bluuebunny/crossref_metadata_2025_split huggingface dataset:
Maternal inflammation has a profound effect on cortical interneuron development in a stage and subtype-specific manner
Authors: Vasistha Navneet A. , Pardo-Navarro Maria , Gasthaus Janina , Weijers Dilys , Müller Michaela K. , García-González Diego , Malwade Susmita , Korshunova Irina , Pfisterer Ulrich , von Engelhardt Jakob , Hougaard Karin S. , Khodosevich Konstantin 
Published: October 2019

AbstractSevere infections during pregnancy are one of the major risk factors for cognitive impairment in the offspring. It has been suggested that maternal inflammation leads to dysfunction of cortical GABAergic interneurons that in turn underlies cognitive impairment of the affected offspring. However, the evidence comes largely from studies of adult or mature brains and how the impairment of inhibitory circuits arises upon maternal inflammation is unknown. Here we show that maternal inflammation affects multiple steps of cortical GABAergic interneuron development, i.e., proliferation of precursor cells, migration and positioning of neuroblasts, as well as neuronal maturation. Importantly, the development of distinct subtypes of cortical GABAergic interneurons was discretely impaired as a result of maternal inflammation. This translated into a reduction in cell numbers, redistribution across cortical regions and layers, and changes in morphology and cellular properties. Furthermore, selective vulnerability of GABAergic interneuron subtypes was associated with the stage of brain development. Thus, we propose that maternally derived insults have developmental stage-dependent effects, which contribute to the complex etiology of cognitive impairment in the affected offspring.
Topological kink plasmons on magnetic-domain boundaries
Authors: Jin Dafei , Xia Yang , Christensen Thomas , Freeman Matthew , Wang Siqi , Fong King Yan , Gardner Geoffrey C. , Fallahi Saeed , Hu Qing , Wang Yuan , Engel Lloyd , Xiao Zhi-Li , Manfra Michael J. , Fang Nicholas X. , Zhang Xiang 
Published: October 2019

AbstractTwo-dimensional topological materials bearing time reversal-breaking magnetic fields support protected one-way edge modes. Normally, these edge modes adhere to physical edges where material properties change abruptly. However, even in homogeneous materials, topology still permits a unique form of edge modes – kink modes – residing at the domain boundaries of magnetic fields within the materials. This scenario, despite being predicted in theory, has rarely been demonstrated experimentally. Here, we report our observation of topologically-protected high-frequency kink modes – kink magnetoplasmons (KMPs) – in a GaAs/AlGaAs two-dimensional electron gas (2DEG) system. These KMPs arise at a domain boundary projected from an externally-patterned magnetic field onto a uniform 2DEG. They propagate unidirectionally along the boundary, protected by a difference of gap Chern numbers ($$\pm1$$
±
1
) in the two domains. They exhibit large tunability under an applied magnetic field or gate voltage, and clear signatures of nonreciprocity even under weak-coupling to evanescent photons.
Molecular mechanism of azoxy bond formation for azoxymycins biosynthesis
Authors: Guo Yuan-Yang , Li Zhen-Hua , Xia Tian-Yu , Du Yi-Ling , Mao Xu-Ming , Li Yong-Quan 
Published: October 2019

AbstractAzoxy bond is an important chemical bond and plays a crucial role in high energy density materials. However, the biosynthetic mechanism of azoxy bond remains enigmatic. Here we report that the azoxy bond biosynthesis of azoxymycins is an enzymatic and non-enzymatic coupling cascade reaction. In the first step, nonheme diiron N-oxygenase AzoC catalyzes the oxidization of amine to its nitroso analogue. Redox coenzyme pairs then facilitate the mutual conversion between nitroso group and hydroxylamine via the radical transient intermediates, which efficiently dimerize to azoxy bond. The deficiency of nucleophilic reactivity in AzoC is proposed to account for the enzyme’s non-canonical oxidization of amine to nitroso product. Free nitrogen radicals induced by coenzyme pairs are proposed to be responsible for the efficient non-enzymatic azoxy bond formation. This mechanism study will provide molecular basis for the biosynthesis of azoxy high energy density materials and other valuable azoxy chemicals.
Transient hysteresis and inherent stochasticity in gene regulatory networks
Authors: Pájaro M. , Otero-Muras I. , Vázquez C. , Alonso A. A. 
Published: October 2019

AbstractCell fate determination, the process through which cells commit to differentiated states is commonly mediated by gene regulatory motifs with mutually exclusive expression states. The classical deterministic picture for cell fate determination includes bistability and hysteresis, which enables the persistence of the acquired cellular state after withdrawal of the stimulus, ensuring a robust cellular response. However, stochasticity inherent to gene expression dynamics is not compatible with hysteresis, since the stationary solution of the governing Chemical Master Equation does not depend on the initial conditions. We provide a quantitative description of a transient hysteresis phenomenon reconciling experimental evidence of hysteretic behaviour in gene regulatory networks with inherent stochasticity: under sufficiently slow dynamics hysteresis is transient. We quantify this with an estimate of the convergence rate to the equilibrium and introduce a natural landscape capturing system’s evolution that, unlike traditional cell fate potential landscapes, is compatible with coexistence at the microscopic level.
A universal ligand mediated method for large scale synthesis of transition metal single atom catalysts
Authors: Yang Hongzhou , Shang Lu , Zhang Qinghua , Shi Run , Waterhouse Geoffrey I. N. , Gu Lin , Zhang Tierui 
Published: October 2019

AbstractThere is interest in metal single atom catalysts due to their remarkable activity and stability. However, the synthesis of metal single atom catalysts remains somewhat ad hoc, with no universal strategy yet reported that allows their generic synthesis. Herein, we report a universal synthetic strategy that allows the synthesis of transition metal single atom catalysts containing Cr, Mn, Fe, Co, Ni, Cu, Zn, Ru, Pt or combinations thereof. Aberration-corrected high-angle annular dark-field scanning transmission electron microscopy and extended X-ray absorption fine structure spectroscopy confirm that the transition metal atoms are uniformly dispersed over a carbon black support. The introduced synthetic method allows the production of carbon-supported metal single atom catalysts in large quantities (>1 kg scale) with high metal loadings. A Ni single atom catalyst exhibits outstanding activity for electrochemical reduction of carbon dioxide to carbon monoxide, achieving a 98.9% Faradaic efficiency at −1.2 V.
ClimCKmap, a spatially, temporally and climatically explicit distribution database for the Italian fauna
Authors: Marta Silvio , Brunetti Michele , Ficetola Gentile Francesco , Stoch Fabio , Amori Giovanni , Cesaroni Donatella , Sbordoni Valerio , Provenzale Antonello 
Published: October 2019

AbstractUnderstanding and counteracting biodiversity losses requires quantitative knowledge on species distribution and abundance across space and time, as well as integrated and interoperable information on climate conditions and climatic changes. In this paper we developed a new biodiversity-climate database for Italy, ClimCKmap, based on the critical analysis, quality estimation and subsequent integration of the CKmap database with several high-resolution climate datasets. The original database was quality-checked for errors in toponym, species name and dating; the retained records were georeferenced and their distribution polygonised via Voronoi tessellation. We then integrated the species distribution information with several high-resolution climatic datasets: average monthly minimum and maximum temperature and total monthly precipitation were reconstructed for each Voronoi cell and year. The resulting database contains 268,977 occurrence records from 8,445 binomials and 16,332 localities, dating between 1680 and 2006 CE. This dataset, fully available at https://doi.org/10.6084/m9.figshare.7906739.v4 and http://hdl.handle.net/21.11125/a91f85cb-befd-4e14-8e83-24f17c4a0491, represents the largest, fully quality-checked, spatially, temporally and climatically explicit distribution database ever assembled for the Italian fauna, now ready for scientific exploitation.
SLE Plasma Profiling Identifies Unique Signatures of Lupus Nephritis and Discoid Lupus
Authors: Smith Michael A. , Henault Jill , Karnell Jodi L. , Parker Melissa L. , Riggs Jeffrey M. , Sinibaldi Dominic , Taylor Devon K. , Ettinger Rachel , Grant Ethan P. , Sanjuan Miguel A. , Kolbeck Roland , Petri Michelle A. , Casey Kerry A. 
Published: October 2019

AbstractSystemic lupus erythematosus (SLE) impacts multiple organ systems, although the causes of many individual SLE pathologies are poorly understood. This study was designed to elucidate organ-specific inflammation by identifying proteins that correlate with SLE organ involvement and to evaluate established biomarkers of disease activity across a diverse patient cohort. Plasma proteins and autoantibodies were measured across seven SLE manifestations. Comparative analyses between pathologies and correlation with the SLE Disease Activity Index (SLEDAI) were used to identify proteins associated with organ-specific and composite disease activity. Established biomarkers of composite disease activity, SLE-associated antibodies, type I interferon (IFN), and complement C3, correlated with composite SLEDAI, but did not significantly associate with many individual SLE pathologies. Two clusters of proteins were associated with renal disease in lupus nephritis samples. One cluster included markers of infiltrating leukocytes and the second cluster included markers of tissue remodelling. In patients with discoid lupus, a distinct signature consisting of elevated immunoglobulin A autoantibodies and interleukin-23 was observed. Our findings indicate that proteins from blood samples can be used to identify protein signatures that are distinct from established SLE biomarkers and SLEDAI and could be used to conveniently monitor multiple inflammatory pathways present in different organ systems.
Development of the equine gut microbiota
Authors: Lindenberg F. , Krych L. , Kot W. , Fielden J. , Frøkiær H. , van Galen G. , Nielsen D. S. , Hansen A. K. 
Published: October 2019

AbstractShortly after birth the mammalian gut is colonized, by a transient microbiota, highly susceptible to environment and diet, that eventually stabilizes and becomes the resident gut microbiota. In a window of opportunity during the colonization, oral tolerance is established towards resident bacteria. In this study, the development of the equine gut microbiota was investigated in ten foals from parturition until post weaning. We found great differences in the core species of the gut microbiota composition between time-matched samples on Day 7 and 20 post-partum. Between day 20 and Day 50 post-partum, we saw the gut microbiota became increasingly dominated by fiber fermenting species. After Day 50, no significant changes in species abundance were observed. Gene expression analysis of pro- and anti-inflammatory cytokines in the blood revealed no significant changes before and after weaning. In summary, relative stability of the gut microbiota was reached within 50 days post-partum and, weaning did not have a major impact on the microbial composition.
Mathematical model for volcanic harmonic tremors
Authors: Montegrossi Giordano , Farina Angiolo , Fusi Lorenzo , De Biase Antonietta 
Published: October 2019

AbstractHarmonic tremors consist in the release of infrasonic energy associated with volcanic activity. The typical frequency range of harmonic tremors is 0.1–12 Hz. We suppose that the harmonic tremors are due to the formation of bubbles entrapped in cavities that oscillate converting thermal energy into mechanic energy. Reproducing the natural phenomenon through an experimental apparatus, we propose here a mathematical model to describe the oscillatory mechanism and to detect the frequency as a function of the main physical parameters. We show that the frequency obtained through the model is in agreement with the one obtained through experimental measurements and with the data available from the literature, proving the consistency of the proposed model.
Upper limb joint kinematics using wearable magnetic and inertial measurement units: an anatomical calibration procedure based on bony landmark identification
Authors: Picerno Pietro , Caliandro Pietro , Iacovelli Chiara , Simbolotti Chiara , Crabolu Michele , Pani Danilo , Vannozzi Giuseppe , Reale Giuseppe , Rossini Paolo Maria , Padua Luca , Cereatti Andrea 
Published: October 2019

AbstractThe estimate of a consistent and clinically meaningful joint kinematics using wearable inertial and magnetic sensors requires a sensor-to-segment coordinate system calibration. State-of-the-art calibration procedures for the upper limb are based on functional movements and/or pre-determined postures, which are difficult to implement in subjects that have impaired mobility or are bedridden in acute units. The aim of this study was to develop and validate an alternative calibration procedure based on the direct identification of palpable anatomical landmarks (ALs) for an inertial and magnetic sensor-based upper limb movement analysis protocol. The proposed calibration procedure provides an estimate of three-dimensional shoulder/elbow angular kinematics and the linear trajectory of the wrist according to the standards proposed by the International Society of Biomechanics. The validity of the method was assessed against a camera-based optoelectronic system during uniaxial joint rotations and a reach-to-grasp task. Joint angular kinematics was found as characterised by a low-biased range of motion (<−2.6°), a low root mean square deviation (RMSD) (<4.4°) and a high waveform similarity coefficient (R2 > 0.995) with respect to the gold standard. Except for the cranio–caudal direction, the linear trajectory of the wrist was characterised by a low-biased range of motion (<11 mm) together with a low RMSD (8 mm) and high waveform similarity (R2 > 0.968). The proposed method enabled the estimation of reliable joint kinematics without requiring any active involvement of the patient during the calibration procedure, complying with the metrological standards and requirements of clinical movement analysis.
Basal Sodium-Dependent Vitamin C Transporter 2 polarization in choroid plexus explant cells in normal or scorbutic conditions
Authors: Ulloa Viviana , Saldivia Natalia , Ferrada Luciano , Salazar Katterine , Martínez Fernando , Silva-Alvarez Carmen , Magdalena Rocio , Oviedo María José , Montecinos Hernán , Torres-Vergara Pablo , Cifuentes Manuel , Nualart Francisco 
Published: October 2019

AbstractVitamin C is incorporated into the cerebrospinal fluid (CSF) through choroid plexus cells. While the transfer of vitamin C from the blood to the brain has been studied functionally, the vitamin C transporter, SVCT2, has not been detected in the basolateral membrane of choroid plexus cells. Furthermore, it is unknown how its expression is induced in the developing brain and modulated in scurvy conditions. We concluded that SVCT2 is intensely expressed in the second half of embryonic brain development and postnatal stages. In postnatal and adult brain, SVCT2 is highly expressed in all choroidal plexus epithelial cells, shown by colocalization with GLUT1 in the basolateral membranes and without MCT1 colocalization, which is expressed in the apical membrane. We confirmed that choroid plexus explant cells (in vitro) form a sealed epithelial structure, which polarized basolaterally, endogenous or overexpressed SVCT2. These results are reproduced in vivo by injecting hSVCT2wt-EYFP lentivirus into the CSF. Overexpressed SVCT2 incorporates AA (intraperitoneally injected) from the blood to the CSF. Finally, we observed in Guinea pig brain under scorbutic condition, that normal distribution of SVCT2 in choroid plexus may be regulated by peripheral concentrations of vitamin C. Additionally, we observed that SVCT2 polarization also depends on the metabolic stage of the choroid plexus cells.
Radiomics and MGMT promoter methylation for prognostication of newly diagnosed glioblastoma
Authors: Sasaki Takahiro , Kinoshita Manabu , Fujita Koji , Fukai Junya , Hayashi Nobuhide , Uematsu Yuji , Okita Yoshiko , Nonaka Masahiro , Moriuchi Shusuke , Uda Takehiro , Tsuyuguchi Naohiro , Arita Hideyuki , Mori Kanji , Ishibashi Kenichi , Takano Koji , Nishida Namiko , Shofuda Tomoko , Yoshioka Ema , Kanematsu Daisuke , Kodama Yoshinori , Mano Masayuki , Nakao Naoyuki , Kanemura Yonehiro 
Published: October 2019

AbstractWe attempted to establish a magnetic resonance imaging (MRI)-based radiomic model for stratifying prognostic subgroups of newly diagnosed glioblastoma (GBM) patients and predicting O (6)-methylguanine-DNA methyltransferase promotor methylation (pMGMT-met) status of the tumor. Preoperative MRI scans from 201 newly diagnosed GBM patients were included in this study. A total of 489 texture features including the first-order feature, second-order features from 162 datasets, and location data from 182 datasets were collected. Supervised principal component analysis was used for prognostication and predictive modeling for pMGMT-met status was performed based on least absolute shrinkage and selection operator regression. 22 radiomic features that were correlated with prognosis were used to successfully stratify patients into high-risk and low-risk groups (p = 0.004, Log-rank test). The radiomic high- and low-risk stratification and pMGMT status were independent prognostic factors. As a matter of fact, predictive accuracy of the pMGMT methylation status was 67% when modeled by two significant radiomic features. A significant survival difference was observed among the combined high-risk group, combined intermediate-risk group (this group consists of radiomic low risk and pMGMT-unmet or radiomic high risk and pMGMT-met), and combined low-risk group (p = 0.0003, Log-rank test). Radiomics can be used to build a prognostic score for stratifying high- and low-risk GBM, which was an independent prognostic factor from pMGMT methylation status. On the other hand, predictive accuracy of the pMGMT methylation status by radiomic analysis was insufficient for practical use.
Airway epithelial cell isolation techniques affect DNA methylation profiles with consequences for analysis of asthma related perturbations to DNA methylation
Authors: Clifford Rachel L. , Patel Jamie , MacIsaac Julia L. , McEwen Lisa M. , Johnson Simon R. , Shaw Dominick , Knox Alan J. , Hackett Tillie-Louise , Kobor Michael S. 
Published: October 2019

AbstractThe airway epithelium forms the interface between the inhaled environment and the lung. The airway epithelium is dysfunctional in asthma and epigenetic mechanisms are considered a contributory factor. We hypothesised that the DNA methylation profiles of cultured primary airway epithelial cells (AECs) would differ between cells isolated from individuals with asthma (n = 17) versus those without asthma (n = 16). AECs were isolated from patients by two different isolation techniques; pronase digestion (9 non-asthmatic, 8 asthmatic) and bronchial brushings (7 non-asthmatic and 9 asthmatic). DNA methylation was assessed using an Illumina Infinium HumanMethylation450 BeadChip array. DNA methylation of AECs clustered by isolation technique and linear regression identified 111 CpG sites differentially methylated between isolation techniques in healthy individuals. As a consequence, the effect of asthmatic status on DNA methylation was assessed within AEC samples isolated using the same technique. In pronase isolated AECs, 15 DNA regions were differentially methylated between asthmatics and non-asthmatics. In bronchial brush isolated AECs, 849 differentially methylated DNA regions were identified with no overlap to pronase regions. In conclusion, regardless of cell isolation technique, differential DNA methylation was associated with asthmatic status in AECs, providing further evidence for aberrant DNA methylation as a signature of epithelial dysfunction in asthma.
Improved gene co-expression network quality through expression dataset down-sampling and network aggregation
Authors: Liesecke Franziska , De Craene Johan-Owen , Besseau Sébastien , Courdavault Vincent , Clastre Marc , Vergès Valentin , Papon Nicolas , Giglioli-Guivarc’h Nathalie , Glévarec Gaëlle , Pichon Olivier , Dugé de Bernonville Thomas 
Published: October 2019

AbstractLarge-scale gene co-expression networks are an effective methodology to analyze sets of co-expressed genes and discover new gene functions or associations. Distances between genes are estimated according to their expression profiles and are visualized in networks that may be further partitioned to reveal communities of co-expressed genes. Creating expression profiles is now eased by the large amounts of publicly available expression data (microarrays and RNA-seq). Although many distance calculation methods have been intensively compared and reviewed in the past, it is unclear how to proceed when many samples reflecting a wide range of different conditions are available. Should as many samples as possible be integrated into network construction or be partitioned into smaller sets of more related samples? Previous studies have indicated a saturation in network performances to capture known associations once a certain number of samples is included in distance calculations. Here, we examined the influence of sample size on co-expression network construction using microarray and RNA-seq expression data from three plant species. We tested different down-sampling methods and compared network performances in recovering known gene associations to networks obtained from full datasets. We further examined how aggregating networks may help increase this performance by testing six aggregation methods.
Performance of landscape composition metrics for predicting water quality in headwater catchments
Authors: Staponites Linda R. , Barták Vojtěch , Bílý Michal , Simon Ondřej P. 
Published: October 2019

AbstractLand use is a predominant threat to the ecological integrity of streams and rivers. Understanding land use-water quality interactions is essential for the development and prioritization of management strategies and, thus, the improvement of water quality. Weighting schemes for land use have recently been employed as methods to advance the predictive power of empirical models, however, their performance has seldom been explored for various water quality parameters. In this work, multiple landscape composition metrics were applied within headwater catchments of Central Europe to investigate how weighting land use with certain combinations of spatial and topographic variables, while implementing alternate distance measures and functions, can influence predictions of water quality. The predictive ability of metrics was evaluated for eleven water quality parameters using linear regression. Results indicate that stream proximity, measured with Euclidean distance, in combination with slope or log-transformed flow accumulation were dominant factors affecting the concentrations of pH, total phosphorus, nitrite and orthophosphate phosphorus, whereas the unweighted land use composition was the most effective predictor of calcium, electrical conductivity, nitrates and total suspended solids. Therefore, both metrics are recommended when examining land use-water quality relationships in small, submontane catchments and should be applied according to individual water quality parameter.