bluuebunny/crossref_metadata_2025_split huggingface dataset:
Irreversible Cysteine‐Selective Protein Labeling Employing Modular Electrophilic Tetrafluoroethylation Reagents
Authors: Václavík Jiří , Zschoche Reinhard , Klimánková Iveta , Matoušek Václav , Beier Petr , Hilvert Donald , Togni Antonio 
Published: February 2017

AbstractFluoroalkylation reagents based on hypervalent iodine are widely used to transfer fluoroalkyl moieties to various nucleophiles. However, the transferred groups have so far been limited to simple structural motifs. We herein report a reagent featuring a secondary amine that can be converted to amide, sulfonamide, and tertiary amine derivatives in one step. The resulting reagents bear manifold functional groups, many of which would not be compatible with the original synthetic pathway. Exploiting this structural versatility and the known high reactivity toward thiols, the new‐generation reagents were used in bioconjugation with an artificial retro‐aldolase, containing an exposed cysteine and a reactive catalytic lysine. Whereas commercial reagents based on maleimide and iodoacetamide labeled both sites, the iodanes exclusively modified the cysteine residue. The study thus demonstrates that modular fluoroalkylation reagents can be used as tools for cysteine‐selective bioconjugation.
A deep learning based strategy for identifying and associating mitotic activity with gene expression derived risk categories in estrogen receptor positive breast cancers
Authors: Romo‐Bucheli David , Janowczyk Andrew , Gilmore Hannah , Romero Eduardo , Madabhushi Anant 
Published: February 2017

AbstractThe treatment and management of early stage estrogen receptor positive (ER+) breast cancer is hindered by the difficulty in identifying patients who require adjuvant chemotherapy in contrast to those that will respond to hormonal therapy. To distinguish between the more and less aggressive breast tumors, which is a fundamental criterion for the selection of an appropriate treatment plan, Oncotype DX (ODX) and other gene expression tests are typically employed. While informative, these gene expression tests are expensive, tissue destructive, and require specialized facilities. Bloom‐Richardson (BR) grade, the common scheme employed in breast cancer grading, has been shown to be correlated with the Oncotype DX risk score. Unfortunately, studies have also shown that the BR grade determined experiences notable inter‐observer variability. One of the constituent categories in BR grading is the mitotic index. The goal of this study was to develop a deep learning (DL) classifier to identify mitotic figures from whole slides images of ER+ breast cancer, the hypothesis being that the number of mitoses identified by the DL classifier would correlate with the corresponding Oncotype DX risk categories. The mitosis detector yielded an average F‐score of 0.556 in the AMIDA mitosis dataset using a 6‐fold validation setup. For a cohort of 174 whole slide images with early stage ER+ breast cancer for which the corresponding Oncotype DX score was available, the distributions of the number of mitoses identified by the DL classifier was found to be significantly different between the high vs low Oncotype DX risk groups (P < 0.01). Comparisons of other risk groups, using both ODX score and histological grade, were also found to present significantly different automated mitoses distributions. Additionally, a support vector machine classifier trained to separate low/high Oncotype DX risk categories using the mitotic count determined by the DL classifier yielded a 83.19% classification accuracy. © 2017 International Society for Advancement of Cytometry
Large grains matter: contrasting bed stability and morphodynamics during two nearly identical experiments
Authors: MacKenzie Lucy G. , Eaton Brett C. 
Published: February 2017

AbstractWhile the stabilizing function of large grains in step‐pool streams has long been recognized, the role they play in gravel‐bed streams is less clear. Most researchers have ignored the role of large grains in gravel‐bed streams, and have assumed that the median bed surface size controls the erodibility of alluvial boundaries. The experiments presented herein challenge this convention. Two experiments were conducted that demonstrate the significant morphodynamic implications of a slight change to the coarse tail of the bed material. The two distributions had the same range of particle sizes, and nearly identical bulk d50 values (1.6 mm); however the d90 of experiment GSD1 was slightly finer (3.7 mm) than that for experiment GSD2 (3.9 mm). Transport rates during GSD1 were nearly four times greater than during GSD2 (even though the dimensionless shear stress was slightly lower), and the channel developed a sinuous pattern with well‐developed riffles, pools and bars. During GSD2 the initial rectangular channel remained virtually unchanged for the duration of the experiment. The relative stability of GSD2 seems to be associated with a slightly larger proportion of stable (large) grains on the bed surface: at the beginning of GSD1, 3.5% of the bed was immobile, while almost twice as much of it (6.1%) was immobile at the beginning of GSD2. The results demonstrate that the largest grains (not the median size) exert first‐order control on channel stability. Copyright © 2017 John Wiley & Sons, Ltd.
Dynamically correct formulations of the linearised Navier–Stokes equations
Authors: Dellar O. J. , Jones B. Ll 
Published: February 2017

SummaryMotivated by the need to efficiently obtain low‐order models of fluid flows around complex geometries for the purpose of feedback control system design, this paper considers the effect on system dynamics of basing plant models on different formulations of the linearised Navier–Stokes equations. We consider the dynamics of a single computational node formed by spatial discretisation of the governing equations in both primitive variables (momentum equation and continuity equation) and pressure Poisson equation formulations. This reveals fundamental numerical differences at the nodal level, whose effects on the system dynamics at the full system level are exemplified by considering the corresponding formulations of a two‐dimensional (2D) channel flow, subjected to a variety of different boundary conditions. Copyright © 2017 John Wiley & Sons, Ltd.
Inflammatory demyelination induces ependymal modifications concomitant to activation of adult (SVZ) stem cell proliferation
Authors: Pourabdolhossein Fereshteh , Gil‐Perotín Sara , Garcia‐Belda Paula , Dauphin Aurelien , Mozafari Sabah , Tepavcevic Vanja , Manuel Garcia Verdugo Jose , Baron‐Van Evercooren Anne 
Published: February 2017

AbstractEpendymal cells (E1/E2) and ciliated B1cells confer a unique pinwheel architecture to the ventricular surface of the subventricular zone (SVZ), and their cilia act as sensors to ventricular changes during development and aging. While several studies showed that forebrain demyelination reactivates the SVZ triggering proliferation, ectopic migration, and oligodendrogenesis for myelin repair, the potential role of ciliated cells in this process was not investigated. Using conventional and lateral wall whole mount preparation immunohistochemistry in addition to electron microscopy in a forebrain‐targeted model of experimental autoimmune encephalomyelitis (tEAE), we show an early decrease in numbers of pinwheels, B1 cells, and E2 cells. These changes were transient and simultaneous to tEAE‐induced SVZ stem cell proliferation. The early drop in B1/E2 cell numbers was followed by B1/E2 cell recovery. While E1 cell division and ependymal ribbon disruption were never observed, E1 cells showed important morphological modifications reflected by their enlargement, extended cytoskeleton, and reinforced cell–cell junction complexes overtime, possibly reflecting protective mechanisms against ventricular insults. Finally, tEAE disrupted motile cilia planar cell polarity and cilia orientation in ependymal cells. Therefore, significant ventricular modifications in ciliated cells occur early in response to tEAE suggesting a role for these cells in SVZ stem cell signalling not only during development/aging but also during inflammatory demyelination. These observations may have major implications for understanding pathophysiology of and designing therapeutic approaches for inflammatory demyelinating diseases such as MS.
Hippocampal subfields at ultra high field MRI: An overview of segmentation and measurement methods
Authors: Giuliano Alessia , Donatelli Graziella , Cosottini Mirco , Tosetti Michela , Retico Alessandra , Fantacci Maria Evelina 
Published: February 2017

ABSTRACTThe hippocampus is one of the most interesting and studied brain regions because of its involvement in memory functions and its vulnerability in pathological conditions, such as neurodegenerative processes. In the recent years, the increasing availability of Magnetic Resonance Imaging (MRI) scanners that operate at ultra‐high field (UHF), that is, with static magnetic field strength ≥7T, has opened new research perspectives. Compared to conventional high‐field scanners, these systems can provide new contrasts, increased signal‐to‐noise ratio and higher spatial resolution, thus they may improve the visualization of very small structures of the brain, such as the hippocampal subfields. Studying the morphometry of the hippocampus is crucial in neuroimaging research because changes in volume and thickness of hippocampal subregions may be relevant in the early assessment of pathological cognitive decline and Alzheimer's Disease (AD). The present review provides an overview of the manual, semi‐automated and fully automated methods that allow the assessment of hippocampal subfield morphometry at UHF MRI, focusing on the different hippocampal segmentation produced. © 2017 The Authors Hippocampus Published by Wiley Periodicals, Inc.
Histamine facilitates GABAergic transmission in the rat entorhinal cortex: Roles of H1 and H2 receptors, Na+‐permeable cation channels, and inward rectifier K+ channels
Authors: Cilz Nicholas I. , Lei Saobo 
Published: February 2017

ABSTRACTIn the brain, histamine (HA) serves as a neuromodulator and a neurotransmitter released from the tuberomammillary nucleus (TMN). HA is involved in wakefulness, thermoregulation, energy homeostasis, nociception, and learning and memory. The medial entorhinal cortex (MEC) receives inputs from the TMN and expresses HA receptors (H1, H2, and H3). We investigated the effects of HA on GABAergic transmission in the MEC and found that HA significantly increased the frequency of spontaneous inhibitory postsynaptic currents (sIPSCs) with an EC50 of 1.3 µM, but failed to significantly alter sIPSC amplitude. HA‐induced increases in sIPSC frequency were sensitive to tetrodotoxin (TTX), required extracellular Ca2+, and persisted when GDP‐β‐S, a G‐protein inactivator, was applied postsynaptically via the recording pipettes, indicating that HA increased GABA release by facilitating the excitability of GABAergic interneurons in the MEC. Recordings from local MEC interneurons revealed that HA significantly increased their excitability as determined by membrane depolarization, generation of an inward current at −65 mV, and augmentation of action potential firing frequency. Both H1 and H2 receptors were involved in HA‐induced increases in sIPSCs and interneuron excitability. Immunohistochemical staining showed that both H1 and H2 receptors are expressed on GABAergic interneurons in the MEC. HA‐induced depolarization of interneurons involved a mixed ionic mechanism including activation of a Na+‐permeable cation channel and inhibition of a cesium‐sensitive inward rectifier K+ channel, although HA also inhibited the delayed rectifier K+ channels. Our results may provide a cellular mechanism, at least partially, to explain the roles of HA in the brain. © 2017 Wiley Periodicals, Inc.
Snow disappearance timing is dominated by forest effects on snow accumulation in warm winter climates of the Pacific Northwest, United States
Authors: Dickerson‐Lange Susan E. , Gersonde Rolf F. , Hubbart Jason A. , Link Timothy E. , Nolin Anne W. , Perry Gwyneth H. , Roth Travis R. , Wayand Nicholas E. , Lundquist Jessica D. 
Published: February 2017

AbstractForests modify snow processes and affect snow water storage as well as snow disappearance timing. However, forest influences on snow accumulation and ablation vary with climate and topography and are therefore subject to temporal and spatial variability. We utilize multiple years of snow observations from across the Pacific Northwest, United States, to assess forest–snow interactions in the relatively warm winter conditions characteristic of maritime and transitional maritime–continental climates. We (a) quantify the difference in snow magnitude and disappearance timing between forests and open areas and (b) assess how forest modifications of snow accumulation and ablation combine to determine whether snow disappears later in the forest or in the open.We find that snow disappearance timing at 12 (out of 14) sites ranges from synchronous in the forest and open to snow persisting up to 13 weeks longer in the open relative to a forested area. By analyzing accumulation and ablation rates up to the day when snow first disappears from the forest, we find that the difference between accumulation rates in the open and forest is larger than the difference between ablation rates. Thus, canopy snow interception and subsequent loss, rather than ablation, set up longer snow duration in the open. However, at two relatively windy sites (hourly average wind speeds up to 8 and 17 m/s), differential snow disappearance timing is reversed: Snow persists 2–5 weeks longer in the forest. At the windiest sites, accumulation rates in the forest and open are similar. Ablation rates are higher in the open, but the difference between ablation rates in the forest and open at these sites is approximately equivalent to the difference at less windy sites. Thus, longer snow retention in the forest at the windiest sites is controlled by depositional differences rather than by reduced ablation rates. These findings suggest that improved quantification of forest effects on snow accumulation processes is needed to accurately predict the effect of forest management or natural disturbance on snow water resources.
Annual runoff assessment in arid and semiarid Mediterranean watersheds under the Budyko's framework
Authors: Viola F. , Caracciolo D. , Forestieri A. , Pumo D. , Noto L.V. 
Published: February 2017

AbstractThe solution of many practical water problems is strictly connected to the availability of reliable and widespread information about runoff. The estimation of mean annual runoff and its interannual variability for any basin over a wide region, even if ungauged, would be fundamental for both water resources assessment and planning and for water quality analysis. Starting from these premises, the main aim of this work is to show a new approach, based on the Budyko's framework, for mapping the mean annual surface runoff and deriving the probability distribution of the annual runoff in arid and semiarid watersheds. As a case study, the entire island of Sicily, Italy, is here proposed. First, time series data of annual rainfall, runoff, and reconstructed series of potential evapotranspiration have been combined within the Budyko's curve framework to obtain regional rules for rainfall partitioning between evapotranspiration and runoff. Then this knowledge has been used to infer long‐term annual runoff at the point scale by means of interpolated rainfall and potential evapotranspiration. The long‐term annual runoff raster layer has been obtained at each pixel of the drainage network, averaging the upstream runoff using advanced spatial analysis techniques within a GIS environment.Furthermore, 2 alternative methods are here proposed to derive the distribution of annual runoff, under the assumption of negligible interannual variations of basin water storage. The first method uses Monte Carlo simulations, combining rainfall and potential evapotranspiration randomly extracted from independent distributions. The second method is based on a simplification of the Budyko's curve and analytically provides the annual runoff distribution as the derived distribution of annual rainfall and potential evapotranspiration. Results are very encouraging: long‐term annual runoff and its distribution have been derived and compared with historical records at several gauged stations, obtaining satisfactory matching.
Influence of hypoxia on the stemness of umbilical cord matrix‐derived mesenchymal stem cells cultured on chitosan films
Authors: Taguchi Takashi , Cho Jane Y. , Hao Jijun , Nout‐Lomas Yvette S. , Kang Kyung‐Sun , Griffon Dominique J. 
Published: February 2017

ABSTRACTChitosan is attractive as a substrate for stem cell expansion because it improves stemness through formation of spheroids. Hypoxia has also been proposed as a strategy to enhance stemness and survival of stem cells afterin vivoimplantation. This study was therefore designed to evaluate the influence of hypoxia on chitosan‐induced behavior of stem cells. Umbilical cord matrix‐derived stem cells were cultured on chitosan film or standard plate under normoxia and hypoxia, for 3 and 7 days. Based on immunophenotyping, chitosan strongly suppresses the expression of CD90 and CD105 cell surface markers, changes partially reversed by combined exposure to hypoxia. Hypoxia generally increased the volume and number of spheroids formed on chitosan, but the cellularity of cultures on chitosan films remained lower than that of standard plates. After 7 days of culture, the expression of stemness related genes (Oct4,Sox2, andNanog) was best stimulated by combined exposure to chitosan and hypoxia. Based on our results, conditioning stem cells for 7 days on chitosan films under hypoxic conditions is recommended to enhance the stemness of stem cells, and minimize cell loss due to lack of attachment on chitosan. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 106B: 501–511, 2018.
Association of expression of selenoprotein P in mRNA and protein levels with metabolic syndrome in subjects with cardiovascular disease: Results of the Selenegene study
Authors: Gharipour Mojgan , Sadeghi Masoumeh , Salehi Mansour , Behmanesh Mehrdad , Khosravi Elham , Dianatkhah Minoo , Haghjoo Javanmard Shaghayegh , Razavi Rouzbeh , Gharipour Amin 
Published: February 2017

AbstractBackgroundSelenoprotein P (SeP) is involved in transporting selenium from the liver to target tissues. Because SeP confers protection against disease by reducing chronic oxidative stress, the present study aimed to assess the level of SeP in the serum of patients with metabolic syndrome (MetS) with a history of cardiovascular disease (CVD).MethodsA cross‐sectional study was conducted in 63 and 71 subjects with and without MetS in the presence of documented CVD. All demographic, anthropometric and cardiometabolic variables (lipids, blood glucose, blood pressure) were assessed. Lifestyle‐related factors and personal history and familial CVD risk factors were recorded. The expression of SELP in mRNA and protein levels in the serum was measured, and MetS was determined using ATPIII criteria. Binary logistic regression analysis demonstrated MetS and SeP to be dependent and independent variables, respectively.ResultsMean of systolic and diastolic blood pressure, triglyceride, high‐density lipoprotein‐cholesterol, fasting blood sugar, body mass index and waist circumference were higher among subjects with MetS (p = 0.05). The mean of selenium was higher among subjects with MetS, whereas the mean of SeP was lower among subjects with MetS (p < 0.001). In the unadjusted model, the SeP had decreased odds for MetS [odds ratio (OR) = 0.995; 95% confidence interval (CI) = 0.989–1.00] (p < 0.04). Furthermore, the association between MetS and SeP levels remained marginally significant even after adjusting for potential confounders such as age, gender, family history, smoking status and nutrition. SeP and waist circumference show a significant relationship (OR =0.995; 95% CI = 0.990–1.00) (p < 0.033).ConclusionsWe have demonstrated a significant decrease in circulating SeP levels according to MetS status in patients with documented cardiovascular disease.
The influence of plant protection by effective microorganisms on the content of bioactive phytochemicals in apples
Authors: Kusznierewicz Barbara , Lewandowska Anna , Martysiak‐Żurowska Dorota , Bartoszek Agnieszka 
Published: February 2017

AbstractBACKGROUNDThe phytochemicals of two apple cultivars (Yellow Transparent and Early Geneva) protected in two ways, conventionally with chemical pesticides or by effective microorganisms (EM), were compared. Two types of components were determined: lipids synthesised constitutively and generated via inducible pathways polyphenols along with antioxidant activity and profiles.RESULTSThe antioxidant activities assessed with ABTS, DPPH and Folin–Ciocalteu reagents were about two‐fold higher in the case of microbiologically protected apples. The qualitative composition of phenolics determined by LC‐DAD‐MS varied between cultivars and the part of apples studied, while the method of protection caused mainly differences in concentration of some groups of polyphenols (hydroxycinnamates, flavanols, dihydrochalcones, flavonols, anthocyanins). The apples from biological cultivation contained about 34–54% more phenolics than these from a conventional orchard. In contrast, lipid composition did not differ significantly between apples originating from conventional and bio‐crops.CONCLUSIONThe results indicate that the advantage of using the EM technology in agriculture may not only be the reduction of consumption of chemical fertilisers and synthetic pesticides, but also, at least in the case of apples, may lead to the production of crops with improved health quality due to the higher content of bioactive phytochemicals. © 2017 Society of Chemical Industry
The composition of cell walls from grape skin in Vitis vinifera intraspecific hybrids
Authors: Apolinar‐Valiente Rafael , Gómez‐Plaza Encarna , Terrier Nancy , Doco Thierry , Ros‐García José María 
Published: February 2017

AbstractBACKGROUNDMonastrell is a red grape cultivar adapted to the dry environmental conditions of Murcia, SE Spain. Its berries seem to be characterized by a rigid cell wall structure, which could make difficult the winemaking process. Cabernet Sauvignon cultivar is used to complement Monastrell wines in this region owing to its high phenolic content with high extractability. This study explores the skin cell wall composition of grapes from plants resulting from intraspecific crosses of Vitis vinifera cultivars Monastrell × Cabernet Sauvignon. Moreover, the morphology of the cell wall material (CWM) from some representative samples was visualized by transmission optical microscopy.RESULTSThe total sugar content of CWM from nine out of ten genotypes of the progeny was lower than that from Monastrell. Seven out of ten genotypes showed lower phenolic content than Cabernet Sauvignon. The CWM from nine out of ten hybrids presented lower protein content than that from Monastrell.CONCLUSIONThis study confirms that skin cell walls from Monastrell × Cabernet Sauvignon hybrid grapes presented major differences in composition compared with their parents. These data could help in the development of new cultivars adapted to the dry conditions of SE Spain and with a cell wall composition favouring extractability. © 2017 Society of Chemical Industry