bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evidence for a palaeo-subglacial lake on the Antarctic continental shelf
Authors: Kuhn Gerhard , Hillenbrand Claus-Dieter , Kasten Sabine , Smith James A. , Nitsche Frank O. , Frederichs Thomas , Wiers Steffen , Ehrmann Werner , Klages Johann P. , Mogollón José M. 
Published: June 2017

AbstractSubglacial lakes are widespread beneath the Antarctic Ice Sheet but their control on ice-sheet dynamics and their ability to harbour life remain poorly characterized. Here we present evidence for a palaeo-subglacial lake on the Antarctic continental shelf. A distinct sediment facies recovered from a bedrock basin in Pine Island Bay indicates deposition within a low-energy lake environment. Diffusive-advection modelling demonstrates that low chloride concentrations in the pore water of the corresponding sediments can only be explained by initial deposition of this facies in a freshwater setting. These observations indicate that an active subglacial meltwater network, similar to that observed beneath the extant ice sheet, was also active during the last glacial period. It also provides a new framework for refining the exploration of these unique environments.
Experimental discrimination of ion stopping models near the Bragg peak in highly ionized matter
Authors: Cayzac W. , Frank A. , Ortner A. , Bagnoud V. , Basko M. M. , Bedacht S. , Bläser C. , Blažević A. , Busold S. , Deppert O. , Ding J. , Ehret M. , Fiala P. , Frydrych S. , Gericke D. O. , Hallo L. , Helfrich J. , Jahn D. , Kjartansson E. , Knetsch A. , Kraus D. , Malka G. , Neumann N. W. , Pépitone K. , Pepler D. , Sander S. , Schaumann G. , Schlegel T. , Schroeter N. , Schumacher D. , Seibert M. , Tauschwitz An. , Vorberger J. , Wagner F. , Weih S. , Zobus Y. , Roth M. 
Published: June 2017

AbstractThe energy deposition of ions in dense plasmas is a key process in inertial confinement fusion that determines the α-particle heating expected to trigger a burn wave in the hydrogen pellet and resulting in high thermonuclear gain. However, measurements of ion stopping in plasmas are scarce and mostly restricted to high ion velocities where theory agrees with the data. Here, we report experimental data at low projectile velocities near the Bragg peak, where the stopping force reaches its maximum. This parameter range features the largest theoretical uncertainties and conclusive data are missing until today. The precision of our measurements, combined with a reliable knowledge of the plasma parameters, allows to disprove several standard models for the stopping power for beam velocities typically encountered in inertial fusion. On the other hand, our data support theories that include a detailed treatment of strong ion-electron collisions.
Tracing the oxygen isotope composition of the upper Earth’s atmosphere using cosmic spherules
Authors: Pack Andreas , Höweling Andres , Hezel Dominik C. , Stefanak Maren T. , Beck Anne-Katrin , Peters Stefan T. M. , Sengupta Sukanya , Herwartz Daniel , Folco Luigi 
Published: June 2017

AbstractMolten I-type cosmic spherules formed by heating, oxidation and melting of extraterrestrial Fe,Ni metal alloys. The entire oxygen in these spherules sources from the atmosphere. Therefore, I-type cosmic spherules are suitable tracers for the isotopic composition of the upper atmosphere at altitudes between 80 and 115 km. Here we present data on I-type cosmic spherules collected in Antarctica. Their composition is compared with the composition of tropospheric O2. Our data suggest that the Earth's atmospheric O2 is isotopically homogenous up to the thermosphere. This makes fossil I-type micrometeorites ideal proxies for ancient atmospheric CO2 levels.
Direct and simultaneous observation of ultrafast electron and hole dynamics in germanium
Authors: Zürch Michael , Chang Hung-Tzu , Borja Lauren J. , Kraus Peter M. , Cushing Scott K. , Gandman Andrey , Kaplan Christopher J. , Oh Myoung Hwan , Prell James S. , Prendergast David , Pemmaraju Chaitanya D. , Neumark Daniel M. , Leone Stephen R. 
Published: June 2017

AbstractUnderstanding excited carrier dynamics in semiconductors is crucial for the development of photovoltaics and efficient photonic devices. However, overlapping spectral features in optical pump-probe spectroscopy often render assignments of separate electron and hole carrier dynamics ambiguous. Here, ultrafast electron and hole dynamics in germanium nanocrystalline thin films are directly and simultaneously observed by ultrafast transient absorption spectroscopy in the extreme ultraviolet at the germanium M4,5 edge. We decompose the spectra into contributions of electronic state blocking and photo-induced band shifts at a carrier density of 8 × 1020 cm−3. Separate electron and hole relaxation times are observed as a function of hot carrier energies. A first-order electron and hole decay of ∼1 ps suggests a Shockley–Read–Hall recombination mechanism. The simultaneous observation of electrons and holes with extreme ultraviolet transient absorption spectroscopy paves the way for investigating few- to sub-femtosecond dynamics of both holes and electrons in complex semiconductor materials and across junctions.
Immune cell-derived cytokines contribute to obesity-related inflammation, fibrogenesis and metabolic deregulation in human adipose tissue
Authors: Caër Charles , Rouault Christine , Le Roy Tiphaine , Poitou Christine , Aron-Wisnewsky Judith , Torcivia Adriana , Bichet Jean-Christophe , Clément Karine , Guerre-Millo Michèle , André Sébastien 
Published: June 2017

AbstractAdipose tissue contains a variety of immune cells, which vary in abundance and phenotype with obesity. The contribution of immune cell-derived factors to inflammatory, fibrotic and metabolic alterations in adipose tissue is not well established in human obesity. Human primary adipose tissue cells, including pre-adipocytes, endothelial cells and mature adipocytes, were used to investigate deregulation of cell- and pathway-specific gene profiles. Among factors known to alter adipose tissue biology, we focus on inflammatory (IL-1β and IL-17) and pro-fibrotic (TGF-β1) factors. rIL-1β and rIL-17 induced concordant pro-inflammatory transcriptional programs in pre-adipocytes and endothelial cells, with a markedly more potent effect of IL-1β than IL-17. None of these cytokines had significant effect on fibrogenesis-related gene expression, contrasting with rTGF-β1-induced up-regulation of extracellular matrix components and pro-fibrotic factors. In mature adipocytes, all three factors promoted down-regulation of genes functionally involved in lipid storage and release. IL-1β and IL-17 impacted adipocyte metabolic genes in relation with their respective pro-inflammatory capacity, while the effect of TGF-β1 occurred in face of an anti-inflammatory signature. These data revealed that IL-1β and IL-17 had virtually no effect on pro-fibrotic alterations but promote inflammation and metabolic dysfunction in human adipose tissue, with a prominent role for IL-1β.
Reconstruction of Complex Directional Networks with Group Lasso Nonlinear Conditional Granger Causality
Authors: Yang Guanxue , Wang Lin , Wang Xiaofan 
Published: June 2017

AbstractReconstruction of networks underlying complex systems is one of the most crucial problems in many areas of engineering and science. In this paper, rather than identifying parameters of complex systems governed by pre-defined models or taking some polynomial and rational functions as a prior information for subsequent model selection, we put forward a general framework for nonlinear causal network reconstruction from time-series with limited observations. With obtaining multi-source datasets based on the data-fusion strategy, we propose a novel method to handle nonlinearity and directionality of complex networked systems, namely group lasso nonlinear conditional granger causality. Specially, our method can exploit different sets of radial basis functions to approximate the nonlinear interactions between each pair of nodes and integrate sparsity into grouped variables selection. The performance characteristic of our approach is firstly assessed with two types of simulated datasets from nonlinear vector autoregressive model and nonlinear dynamic models, and then verified based on the benchmark datasets from DREAM3 Challenge4. Effects of data size and noise intensity are also discussed. All of the results demonstrate that the proposed method performs better in terms of higher area under precision-recall curve.
Statistical Analysis of Zebrafish Locomotor Behaviour by Generalized Linear Mixed Models
Authors: Liu Yiwen , Ma Ping , Cassidy Paige A. , Carmer Robert , Zhang Gaonan , Venkatraman Prahatha , Brown Skye A. , Pang Chi Pui , Zhong Wenxuan , Zhang Mingzhi , Leung Yuk Fai 
Published: June 2017

AbstractUpon a drastic change in environmental illumination, zebrafish larvae display a rapid locomotor response. This response can be simultaneously tracked from larvae arranged in multi-well plates. The resulting data have provided new insights into neuro-behaviour. The features of these data, however, present a challenge to traditional statistical tests. For example, many larvae display little or no movement. Thus, the larval responses have many zero values and are imbalanced. These responses are also measured repeatedly from the same well, which results in correlated observations. These analytical issues were addressed in this study by the generalized linear mixed model (GLMM). This approach deals with binary responses and characterizes the correlation of observations in the same group. It was used to analyze a previously reported dataset. Before applying the GLMM, the activity values were transformed to binary responses (movement vs. no movement) to reduce data imbalance. Moreover, the GLMM estimated the variations among the effects of different well locations, which would eliminate the location effects when two biological groups or conditions were compared. By addressing the data-imbalance and location-correlation issues, the GLMM effectively quantified true biological effects on zebrafish locomotor response.
CT-Based Local Distribution Metric Improves Characterization of COPD
Authors: Hoff Benjamin A. , Pompe Esther , Galbán Stefanie , Postma Dirkje S. , Lammers Jan-Willem J. , ten Hacken Nick H. T. , Koenderman Leo , Johnson Timothy D. , Verleden Stijn E. , de Jong Pim A. , Mohamed Hoesein Firdaus A. A. , van den Berge Maarten , Ross Brian D. , Galbán Craig J. 
Published: June 2017

AbstractParametric response mapping (PRM) of paired CT lung images has been shown to improve the phenotyping of COPD by allowing for the visualization and quantification of non-emphysematous air trapping component, referred to as functional small airways disease (fSAD). Although promising, large variability in the standard method for analyzing PRMfSAD has been observed. We postulate that representing the 3D PRMfSAD data as a single scalar quantity (relative volume of PRMfSAD) oversimplifies the original 3D data, limiting its potential to detect the subtle progression of COPD as well as varying subtypes. In this study, we propose a new approach to analyze PRM. Based on topological techniques, we generate 3D maps of local topological features from 3D PRMfSAD classification maps. We found that the surface area of fSAD (SfSAD) was the most robust and significant independent indicator of clinically meaningful measures of COPD. We also confirmed by micro-CT of human lung specimens that structural differences are associated with unique SfSAD patterns, and demonstrated longitudinal feature alterations occurred with worsening pulmonary function independent of an increase in disease extent. These findings suggest that our technique captures additional COPD characteristics, which may provide important opportunities for improved diagnosis of COPD patients.
Role of flagella and type four pili in the co-migration of Burkholderia terrae BS001 with fungal hyphae through soil
Authors: Yang Pu , Zhang Miaozhi , van Elsas Jan Dirk 
Published: June 2017

AbstractBurkholderia terrae BS001 has previously been found to be able to disperse along with growing fungal hyphae in soil, with the type-3 secretion system having a supportive role in this movement. In this study, we focus on the role of two motility- and adherence-associated appendages, i.e. type-4 pili (T4P) and flagella. Electron microcopy and motility testing revealed that strain BS001 produces polar flagella and can swim on semi-solid R2A agar. Flagellum- and T4P-negative mutants were then constructed to examine the ecological roles of the respective systems. Both in liquid media and on swimming agar, the mutant strains showed similar fitness to the wild-type strain in mixed culture. The flagellar mutant had completely lost its flagella, as well as its swimming capacity. It also lost its co-migration ability with two soil-exploring fungi, Lyophyllum sp. strain Karsten and Trichoderma asperellum 302, in soil microcosms. In contrast, the T4P mutant showed reduced surface twitching motility, whereas its co-migration ability in competition with the wild-type strain was slightly reduced. We conclude that the co-migration of strain BS001 with fungal hyphae through soil is dependent on the presence of functional flagella conferring swimming motility, with the T4P system having a minor effect.
Imbalance-Aware Machine Learning for Predicting Rare and Common Disease-Associated Non-Coding Variants
Authors: Schubach Max , Re Matteo , Robinson Peter N. , Valentini Giorgio 
Published: June 2017

AbstractDisease and trait-associated variants represent a tiny minority of all known genetic variation, and therefore there is necessarily an imbalance between the small set of available disease-associated and the much larger set of non-deleterious genomic variation, especially in non-coding regulatory regions of human genome. Machine Learning (ML) methods for predicting disease-associated non-coding variants are faced with a chicken and egg problem - such variants cannot be easily found without ML, but ML cannot begin to be effective until a sufficient number of instances have been found. Most of state-of-the-art ML-based methods do not adopt specific imbalance-aware learning techniques to deal with imbalanced data that naturally arise in several genome-wide variant scoring problems, thus resulting in a significant reduction of sensitivity and precision. We present a novel method that adopts imbalance-aware learning strategies based on resampling techniques and a hyper-ensemble approach that outperforms state-of-the-art methods in two different contexts: the prediction of non-coding variants associated with Mendelian and with complex diseases. We show that imbalance-aware ML is a key issue for the design of robust and accurate prediction algorithms and we provide a method and an easy-to-use software tool that can be effectively applied to this challenging prediction task.
High-Resolution Magnetic Resonance Imaging of the Regenerating Adult Zebrafish Heart
Authors: Koth Jana , Maguire Mahon L. , McClymont Darryl , Diffley Leonie , Thornton Victoria L. , Beech John , Patient Roger K. , Riley Paul R. , Schneider Jürgen E. 
Published: June 2017

AbstractThe adult zebrafish is a well-established model for studying heart regeneration, but due to its tissue opaqueness, repair has been primarily assessed using destructive histology, precluding repeated investigations of the same animal. We present a high-resolution, non-invasive in vivo magnetic resonance imaging (MRI) method incorporating a miniature respiratory and anaesthetic perfusion set-up for live adult zebrafish, allowing for visualization of scar formation and heart regeneration in the same animal over time at an isotropic 31 µm voxel resolution. To test the method, we compared well and poorly healing cardiac ventricles using a transgenic fish model that exhibits heat-shock (HS) inducible impaired heart regeneration. HS-treated groups revealed persistent scar tissue for 10 weeks, while control groups were healed after 4 weeks. Application of the advanced MRI technique allowed clear discrimination of levels of repair following cryo- and resection injury for several months. It further provides a novel tool for in vivo time-lapse imaging of adult fish for non-cardiac studies, as the method can be readily applied to image wound healing in other injured or diseased tissues, or to monitor tissue changes over time, thus expanding the range of questions that can be addressed in adult zebrafish and other small aquatic species.
One dimensional transport in silicon nanowire junction-less field effect transistors
Authors: Mirza Muhammad M. , Schupp Felix J. , Mol Jan A. , MacLaren Donald A. , Briggs G. Andrew D. , Paul Douglas J. 
Published: June 2017

AbstractJunction-less nanowire transistors are being investigated to solve short channel effects in future CMOS technology. Here we demonstrate 8 nm diameter silicon nanowire junction-less transistors with metallic doping densities which demonstrate clear 1D electronic transport characteristics. The 1D regime allows excellent gate modulation with near ideal subthreshold slopes, on- to off-current ratios above 108 and high on-currents at room temperature. Universal conductance scaling as a function of voltage and temperature similar to previous reports of Luttinger liquids and Coulomb gap behaviour at low temperatures suggests that many body effects including electron-electron interactions are important in describing the electronic transport. This suggests that modelling of such nanowire devices will require 1D models which include many body interactions to accurately simulate the electronic transport to optimise the technology but also suggest that 1D effects could be used to enhance future transistor performance.
Lipopolysaccharides induced inflammatory responses and electrophysiological dysfunctions in human-induced pluripotent stem cell derived cardiomyocytes
Authors: Yücel Gökhan , Zhao Zhihan , El-Battrawy Ibrahim , Lan Huan , Lang Siegfried , Li Xin , Buljubasic Fanis , Zimmermann Wolfram-Hubertus , Cyganek Lukas , Utikal Jochen , Ravens Ursula , Wieland Thomas , Borggrefe Martin , Zhou Xiao-Bo , Akin Ibrahim 
Published: June 2017

AbstractSevere infections like sepsis lead frequently to cardiomyopathy. The mechanisms are unclear and an optimal therapy for septic cardiomyopathy still lacks. The aim of this study is to establish an endotoxin-induced inflammatory model using human induced pluripotent stem cell (hiPSC) derived cardiomyocytes (hiPSC-CMs) for mechanistic and therapeutic studies. hiPSC-CMs were treated by lipopolysaccharide (LPS) in different concentrations for different times. ELISA, FACS, qPCR, and patch-clamp techniques were used for the study. TLR4 (Toll-like receptor 4) and its associated proteins, CD14, LBP (lipopolysaccharide binding protein), TIRAP (toll-interleukin 1 receptor domain containing adaptor protein), Ly96 (lymphocyte antigen 96) and nuclear factor kappa B as well as some pro-and anti-inflammatory factors are expressed in hiPSC-CMs. LPS-treatment for 6 hours increased the expression levels of pro-inflammatory and chemotactic cytokines (TNF-a, IL-1ß, IL-6, CCL2, CCL5, IL-8), whereas 48 hour-treatment elevated the expression of anti-inflammatory factors (IL-10 and IL-6). LPS led to cell injury resulting from exaggerated cell apoptosis and necrosis. Finally, LPS inhibited small conductance Ca2+-activated K+ channel currents, enhanced Na+/Ca2+-exchanger currents, prolonged action potential duration, suggesting cellular electrical dysfunctions. Our data demonstrate that hiPSC-CMs possess the functional reaction system involved in endotoxin-induced inflammation and can model some bacterium-induced inflammatory responses in cardiac myocytes.
Pretreatment C-reactive protein to albumin ratio for predicting overall survival in advanced pancreatic cancer patients
Authors: Hang Junjie , Xue Peng , Yang Haiyan , Li Shaobo , Chen Donghui , Zhu Lifei , Huang Weiyi , Ren Shujuan , Zhu Yue , Wang Liwei 
Published: June 2017

AbstractAlthough previous studies demonstrated that elevated C-reactive protein to albumin ratio (CAR) predicted poor prognosis in various solid tumors, little was known about the prognostic value of CAR in patients with advanced pancreatic cancer (APC). The aim of the present study was to assess CAR as one independent prognostic factor in predicting overall survival (OS) in APC patients who had received palliative chemotherapy. Data of 142 APC patients who received palliative chemotherapy between 2009 and 2014 were retrospectively documented. We classified the patients into two groups based on the optimal cutoff value of CAR identified by generating receiver operating characteristics (ROC) curve. The clinicopathological parameters were compared between two CAR groups. Pearson correlation test showed that the level of C-reactive protein (CRP) was inversely correlated with albumin (r = −0.387; P < 0.001). Kaplan-Meier analysis demonstrated overall survival (OS) was significantly longer in CAR < 0.156 group than CAR ≥ 0.156 group (11.2 vs 5.9 months, P < 0.001). CAR was an independent prognostic factor for OS in the Cox regression model (HR, 1.623; 95% CI, 1.093–2.410; P = 0.016). Furthermore, the discrimination ability of CAR (AUC = 0.648, P = 0.025) was slightly higher than that of other inflammation-based factors. Therefore, pretreatment CAR could be an independent prognostic biomarker for APC patients.
Simplifying the design of microstructured optical fibre pressure sensors
Authors: Osório Jonas H. , Chesini Giancarlo , Serrão Valdir A. , Franco Marcos A. R. , Cordeiro Cristiano M. B. 
Published: June 2017

AbstractIn this paper, we propose a way to simplify the design of microstructured optical fibres with high sensitivity to applied pressure. The use of a capillary fibre with an embedded core allows the exploration of the pressure-induced material birefringence due to the capillary wall displacements and the photoelastic effect. An analytical description of pressure-induced material birefringence is provided, and fibre modal characteristics are explored through numerical simulations. Moreover, a capillary fibre with an embedded core is fabricated and used to probe pressure variations. Even though the embedded-core fibre has a non-optimized structure, measurements showed a pressure sensitivity of (1.04 ± 0.01) nm/bar, which compares well with more complex, specially designed fibre geometries reported in the literature. These results demonstrate that this geometry enables a novel route towards the simplification of microstructured fibre-based pressure sensors.
RETRACTED ARTICLE:
ω-3 free fatty acids and all-trans retinoic acid
synergistically induce growth inhibition of three subtypes of breast
cancer cell lines
Authors: Lin Guangxiao , Zhu Shenglong , Wu Yikuan , Song Ci , Wang Wanjing , Zhang Yuan , Chen Yue-Lei , He Zhao 
Published: June 2017

AbstractAll-trans retinoic acid (ATRA), one of vitamin A
derivatives, shows greater growth inhibition of breast cancer cell
for ER-positive than ER-negative cells, while triple negative breast
cancer cell such as MDA-MB-231 cell is poorly responsive to ATRA
treatment. In this study, we found that combination of ω-3 free fatty acids (ω-3 FFAs) and ATRA exhibited
synergistic inhibition of cell growth in three subtypes
(ER+ MCF7,
HER2+ SK-BR-3, Triple negative
HCC1806 and MDA-MB-231 cells) of human breast cancer cell lines. The
combined treatment of ω-3 FFAs
and ATRA resulted in cell cycle arrest. ω-3 FFAs combined with ATRA synergistically provoked
cell apoptosis via the caspase signals but not p53. These findings
suggest that combined chemotherapy of ω-3 FFAs with ATRA is beneficial for improvement of
ATRA sensitivity in breast cancer cells.