bluuebunny/crossref_metadata_2025_split huggingface dataset:
A comprehensive approach to analyzing community dynamics using rank abundance curves
Authors: Avolio Meghan L. , Carroll Ian T. , Collins Scott L. , Houseman Gregory R. , Hallett Lauren M. , Isbell Forest , Koerner Sally E. , Komatsu Kimberly J. , Smith Melinda D. , Wilcox Kevin R. 
Published: October 2019

AbstractUnivariate and multivariate methods are commonly used to explore the spatial and temporal dynamics of ecological communities, but each has limitations, including oversimplification or abstraction of communities. Rank abundance curves (RACs) potentially integrate these existing methodologies by detailing species‐level community changes. Here, we had three goals: first, to simplify analysis of community dynamics by developing a coordinated set of R functions, and second, to demystify the relationships among univariate, multivariate, and RACs measures, and examine how each is influenced by the community parameters as well as data collection methods. We developed new functions for studying temporal changes and spatial differences in RACs in an update to the R package library(“codyn”), alongside other new functions to calculate univariate and multivariate measures of community dynamics. We also developed a new approach to studying changes in the shape of RAC curves. The R package update presented here increases the accessibility of univariate and multivariate measures of community change over time and difference over space. Next, we use simulated and real data to assess the RAC and multivariate measures that are output from our new functions, studying (1) if they are influenced by species richness and evenness, temporal turnover, and spatial variability and (2) how the measures are related to each other. Lastly, we explore the use of the measures with an example from a long‐term nutrient addition experiment. We find that the RAC and multivariate measures are not sensitive to species richness and evenness and that all the measures detail unique aspects of temporal change or spatial differences. We also find that species reordering is the strongest correlate of a multivariate measure of compositional change and explains most community change observed in long‐term nutrient addition experiment. Overall, we show that species reordering is potentially an understudied determinant of community changes over time or differences between treatments. The functions developed here should enhance the use of RACs to further explore the dynamics of ecological communities.
Suppressor of cytokine signalling 3 is crucial for interleukin‐7 receptor re‐expression after T‐cell activation and interleukin‐7 dependent proliferation
Authors: Güler Alptekin , Lopez Venegas Miguel , Adankwah Ernest , Mayatepek Ertan , Nausch Norman , Jacobsen Marc 
Published: October 2019

AbstractSOCS3 is a crucial feedback inhibitor of several cytokine pathways with potential regulatory functions during T cell receptor activation. A role of SOCS3 in IL‐7‐dependent homeostatic mechanisms has been assumed but the underlying mechanisms remain unclear. We investigated the role of SOCS3 in IL‐7 receptor α‐chain (IL‐7Rα) expression and IL‐7 effects on activated human CD4+ T cells. SOCS3 expression modulation by lentiviral transduction combined with T cell phenotyping, receptor signalling analysis, and a novel competitive in vitro assay were applied. Time course analyses following T‐cell activation showed IL‐7Rα re‐expression after initial down‐regulation that was accompanied by increased SOCS3 expression starting on day 2. T cells with low SOCS3 expression (SOCS3kd) had decreased IL‐7Rα levels due to impaired re‐expression. SOCS3 mediated effects on IL‐7Rα were not affected by recombinant IL‐7 or blocking of IL‐2. We found no evidence for SOCS3 effects on IL7RA transcriptional regulation. Functionally, SOCS3kd T cells showed decreased IL‐7‐dependent proliferation as compared to vector control T cells under competitive in vitro conditions. This impaired IL‐7 response of SOCS3kd T cells was accompanied by decreased STAT5 phosphorylation late during IL‐7 signalling. We identified a novel SOCS3 function in IL‐7Rα regulation during T‐cell activation with crucial implications for IL‐7‐dependent mechanisms.
Implications of genetic diagnostics in epilepsy surgery candidates: A single‐center cohort study
Authors: Sanders Maurits W. C. B. , Lemmens Cynthia M. C. , Jansen Floor E. , Brilstra Eva H. , Koeleman Bobby P. C. , Braun Kees P. J. ,   the Dutch Collaborative Epilepsy Surgery Program (LWEC)
Published: October 2019

AbstractObjectiveGenetic causes are increasingly identified in patients with focal epilepsy. These genetic causes may be related to the effectiveness of epilepsy surgery. We aimed to assess the use and yield of genetic testing in a large cohort of patients who were evaluated for epilepsy surgery.MethodsWe performed a retrospective single‐center consecutive cohort study of patients who were evaluated for surgery between 1990 and 2016. Within this cohort, we assessed the use of genetic testing—either before or after presurgical decision‐making. We evaluated genetic results as well as the outcome of presurgical decision‐making and surgery, and compared these end points for different subgroups—especially MRI‐positive vs MRI‐negative patients. Patients with tuberous sclerosis (TSC) and KRIT1 mutations were excluded from analysis.ResultsOf the 2385 epilepsy patients who were evaluated for surgery, 1280 (54%) received surgical treatment in our center. Of the entire cohort, 325 (14%) underwent genetic testing, comprising 156 of 450 MRI‐negative patients (35%) vs 169 of 1935 MRI‐positive patients (9%). A genetic cause of epilepsy was found in 40 of the 325 patients (12%, 2% of the entire cohort), mainly consisting of mutations in ion channel function and synaptic transmission genes, and mTOR pathway gene mutations. Three of the seven patients with mTOR pathway gene mutations underwent surgery; two achieved complete seizure freedom. One of the 17 patients with germline mutations in ion channel function and synaptic transmission genes received resective surgery but was not rendered seizure‐free; two other patients underwent invasive intracranial EEG‐monitoring before being rejected.SignificanceThis study shows that genetic testing is increasingly applied in focal epilepsy patients who are considered for epilepsy surgery. The diagnostic yield of genetic testing is highest in next generation sequencing techniques, and the outcome of genetic testing assists selecting eligible patients for invasive intracranial monitoring and resective surgery.
Der vergessene Mann
Authors: Gromoll Jörg , Schiffer Christian , Tüttelmann Frank 
Published: October 2019

AbstractDie Ursachen für Unfruchtbarkeit und ungewollte Kinderlosigkeit von Paaren können bei Frau und Mann liegen. Doch die „reproduktive Gesundheit“ des männlichen Geschlechts wurde lange vernachlässigt. Nun setzt die Forschung auf einen Blickwechsel.
Reliability of wavefront shaping based on coherent optical adaptive technique in deep tissue focusing
Authors: Hu Lejia , Hu Shuwen , Li Younong , Gong Wei , Si Ke 
Published: October 2019

AbstractWavefront shaping can compensate the wavefront distortions in deep tissue focusing, leading to an improved penetration depth. However, when using the backscattered signals as the feedback, unexpected compensation bias may be introduced, resulting in focusing position deviations or even no focus in the illumination focal plane. Here we investigated the reliability of wavefront shaping based on coherent optical adaptive technique in deep tissue focusing by measuring the position deviations between the foci in the illumination focal plane and the epi‐detection plane. The experimental results show that when the penetration depth reaches 150 μm in mouse brain tissue (with scattering coefficient ~22.42 mm−1) using a 488 nm laser and an objective lens with 0.75 numerical aperture, the center of the real focus will deviate out of one radius range of the Airy disk while the optimized focus in the epi‐detection plane maintained basically at the center. With the penetration depth increases, the peak to background ratio of the focus in the illumination focal plane decreases faster than that in the epi‐detection plane. The results indicate that when the penetration depth reaches 150 μm, feedback based on backscattered signals will make wavefront shaping lose its reliability, which may provide a guidance for applications of non‐invasive precise optogenetics or deep tissue optical stimulation using wavefront shaping methods. A, Intensity distribution in the epi‐detection plane and the illumination focal plane before and after correction, corresponding to brain sections with 250 and 300 μm thickness, respectively. Scale bar is 2 μm. B, Averaged focusing deviations in the epi‐detection plane (optimized) and the illumination focal plane (monitored) after compensation. The unit of the ordinate is one Airy disk diameter. Black dashed line represents one Airy disk radius. Bars represent the SE of each measurement set.
Preparation and oil–water separation of 3D kapok fiber‐reduced graphene oxide aerogel
Authors: Luo Zirong , Li Dandan , Tan Shaozao , Huang Langhuan 
Published: October 2019

AbstractBACKGROUNDOil spills from oil tankers and ships or industrial accidents have serious impacts on the ecological environment. There is an urgent need for finding effective ways to resolve these problems. The use of low‐cost and efficient adsorbents is considered to be one of the most effective ways.RESULTSIn this study, an ultra‐light 3D kapok fiber‐reduced graphene oxide (TKF‐rGO) aerogel was prepared by a simple and green one‐step hydrothermal method. The kapok fiber used as skeleton was embedded in a graphene network to successfully form a 3D aerogel structure. The as‐prepared TKF‐rGO aerogel featured low density, excellent mechanical strength, high thermal stability, and high hydrophobic lipophilicity. Furthermore, continuous oil–water separation could be achieved by the aerogel when connected to a vacuum system. The adsorption capacity of TKF‐rGO aerogel for various common oil products and organic solvents was 1.5‐fold greater than that of pure rGO aerogel and six‐fold greater than that of polypropylene melt spray, respectively. In addition, the initial adsorption capacity of the as‐prepared TKF‐rGO aerogel was maintained at 94% after eight cycles.CONCLUSIONThe TKF‐rGO aerogel could be synthesized by a low‐cost and green method, which was suitable for commercial production, and showed competitive adsorption capacities for oil removal. Thus, the TKF‐rGO aerogel is expected to be employed as a promising adsorbent in the removal of oil spill or hazardous organic solvents from water. © 2019 Society of Chemical Industry
Solvent Effect on the Relative Quantum Yield and Preferential Solvation of Biologically Active Coumarin Derivative
Authors: Koppal Varsha V. , Patil P. G. , Melavanki Raveendra , Kusanur Raviraj , Patil N. R. 
Published: October 2019

AbstractThis paper aims at studying the relative quantum yield and preferential solvation of biologically active coumarin derivative ethyl 8‐methoxy‐2‐oxo‐2H‐chromene‐3‐carboxylate (8EMOHCC) in different solvents and solvent mixture acetonitrile and dioxane (ACN + DXN). It is observed that the quantum yield of the title molecule increases with decrease in the solvent polarity that may be due to bathochromic effect and intermolecular charge transfer. Further, the ground state preferential solvation index (i.e., δs2) showed negative values in different binary solvent mixtures.
Analysis of Pure Collisional Quenching of 2‐Isopropylphenyl Boronic Acid Using Linear S–V Plots
Authors: Patil Sanmati S. , Sharma Kalpana , Melavanki Raveendra , Muttannavar Venktesh T. , Patil N. R. 
Published: October 2019

AbstractThe steady state studies of fluorescence quenching of excitation energy of heterocyclic compound namely 2‐isopropylphenyl boronic acid (2IPBA) by aniline quencher was carried out in 1,4‐dioxane (DX), toluene (TL), methanol (ML), heptane (HP), nonane (NN), butanol (BL), and propanol (PL) solvents with a view to understand the role of diffusion in the quenching mechanism. The quenching process is studied in the selected solvents using steady state method by linear S‐V plots.
Study of Rayleigh to Compton Scattering Ratio and Effective Atomic Number as a Function of Photon Energy and Scattering Angle
Authors: Manjunath A. , Mahalesh D. , Biradar Balaji , Kerur B. R. , Pushpanjali G. M. 
Published: October 2019

AbstractFor photon energies below 1 MeV the predominant phenomenon involved is photoelectric absorption, coherent scattering (Rayleigh), and incoherent scattering (Compton). Biological samples with small thickness attenuate the transmitted beam very little and the application of transmission technique is not possible, when atomic number variations are more significant. Indeed, the Rayleigh to Compton scattering ratio enables the material to be characterized only by its atomic number, independent of the material density or of the attenuation inside the tested object. Hence, evaluation of the parameter “effective atomic number” is still necessary to characterize the measurement sensibility and to establish a correlation with the estimated Rayleigh to Compton scattering ratio.
Omics‐based Identification of Glycan Structures as Biomarkers for a Variety of Diseases
Authors: Akiyoshi Sayaka , Iwata Michio , Berenger Francois , Yamanishi Yoshihiro 
Published: October 2019

AbstractGlycans play important roles in cell communication, protein interaction, and immunity, and structural changes in glycans are associated with the regulation of a range of biological pathways involved in disease. However, our understanding of the detailed relationships between specific diseases and glycans is very limited. In this study, we proposed an omics‐based method to investigate the correlations between glycans and a wide range of human diseases. We analyzed the gene expression patterns of glycogenes (glycosyltransferases and glycosidases) for 79 different diseases. A biological pathway‐based glycogene signature was constructed to identify the alteration in glycan biosynthesis and the associated glycan structures for each disease state. The degradation of N‐glycan and keratan sulfate, for example, may promote the growth or metastasis of multiple types of cancer, including endometrial, gastric, and nasopharyngeal. Our results also revealed that commonalities between diseases can be interpreted using glycogene expression patterns, as well as the associated glycan structure patterns at the level of the affected pathway. The proposed method is expected to be useful for understanding the relationships between glycans, glycogenes, and disease and identifying disease‐specific glycan biomarkers.
Naringenin Exerts Cardiovascular Protective Effect in a Palmitate‐Induced Human Umbilical Vein Endothelial Cell Injury Model via Autophagy Flux Improvement
Authors: Zhao Qiang , Yang Hongyan , Liu Fen , Luo Junyi , Zhao Qian , Li Xiaomei , Yang Yining 
Published: October 2019

ScopePalmitic acid (PA) contributes to the pathogenesis of cardiovascular disease by promoting endothelial dysfunction, while naringenin, most abundant in oranges, has been shown to exert multiple beneficial effects on the human cardiovascular system. This study explores whether naringenin prevents PA‐induced apoptosis in human umbilical vein endothelial cells (HUVECs).Methods and ResultsTreatment of PA for at least 24 h causes observable decrease in levels of cell viability, oxidative stress, disorder of autophagy flux, and apoptosis in HUVECs. Naringenin enhances the viability of the PA‐treated HUVECs and, additionally, effectively decreases oxidative stress by scavenging ROS, and increasing the SOD2 level and GPx activity. Autophagy flux is protected by naringenin, as evidenced by the decreases in the ratio of LC3B‐II/I, expression level of p62 and number of autophagosomes, and the increase in the number of autolysosomes in the PA‐induced HUVECs. These effects are confirmed by the oxidative stress inhibitor N‐acetyl‐cysteine and autophagy inhibitor chloroquine. The molecular data indicate that the protective effects of naringenin on autophagy flux may also be regulated via the JNK pathway, as verified via the application of JNK inhibitor SP600125.ConclusionThese findings provide a possible mechanism by which naringenin prevents endothelial dysfunction and cardiovascular diseases.
A compact and high‐selectivity tri‐band bandpass filter based on symmetrical stub‐loaded square ring resonator
Authors: Liu Liang , Liang Xianling , Jin Ronghong , Bai Xudong , Fan Haijun , Geng Junping 
Published: October 2019

AbstractA compact tri‐band bandpass filter is presented in this article, whose three passbands are realized by the lowest three resonant modes of a new structure of symmetrical stub‐loaded square ring resonator. The filter features a compact size of 0.049
λ
g2 (
λ
g is the guided wavelength) as well as a high selectivity with nine transmission zeros. In addition, by using the odd‐ and even‐mode analysis, its center frequencies can be easily tuned to the desired frequencies by the identical‐number parameters, namely, the lengths of short‐, open‐, and square ring‐stubs. To validate the proposed design, a tri‐band bandpass filter with center frequencies of 2.4, 3.5, and 5.2 GHz was designed, simulated, and measured. The measurement results agree well with the simulation results.
Feasibility of two‐dimensional dose distribution deconvolution using convolution neural networks
Authors: Cheon Wonjoong , Kim Sung Jin , Kim Kyuseok , Lee Moonhee , Lee Jinhyeop , Jo Kwanghyun , Cho Sungkoo , Cho Hyosung , Han Youngyih 
Published: October 2019

PurposeThe purpose of this study was to investigate the feasibility of two‐dimensional (2D) dose distribution deconvolution using convolutional neural networks (CNNs) instead of an analytical approach for an in‐house scintillation detector that has a detector‐interface artifact in the penumbra region.MethodsDatasets of 2D dose distributions were acquired from a medical linear accelerator of Novalis Tx. The datasets comprise two different sizes of square radiation fields and 13 clinical intensity‐modulated radiation treatment (IMRT) plans. These datasets were divided into two datasets (training and test) to train and validate the developed network, called PenumbraNet, which is a shallow linear CNN. The PenumbraNet was trained to transform the measured dose distribution [M(x, y)] to calculated distribution [D(x, y)] by the treatment planning system. After training of the PenumbraNet was completed, the performance was evaluated using test data, which were 10 × 10 cm2 open field and ten clinical IMRT cases. The corrected dose distribution [C(x, y)] was evaluated against D(x, y) with 2%/2 mm and 3%/3 mm criteria of the gamma index for each field. The M(x, y) and deconvolved dose distribution with the analytically obtained kernel using Wiener filtering [A(x, y)] were also evaluated for comparison. In addition, we compared the performance of the shallow depth of linear PenumbraNet with that of nonlinear PenumbraNet and a deep nonlinear PenumbraNet within the same training epoch.ResultsThe mean gamma passing rates were 84.77% and 95.81% with 3%/3 mm gamma criteria for A(x, y) and C(x, y) of the PenumbraNet, respectively. The mean gamma pass rates of nonlinear PenumbraNet and the deep depth of nonlinear PenumbraNet were 96.62%, 93.42% with 3%/3 mm gamma criteria, respectively.ConclusionsWe demonstrated the feasibility of the PenumbraNets for 2D dose distribution deconvolution. The nonlinear PenumbraNet which has the best performance improved the gamma passing rate by 11.85% from the M(x, y) at 3%/3 mm gamma criteria.
Electromagnetic wave propagation in a fast pulse line ion accelerator
Authors: Behbahani Reza A. , Diot Quentin , Kavanagh Brian , Serkova Natalie J. , Miften Moyed , Westerly David C. 
Published: October 2019

PurposeThe pulse line ion accelerator (PLIA) is a low‐cost accelerator concept originally designed to accelerate heavy ions. Our group has been investigating the use of PLIA to accelerate light ions and believe a multi‐stage PLIA could be useful for short half‐life PET isotope production. The goal of this work was to develop a single prototype fast PLIA structure and demonstrate electromagnetic wave propagation using a high‐voltage pulser.Materials and methodsA 1.6 m fast PLIA structure (wave speed > 107 m/s) was constructed along with a high‐voltage, sinusoidal pulse generator. The latter uses capacitive voltage doubling and spark gap switching. A step‐up transformer couples voltage from the pulser to the PLIA coil. Voltage measurements on the coil were made in air using a high‐voltage resistive probe, while capacitive probes placed along the length of the PLIA were used to measure wave propagation with the PLIA structure filled with transformer oil.ResultsVoltage measurements acquired on the primary and secondary coils of the transformer coupler in air demonstrated a peak‐to‐peak voltage step‐up of 4.2 relative to the pulser DC charging voltage. The maximum voltage time‐rate‐of‐change on the PLIA coil was 0.76 × 1013 V/s. Capacitive probe measurements indicated voltage oscillations on the PLIA coil with half‐period equal to 43 ± 0.9 ns and wave speed (with oil) of 1.2 × 107 m/s. Average and peak accelerating gradients were conservatively estimated to be 0.44 and 0.60 MV/m, respectively, with a charging voltage of 55 kV. Wave propagation was demonstrated at these gradients without flashover at a vacuum pressure of 9 × 10−6 Torr. Submerging the pulser in oil would allow for charging voltages up to 150 kV and produce accelerating gradients >1.2 MV/m.ConclusionsUse of a multi‐stage, fast PLIA for light ion acceleration could provide a low‐cost complement to cyclotrons for the production of short half‐life isotopes used for PET imaging, including carbon‐11, nitrogen‐13, oxygen‐15, and fluorine‐18.
Influence of initiator on the curing of unsaturated polyester resin at 100 °C
Authors: Delaite Christelle , Bistac Sophie , Dreyer Elodie , Schuller Anne‐Sophie 
Published: October 2019

AbstractSheet molding compound (SMC) parts are fiber‐reinforced unsaturated polyester (UP) composites molded at 140–170 °C under a pressure of 60–100 bar. For economic and ecological reasons, the aim of this research project is to develop new SMC formulations to modify the molding conditions. For this, SMC formulations were modified and optimized to decrease the molding temperature to 100 °C. The strategy was to change the catalytic system (peroxides) in order to obtain highly reactive formulations at 100 °C. First, the temperatures of initiation of the reaction were determined by rheological and DSC measurements for each peroxide. Second, the UP resin crosslinking kinetics were measured for the various peroxides during an isothermal curing at 100 °C. The results obtained with the three experimental methods are compared and discussed. Finally, the laboratory analyses were validated by SMC molding trials. © 2019 Society of Chemical Industry