bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nosocomial urinary tract infections caused by extended-spectrum beta-lactamase uropathogens: Prevalence, pathogens, risk factors, and strategies for infection control
Authors: Bouassida Khaireddine , Jaidane Mehdi , Bouallegue Olfa , Tlili Ghassen , Naija Habiba , Mosbah Ali Tahar 
Published: March 2016

Introduction: Our goal was to investigate the prevalence and antibiogram pattern of extended spectrum beta-lactamase (ESBL) production among uropathogens using isolates from urine samples collected at the Department of Urology in the Sahloul Hospital, Tunisia We also aimed to identify the risk factors for nosocomial urinary tract infections (UTIs) in patients who underwent transurethral resection of the prostate (TURP) and the measures for infection control.Methods: Laboratory records of a five-year period from January 2004 to December 2008 were submitted for retrospective analysis to determine the incidence of ESBL infections. A total of 276isolates were collected. A case-control study involving comparisons between two groups of patients who underwent TURP was performed to determine the risk factors for ESBL infection. Group 1, designated case subjects, included 51 patients with nosocomial UTI after TURP. Group 2, designated control subjects, consisted of 58 randomly selected patients who underwent TURP without nosocomialUTI in the same period. Factors suspected to be implicated in the emergence of ESBL infection were compared between the two groups in order to identify risk factors for infection. A univariate regression analysis was performed, followed by a multivariate one.Results: The annual prevalence of ESBL infection ranged from 1.3‒2.5%. After performing univariate and multivariate regression analysis, the main risk factors for ESBL infections were identified as: use of antibiotics the year preceding the admission, duration of catheter use, and bladder washout (p=0.012, p=0.019, and p<0.001.Conclusions: Urologists have to perform a good hemostasis, especially in endoscopic resections, in order to avoid bladder irrigation and bladder washout and to reduce the time of bladder catheterization, which is a strong risk factor of nosocomial UTIs.
Profil évolutif et pronostic des tumeurs urothéliales de la vessie chez le sujet jeune
Authors: Bouzouita Abderrazak , Saadi Ahmed , Kerkeni Walid , Chakroun Marouene , Cherif Mohamed , Ayed Haroun , Selmi Selim , Derouiche Amine , Benslama Riadh Mohamed , Chebil Mohamed 
Published: March 2016

But : Les tumeurs urothéliales de la vessie sont rares chez le jeune adulte. Leur profil évolutif et leur pronostic restent matière à controverse. Nous rapportons notre expérience à propos de 54 patients.Méthodologie : Entre 1990 et 2010, 54 patients de moins de 40 ans au moment du diagnostic ont été traités pour carcinome à cellules transitionnelles de la vessie. Nous avons étudié le profil évolutif de ces tumeurs en séparant les patients en deux groupes (moins de 30 ans, et 30 à 40 ans). Résultats : La tumeur n’infiltrait pas le muscle vésical dans 37 cas et l’infiltrait dans 17 cas. Pour les tumeurs n’infiltrant pas le muscle vésical, elles étaient de stade Ta dans 20 cas et de grade I-II dans 36 cas. Le pronostic de ces tumeurs était meilleur avant l’âge de 30 ans avec un taux de récidive de 15,3 % sans progression. Pour les patients de 30 à 40 ans, le taux de récidive était de 33,3 %, et 25 % des tumeurs qui ont récidivé ont présenté une progression du stade. Pour les tumeurs infiltrant le muscle vésical, le pronostic était sombre (localement avancées dans neuf cas et métastatiques d’emblée dans cinq cas).Conclusion : Le profil évolutif des tumeurs n’infiltrant pas le muscle vésical a semblé meilleur avant l’âge de 30 ans. Entre 30 et 40 ans, le profil évolutif s’est approché de celui des sujets âgés. Les tumeursinfiltrantes étaient souvent évoluées et agressives, évoquant un potentiel évolutif particulier.
Strain-induced reversible modulation of the magnetic anisotropy in perpendicularly magnetized metals deposited on a flexible substrate
Authors: Ota Shinya , Hibino Yuki , Bang Do , Awano Hiroyuki , Kozeki Takahiro , Akamine Hirokazu , Fujii Tatsuya , Namazu Takahiro , Takenobu Taishi , Koyama Tomohiro , Chiba Daichi 
Published: March 2016

Abstract
In this study, the strain-induced change in the magnetic anisotropy of perpendicularly magnetized thin metals (TbFeCo and Pt/Co/Pt) deposited on a polyethylene naphthalate flexible substrate was investigated. The in-plane uniaxial tensile strain was reversibly applied up to 2%. The magnetic anisotropy was reversibly changed in both samples with applied stress. In the TbFeCo film, a marked change in magnetic anisotropy energy of 1.2 × 105 J/m3 was observed. In the Pt/Co/Pt film, where the thickness of Co was 2–4 monolayers, the stress-induced changes in interface and volume contributions to magnetic anisotropy were individually determined.
High-speed and high-efficiency Si optical modulator with MOS junction, using solid-phase crystallization of polycrystalline silicon
Authors: Fujikata Junichi , Takahashi Masashi , Takahashi Shigeki , Horikawa Tsuyoshi , Nakamura Takahiro 
Published: March 2016

Abstract
We developed a high-speed and high-efficiency MOS-capacitor-type Si optical modulator (Si-MOD) by applying a low optical loss and a low resistivity of a polycrystalline silicon (poly-Si) gate with large grains. To achieve a low resistivity of a poly-Si film, a P-doped poly-Si film based on Si2H6 solid-phase crystallization (SPC) was developed, which showed a comparable resistivity to that of P-doped single-crystal Si. In addition, high-temperature annealing (HTA) after SPC was effective for realizing low optical loss. We designed the optimum Si-MOD structure and demonstrated a very high modulation efficiency of 0.3 V cm, which is very efficient among the Si-MODs developed thus far. High-speed (15 Gbps) operation was achieved with a small footprint of the 200-µm-long phase shifter and a low drive voltage of 1.5 Vpp at a low optical insertion loss of −2.2 dB and 1.55 µm wavelength.
Angle-resolved photoelectron spectroscopy study of initial stage of thermal oxidation on 4H-SiC(0001)
Authors: Arai Hitoshi , Nohira Hiroshi 
Published: March 2016

Abstract
A key to improving the performance of SiC MOSFETs is to clarify the SiO2/SiC interface structure formed by thermal oxidation. We have investigated the initial stage of thermal oxidation on 4H-SiC(0001) by angle-resolved photoelectron spectroscopy. From the changes in the Si 2p3/2 and C 1s photoelectron spectra, the changes in the chemical bonding state of the SiO2/SiC structure with the progress of thermal oxidation were observed. We also found that the intensity of C–O bonds in the case of 4H-SiC(0001) was smaller than that in the case of 4H-SiC(

) with the same oxide thickness and that the oxidation rate of 4H-SiC(0001) is already slower than that of 4H-SiC(

) in the early stage of oxidation.
Modeling of nonlinear thermal resistance in FinFETs
Authors: Kompala Bala Krishna , Kushwaha Pragya , Agarwal Harshit , Khandelwal Sourabh , Duarte Juan-Pablo , Hu Chenming , Chauhan Yogesh Singh 
Published: March 2016

Abstract
In this paper, self-consistent three-dimensional (3D) device simulations for exact analysis of thermal transport in FinFETs are performed. We analyze the temperature rise in FinFET devices with the variation in the number of fins (N
fin), shape of fins and fin pitch (F
pitch). We investigate that the thermal resistance R
th has nonlinear dependency on N
fin and F
pitch. We formulate a model for thermal resistance behavior correctly with N
fin and F
pitch variation. The proposed formulation is implemented in industry standard Berkeley short-channel independent gate FET model for common multi-gate transistors (BSIM-CMG) and validated with both experimental data and TCAD simulations.
Analysis and reduction of leakage current of 2 kV monolithic isolator with wide trench spiral isolation structure
Authors: Takeuchi Yusuke , Kuroda Rihito , Sugawa Shigetoshi 
Published: March 2016

Abstract
In this work, the origin of the leakage current of a highly area-efficient silicon-on-insulator (SOI) monolithic isolator using a spiral trench isolation structure is clarified by experimental and simulation analyses and its reduction method is proposed. It was found that parasitic MOSFET inversion and accumulation channels formed at the SOI and buried oxide (BOX) interface are the origins of leakage current. To reduce the leakage current, adequate SOI spiral length and width and BOX layer thickness are proposed for various voltage usages and show the possibility of 4 kV voltage tolerance and 500 MΩ isolation resistivity.
Computational inference of H3K4me3 and H3K27ac domain length
Authors: Zubek Julian , Stitzel Michael L. , Ucar Duygu , Plewczynski Dariusz M. 
Published: March 2016

Background.Recent epigenomic studies have shown that the length of a DNA region covered by an epigenetic mark is not just a byproduct of the assaying technologies and has functional implications for that locus. For example, expanded regions of DNA sequences that are marked by enhancer-specific histone modifications, such as acetylation of histone H3 lysine 27 (H3K27ac) domains coincide with cell-specific enhancers, known as super or stretch enhancers. Similarly, promoters of genes critical for cell-specific functions are marked by expanded H3K4me3 domains in the cognate cell type, and these can span DNA regions from 4–5kb up to 40–50kb in length. These expanded H3K4me3 domains are known as buffer domains or super promoters.Methods.To ask what correlates with—and potentially regulates—the length of loci marked with these two important histone marks, H3K4me3 and H3K27ac, we built Random Forest regression models. With these models, we computationally identified genomic and epigenomic patterns that are predictive for the length of these marks in seven ENCODE cell lines.Results.We found that certain epigenetic marks and transcription factors explain the variability of the length of H3K4me3 and H3K27ac marks across different cell types, which implies that the lengths of these two epigenetic marks are tightly regulated in a given cell type. Our source code for the regression models and data can be found at our GitHub page:https://github.com/zubekj/broad_peaks.Discussion.Our Random Forest based regression models enabled us to estimate the individual contribution of different epigenetic marks and protein binding patterns to the length of H3K4me3 and H3K27ac deposition patterns, therefore potentially revealing genomic signatures at cell specific regulatory elements.
Stochastic filtering for determining gravity variations for decade‐long time series of GRACE gravity
Authors: Wang Lei , Davis James L. , Hill Emma M. , Tamisiea Mark E. 
Published: March 2016

AbstractWe present a new stochastic filter technique for statistically rigorous separation of gravity signals and correlated “stripe” noises in a series of monthly gravitational spherical harmonic coefficients (SHCs) produced by the Gravity Recovery and Climate Experiment (GRACE) satellite mission. Unlike the standard destriping process that removes the stripe contamination empirically, the stochastic approach simultaneously estimates gravity signals and correlated noises relying on covariance information that reflects both the spatial spectral features and temporal correlations among them. A major benefit of the technique is that by estimating the stripe noise in a Bayesian framework, we are able to propagate statistically rigorous covariances for the destriped GRACE SHCs, i.e. incorporating the impact of the destriping on the SHC uncertainties. The Bayesian approach yields a natural resolution for the gravity signal that reflects the correlated stripe noise, and thus achieve a kind of spatial smoothing in and of itself. No spatial Gaussian smoothing is formally required although it might be useful for some circumstances. Using the stochastic filter, we process a decade‐length series of GRACE monthly gravity solutions, and compare the results with GRACE Tellus data products that are processed using the “standard” destriping procedure. The results show that the stochastic filter is able to remove the correlated stripe noise to a remarkable degree even without an explicit smoothing step. The estimates from the stochastic filter for each destriped GRACE field are suitable for Bayesian integration of GRACE with other geodetic measurements and models, and the statistically rigorous estimation of the time‐varying rates and seasonal cycles in GRACE time series.
Basin‐scale assessment of the land surface water budget in the National Centers for Environmental Prediction operational and research NLDAS‐2 systems
Authors: Xia Youlong , Cosgrove Brian A. , Mitchell Kenneth E. , Peters‐Lidard Christa D. , Ek Michael B. , Brewer Michael , Mocko David , Kumar Sujay V. , Wei Helin , Meng Jesse , Luo Lifeng 
Published: March 2016

AbstractThe purpose of this study is to evaluate the components of the land surface water budget in the four land surface models (Noah, SAC‐Sacramento Soil Moisture Accounting Model, (VIC) Variable Infiltration Capacity Model, and Mosaic) applied in the newly implemented National Centers for Environmental Prediction (NCEP) operational and research versions of the North American Land Data Assimilation System version 2 (NLDAS‐2). This work focuses on monthly and annual components of the water budget over 12 National Weather Service (NWS) River Forecast Centers (RFCs). Monthly gridded FLUX Network (FLUXNET) evapotranspiration (ET) from the Max‐Planck Institute (MPI) of Germany, U.S. Geological Survey (USGS) total runoff (Q), changes in total water storage (dS/dt, derived as a residual by utilizing MPI ET and USGS Q in the water balance equation), and Gravity Recovery and Climate Experiment (GRACE) observed total water storage anomaly (TWSA) and change (TWSC) are used as reference data sets. Compared to these ET and Q benchmarks, Mosaic and SAC (Noah and VIC) in the operational NLDAS‐2 overestimate (underestimate) mean annual reference ET and underestimate (overestimate) mean annual reference Q. The multimodel ensemble mean (MME) is closer to the mean annual reference ET and Q. An anomaly correlation (AC) analysis shows good AC values for simulated monthly mean Q and dS/dt but significantly smaller AC values for simulated ET. Upgraded versions of the models utilized in the research side of NLDAS‐2 yield largely improved performance in the simulation of these mean annual and monthly water component diagnostics. These results demonstrate that the three intertwined efforts of improving (1) the scientific understanding of parameterization of land surface processes, (2) the spatial and temporal extent of systematic validation of land surface processes, and (3) the engineering‐oriented aspects such as parameter calibration and optimization are key to substantially improving product quality in various land data assimilation systems.
SST‐forced interdecadal deepening of the winter India‐Burma trough since the 1950s
Authors: Lu Bo , Ren Hong‐Li 
Published: March 2016

AbstractThe winter India‐Burma Trough (IBT) has undergone a pronounced interdecadal deepening since the 1950s, which led to the significant rainfall increasing over the eastern Indochina Peninsula and south China. To better understand such an observed IBT change, this study examines the responses of the IBT to the upstream subtropical jet, historical anthropogenic forcing, and tropical sea surface temperature (SST). Results show that the SST warming that occurs in the eastern tropical Indian Ocean (ETIO) is the primary cause of the observed interdecadal IBT deepening. The remarkable SST warming leads to a reduction of sea level pressure (SLP) over ETIO by diabatic heating. In association with the change of zonal SLP gradient, the westerly wind anomalies are observed. The northern flank of the westerlies further induces a cyclonic Rossby wave response over the Bay of Bengal. As a result, the winter IBT is intensified. This attribution can be supported by the simulations of atmosphere general circulation models forced by historical SST, in which the observed IBT changes are well simulated on both interdecadal and interannual time scales.
Benchmarking wide swath altimetry‐based river discharge estimation algorithms for the Ganges river system
Authors: Bonnema Matthew G. , Sikder Safat , Hossain Faisal , Durand Michael , Gleason Colin J. , Bjerklie David M. 
Published: March 2016

AbstractThe objective of this study is to compare the effectiveness of three algorithms that estimate discharge from remotely sensed observables (river width, water surface height, and water surface slope) in anticipation of the forthcoming NASA/CNES Surface Water and Ocean Topography (SWOT) mission. SWOT promises to provide these measurements simultaneously, and the river discharge algorithms included here are designed to work with these data. Two algorithms were built around Manning's equation, the Metropolis Manning (MetroMan) method, and the Mean Flow and Geomorphology (MFG) method, and one approach uses hydraulic geometry to estimate discharge, the at‐many‐stations hydraulic geometry (AMHG) method. A well‐calibrated and ground‐truthed hydrodynamic model of the Ganges river system (HEC‐RAS) was used as reference for three rivers from the Ganges River Delta: the main stem of Ganges, the Arial‐Khan, and the Mohananda Rivers. The high seasonal variability of these rivers due to the Monsoon presented a unique opportunity to thoroughly assess the discharge algorithms in light of typical monsoon regime rivers. It was found that the MFG method provides the most accurate discharge estimations in most cases, with an average relative root‐mean‐squared error (RRMSE) across all three reaches of 35.5%. It is followed closely by the Metropolis Manning algorithm, with an average RRMSE of 51.5%. However, the MFG method's reliance on knowledge of prior river discharge limits its application on ungauged rivers. In terms of input data requirement at ungauged regions with no prior records, the Metropolis Manning algorithm provides a more practical alternative over a region that is lacking in historical observations as the algorithm requires less ancillary data. The AMHG algorithm, while requiring the least prior river data, provided the least accurate discharge measurements with an average wet and dry season RRMSE of 79.8% and 119.1%, respectively, across all rivers studied. This poor performance is directly traced to poor estimation of AMHG via a remotely sensed proxy, and results improve commensurate with MFG and MetroMan when prior AMHG information is given to the method. Therefore, we cannot recommend use of AMHG without inclusion of this prior information, at least for the studied rivers. The dry season discharge (within‐bank flow) was captured well by all methods, while the wet season (floodplain flow) appeared more challenging. The picture that emerges from this study is that a multialgorithm approach may be appropriate during flood inundation periods in Ganges Delta.
Investigation of the kinetics of water uptake into partially saturated shales
Authors: Roshan H. , Andersen M. S. , Rutlidge H. , Marjo C. E. , Acworth R. I. 
Published: March 2016

AbstractSeveral processes have been proposed to describe the low recovery of hydraulic fracturing fluid in unconventional shale reservoirs which has caused both technical and environmental concerns. This study describes novel hydraulic experiments to quantitatively investigate the kinetics of water uptake into partially saturated shale through investigating the pressure response of injecting fluids (NaCl, KCl, MgCl2, and CaCl2 with different ionic concentrations) into crushed and sieved shale fragments. The results of the study indicate that the cumulative water uptake under pressure is likely to be controlled by three processes: surface hydration, capillary hydration including advective flow, and osmotic hydration. Each of these processes is a function of the differences between the in situ pore fluid and the injection fluid (solution chemistry and concentration) and the shale physicochemical properties, in particular the contact surface area, pore diameter, and the Cation Exchange Capacity (CEC). The uptake is not instantaneous, but is diffusion limited, with the rate governed by a number of kinetic processes. Uptake proceeds in three stages, each associated with a different process: (1) predominantly surface hydration, (2) predominantly capillary hydration and finally, (3) predominantly osmotic hydration. It was also shown that shale can take up a significant amount of water compared to its available solid volume. However, contrary to the conventional understanding, the increase in salinity of the injection fluid does not necessarily lead to reduced water uptake into shales, but is dependent on the type and concentration of cations within the shale and injecting fluid.
Snow process estimation over the extratropical Andes using a data assimilation framework integrating MERRA data and Landsat imagery
Authors: Cortés Gonzalo , Girotto Manuela , Margulis Steven 
Published: March 2016

AbstractA data assimilation framework was implemented with the objective of obtaining high‐resolution retrospective snow water equivalent (SWE) estimates over several Andean study basins. The framework integrates Landsat fractional snow covered area (fSCA) images, a land surface and snow depletion model, and the Modern Era Retrospective Analysis for Research and Applications (MERRA) reanalysis as a forcing data set. The outputs are SWE and fSCA fields (1985–2015) at a resolution of 90 m that are consistent with the observed depletion record. Verification using in‐situ snow surveys showed significant improvements in the accuracy of the SWE estimates relative to forward model estimates, with increases in correlation (0.49–0.87) and reductions in root mean square error (0.316 m to 0.129 m) and mean error (−0.221 m to 0.009 m). A sensitivity analysis showed that the framework is robust to variations in physiography, fSCA data availability and a priori precipitation biases. Results from the application to the headwater basin of the Aconcagua River showed how the forward model versus the fSCA‐conditioned estimate resulted in different quantifications of the relationship between runoff and SWE, and different correlation patterns between pixel‐wise SWE and ENSO. The illustrative results confirm the influence that ENSO has on snow accumulation for Andean basins draining into the Pacific, with ENSO explaining approximately 25% of the variability in near‐peak (1 September) SWE values. Our results show how the assimilation of fSCA data results in a significant improvement upon MERRA‐forced modeled SWE estimates, further increasing the utility of the MERRA data for high‐resolution snow modeling applications.
Isotope Targeted Glycoproteomics (IsoTaG) to Characterize Intact, Metabolically Labeled Glycopeptides from Complex Proteomes
Authors: Woo Christina M. , Bertozzi Carolyn R. 
Published: March 2016

AbstractProtein glycosylation plays many critical roles in biological function and creates the most diversity of all post‐translational modifications (PTMs). Glycan structural diversity is directly correlated with difficulty in characterizing the intact glycoproteome by mass spectrometry (MS). In this protocol, we describe a novel mass‐independent chemical glycoproteomics platform for characterizing intact, metabolically labeled glycopeptides from complex proteomes, termed Isotope Targeted Glycoproteomics (IsoTaG). To use IsoTaG, cell culture samples are metabolically labeled with an azido‐ or alkynyl‐sugar. Metabolically labeled glycoproteins are then tagged using Click chemistry and enriched with an isotopic recoding biotin probe. Intact glycopeptides are recovered by cleavage of the probe, analyzed with directed MS, and assigned by targeted mass‐independent data analysis. The outlined procedure is well defined in cell culture and has been executed with over 15 cell lines. © 2016 by John Wiley & Sons, Inc.