bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic profiling identifies GPC5 amplification in association with sarcomatous transformation in a subset of uterine carcinosarcomas
Authors: Chui M Herman , Have Cherry , Hoang Lien N , Shaw Patricia , Lee Cheng‐Han , Clarke Blaise A 
Published: December 2017

AbstractUterine carcinosarcoma, also known as Malignant Mixed Müllerian Tumour, is a high‐grade biphasic neoplasm composed of sarcomatous elements thought to originate via transdifferentiation from high‐grade endometrial carcinoma. To identify molecular factors contributing to the histogenesis of this tumour, we analyzed DNA extracted from matched carcinoma and sarcoma components from 12 cases of carcinosarcoma by a molecular inversion probe microarray to assess genomic copy number alterations (CNAs) and allelic imbalances. Widespread CNAs were identified in tumours with serous histology in the carcinoma component (9/12), while the remaining three cases with endometrioid carcinoma were near‐diploid. Quantification of the extent of genomic aberrations revealed a significant increase in sarcoma relative to carcinoma in tumours with well‐delineated histologic components. Focal amplification of 13q31.3 was identified in 6/12 profiled tumours, of which four harboured the aberration exclusively in the sarcoma component. This result was verified by fluorescence in situ hybridization against GPC5, the only gene situated within the minimal region of amplification. In a validation cohort composed of 97 carcinosarcomas and other uterine sarcomas, amplification of GPC5 (GPC5/CEP13 ratio ≥ 2.2) was identified in 11/97 (11.3%) cases (9/64 carcinosarcoma, 1/3 rhabdomyosarcoma, 1/21 leiomyosarcoma, 0/8 adenosarcoma, 0/1 undifferentiated endometrial sarcoma) and an additional 4 (2.8%) cases had low level gains (GPC5/CEP13 ratio ≥1.5 but <2.2). The functional relevance of Glypican‐5, the gene product of GPC5, in regulating differentiation and lineage commitment was demonstrated in an endometrial carcinoma cell line in vitro. In conclusion, we identified GPC5 amplification as a molecular event mediating epithelial‐mesenchymal transdifferentiation in a subset of uterine carcinosarcomas.
Rapid amplification of prions from variant Creutzfeldt–Jakob disease cerebrospinal fluid
Authors: Barria Marcelo A , Lee Andrew , Green Alison JE , Knight Richard , Head Mark W 
Published: December 2017

AbstractHuman prion diseases constitute a group of infectious and invariably fatal neurodegenerative disorders associated with misfolding of the prion protein. Variant Creutzfeldt–Jakob disease (vCJD) is a zoonotic prion disease linked to oral exposure to the infectious agent that causes bovine spongiform encephalopathy (BSE) in cattle. The most recent case of definite vCJD was heterozygous (MV) at polymorphic codon 129 of the prion protein gene PRNP while all of the previous 177 definite or probable vCJD cases who underwent genetic analysis were methionine homozygous (MM). Retrospective prevalence studies conducted on lympho‐reticular tissue suggest that the number of asymptomatic vCJD carriers in the United Kingdom might be around 1 in 2000 people. In addition, there have been four known cases of the transmission of vCJD infection via blood transfusion. For these reasons, a sensitive, reliable, and fast diagnostic test is currently needed. We describe a rapid and highly sensitive seeding conversion assay that detects disease‐associated prion protein in the brain and cerebrospinal fluid in vCJD after 48–96 h of amplification, with 100% sensitivity and specificity. This method can amplify prions from definite, probable, and possible vCJD cases from patients who are either MM or MV at PRNP‐codon 129.
Co‐administration of Antimicrobial Peptides Enhances Toll‐like Receptor 4 Antagonist Activity of a Synthetic Glycolipid
Authors: Facchini Fabio A. , Coelho Helena , Sestito Stefania E. , Delgado Sandra , Minotti Alberto , Andreu David , Jiménez‐Barbero Jesús , Peri Francesco 
Published: December 2017

AbstractThis study examines the effect of co‐administration of antimicrobial peptides and the synthetic glycolipid FP7, which is active in inhibiting inflammatory cytokine production caused by TLR4 activation and signaling. The co‐administration of two lipopolysaccharide (LPS)‐neutralizing peptides (a cecropin A–melittin hybrid peptide and a human cathelicidin) enhances by an order of magnitude the potency of FP7 in blocking the TLR4 signal. Interestingly, this is not an additional effect of LPS neutralization by peptides, because it also occurs if cells are stimulated by the plant lectin phytohemagglutinin, a non‐LPS TLR4 agonist. Our data suggest a dual mechanism of action for the peptides, not exclusively based on LPS binding and neutralization, but also on a direct effect on the LPS‐binding proteins of the TLR4 receptor complex. NMR experiments in solution show that peptide addition changes the aggregation state of FP7, promoting the formation of larger micelles. These results suggest a relationship between the aggregation state of lipid A‐like ligands and the type and intensity of the TLR4 response.
Method Evaluations for Adsorption Free Energy Calculations at the Solid/Water Interface through Metadynamics, Umbrella Sampling, and Jarzynski's Equality
Authors: Wei Qichao , Zhao Weilong , Yang Yang , Cui Beiliang , Xu Zhijun , Yang Xiaoning 
Published: December 2017

AbstractConsiderable interest in characterizing protein/peptide–surface interactions has prompted extensive computational studies on calculations of adsorption free energy. However, in many cases, each individual study has focused on the application of free energy calculations to a specific system; therefore, it is difficult to combine the results into a general picture for choosing an appropriate strategy for the system of interest. Herein, three well‐established computational algorithms are systemically compared and evaluated to compute the adsorption free energy of small molecules on two representative surfaces. The results clearly demonstrate that the characteristics of studied interfacial systems have crucial effects on the accuracy and efficiency of the adsorption free energy calculations. For the hydrophobic surface, steered molecular dynamics exhibits the highest efficiency, which appears to be a favorable method of choice for enhanced sampling simulations. However, for the charged surface, only the umbrella sampling method has the ability to accurately explore the adsorption free energy surface. The affinity of the water layer to the surface significantly affects the performance of free energy calculation methods, especially at the region close to the surface. Therefore, a general principle of how to discriminate between methodological and sampling issues based on the interfacial characteristics of the system under investigation is proposed.
The role of shame and self‐compassion in psychotherapy for narcissistic personality disorder: An exploratory study
Authors: Kramer Ueli , Pascual‐Leone Antonio , Rohde Kristina B. , Sachse Rainer 
Published: December 2017

AbstractThis process‐outcome study aims at exploring the role of shame, self‐compassion, and specific therapeutic interventions in psychotherapy for patients with narcissistic personality disorder (NPD). This exploratory study included a total of N = 17 patients with NPD undergoing long‐term clarification‐oriented psychotherapy. Their mean age was 39 years, and 10 were male. On average, treatments were 64 sessions long (range between 45 and 99). Sessions 25 and 36 were rated using the Classification of Affective Meaning States and the Process‐Content‐Relationship Scale. Outcome was assessed using the Symptom Check List‐90 and Beck Depression Inventory‐II. Between Sessions 25 and 36, a small decrease in the frequency of shame was found (d = .30). In Session 36, the presence of self‐compassion was linked with a set of specific therapist interventions (process‐guidance and treatment of behaviour‐underlying assumptions; 51% of variance explained and adjusted). This study points to the possible central role of shame in the therapeutic process of patients with NPD. Hypothetically, one way of resolving shame is, for the patient, to access underlying self‐compassion.
Environmentally Responsible Consumption: Construct Definition, Scale Development, and Validation
Authors: Gupta Sudhanshu , Agrawal Richa 
Published: December 2017

AbstractMost environmental problems are rooted in human behaviour, especially consumption. While not consuming is not an option, it would help if all consumption could be measured for environmental responsibility. This study conceptualizes and operationalizes environmentally responsible consumption (ERC), and develops a standardized scale for measuring the same. Depth interviews, blog data analysis, and customer surveys were conducted to develop a standardized 38‐item ERC scale that captures ten unique behaviours pertaining to acquisition, use, and disposal. The scale is an improvement over available measures and compares favourably on several key parameters. The ERC scale could be potentially used by governmental and non‐governmental bodies, policymakers, and environmental groups, for gaining insights into current consumption behaviours of the general public or specific target groups, identifying specific behaviour/s that need improvement, and targeting and tracking such behaviours over time. It could also be used by businesses for identifying opportunities in green products and/or services. Copyright © 2017 John Wiley & Sons, Ltd and ERP Environment
Deconvolution model to resolve cytometric microbial community patterns in flowing waters
Authors: Amalfitano Stefano , Fazi Stefano , Ejarque Elisabet , Freixa Anna , Romaní Anna M. , Butturini Andrea 
Published: December 2017

AbstractFlow cytometry is suitable to discriminate and quantify aquatic microbial cells within a spectrum of fluorescence and light scatter signals. Using fixed gating and operational settings, we developed a finite distribution mixture model, followed by the Voronoi tessellation, to resolve bivariate cytometric profiles into cohesive subgroups of events. This procedure was applied to outline recurrent patterns and quantitative changes of the aquatic microbial community along a river hydrologic continuum. We found five major subgroups within each of the commonly retrieved populations of cells with Low and High content of Nucleic Acids (namely, LNA, and HNA cells). Moreover, the advanced analysis allowed assessing changes of community patterns perturbed by a wastewater feed. Our approach for cytometric data deconvolution confirmed that flow cytometry could represent a prime candidate technology for assessing microbial community patterns in flowing waters. © 2017 International Society for Advancement of Cytometry
Optimal deployment of femtocells using cost function
Authors: Akindeji Akinlabi , Joseph Meera 
Published: December 2017

SummaryIn fact, the demand for mobile data has turned out to be one of the most pressing needs of the human race. In more details, the researcher deals with the voice calling performance and good network signal, which are needed to achieve the above. The femtocells are mostly designed for indoor environments. It enables voice calling and traffic loading, where it improves network coverage. Thus, a femtocell is deployed for signal improvement in the indoor setting. Interference occurs among femtocells. The optimisation of femtocells depends on system factors that require performance and capacity of the network for indoor users. In the above circumstance, the authors considered using the cost function to optimise the mobile coverage, whereby reducing the interference within the users. Adequate MATLAB simulation was utilised for this study. The simulated results were satisfactory since they illustrate the benefits of the methods for the service performance.
Geological record of marine tsunami backwash: The role of the hydraulic jump
Authors: Slootman Arnoud , Simpson Guy , Castelltort Sébastien , de Boer Poppe L. 
Published: December 2017

AbstractTsunamis are marked by distinct phases of uprush during coastal inundation and backwash when tsunami water recedes. Especially in the case of a steep coastal profile, the return flow may operate in a Froude‐supercritical regime, eroding the flooded area and transporting large volumes of sediment seawards. Important sediment accumulation occurs when the supercritical flow goes through a hydraulic jump where it becomes subcritical upon deceleration. An inferred example in coarse‐grained, mixed carbonates from the Lower Pleistocene on Rhodes (Greece) is described, with offshore bars up to 10 m long with scour‐and‐fill structures and steep antidune stratification. In finer‐grained sandy depositional systems such structures may be much longer, up to hundreds of metres. It is suggested here that, analogous to some turbidite beds, the apparent lack of structures or the presence of faint stratification that is common for graded sand layers within marine tsunamiites may in fact consist of extremely low‐angle, landward‐dipping backset‐strata that formed under a landward‐migrating hydraulic jump during the basinward retreat of tsunami water. Numerical simulations that focus on the internal stratification of backwash‐generated offshore bars support this hypothesis. The recognition of such deposits in the sedimentary record enlarges the toolbox for assessing the past frequency of tsunamis in coastal areas.
Protecting and Restoring Biodiversity across the Freshwater, Coastal and Marine Realms: Is the existing EU policy framework fit for purpose?
Authors: Rouillard Josselin , Lago Manuel , Abhold Katrina , Roeschel Lina , Kafyeke Terri , Klimmek Helen , Mattheiß Verena 
Published: December 2017

AbstractWhile some progress has been made, Europe is far from achieving its policy objective of healthy aquatic ecosystems. This paper presents an integrated assessment of how EU policies influence aquatic biodiversity, in order to determine how EU policies and laws contribute to achieving and/or hindering EU and international biodiversity targets. The paper also discusses whether European policy has a synergistic or conflicting mix of instruments to address the main problems facing aquatic biodiversity, and whether gaps in the existing policy framework exist. The integrated policy review assessment presented in this paper is based on the application of the drivers–pressures–state–impact–responses (DPSIR) framework to six known pressures on aquatic biodiversity, selected to provide a representative range: nitrogen pollution, species extraction, invasive alien species, water abstraction, alterations to morphology, and plastic waste. The DPSIR framework is used to characterize these pressures and how they are influenced by underpinning socio‐economic drivers and major European policies. The conclusions highlight that the policy framework is most developed when it comes to defining environmental targets and sets a number of instruments to reduce pressures by encouraging the adoption of more resource‐efficient practices, but it becomes less specific when tackling sectors (drivers) and supporting more environmental sound economic development. © 2017 The Authors. Environmental Policy and Governance published by ERP Environment and John Wiley & Sons Ltd
Altered toll‐like receptor responsiveness underlies a dominant heritable defect in B cell tolerance in autoimmune New Zealand Black mice
Authors: Clark Amy G. , Buckley Elizabeth S. , Foster Mary H. 
Published: December 2017

AbstractSystemic lupus erythematosus is a debilitating autoimmune disease in which autoantibodies and autoreactive T cells destroy kidneys and other organs. Disease is clinically and genetically heterogeneous, suggesting that underlying mechanisms vary between patients. We previously used an autoantibody transgenic mouse reporter system to examine the effect of different autoimmune backgrounds on B‐cell tolerance, failure of which is a fundamental defect in lupus. We identified a defect consistent with reversible anergy induced by endotoxin stimulation of B cells from Ig transgenic New Zealand Black (NZB) mice. Herein we report that the tolerance defect is revealed by TLR7 and TLR9 as well as TLR4 ligands, with additive effect, and is partially reversed by Mek inhibition. Gene expression analysis reveals significant differences in transcription of multiple TLR pathway genes and ptpn22 in stimulated NZB compared to B6 B cells. Additionally, the defect is detected in Ig transgenic NZB F1 hybrid strains (NZBxNZW)F1 and (B6xNZB)F1. These results implicate an inherited defect wherein NZB anergic B cells maintain coordinated TLR/BCR signaling that permits autoantibody production. Agents targeting these pathways may have therapeutic benefit in the subset of lupus patients that manifest similar defects in B‐cell regulation.
Enzyme Catalysis Induced Polymer Growth in Nanochannels: A New Approach to Regulate Ion Transport and to Study Enzyme Kinetics in Nanospace
Authors: Dai Huang , Li Yuqing , Fu Yingchun , Li Yanbin 
Published: December 2017

AbstractMethod that could regulate the ion transport in nanochannel in an efficient and rapid manner is still a challenge. Here, we introduced enzyme‐catalysis‐induced polymer growth in nanochannels to develop a new method to regulate the ion transport and evaluate the enzyme catalysis kinetics in nano‐space. As a model enzyme, Horseradish peroxidase (HRP) was immobilized in the nanochannels through a volume‐controlled‐drying method. In the presence of H2O2, HRP catalyzed o‐phenylenediamine (o‐PD) to trigger its polymer growth, in turn blocked the ion transport and led to the decrease of the ion current. Taking advantages of the high efficiency of enzyme catalysis and the nano‐confinement of nanochannels, the system readily achieved blocking ratios of ion current even reaching 99.6 % of the initial. Based on above concept, we developed a new method to evaluate the enzyme catalysis kinetics in nano‐confined space. By comparing with those in free state in solution and absorbed on planar surface, HRP confined in nanochannels presented similar apparent Michaelis constant (Km) values for the substrate H2O2 but much higher Km values for the substrate o‐PD, due to the steric hindrance and diffusion suppression. The enzyme‐catalysis‐induced polymerization in nanochannels might lead to new concept for the nano‐blocking/switching and provide a new platform for single molecule analysis and detection.
Evaluation of ASCE 7 equations for designing acceleration‐sensitive nonstructural components using data from instrumented buildings
Authors: Anajafi Hamidreza , Medina Ricardo A. 
Published: December 2017

SummaryThis study uses instrumented buildings and models of code‐based designed buildings to validate the results of previous studies that highlighted the need to revise the ASCE 7 Fp equation for designing nonstructural components (NSCs) through utilizing oversimplified linear and nonlinear models. The evaluation of floor response spectra of a large number of instrumented buildings illustrates that, unlike the ASCE 7 approach, the in‐structure and the component amplification factors are a function of the ratio of NSC period to the supporting building modal periods, the ground motion intensity, and the NSC location. It is also shown that the recorded ground motions at the base of instrumented buildings in most cases are significantly lower than design earthquake (DE) ground motions. Because ASCE 7 is meant to provide demands at a DE level, for a more reliable evaluation of the Fp equation, 2 representative archetype buildings are designed based on the ASCE 7‐16 seismic provisions and exposed to various ground motion intensity levels (including those consistent with the ones experienced by instrumented buildings and the DE). Simulation results of the archetype buildings, consistent with previous numerical studies, illustrate the tendency of the ASCE 7 in‐structure amplification factor, [1 + 2(z/h)], to significantly overestimate demands at all floor levels and the ASCE 7 limit of
to in many cases underestimate the calculated NSC amplification factors. Furthermore, the product of these 2 amplification factors (that represents the normalized peak NSC acceleration) in some cases exceeds the ASCE 7 equation by a factor up to 1.50.
Interbuilding interpolation of peak seismic response using spatially correlated demand parameters
Authors: Sun Han , Burton Henry , Zhang Yu , Wallace John 
Published: December 2017

SummarySeismic structural responses recorded in instrumented buildings during an earthquake are used to provide insights into the demands placed on neighboring, noninstrumented buildings, using a framework to interpolate structural response demands across buildings. The interbuilding interpolation model relies on the spatial and structural correlations of responses in coregionally located buildings subjected to a seismic event. A dataset of response demands for a portfolio of reinforced concrete moment frame buildings is generated by performing nonlinear response history analyses on structural models using ground motions recorded from historical scenario earthquakes. The dataset is used to characterize the correlation between seismic demands across different buildings. Semivariograms are used to model spatial and structural correlations and then incorporated into a kriging algorithm, which forms the basis of the interpolation models. The effect of several model and dataset attributes and assumptions, for example, using intensity‐measure‐based versus engineering demand parameter‐based semivariograms, and size of training dataset relative to portfolio, on the overall performance are evaluated along with the limitations of the proposed model.
Influence of DEM resolution on modelling hydrological connectivity in a complex agricultural catchment with woody crops
Authors: López‐Vicente M. , Álvarez S. 
Published: December 2017

AbstractDigital elevation model (DEM) resolution influences hydrological simulation. However, its influence when modelling hydrological connectivity (HC) in woody crops remains to be seen. We assessed surface topography, microtopography and HC in an agricultural sub‐catchment (27.4 ha) using six photogrammetry‐derived DEMs with 0.03, 0.05, 0.1, 0.2, 0.5 and 1 m cell sizes. Land uses included vineyards, olive groves, cereal fields, and forestry patches. We ran an updated version of Borselli's HC index (IC) using the D‐Infinity approach. We assessed HC in woody crops at high spatial resolution for the first time. After analysing the differences in the contributing area, the flow width, the soil roughness, the convergence index and the IC (normalised and non‐normalised) at different scales (hillslope, land uses and compartments, ephemeral gullies, depositional areas and the sub‐catchment outlet) and accounting for the field vertical components, we propose an optimum DEM resolution (0.2 m) to improve modelling of structural HC in woody crops. The modelled hydrological features at this threshold resolution matched well with the geomorphic features associated with the short‐ and medium‐term patterns of soil redistribution. Higher DEM resolutions, especially at 0.03 and 0.05 m, introduced bias in the input data and the IC computations. Finally, we observed good agreement between the outputs at the lowest resolution, 1 × 1 m, and the long‐term soil redistribution patterns (functional connectivity). Copyright © 2017 John Wiley & Sons, Ltd.