bluuebunny/crossref_metadata_2025_split huggingface dataset:
The first non Clostridial botulinum-like toxin cleaves VAMP within the juxtamembrane domain
Authors: Zornetta Irene , Azarnia Tehran Domenico , Arrigoni Giorgio , Anniballi Fabrizio , Bano Luca , Leka Oneda , Zanotti Giuseppe , Binz Thomas , Montecucco Cesare 
Published: July 2016

AbstractThe genome of Weissella oryzae SG25T was recently sequenced and a botulinum neurotoxin (BoNT) like gene was identified by bioinformatics methods. The typical three-domains organization of BoNTs with a N-terminal metalloprotease domain, a translocation and a cell binding domains could be identified. The BoNT family of neurotoxins is rapidly growing, but this was the first indication of the possible expression of a BoNT toxin outside the Clostridium genus. We performed molecular modeling and dynamics simulations showing that the 50 kDa N-terminal domain folds very similarly to the metalloprotease domain of BoNT/B, whilst the binding part is different. However, neither the recombinant metalloprotease nor the binding domains showed cross-reactivity with the standard antisera that define the seven serotypes of BoNTs. We found that the purified Weissella metalloprotease cleaves VAMP at a single site untouched by the other VAMP-specific BoNTs. This site is a unique Trp-Trp peptide bond located within the juxtamembrane segment of VAMP which is essential for neurotransmitter release. Therefore, the present study identifies the first non-Clostridial BoNT-like metalloprotease that cleaves VAMP at a novel and relevant site and we propose to label it BoNT/Wo.
Fibroblast growth factor rescues brain endothelial cells lacking presenilin 1 from apoptotic cell death following serum starvation
Authors: Gama Sosa Miguel A. , De Gasperi Rita , Hof Patrick R. , Elder Gregory A. 
Published: July 2016

AbstractPresenilin 1 (Psen1) is important for vascular brain development and is known to influence cellular stress responses. To understand the role of Psen1 in endothelial stress responses, we investigated the effects of serum withdrawal on wild type (wt) and Psen1−/− embryonic brain endothelial cells. Serum starvation induced apoptosis in Psen1−/− cells but did not affect wt cells. PI3K/AKT signaling was reduced in serum-starved Psen1−/− cells and this was associated with elevated levels of phospho-p38 consistent with decreased pro-survival AKT signaling in the absence of Psen1. Fibroblast growth factor (FGF1 and FGF2), but not vascular endothelial growth factor (VEGF) rescued Psen1−/− cells from serum starvation induced apoptosis. Inhibition of FGF signaling induced apoptosis in wt cells under serum withdrawal, while blocking γ-secretase activity had no effect. In the absence of serum, FGF2 immunoreactivity was distributed diffusely in cytoplasmic and nuclear vesicles of wt and Psen1−/− cells, as levels of FGF2 in nuclear and cytosolic fractions were not significantly different. Thus, sensitivity of Psen1−/− cells to serum starvation is not due to lack of FGF synthesis but likely to effects of Psen1 on FGF release onto the cell surface and impaired activation of the PI3K/AKT survival pathway.
Transcriptome sequencing wide functional analysis of human mesenchymal stem cells in response to TLR4 ligand
Authors: Kim Sun Hwa , Das Amitabh , Chai Jin Choul , Binas Bert , Choi Mi Ran , Park Kyoung Sun , Lee Young Seek , Jung Kyoung Hwa , Chai Young Gyu 
Published: July 2016

AbstractDue to their multipotentiality and immunomodulation, human mesenchymal stem cells (hMSCs) are widely studied for the treatment of degenerative and inflammatory diseases. Transplantation of hMSCs to damaged tissue is a promising approach for tissue regeneration. However, the physiological mechanisms and regulatory processes of MSC trafficking to injured tissue are largely unexplored. Here, we evaluated the gene expression profile and migratory potential of hMSCs upon stimulation with the TLR4 ligand lipopolysaccharide (LPS). Using RNA sequencing, we identified unique induction patterns of interferon stimulated genes, cytokines and chemokines involved in chemotaxis and homing. The −950 to +50 bp regions of many of these LPS-responsive genes were enriched with putative binding motifs for the transcription factors (TFs) interferon regulatory factor (IRF1) and nuclear factor kappa B (NF-κB1, REL), which were also induced by LPS along with other TFs. Chromatin immunoprecipitation assays showed that IRF1 bound within their target genes promoter region. In addition, IRF1 attenuation significantly down-regulated interferon stimulated genes as well as key cytokines. Furthermore, using pharmacological inhibitors, we showed that the NF-κB and phosphatidylinositol 3-kinase (PI3K) pathways regulate the migratory and cytokines/chemokines response to LPS. These unprecedented data suggest that IRF1 and NF-κB orchestrate the TLR4-primed immunomodulatory response of hMSCs and that this response also involves the PI3K pathway.
Identification of apolipoprotein using feature selection technique
Authors: Tang Hua , Zou Ping , Zhang Chunmei , Chen Rong , Chen Wei , Lin Hao 
Published: July 2016

AbstractApolipoprotein is a kind of protein which can transport the lipids through the lymphatic and circulatory systems. The abnormal expression level of apolipoprotein always causes angiocardiopathy. Thus, correct recognition of apolipoprotein from proteomic data is very crucial to the comprehension of cardiovascular system and drug design. This study is to develop a computational model to predict apolipoproteins. In the model, the apolipoproteins and non-apolipoproteins were collected to form benchmark dataset. On the basis of the dataset, we extracted the g-gap dipeptide composition information from residue sequences to formulate protein samples. To exclude redundant information or noise, the analysis of various (ANOVA)-based feature selection technique was proposed to find out the best feature subset. The support vector machine (SVM) was selected as discrimination algorithm. Results show that 96.2% of sensitivity and 99.3% of specificity were achieved in five-fold cross-validation. These findings open new perspectives to improve apolipoproteins prediction by considering the specific dipeptides. We expect that these findings will help to improve drug development in anti-angiocardiopathy disease.
Network impulse response based‐on fault location method for fault location in power distribution systems
Authors: Abad Marta , García‐Gracia Miguel , El Halabi Nabil , López Andía Diego 
Published: July 2016

This study proposes a new time‐domain fault location method based on the impulse response (image) of a power system. The proposed algorithm captures an electrical image of the power system in normal operation by injecting a train of impulses. Following fault detection, an updated electrical image is acquired and compared with the normal operating image. The comparison between both images, in time domain, permits the estimation of the distance to the fault. The performance of the proposed method has been evaluated in a 20 kV distribution system modelled in power systems computer‐aided design/electro‐magnetic transient design and control (PSCAD/EMTDC). Moreover, laboratory and field tests in a 15 kV overhead line have been carried out to verify and validate model accuracy and performance. Results show a considerable improvement in the accuracy of fault distance estimation compared with existing algorithms. A relevant advantage of the proposed method is its high immunity to ground resistivity, fault resistance and fault type and location in the distribution system.
Looking into introspection
Authors: Dąbrowska Ewa 
Published: July 2016

Introspective judgments are often used in linguistics to obtain information about speakers’ mental representations of language. This chapter addresses two questions, namely: what shapes speakers’ judgments, and what such judgments provide information about. I argue that speakers’ judgments are influenced by their theories of language, which in turn are partly shaped by our experience with written language. The fundamental units that linguists use in their analyses – phonemes, words, and sentences – are largely products of a particular written tradition; and grammaticality judgments about isolated sentences are, to a considerable extent, judgments about what is acceptable in written language. Thus, linguistic intuitions are not direct reflections of mental representations of linguistic knowledge, but of speakers’ sensitivity to socially constituted norms.
Lexical and grammatical dimensions of metaphor – a Cognitive Grammar perspective
Authors: Taraszka-Drożdż Barbara 
Published: July 2016

Metaphor – a popular issue in Cognitive Linguistics – is also a topic discussed within Cognitive Grammar (e.g. Langacker 2000, 2008). There, metaphor is viewed as a type of semantic extension that can be characterized at different levels of schematicity. This approach inevitably evokes the notion of meaning and, from the perspective of CG, meaning is not only the conceptual content but also the manner in which this content is construed. Adopting this type of analysis, we indicate the resultant interplay between lexical and grammatical dimensions in the account of metaphorical extensions. To achieve this aim, we analyze metaphorical extensions of French lexical items referring to light.
Towards an experientially-based classification of motion situations
Authors: WoŹny Jacek 
Published: July 2016

The concepts of motion and force are both extensively discussed in cognitive linguistics literature. However, they are discussed separately. The first – usually in the context of ‘motion situations’ (e.g. Talmy 2000; Slobin 2003; Zlatev 2007; Zlatev et al. 2010, 2012), the other – as part of the Force Dynamics framework, which was developed by Talmy (1976, 1988, 2000) and adopted by, for example, Sweetser (1982, 1991), Johnson (1987), Boye (2001), Vandenberghe (2002), and Da Silva (2003). The aim of this chapter is to argue that the concepts of force and motion should not be isolated but considered as two inseparable parts of force-motion events.
S2 from Equine infectious anemia virus is an infectivity factor which counteracts the retroviral inhibitors SERINC5 and SERINC3
Authors: Chande Ajit , Cuccurullo Cristiana , Rosa Annachiara , Ziglio Serena , Carpenter Susan , Pizzato Massimo 
Published: July 2016

ABSTRACTThe lentivirus equine infectious anemia virus (EIAV) encodes S2, a pathogenic determinant important for virus replication and disease progression in horses. No molecular function has yet been linked to this accessory protein. We now report that S2 can replace the activity of Nef on HIV-1 infectivity, being required to antagonize the inhibitory activity of SERINC proteins on Nef-defective HIV-1. Similar to Nef, S2 excludes SERINC5 from virus particles and requires an ExxxLL motif predicted to recruit the clathrin adaptor AP2. Accordingly, a functional endocytic machinery is essential for S2-mediated infectivity enhancement, which is impaired by inhibitors of clathrin-mediated endocytosis. In addition to retargeting SERINC5 to a late endosomal compartment, S2 promotes the host factor degradation. Emphasizing the similarity with Nef, we show that S2 is myristoylated and, compatible with a crucial role of the post-translational modification, its N-terminal glycine is required for the anti-SERINC5 activity.EIAV-derived vectors devoid of S2 are less susceptible than HIV-1 to the inhibitory effect of both human and equine SERINC5. We then identified the envelope glycoprotein of EIAV as a determinant which also modulates retrovirus susceptibility to SERINC5, indicating a bi-modular ability of the equine lentivirus to counteract the host factor.S2 shares no sequence homology with other retroviral factors known to counteract SERINC5. Adding to primate lentivirus Nef and gammaretrovirus glycoGag, the accessory protein from EIAV makes another example of a retroviral virulence determinant which independently evolved SERINC5-antagonizing activity. SERINC5 therefore plays a critical role for the interaction of the host with diverse retrovirus pathogens.Significance StatementSERINC5 and SERINC3 are recently discovered cellular inhibitors of retroviruses, which are incorporated into virus particles and impair their ability to propagate the infection to target cells. Only two groups of viruses (represented by HIV-1 and MLV) have so far been identified to have evolved the ability of counteracting SERINC inhibition. We now discovered that Equine infectious anemia virus, which causes a debilitating disease in horses, also acquired the ability to protect the virus particle from inhibition by SERINC5 and SERINC3, using its small protein S2. The evidence that three different retroviruses have independently evolved the ability to elude inhibition bySERINC5 and SERINC3 indicates that these cellular factors play a fundamental role against various retrovirus pathogens.
Structure of Topologically Associating Domains and gene regulation embedded in the 5C data revealed by a polymer model and stochastic simulations
Authors: Shukron O. , Holcman D. 
Published: July 2016

AbstractChromatin organization is probed by chromosomal capture data, from which the encounter probability (EP) between genomic sites is represented in a large matrix. However, this matrix is obtained by averaging the EP over cell population, where diagonal blocks called TADs, contains hidden information about sub-chromatin organization. Our aim here is to elucidate the relationship between TADs structure and gene regulation. For this end, we reconstruct the chromatin dynamics from the EP matrix using polymer model and explore the transient properties, constrained by the statistics of the data. To construct the polymer, we use the EP decay in two steps: first, to account for TADs, we introduce random connectors inside a restricted region defining the TADs. Second, we account for long-range frequent specific genomic interactions in the polymer architecture. Finally, stochastic simulations show that only a small number of randomly placed connectors are required to reproduce the EP of TADs, and allow us to compute the mean first time and the conditional encounter probability of three key genomic sites to meet. These encounter times reveal how chromatin can self-regulate. The present polymer construction is generic and can be used to study steady-state and transient properties of chromatin constrained on 5C data.
Dispersal: a central and independent trait in life history
Authors: Bonte Dries , Dahirel Maxime 
Published: July 2016

AbstractThe study of trade-offs among major life history components (age at maturity, lifespan and reproduction) allowed the development of a quantitative framework to understand how environmental variation shapes patterns of biodiversity among and within species.Because every environment is inherently spatially structured, and in most cases temporally variable, individuals need to move within and among habitats to maximize fitness. Dispersal is often assumed to be tightly integrated into life histories through genetic correlations with other vital traits. This assumption is particularly strong within the context of a fast-slow continuum of life-history variation. Such a framework is to date used to explain many aspects of population and community dynamics. Evidence for a consistent and context-independent integration of dispersal in life histories is, however, weak. We therefore advocate the explicit integration of dispersal into life history theory as a principal axis of variation influencing fitness, that is free to evolve, independently of other life history traits.We synthesize theoretical and empirical evidence on the central role of dispersal and its evolutionary dynamics on the spatial distribution of ecological strategies and its impact on population spread, invasions and coexistence. By applying an optimality framework we show that the inclusion of dispersal as an independent dimension of life histories might substantially change our view on evolutionary trajectories in spatially structured environments.Because changes in the spatial configuration of habitats affect the costs of movement and dispersal, adaptations to reduce these costs will increase phenotypic divergence among and within populations. We outline how this phenotypic heterogeneity is anticipated to further impact population and community dynamics.
Nkx2.1 regulates the proliferation and cell fate of telencephalic astrocytes during embryonic development
Authors: Minocha Shilpi , Valloton Delphine , Arsenijevic Yvan , Cardinaux Jean-René , Dreier Guidi Raffaella , Hornung Jean-Pierre , Lebrand Cécile 
Published: July 2016

AbstractThe homeodomain transcription factor Nkx2.1 controls cell differentiation of telencephalic GABAergic interneurons and oligodendrocytes. Here, we show that Nkx2.1 additionally regulates astrogliogenesis of the telencephalon from embryonic day (E) 14.5 to E16.5. Our work aims to identify the different mechanisms by which Nkx2.1 controls telencephalic astrogliogenesis. InNkx2.1-/-, a drastic loss of astrocytes is observed which is not related to cell death.In vivoanalysis using BrdU incorporation reveals that Nkx2.1 affects the proliferation of ventral neural stem cells that generate early astrocytes.In vitroneurosphere assays show that Nkx2.1 additionally affects the differentiation step of Nkx2.1-derived astrocytes. Chromatin immunoprecipitation andin vitroco-transfection studies of a Nkx2.1-expressing plasmid indicate that Nkx2.1 binds to the promoter of astroglial differentiation gene GFAP, and regulates its expression. Hence, Nkx2.1 controls astroglial production spatiotemporally in embryos by regulating stem cell division and specification of the contributing Nkx2.1+precursors.
Identifying the Interdependence Between Monetary Policy and Financial Stress: Evidence from China
Authors: Li Rong , Tian Xiaohui 
Published: July 2016

AbstractWe estimate the interdependence between Chinese monetary policy and financial stress using structural vector autoregression. To solve the simultaneity problem, we employ a strategy including both short‐run and long‐run restrictions that maintains the qualitative properties of monetary policy shocks derived from the literature. This method is applied to Chinese monthly data, together with a newly constructed index of financial stress in this paper. Our findings suggest there exists strong interdependence between monetary policy and financial stress. The financial stress index increases immediately by 0.4 of its standard deviation after a monetary policy shock that raises the M2 growth rate by 1 percentage point. An increase of financial stress by one standard deviation leads to a decline in the M2 growth rate by 2 percentage points.
Subterranean termite (Blattodea: Termitoidae) pests in metropolitan Brisbane, Australia, 1997–2006: patterns and implications
Authors: Peters Brenton C , Perkins Lynda E , Cochrane Gary H , Zalucki Myron P 
Published: July 2016

AbstractThe distribution and abundance of subterranean termites in Brisbane, Australia, has not previously been investigated, despite the sub‐tropical climate being favourable for these xylophagous insects which often cause damage to the built environment. Data on the incidence of termite infestations, including taxonomic identity, locality and site of infestation within premises were collected by a large commercial pest management company in metropolitan Brisbane during a ten‐year period (1997 – 2006). General Linear Models based on a negative binomial distribution were used to examine the influence of the climatic variables of rainfall and Southern Oscillation Index (SOI), and the demographic variables of premise density and socioeconomic status, on the number of termite infestations found. Two genera of termites dominated: Schedorhinotermes, which was the most abundant both indoors and outdoors, and Coptotermes. That Schedorhinotermes spp. were the major xylophagous subterranean termites recorded is unique in Australian capital cities where Coptotermes spp. usually dominate. The patterns of abundance and distribution of both genera are discussed with respect to their differing biology. SOI, premise density per ha and household income all significantly explained the variation in termite abundance reported across metropolitan Brisbane over the 10 year study. Our results shows the potential for using SOI as a predictor of termite activity. Further study is needed to more accurately correlate the key drivers of termite activity with the incidence of termite infestations in premises.
Rhinovirus‐specific antibody responses in preschool children with acute wheeze reflect severity of respiratory symptoms
Authors: Stenberg‐Hammar K. , Niespodziana K. , Söderhäll C. , James A. , Cabauatan C.R. , Konradsen J. R. , Melén E. , van Hage M. , Valenta R. , Hedlin G. 
Published: July 2016

AbstractBackgroundSome children with rhinovirus (RV) infections wheeze, but it is unknown whether this is due to more virulent strains of virus or differences in host immune responses. The aim of this study was to investigate the RV species‐specific antibody responses measured at a follow‐up visit in preschool children in relation to reported time with respiratory symptoms and the presence of different RV species during an acute episode of wheeze.MethodNasopharyngeal swabs and blood samples were taken among 120 preschool children (<4 years of age) at an acute episode of wheeze and at a follow‐up visit (median 11 weeks later). Nested PCR was used to detect different RV strains, and serum levels of IgG1 against purified recombinant VP1 proteins from representatives of the three RV species (RV‐A, RV‐B, and RV‐C) were measured by ELISA.ResultsRhinovirus was detected in 74% (n = 80/108) of the children at the acute visit, and RV‐C was the most common subtype (n = 59/80, 74%). An increase in RV‐specific IgG1 was seen in 61% (n = 73) of the children at follow‐up, most frequently against RV‐A (n = 61/73, 86%) irrespective of the RV strains detected by PCR. Increases in RV‐specific IgG1 against RV‐A or against RV‐A and RV‐C were significantly associated with more respiratory symptoms (p = 0.03, p = 0.007).ConclusionAntibody response to recombinant RV VP1 proteins was associated with longer time with respiratory symptoms.