bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neutrophil trafficking to lymphoid tissues: physiological and pathological implications
Authors: Voisin Mathieu‐Benoit , Nourshargh Sussan 
Published: December 2018

AbstractRecent advances have provided evidence for the involvement of neutrophils in both innate and adaptive immunity, robustly challenging the old dogma that neutrophils are short‐lived prototypical innate immune cells solely involved in acute responses to microbes and exerting collateral tissue damage. There is now ample evidence showing that neutrophils can migrate into different compartments of the lymphoid system where they contribute to the orchestration of the activation and/or suppression of lymphocyte effector functions in homeostasis and during chronic inflammation, such as autoimmune disorders and cancer. In support of this notion, neutrophils can generate a wide range of cytokines and other mediators capable of regulating the survival, proliferation and functions of both T and B cells. In addition, neutrophils can directly engage with lymphocytes and promote antigen presentation. Furthermore, there is emerging evidence of the existence of distinct and diverse neutrophil phenotypes with immunomodulatory functions that characterise different pathological conditions, including chronic and autoimmune inflammatory conditions. The aim of this review is to discuss the mechanisms implicated in neutrophil trafficking into the lymphoid system and to provide an overview of the immuno‐regulatory functions of neutrophils in health and disease in the context of adaptive immunity. Copyright © 2018 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
High‐throughput sequencing identifies aetiology‐dependent differences in ductular reaction in human chronic liver disease
Authors: Govaere Olivier , Cockell Simon , Van Haele Matthias , Wouters Jasper , Van Delm Wouter , Van den Eynde Kathleen , Bianchi Arianna , van Eijsden Rudy , Van Steenbergen Werner , Monbaliu Diethard , Nevens Frederik , Roskams Tania 
Published: December 2018

AbstractDuctular reaction (DR) represents the activation of hepatic progenitor cells (HPCs) and has been associated with features of advanced chronic liver disease; yet it is not clear whether these cells contribute to disease progression and how the composition of their micro‐environment differs depending on the aetiology. This study aimed to identify HPC‐associated signalling pathways relevant in different chronic liver diseases using a high‐throughput sequencing approach. DR/HPCs were isolated using laser microdissection from patient samples diagnosed with HCV or primary sclerosing cholangitis (PSC), as models for hepatocellular or biliary regeneration. Key signals were validated at the protein level for a cohort of 56 patients (20 early and 36 advanced stage). In total, 330 genes were significantly differentially expressed between the HPCs in HCV and PSC. Recruitment and homing of inflammatory cells were distinctly different depending on the aetiology. HPCs in PSC were characterised by a response to oxidative stress (e.g. JUN, VNN1) and neutrophil‐attractant chemokines (CXCL5, CXCL6, IL‐8), whereas HPCs in HCV were identified by T‐ and B‐lymphocyte infiltration. Moreover, we found that communication between HPCs and macrophages was aetiology driven. In PSC, a high frequency of CCL28‐positive macrophages was observed in the portal infiltrate, already in early disease in the absence of advanced fibrosis, while in HCV, HPCs showed a strong expression of the macrophage scavenger receptor MARCO. Interestingly, DR/HPCs in PSC showed more deposition of ECM (e.g. FN1, LAMC2, collagens) compared to HCV, where an increase of pro‐invasive genes (e.g. PDGFRA, IGF2) was observed. Additionally, endothelial cells in the vicinity of DR/HPCs showed differential immunopositivity (e.g. IGF2 and INHBA expression). In conclusion, our data shine light on the role of DR/HPCs in immune signalling, fibrogenesis and angiogenesis in chronic liver disease. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Does Intrinsic Disorder in Proteins Favor Their Interaction with Lipids?
Authors: Deryusheva Evgenia , Nemashkalova Ekaterina , Galloux Marie , Richard Charels‐Adrien , Eléouët Jean‐François , Kovacs Denis , Van Belle Karo , Tompa Peter , Uversky Vladimir , Permyakov Sergei 
Published: December 2018

AbstractIntrinsically disordered proteins (IDPs) are implicated in a range of human diseases, some of which are associated with the ability to bind to lipids. Although the presence of solvent‐exposed hydrophobic regions in IDPs should favor their interactions with low‐molecular‐weight hydrophobic/amphiphilic compounds, this hypothesis has not been systematically explored as of yet. In this study, the analysis of the DisProt database with regard to the presence of lipid‐binding IDPs (LBIDPs) reveals that they comprise, at least, 15% of DisProt entries. LBIDPs are classified into four groups by ligand type, functional categories, domain structure, and conformational state. 57% of LBIDPs are classified as ordered according to the CH‐CDF analysis, and 70% of LBIDPs possess lengths of disordered regions below 50%. To investigate the lipid‐binding properties of IDPs for which lipid binding is not reported, three proteins from different conformational groups are rationally selected. They all are shown to bind linoleic (LA) and oleic (OA) acids with capacities ranging from 9 to 34 LA/OA molecules per protein molecule. The association with LA/OA causes the formation of high‐molecular‐weight lipid–protein complexes. These findings suggest that lipid binding is common among IDPs, which can favor their involvement in lipid metabolism.
C―H···O hydrogen bonding interactions for sterically hindered phenols and their phenoxyl radicals
Authors: Wang Jinhu , Liu Chunli , Liu Xuejing , Shao Linjun , Zhang Xian‐Man 
Published: December 2018

AbstractSterically hindered phenols have been widely used as chain‐breaking antioxidants in chemical and polymeric industries, and the remarkable stabilities of their phenoxyl radicals are generally attributed to the steric effects and resonance stabilization of the unpaired electron into the aromatic ring. Non‐covalent interaction (NCI) analysis shows that there are four intramolecular C―H···O hydrogen bonds between oxygen atom and theortho t‐butyl C―H bonds for the sterically hindered phenoxyl radicals and their phenolic precursors. The C―H···O hydrogen bonds can be directly visualized and quantified from the reduced density gradient NCI isosurfaces and atoms‐in‐molecules analysis, respectively. Furthermore, the phenolic O―H bond strength decreases gradually with increasing volume of theorthoalkyl substituents in three different phenol model systems (Table 5). The nice linear correlation of the O―H bond dissociation enthalpies with the Taft's steric parameters (Figure 8) provides additional evidences to support formation of the intramolecular C―H···O hydrogen bonds between oxygen atom and theortho t‐alkyl C―H bonds.
Geomorphology of Gullies at Thomas Lee Inlet, Devon Island, Canadian High Arctic
Authors: Godin Etienne , Osinski Gordon R. , Harrison Tanya N. , Pontefract Alexandra , Zanetti Michael 
Published: December 2018

AbstractSlopes in and around Thomas Lee Inlet (Devon Island, Nunavut, Canada) are eroded by means of gullying, yet the driving factors, such as the nature of the substrate and availability of different sources for water, influencing gully morphology remain poorly understood. Here we investigate the factors that contribute to gully formation using a combination of satellite mapping, field observations and statistical analysis of morphological data. In total, 161 gullies were mapped within the 126 km2 study area. Factors linked to gullies, such as the nature of its substrate and the presence of glaciers, were integrated into a spatial geodatabase. A Factor Analysis of Mixed Data performed on the geodatabase was used to discriminate which factors may influence gully geometry. Our results show that the type of geological formation has a strong impact on gully slope. In addition, supplemental sources of water are often found near alcoves of the steep, longer and mature gullies, and levees often form in their aprons. Immature debris flow‐like gullies were dryer and found on short and variable (from steep to gentle) slopes. This detailed study of the rocky and arid Thomas Lee Inlet plateaus and slopes provides the first insight into gullied slopes as a hydrological component connecting upland units to downslope in this area.
Open‐Circuit Ultrafast Generation of Nanoscopic Toroidal Moments: The Swift Phase Generator
Authors: Wätzel Jonas , Berakdar Jamal 
Published: December 2018

AbstractEfficient and flexible schemes for a swift, field‐free control of the phase in quantum devices have far‐reaching impact on energy‐saving operation of quantum computing, data storage, and sensoring nanodevices. A novel approach for an ultrafast generation of a field‐free vector potential that is tunable in duration, sign, and magnitude, allowing to impart non‐invasive, spatiotemporally controlled changes to the quantum nature of nanosystems is reported. The method relies on triggering a steady‐state toroidal moment in a donut‐shaped nanostructure that serves as a vector‐potential generator and quantum phase modulator. Irradiated by moderately intense, few cycle THz pulses with appropriately shaped polarization states, the nano donut is brought to a steady‐state where a nearby object does not experience electric or magnetic fields but feels the photo‐generated vector potential. Designing the time structure of the driving THz pulses allows for launching picosecond trains of vector potentials which is the key for a contact‐free optimal control of quantum coherent states. This research can trigger a new class of ultrafast quantum devices operated and switched in an energy‐efficient, contact and field‐free manner, enabling new techniques for use in quantum information, magnetic nanostructures, and superconducting tunnel junctions as well as in toroidally ordered systems and multiferroics.
Perinatal mortality and morbidity in triplet pregnancy according to chorionicity: systematic review and meta‐analysis
Authors: Curado J. , D'antonio F. , Papageorghiou A. T. , Bhide A. , Thilaganathan B. , Khalil A. 
Published: December 2018

ABSTRACTObjectiveThe incidence of perinatal mortality and morbidity in triplet pregnancies according to chorionicity is yet to be established. The aim of this systematic review was to quantify perinatal mortality and morbidity in trichorionic triamniotic (TCTA), dichorionic triamniotic (DCTA) and monochorionic triamniotic (MCTA) triplets.MethodsMEDLINE, EMBASE and CINAHL databases were searched in December 2017 for literature published in English describing outcomes of DCTA, TCTA and/or MCTA triplet pregnancies. Primary outcomes were intrauterine death (IUD), neonatal death, perinatal death (PND) and gestational age at birth. Secondary outcomes comprised respiratory, neurological and infectious morbidity, as well as a composite score of neonatal morbidity. Data regarding outcomes were extracted from the included studies. Random‐effects meta‐analysis was used to estimate the risk of mortality and morbidity and to compute the difference in gestational age at birth between TCTA and DCTA triplet pregnancies.ResultsNine studies (1373 triplet pregnancies, of which 1062 were TCTA, 261 DCTA and 50 MCTA) were included in the analysis. The risk of PND was higher in DCTA than in TCTA triplet pregnancies (odds ratio (OR), 3.3 (95% CI, 1.3–8.0)), mainly owing to the higher risk of IUD in DCTA triplet pregnancies (OR, 4.6 (95% CI, 1.8–11.7)). There was no difference in gestational age at birth between TCTA and DCTA triplets (mean difference, 1.1 weeks (95% CI, –0.3 to 2.5 weeks); I2 = 85%; P = 0.12). Neurological morbidity occurred in 2.0% (95% CI, 1.1–3.3%) of TCTA and in 11.6% (95% CI, 1.1–40.0%) of DCTA triplets. Respiratory and infectious morbidity affected 28.3% (95% CI, 20.7–36.8%) and 4.2% (95% CI, 2.8–5.9%) of TCTA and 34.0% (95% CI, 21.5–47.7%) and 7.1% (95% CI, 2.7–13.3%) of DCTA triplets, respectively. The incidence of composite morbidity in TCTA and DCTA triplets was 29.6% (95% CI, 21.1–38.9%) and 34.0% (95% CI, 21.5–47.7%), respectively. When translating these figures into a risk analysis, the risk of neurological morbidity (OR, 5.4 (95% CI, 1.6–18.3)) was significantly higher in DCTA than in TCTA triplets, while there was no significant difference in the other morbidities explored. Only one study reported on outcomes of MCTA pregnancies, hence, no formal comparison with the other groups was performed.ConclusionDCTA triplets are at higher risk of perinatal mortality and morbidity than are TCTA triplets. Copyright © 2018 ISUOG. Published by John Wiley & Sons Ltd.
Does levator ani hiatal area configuration affect pelvic organ prolapse?
Authors: Xuan Y. , Friedman T. , Dietz H. P. 
Published: December 2018

ABSTRACTObjectiveLevator ani trauma and hiatal overdistension have been shown to be associated with female pelvic organ prolapse (POP); however, the role of the shape of the levator hiatus in POP has not been examined to date. The aim of this study was to investigate the association between the configuration of the levator ani hiatus and POP.MethodsThis was a retrospective study of 547 women who attended a tertiary urogynecological center for symptoms of pelvic floor and lower urinary tract dysfunction between October 2014 and August 2016. All women underwent a standardized interview and prolapse assessment using the International Continence Society (ICS) Pelvic Organ Prolapse Quantification (POP‐Q) method and four‐dimensional translabial ultrasound (TLUS). Measurements of the hiatal anteroposterior diameter (APD), coronal diameter (CD) and hiatal area (HA), at rest and on maximal Valsalva maneuver, and those of organ descent were performed offline at a later date by an investigator blinded to all other data. Hiatal configuration was defined as the ratio APD/CD. Associations between HA and HA adjusted by APD/CD at rest and on maximal Valsalva and symptoms and signs of prolapse were analyzed statistically using logistic regression modelling.ResultsThe mean age of the women was 54 ± 13.6 (range, 16–89) years. Of the 547 women included, 241 (44%) presented with prolapse symptoms. Clinically significant POP was detected in 406 (74%) patients and significant prolapse on TLUS was detected in 331 (61%). Hiatal ballooning was observed in 310 (57%) women and this was strongly associated with signs and symptoms of POP. HA at rest and on Valsalva was associated with significant POP both on clinical examination and on TLUS. Adjusted odds ratios for hiatal shape showed no effect of the hiatal configuration on the association between HA and POP.ConclusionHiatal shape does not seem to influence the association between HA and symptoms and signs of prolapse. Copyright © 2018 ISUOG. Published by John Wiley & Sons Ltd.
Formatting biological big data for modern machine learning in drug discovery
Authors: Duran‐Frigola Miquel , Fernández‐Torras Adrià , Bertoni Martino , Aloy Patrick 
Published: December 2018

Biological data is accumulating at an unprecedented rate, escalating the role of data‐driven methods in computational drug discovery. This scenario is favored by recent advances in machine learning algorithms, which are optimized for huge datasets and consistently beat the predictive performance of previous art, rapidly approaching human expert reasoning. The urge to couple biological data to cutting‐edge machine learning has spurred developments in data integration and knowledge representation, especially in the form of heterogeneous, multiplex and semantically‐rich biological networks. Today, thanks to the propitious rise in knowledge embedding techniques, these large and complex biological networks can be converted to a vector format that suits the majority of machine learning implementations. Here, we explain why this can be particularly transformative for drug discovery where, for decades, customary chemoinformatics methods have employed vector descriptors of compound structures as the standard input of their prediction tasks. A common vector format to represent biology and chemistry may push biological information into most of the existing steps of the drug discovery pipeline, boosting the accuracy of predictions and uncovering connections between small molecules and other biological entities such as targets or diseases.This article is categorized under:
Computer and Information Science > Databases and Expert Systems
Computer and Information Science > Chemoinformatics
Reconsidering Sovereignty, Ownership and Consent in Natural Resource Contracts: From Concepts to Practice
Authors: Cotula Lorenzo 
Published: December 2018

AbstractA wave of commercial investments in the natural resource sectors has rekindled debates about the place of contracts in the interface between economic governance and control over natural resources. Contracts between investors and states have provided the legal basis for many natural resource projects. They have also formed the object of renegotiations and disputes. Meanwhile, community-investor agreements have emerged as a strategy to promote local support for the business or advance local claims to natural resources. This chapter interrogates the fundamental parameters on which resource-related contracting rests. It first examines, based on positive law, the foundations of natural resource contracts, focusing on the notions of sovereignty, ownership and consent. This conceptual exploration highlights that, while consent underpins the contract, the legal construction of (state) sovereignty and (resource) ownership sets parameters for the expression of consent—namely, the actors whose consent is required, the processes through which consent is formed and manifested, and the bounds within which consent can lawfully operate. The chapter then distils some practical implications for natural resource contracts, focusing on illustrative issues relating both to the substantive and procedural dimensions of investor-state contracts, and to reframing the contracting process around a wider range of resource right holders and affected actors. The findings provide pointers for piecing together the diverse and possibly conflicting commercial and non-commercial interests that are at stake in natural resource contracts.
Empirical Run‐Time Bias Correction for Antarctic Regional Climate Projections With a Stretched‐Grid AGCM
Authors: Krinner Gerhard , Beaumet Julien , Favier Vincent , Déqué Michel , Brutel‐Vuilmet Claire 
Published: December 2018

AbstractThis work presents snapshot simulations of the late 20th and late 21st century Antarctic climate under the RCP8.5 scenario carried out with an empirically bias‐corrected global atmospheric general circulation model (AGCM), forced with bias‐corrected sea‐surface temperatures and sea ice and run with about 100‐km resolution over Antarctica. The bias correction substantially improves the simulated mean late 20th century climate. The simulated atmospheric circulation of the bias‐corrected model compares very favorably to the best available AMIP (Atmospheric Model Intercomparison Project)‐type climate models. The simulated interannual circulation variability is improved by the bias correction. Depending on the metric, a slight improvement or degradation is found in the simulated variability on synoptic timescales. The simulated climate change over the 21st century is broadly similar in the corrected and uncorrected versions of the atmospheric model, and atmospheric circulation patterns are not geographically “pinned” by the applied bias correction. These results suggest that the method presented here can be used for bias‐corrected climate projections. Finally, the authors discuss different possible choices in terms of the place of bias corrections and other intermediate steps in the modeling chain leading from global coupled climate simulations to impact assessment.
Energy autonomous electronic skin
Authors: García Núñez Carlos , Manjakkal Libu , Dahiya Ravinder 
Published: December 2018

AbstractEnergy autonomy is key to the next generation portable and wearable systems for several applications. Among these, the electronic-skin or e-skin is currently a matter of intensive investigations due to its wider applicability in areas, ranging from robotics to digital health, fashion and internet of things (IoT). The high density of multiple types of electronic components (e.g. sensors, actuators, electronics, etc.) required in e-skin, and the need to power them without adding heavy batteries, have fuelled the development of compact flexible energy systems to realize self-powered or energy-autonomous e-skin. The compact and wearable energy systems consisting of energy harvesters, energy storage devices, low-power electronics and efficient/wireless power transfer-based technologies, are expected to revolutionize the market for wearable systems and in particular for e-skin. This paper reviews the development in the field of self-powered e-skin, particularly focussing on the available energy-harvesting technologies, high capacity energy storage devices, and high efficiency power transmission systems. The paper highlights the key challenges, critical design strategies, and most promising materials for the development of an energy-autonomous e-skin for robotics, prosthetics and wearable systems. This paper will complement other reviews on e-skin, which have focussed on the type of sensors and electronics components.
Soundness and completeness of quantum root-mean-square errors
Authors: Ozawa Masanao 
Published: December 2018

AbstractDefining and measuring the error of a measurement is one of the most fundamental activities in experimental science. However, quantum theory shows a peculiar difficulty in extending the classical notion of root-mean-square (rms) error to quantum measurements. A straightforward generalization based on the noise-operator was used to reformulate Heisenberg’s uncertainty relation on the accuracy of simultaneous measurements to be universally valid and made the conventional formulation testable to observe its violation. Recently, its reliability was examined based on an anomaly that the error vanishes for some inaccurate measurements, in which the meter does not commute with the measured observable. Here, we propose an improved definition for a quantum generalization of the classical rms error, which is state-dependent, operationally definable, and perfectly characterizes accurate measurements. Moreover, it is shown that the new notion maintains the previously obtained universally valid uncertainty relations and their experimental confirmations without changing their forms and interpretations, in contrast to a prevailing view that a state-dependent formulation for measurement uncertainty relation is not tenable.