bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparing the Chemical Structure and Protein Content of ChEMBL, DrugBank, Human Metabolome Database and the Therapeutic Target Database
Authors: Southan Christopher , Sitzmann Markus , Muresan Sorel
Published: December 2013

ChEMBL, DrugBank, Human Metabolome Database and the Therapeutic Target Database are resources of curated chemistry‐to‐protein relationships widely used in the chemogenomic arena. In this work we have extended an earlier analysis (PMID 22821596) by comparing chemistry and protein target content between 2010 and 2013. For the former, details are presented for overlaps and differences, statistics of stereochemistry as well as stereo representation and MW profiles between the four databases. For 2013 our results indicate quality improvements, major expansion, increased achiral structures and changes in MW distributions. An orthogonal comparison of chemical content with different sources inside PubChem highlights further interpretable differences. Expansion of protein content by UniProt IDs is also recorded for 2013 and Gene Ontology comparisons for human‐only sets indicate differences. These emphasise the expanding complementarity of chemistry‐to‐protein relationships between sources, although different criteria are used for their capture.
NMR study of O and N, O‐substituted 8‐quinolinol derivatives
Authors: Mastoor Sobia , Faizi Shaheen , Saleem Rubeena , Siddiqui Bina Shaheen
Published: December 2013

The 1H and 13C NMR spectral study of several biologically active derivatives of 8‐quinolinol have been made through extensive NMR studies including homodecoupling and 2D‐NMR experiments such as COSY‐45°, NOESY, and HeteroCOSY. Electron donating resonance and electron withdrawing inductive effect of several groups showed marked changes in chemical shifts of nuclei at the seventh positions of O‐substituted quinolinols (2–15). Although in N‐alkyl, 8‐alkoxyquinolinium halides (16–21), ring A rightly showed low frequency chemical shift values. Copyright © 2013 John Wiley & Sons, Ltd.
Integrated Laplacian‐based phase unwrapping and background phase removal for quantitative susceptibility mapping
Authors: Li Wei , Avram Alexandru V. , Wu Bing , Xiao Xue , Liu Chunlei
Published: December 2013

Quantitative susceptibility mapping (QSM) is a recently developed MRI technique that provides a quantitative measure of tissue magnetic susceptibility. To compute tissue magnetic susceptibilities based on gradient echoes, QSM requires reliable unwrapping of the measured phase images and removal of contributions caused by background susceptibilities. Typically, the two steps are performed separately. Here, we present a method that simultaneously performs phase unwrapping and HARmonic (background) PhasE REmovaL using the LAplacian operator (HARPERELLA). Both numerical simulations and in vivo human brain images show that HARPERELLA effectively removes both phase wraps and background phase, whilst preserving all low spatial frequency components originating from brain tissues. When compared with other QSM phase preprocessing techniques, such as path‐based phase unwrapping followed by background phase removal, HARPERELLA preserves the tissue phase signal in gray matter, white matter and cerebrospinal fluid with excellent robustness, providing a convenient and accurate solution for QSM. The proposed algorithm is provided, together with QSM and susceptibility tensor imaging (STI) tools, in a shared software package named ‘STI Suite’. Copyright © 2013 John Wiley & Sons, Ltd.
Study of a numerical scheme for miscible two‐phase flow in porous media
Authors: Eymard Robert , Schleper Veronika
Published: December 2013

We study the convergence of a finite volume scheme for a model of miscible two‐phase flow in porous media. In this model, one phase can dissolve into the other one. The convergence of the scheme is proved thanks to an estimate on the two pressures, which allows to prove some estimates on the discrete time derivative of some nonlinear functions of the unknowns. Monotony arguments allow to show some properties on the limits of these functions. A key point in the scheme is to use particular averaging formula for the dissolution function arising in the space term. © 2013 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq 30: 723–748, 2014
The local superconvergence of the linear finite element method for the poisson problem
Authors: He Wen‐ming , Cui Jun‐Zhi , Zhu Qi‐ding , Wen Zhong‐liang
Published: December 2013

Assume that . In this study, the Richardson extrapolation for the tensor‐product block element and the linear finite element theory of the Green's function will be combined to study the local superconvergence of finite element methods for the Poisson equation in a bounded polytopic domain (polygonal or polyhedral domain for ), where a family of tensor‐product block partitions
is not required or the solution need not have high global
smoothness. We present a special family of partitions satisfying, for any , e is a tensor‐product block whenever where
denotes the distance between e and . By the linear finite element
theory of the Green's function and the Richardson extrapolation for
the tensor‐product block element, we obtain the local
superconvergence of the displacement for the linear finite element
method over the special family of partitions . © 2013 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq 30: 930–946, 2014
Application of Person‐Centered Analytic Methodology in Longitudinal Research: Exemplars From the Women's Health Initiative Clinical Trial Data
Authors: Zaslavsky Oleg , Cochrane Barbara B. , Herting Jerald R. , Thompson Hilaire J. , Woods Nancy F. , LaCroix Andrea
Published: December 2013

Despite the variety of available analytic methods, longitudinal research in nursing has been dominated by use of a variable‐centered analytic approach. The purpose of this article is to present the utility of person‐centered methodology using a large cohort of American women 65 and older enrolled in the Women's Health Initiative Clinical Trial (N = 19,891). Four distinct trajectories of energy/fatigue scores were identified. Levels of fatigue were closely linked to age, socio‐demographic factors, comorbidities, health behaviors, and poor sleep quality. These findings were consistent regardless of the methodological framework. Finally, we demonstrated that energy/fatigue levels predicted future hospitalization in non‐disabled elderly. Person‐centered methods provide unique opportunities to explore and statistically model the effects of longitudinal heterogeneity within a population. © 2013 Wiley Periodicals, Inc.
Predictors of Attrition Among Rural Breast Cancer Survivors
Authors: Meneses Karen , Azuero Andres , Su Xiaogang , Benz Rachel , McNees Patrick
Published: December 2013

Attrition can jeopardize both internal and external validity. The goal of this secondary analysis was to examine predictors of attrition using baseline data of 432 participants in the Rural Breast Cancer Survivors study. Attrition predictors were conceptualized based on demographic, social, cancer treatment, physical health, and mental health characteristics. Baseline measures were selected using this conceptualization. Bivariate tests of association, discrete‐time Cox regression models and recursive partitioning techniques were used in analysis. Results showed that 100 participants (23%) dropped out by Month 12. Non‐linear tree analyses showed that poor mental health and lack of health insurance were significant predictors of attrition. Findings contribute to future research efforts to reduce research attrition among rural underserved populations. © 2013 Wiley Periodicals, Inc.
A Reformulated Low‐Rank ADI Iteration with Explicit Residual Factors
Authors: Benner Peter , Kürschner Patrick , Saak Jens
Published: December 2013

Based on our recent findings [1, 2] regarding the low‐rank ADI iteration for large‐scale Lyapunov equations, we propose a mathematically equivalent formulation of the LR‐ADI whose iteration is directly connected to low rank factors of the Lyapunov residual. If complex shift parameters occur and are handled efficiently [1], this reformulation is slightly more efficient from a computational point of view, since it guarantees that the right hand sides of all linear systems that need to be solved are real. (© 2013 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Accuracy of two‐phase flow simulations: The Taylor Flow benchmark
Authors: Aland Sebastian , Lehrenfeld Christoph , Marschall Holger , Meyer Christoph , Weller Stephan
Published: December 2013

We detail on the relevance and characteristics of a Taylor Flow benchmark recently proposed within the framework of the Priority Program ‘Transport Processes at Fluidic Interfaces’ by the German Research Foundation (DFG‐SPP1506). (© 2013 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The next level of complexity: Crosstalk of posttranslational modifications
Authors: Venne A. Saskia , Kollipara Laxmikanth , Zahedi René P.
Published: December 2013

Beside gene expression and translational control, which are relatively slow, PTM of proteins represents the major level of regulation, from very fast and reversible to slow or irreversible processes. PTMs affect protein structure and act as molecular switches, which regulate the interaction of proteins with DNA, cofactors, lipids, and other proteins. In the past few years, evidence for extensive crosstalk between PTMs has accumulated. The combination of different PTMs on protein surfaces can create a “PTM code,” which can be recognized by specific effectors to initiate/inhibit downstream events, only inducing/retaining a signal once the complementary incoming signals are present at the same time and place. Although MS‐based proteomics has substantially improved our knowledge about PTMs, currently sensitive and dedicated analytical strategies are available only for few different types of PTM. Several recent studies focused on the combinatorial analysis of PTMs, but preferentially utilized peptide‐centric bottom‐up strategies might be too restricted to decipher complex PTM codes. Here, we discuss the current state of PTM crosstalk research and how proteomics may contribute to understanding PTM codes, representing the next level of complexity and one of the biggest challenges for future proteomics research.
Usefulness of cerebral NIRS in detecting the effects of pediatric sleep apnea
Authors: Ullman Nachman , Anas Nick G. , Izaguirre Estela , Haugen Wendy , Ortiz Heather , Arguello Oscar , Nickerson Bruce , Mink Richard B.
Published: December 2013

Background

Children with sleep apnea have increased morbidity if the sleep apnea is untreated. Polysomnography (PSG) is used to detect sleep apnea, but in children, there are technical difficulties that make the diagnosis more difficult. Cerebral near infrared spectroscopy (NIRS) has the ability to detect tissue hypoxia by measuring regional oxygen saturation (rSO2). We hypothesized that when used as an adjunct to PSG testing, cerebral NIRS would better detect the effects of sleep apnea in children than arterial pulse oximetry (SpO2). Specifically, we aimed to show that the apnea/hypopnea index (AHI) calculated with rSO2 from the NIRS would be greater than that calculated with SpO2.

Methods

Forty‐seven patients under 18 years of age who underwent PSG testing for sleep apnea were evaluated. Cerebral NIRS was utilized in addition to PSG. The AHI was calculated using SpO2 and compared to the AHI calculated using the rSO2. A pediatric pulmonologist who was unaware of the NIRS data evaluated each patient for sleep apnea. Data are median (interquartile range).

Results

The median AHI(rSO2) was 2.4(1.2,5.1), significantly greater (P < 0.0001) than the AHI(SpO2) of 0.7(0.4,1.2). Four patients were diagnosed with sleep apnea; however, only one had an AHI(SpO2) ≥ 5, a typical threshold for the diagnosis of sleep apnea. All 4 subjects had an AHI(rSO2) ≥ 5 but 10 patients without sleep apnea had a value ≥5. The sensitivity and specificity for using the AHI(rSO2) to diagnose sleep apnea was 100% and 76.7%, respectively.

Conclusion

Consistent with the ability of NIRS to detect tissue hypoxia, we found that the AHI calculated with rSO2 was greater than that using SpO2. We conclude that NIRS has potential as a valuable adjunct to PSG in evaluating patients for sleep apnea and warrants further investigation for this purpose. Pediatr Pulmonol. 2014; 49:1036–1042. © 2013 Wiley Periodicals, Inc.
Risk Factors for First Time Incidence Sciatica: A Systematic Review
Authors: Cook Chad E. , Taylor Jeffrey , Wright Alexis , Milosavljevic Steven , Goode Adam , Whitford Maureen
Published: December 2013

Background and Purpose

Characteristically, sciatica involves radiating leg pain that follows a dermatomal pattern along the distribution of the sciatic nerve. To our knowledge, there are no studies that have investigated risk factors associated with first time incidence sciatica. The purpose of the systematic review was to identify the longitudinal risk factors associated with first time incidence sciatica and to report incidence rates for the condition. For the purposes of this review, first time incidence sciatica was defined as either of the following: 1) no prior history of sciatica or 2) transition from a pain‐free state to sciatica. Studies included subjects of any age from longitudinal, observational, cohort designs.

Methods

The study was a systematic review. Eight of the 239 articles identified by electronic search strategies met the inclusion criteria.

Results

Risk factors and their respective effect estimates were reported using descriptive analysis and the preferred reporting items for systematic reviews and meta‐analyses guidelines. Modifiable risk factors included smoking, obesity, occupational factors and health status. Non‐modifiable factors included age, gender and social class. Incidence rates varied among the included studies, in part reflecting the variability in the operationalized definition of sciatica but ranged from <1% to 37%.

Discussion

A majority of the identified risk factors associated with first time sciatica are modifiable, suggesting the potential benefits of primary prevention. In addition, those risk factors are also associated with unhealthy lifestyles, which may function concomitantly toward the development of sciatica. Sciatica as a diagnosis is inconsistently defined among studies. Copyright © 2013 John Wiley & Sons, Ltd.
Yb3+ site occupation and host sensitization luminescence of a novel near‐infrared emitting Sr2CaMoO6:Yb3+ phosphor
Authors: Wang Enyan , Zhou Wenli , Liu Chunmeng , Wang Jing , Kuang Xiaojun , Ye Yanmei , Tang Jinke , Su Qiang
Published: December 2013

The host sensitized near‐infrared (NIR) emitting phosphor Sr2CaMoO6:Yb3+ was fabricated by the solid state reaction method. The structural refinement and Raman spectra elucidate that Yb3+ ions preferentially occupy Ca2+ sites. The phosphor can harvest ultraviolet (UV)–blue photons and exhibits intense NIR emission at around 1012 nm with full‐width‐at‐half‐maximum of 1635 cm–1. Moreover, the absolute NIR photoluminesence quantum yield (PLQY) is estimated to be about 9%. The Sr2CaMoO6:Yb3+ phosphor may be a promising luminescence downshifting material for improving the spectral response of solar cells in the UV region. (© 2014 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Low O2 Master Bag for Beef Patties: Effects of Primary Package Permeability and Structure
Authors: Uboldi Eleonora , Lamperti Mirka , Limbo Sara
Published: December 2013

The contribution of the structure and permeability of case‐ready units on the colour changes of ground beef patties during low O2 storage in master bags, aerobic blooming and display life was investigated. We selected the following case‐ready solutions: PVC 8000 + closed‐cell expanded polystyrene (EPS) tray, PVC 20000 + closed‐cell EPS tray, linear low‐density polyethylene (LLDPE) 26000 + closed‐cell EPS tray and PVC 20000 + open‐cell EPS tray. Patties packaged onto a closed‐cell tray and wrapped with PVC 20000, but never stored in master bag, were taken as a control. We monitored oxygen depletion in the headspace of the master bags, the microbiological indexes and the appearance of the patties (colorimetric measurements and scanning images). During the storage in master bags, the use of a very high permeability wrapping film and an open‐cell EPS tray allowed the best colour stability of the bottom and upper sides of patties through 7 days. After master bag opening, the same combination of materials favoured the blooming of the upper surface pigments of the product and the stability of the oxygenated pigments during the display life. Moreover, the open‐cell trays helped in reducing the discolouration of the bottom side of patties. Hence, this low O2 master bag system can enhance the colour stability of ground beef patties and therefore extend their distribution life. Copyright © 2013 John Wiley & Sons, Ltd.
Promoting University Students' Engagement in Learning Through Instructor‐Initiated EFL Writing Groups
Authors: Mutwarasibo Faustin
Published: December 2013

This article examines how to promote university students' engagement in learning by means of instructor‐initiated English as a foreign language (EFL) writing groups. The research took place in Rwanda and was undertaken as a case study involving 34 second‐year undergraduate students, divided into 12 small working groups, and one instructor. The data were collected by means of open‐ended group interviews carried out after each of the 12 groups had finished writing an essay in English. In their responses, students acknowledged having improved their interpersonal and collaborative skills through EFL group writing. Students also indicated that, while discussing and interacting with their group members and with the support from their instructor, they improved their English vocabulary, gained new ideas and perspectives, and enhanced their learning about text coherence, all of which led to improvement in their EFL writing. However, a minority of students did not appreciate writing together, due to continued internal disagreements and member incompatibility. The author proposes strategies to make group work an effective learning tool inside and outside the classroom, particularly in EFL contexts.
Biomolecular motors in nanoscale materials, devices, and systems
Authors: Bachand George D. , Bouxsein Nathan F. , VanDelinder Virginia , Bachand Marlene
Published: December 2013

Biomolecular motors are a unique class of intracellular proteins that are fundamental to a considerable number of physiological functions such as DNA replication, organelle trafficking, and cell division. The efficient transformation of chemical energy into useful work by these proteins provides strong motivation for their utilization as nanoscale actuators in ex vivo, meso‐ and macro‐scale hybrid systems. Biomolecular motors involved in cytoskeletal transport are quite attractive models within this context due to their ability to direct the transport of nano‐/micro‐scale objects at rates significantly greater than diffusion, and in the absence of bulk fluid flow. As in living organisms, biomolecular motors involved in cytoskeletal transport (i.e., kinesin, dynein, and myosin) function outside of their native environment to dissipatively self‐assemble biological, biomimetic, and hybrid nanostructures that exhibit nonequilibrium behaviors such as self‐healing. These systems also provide nanofluidic transport function in hybrid nanodevices where target analytes are actively captured, sorted, and transported for autonomous sensing and analytical applications. Moving forward, the implementation of biomolecular motors will continue to enable a wide range of unique functionalities that are presently limited to living systems, and support the development of nanoscale systems for addressing critical engineering challenges.

This article is categorized under:

Diagnostic Tools > Biosensing

Diagnostic Tools > Diagnostic Nanodevices

Nanotechnology Approaches to Biology > Nanoscale Systems in Biology
Candidates for Limited Lateral Neck Dissection among Patients with Metastatic Papillary Thyroid Carcinoma
Authors: Kang Byung Chul , Roh Jong‐Lyel , Lee Jeong Hyun , Cho Kyung‐Ja , Gong Gyungyub , Choi Seung‐Ho , Nam Soon Yuhl , Kim Sang Yoon
Published: December 2013

Background

Papillary thyroid carcinoma (PTC) is associated with an excellent prognosis but frequently spreads to regional lymph nodes. The extent of neck dissection, particularly routine level II or V lymphadenectomy, is still controversial as it may lead to spinal accessory nerve injury and associated postoperative morbidities. We assessed the diagnostic value of preoperative ultrasonography (US) plus computed tomography (CT) for detecting metastatic lymph nodes and for identifying predictors of level II or V metastasis in patients with PTC.

Methods

The results of US and CT were compared with histopathologic findings at various neck levels in 209 previously untreated PTC patients with lateral cervical nodal metastases who underwent total thyroidectomy with central and lateral neck dissection. Clinicopathologic predictors for level II or V metastases were identified.

Results

Pathologic metastases to level II and V were observed in 53.6 and 25.4 % of patients, respectively. Occult metastases were found in 34.5 and 16.8 %, respectively. The sensitivities of US plus CT for levels II and V were 64.6 and 50.9 %, respectively. Image‐based, isolated lateral level IV involvement and macroscopic extranodal extension were independently associated with level II metastasis or either level II or V metastasis (p < 0.01). Macroscopic extranodal extension was also independently associated with level V metastasis (p = 0.001).

Conclusions

Patients with image‐based, isolated lateral level IV involvement and no macroscopic extranodal extension are potential candidates for limited level III–IV dissection or prophylactic level II lymphadenectomy omission. Level V lymphadenectomy may be omitted in patients without macroscopic extranodal extension.
Parameter estimation for reaction‐diffusion models of biological invasions
Authors: Soubeyrand Samuel , Roques Lionel
Published: December 2013

In this note, we discuss parameter estimation for population models based on partial differential equations (PDEs). Parametric estimation is first considered in the perspective of inverse problems (i.e., when the observation of the solution of a PDE is exactly observed or noise‐free). Then, adopting the point of view of statistics, we turn to parametric estimation for PDEs using more realistic noisy measurements. The approach that we describe uses mechanistic‐statistical models which combine (1) a PDE‐based submodel describing the dynamic under study and (2) a stochastic submodel describing the observation process. This Note is expected to contribute to bridge the gap between modelers using PDEs and population ecologists collecting and analyzing spatio‐temporal data.
Detection of the horizontal spatial structure of soil fungal communities in a natural forest
Authors: Kadowaki Kohmei , Sato Hirotoshi , Yamamoto Satoshi , Tanabe Akifumi S. , Hidaka Amane , Toju Hirokazu
Published: December 2013

Soil microbes are considered to be a key determinant of the aboveground plant community. They are not distributed uniformly in the environment, and their activity, abundance, and ecosystem functioning could vary across localities, characterized by high β‐diversity. Investigating factors that contribute to high β‐diversity can help infer the possible mechanisms of microbial community assembly, and predict the scale and extent of impacts that soil microbes have on the plant community. Because soil systems consist of multiple horizons (i.e., vertical stratification) associated with different soil properties, complete understanding of high β‐diversity requires consideration of both horizontal and vertical spatial structures of soil microbial communities. We studied the community composition of soil fungi from the O‐ and A‐horizons in a Castanopsis‐dominated temperate forest, and compared horizontal spatial autocorrelation in species composition between the two soil horizons (O‐ versus A‐horizons). Pyrosequencing analysis yielded 67,129 sequencing reads, summed across all the 48 forest soil samples. Clustering analysis resulted in 597 molecular operational taxonomic units (OTUs), 68 % of which were identified as fungi, represented by four phyla. The Mantel test revealed that the O‐horizon communities are spatially clustered, and the observed high β‐diversity was driven not only by changes in OTUs present, but also by high turnover in identities of OTUs in soil samples. Furthermore, Mantel correlogram analysis showed that the O‐horizon communities resembled each other in composition within the range of 50 m, whereas the A‐horizon communities lacked such horizontal autocorrelation. These differences in the scale patchiness could arise from two processes: (1) that environmental conditions could show higher heterogeneity in finer scale at the A‐horizon than at the O‐horizon; and/or (2) dispersal could be more frequent at the O‐horizon than the A‐horizon. The present study suggests that either environmental filtering (i.e., the niche‐based process) or dispersal limitation (i.e., neutral process) could characterize the observed patterns of spatial clustering in the soil fungal community.
Vulnerability of phenological synchrony between plants and pollinators in an alpine ecosystem
Authors: Kudo Gaku
Published: December 2013

The relationship between flowering phenology and abundance of bumble bees (Bombusspp.) was investigated using 2 years of phenological data collected in an alpine region of northern Japan. Abundance ofBombusspecies was observed along a fixed transect throughout the flowering season. The number of flowering species was closely related to the floral resources for pollinators at the community scale. In the year with typical weather, the first flowering peak corresponded to the emergence time of queen bees from hibernation, while the second flowering peak corresponded to the active period of worker bees. In the year with an unusually warm spring, however, phenological synchrony between plants and bees was disrupted. Estimated emergence of queen bees was 10 days earlier than the first flowering date owing to earlier soil thawing and warming. However, subsequent worker emergence was delayed, indicating slower colony development. The flowering season finished 2 weeks earlier in the warm‐spring year in response to earlier snowmelt. A common resident species in the alpine environment,B. hypocrita sapporoensis, flexibly responded to the yearly fluctuation of flowering. In contrast, population dynamics of otherBombusspecies were out of synchrony with the flowering: their frequencies were highest at the end of the flowering season in the warm‐spring year. Therefore, phenological mismatch between flowers and pollinators is evident during warm years, which may become more prevalent in a warmer climate. To understand the mechanism of phenological mismatch in the pollination system of the alpine ecosystem, ground temperature, snowmelt regime, and life cycle of pollinators are key factors.
Nonlinear Random-Effects Mixture Models for Repeated Measures
Authors: Codd Casey L. , Cudeck Robert
Published: December 2013

A mixture model for repeated measures based on nonlinear functions with random effects is reviewed. The model can include individual schedules of measurement, data missing at random, nonlinear functions of the random effects, of covariates and of residuals. Individual group membership probabilities and individual random effects are obtained as empirical Bayes predictions. Although this is a complicated model that combines a mixture of populations, nonlinear regression, and hierarchical models, it is straightforward to estimate by maximum likelihood using SAS PROC NLMIXED. Many different models can be studied with this procedure. The model is more general than those that can be estimated with most special purpose computer programs currently available because the response function is essentially any form of nonlinear regression. Examples and sample code are included to illustrate the method.
TGF‐β1 induces EMT reprogramming of porcine bladder urothelial cells into collagen producing fibroblasts‐like cells in a Smad2/Smad3‐dependent manner
Authors: Islam Syed S. , Mokhtari Reza Bayat , El Hout Yaser , Azadi M. A. , Alauddin M. , Yeger Herman , Farhat Walid A.
Published: December 2013

Activation of fibroblasts and their differentiation into myofibroblasts, excessive collagen production and fibrosis occurs in a number of bladder diseases. Similarly, conversion of epithelial cells into mesenchymal cells (EMT) has been shown to increase fibroblasts like cells. TGF‐β1 can induce the EMT and the role of TGF‐β1‐induced EMT during bladder injury leading to fibrosis and possible organ failure is gaining increasing interest. Here we show that EMT and fibrosis in porcine bladder urothelial (UC) cells are Smad dependent. Fresh normal porcine bladder urothelial cells were grown in culture with or without TGF‐β1 and EMT markers were assessed. TGF‐β1 treatment induced changes in cellular morphology as depicted by a significant decrease in the expression of E‐cadherin and corresponding increase in N‐cadherin and α‐SMA. We knocked down Smad2 and Smad3 by Smad specific siRNA. Downregulation of E‐cadherin expression by TGF‐β1 was Smad3‐dependent, whereas N‐cadherin and α‐SMA were dependent on both Smad2 and Smad3. Connective tissue growth factor (CTGF/CCN2), matrix metalloproteinase‐2 and ‐9 (MMP‐2, MMP‐9) has been shown to play important roles in the pathogenesis of fibrosis. Induction of these genes by TGF‐β1 was found to be time dependent. Upregulation of CTGF/CCN2 by TGF‐β1 was Smad3 dependent; whereas MMP‐2 was Smad2 dependent. Smad2 and Smad3 both participated in MMP‐9 expression. TGF‐β1 reprogrammed mesenchymal fibroblast like cells robustly expressed collagen I and III and these was inhibited by SB‐431542, a TGF‐β receptor inhibitor. Our results indicate that EMT of porcine bladder UC cells is TGF‐β1 dependent and is mediated through Smad2 and Smad3. TGF‐β1 may be an important factor in the development of bladder fibrosis via an EMT mechanism. This identifies a potential amenable therapeutic target.
Millennial- to centennial-scale climate periodicities and forcing mechanisms in the westernmost Mediterranean for the past 20,000 yr
Authors: Rodrigo-Gámiz Marta , Martínez-Ruiz Francisca , Rodríguez-Tovar Francisco J. , Jiménez-Espejo Francisco J. , Pardo-Igúzquiza Eulogio
Published: December 2013

Cyclostratigraphic analysis conducted on a continuous high-resolution marine record from the western most Mediterranean reveals well-identified paleoclimate cycles for the last 20,000 yr. The detrital proxies used (Si/Al, Ti/Al, Zr/Al, Mg/Al, K/Al, Rb/Al) are related to different sediment-transport mechanisms, including eolian dust and fluvial runoff, which involve fluctuations in the atmosphere–hydrosphere systems. These fluctuations are accompanied by changes in marine productivity (supported by Ba/Al) and bottom-water redox conditions (Cu/Al, V/Al, Zn/Al, Fe/Al, Mn/Al, U/Th). Spectral analysis conducted using the Lomb–Scargle periodogram and the achieved significance level implemented with the permutation test allowed us to establish major periodicities at 1300, 1515, 2000, and 5000 yr, and secondary peaks at 650, 1087, and 3000 yr. Some of these cycles also agree with those previously described in the North Atlantic Ocean and circum-Mediterranean records. The periodicities obtained at 2000 and 5000 yr support a global connection with records distributed at high, mid, and low latitudes associated with solar activity, monsoonal regime and orbital forcing. The 1300- and 1515-yr cycles appear to be linked with North Atlantic climate variability and the African monsoon system. Thus, the analyzed record provides evidence of climate cycles and plausible forcing mechanisms coupled with ocean–atmosphere fluctuations.
Facing Cultural Diversity
Authors: Fasel Nicole , Green Eva G. T. , Sarrasin Oriane
Published: December 2013

Negative attitudes toward immigrants are widespread in Western societies, and research has repeatedly attempted to explain such attitudes with the presence of cultural diversity arising from a high number of immigrants. Highlighting how political psychology integrates individual and contextual levels of explanation, the present paper aims to overview research that reaches beyond this narrow focus of diversity (i.e., immigrant proportion) to understand anti-immigrant attitudes in culturally diverse societies. First, we present research that reconciles two opposing intergroup mechanisms – contact and threat – both triggered by a high proportion of immigrants. Second, emphasis is placed on ideological climates, a novel contextual antecedent of anti-immigrant attitudes understood as collectively shared norms and values permeating all spheres of social life. Ideological climates influence anti-immigrant attitudes beyond individual characteristics and further shape individuals’ responses to cultural diversity. Third, the paper extends existing research on a Person × Context interaction approach to anti-immigrant attitudes and suggests how cultural diversity and ideological climates differentially impact the link between individual-level ideologies and anti-immigrant attitudes. The growing field of multilevel research on anti-immigrant attitudes is overviewed and empirical illustrations of our recent research in Switzerland are provided. We conclude by discussing the benefits and further challenges of integrating individual and contextual antecedents in political psychology and beyond.
Theories of Socio-Political Change and the Dynamics of Sub-Group Versus Superordinate Interests
Authors: Reynolds Katherine J. , Jones Benjamin M. , O’Brien Kerry , Subasic Emina
Published: December 2013

Social change is a core topic within political and social psychology. In light of recent world-wide protest movements directed at social change it is timely to reflect on where current theory and research on socio-political change stands, what the unresolved issues are, and what the necessary next steps. In this paper, three dominant theoretical models are critically evaluated – social identity theory, social dominance theory, and system justification theory – and points of similarity and divergence are highlighted. In addition, it is argued that inclusion of different levels of self-categorization and associated self-interest in the theories has the potential to provide a more “integrated” account of the psychological processes that underpin both system stability and system change.
Assessment of Nontechnical Skills
Authors: Roth Wolff-Michael , Mavin Timothy J.
Published: December 2013

The assessment of pilots’ performances and more specifically their nontechnical skills turns out to be difficult because researchers and practitioners find that inter-rater reliability tends to be moderate to low. In this study, we proposed, consistent with field observations, that assessment is a categorization rather than a measurement issue. Categorization, even though, and especially when, based on imprecise information and assessments, can be modeled mathematically using fuzzy logic. We present the structure of the approach and provide an example from a large database of pilots providing reasons for their assessments of other pilots’ (simulator) flying performances. Considering the implications, we discuss possibilities for using the variations in performance ratings positively, as a source for learning and resilience building.
Ergonomic Assessment of Pilot Workplace
Authors: Robinski Maxi , Stein Michael
Published: December 2013

This article presents the development and application of a tool for the ergonomic evaluation of helicopter simulators at a German Army aviation school. We will illustrate excerpts of two assessments and the derivation of technical change requirements by analyzing shifts in expert ratings. Our questionnaire consisted of the categories realism, reference recognition capability, visual characteristics, and training success, and was sensitive to the assessment of simulator modifications: For instance, although the projectors had been replaced, the brightness of the projections received a significantly worse rating, t(48.00) = -4.42, p < .000, implying the need for a continuous technical development with reference to the illumination impression of operators. Results are discussed with regard to simulator sickness and training success.
Aneurysmal Remodeling in the Circle of Willis after Carotid Occlusion in an Experimental Model
Authors: Tutino Vincent M , Mandelbaum Max , Choi Hoon , Pope Liza C , Siddiqui Adnan , Kolega John , Meng Hui
Published: December 2013

Carotid occlusions are associated with de novo intracranial aneurysm formation in clinical case reports, but this phenomenon is not widely studied. We performed bilateral carotid ligation ( n=9) in rabbits to simulate carotid occlusion, and sham surgery ( n=3) for control. Upon euthanasia ( n=3 at 5 days, n=6 at 6 months post ligation, and n=3 at 5 days after sham operation), vascular corrosion casts of the circle of Willis (CoW) were created. Using scanning electron microscopy, we quantified gross morphologic, macroscopic, and microscopic changes on the endocasts and compared findings with histologic data. At 5 days, CoW arteries of ligated animals increased caliber. The posterior communicating artery (PCom) increased length and tortuosity, and the ophthalmic artery (OA) origin presented preaneurysmal bulges. At 6 months, calibers were unchanged from 5 days, PComs further increased tortuosity while presenting segmental dilations, and the OA origin and basilar terminus presented preaneurysmal bulges. This exploratory study provides evidence that flow increase after carotid occlusion produces both compensatory arterial augmentation and pathologic remodeling such as tortuosity and saccular/fusiform aneurysm. Our findings may have considerable clinical implications, as these lesser-known consequences should be considered when managing patients with carotid artery disease or choosing carotid ligation as a therapeutic option.
Cerebral Oxygen Metabolism in Neonates with Congenital Heart Disease Quantified by MRI and Optics
Authors: Jain Varsha , Buckley Erin M , Licht Daniel J , Lynch Jennifer M , Schwab Peter J , Naim Maryam Y , Lavin Natasha A , Nicolson Susan C , Montenegro Lisa M , Yodh Arjun G , Wehrli Felix W
Published: December 2013

Neonatal congenital heart disease (CHD) is associated with altered cerebral hemodynamics and increased risk of brain injury. Two novel noninvasive techniques, magnetic resonance imaging (MRI) and diffuse optical and correlation spectroscopies (diffuse optical spectroscopy (DOS), diffuse correlation spectroscopy (DCS)), were employed to quantify cerebral blood flow ( CBF) and oxygen metabolism ( CMRO2) of 32 anesthetized CHD neonates at rest and during hypercapnia. Cerebral venous oxygen saturation ( Sv O2) and CBF were measured simultaneously with MRI in the superior sagittal sinus, yielding global oxygen extraction fraction ( OEF) and global CMRO2 in physiologic units. In addition, microvascular tissue oxygenation ( StO2) and indices of microvascular CBF (BFI) and CMRO2 ( CMRO2i) in the frontal cortex were determined by DOS/DCS. Median resting-state MRI-measured OEF, CBF, and CMRO2 were 0.38, 9.7 mL/minute per 100 g and 0.52 mL O2/minute per 100 g, respectively. These CBF and CMRO2 values are lower than literature reports for healthy term neonates (which are sparse and quantified using different methods) and resemble values reported for premature infants. Comparison of MRI measurements of global Sv O2, CBF, and CMRO2 with corresponding local DOS/DCS measurements demonstrated strong linear correlations ( R2=0.69, 0.67, 0.67; P<0.001), permitting calibration of DOS/DCS indices. The results suggest that MRI and optics offer new tools to evaluate cerebral hemodynamics and metabolism in CHD neonates.
Goldstone and Higgs modes of photons inside a cavity
Authors: Yi-Xiang Yu , Ye Jinwu , Liu Wu-Ming
Published: December 2013

Goldstone and Higgs modes have been detected in various condensed matter, cold atom and particle physics experiments. Here, we demonstrate that the two modes can also be observed in optical systems with only a few (artificial) atoms inside a cavity. We establish this connection by studying the U(1)/Z2 Dicke model where N qubits (atoms) coupled to a single photon mode. We determine the Goldstone and Higgs modes inside the super-radiant phase and their corresponding spectral weights by performing both 1/J = 2/N expansion and exact diagonalization (ED) study at a finite N. We find nearly perfect agreements between the results achieved by the two approaches when N gets down even to N = 2. The quantum finite size effects at a few qubits make the two modes quite robust against an effectively small counterrotating wave term. We present a few schemes to reduce the critical coupling strength, so the two modes can be observed in several current available experimental systems by just conventional optical measurements.
Achieving low voltage half electrolysis with a supercapacitor electrode
Authors: Peng Chuang , Hu Di , Chen George Z.
Published: December 2013

Half electrolysis consists of one faradaic reaction and a supercapacitor double layer charging process. In such a configuration, the product of the electrolysis is only generated in the vicinity of one electrode. Furthermore the electrolysis voltage and electric energy consumption are significantly reduced.
Discovery of BET bromodomain inhibitors and their role in target validation
Authors: Müller S. , Knapp S.
Published: December 2013

Publicly available bromodomain inhibitors led to discoveries of key functions of BET-proteins in disease and development of new therapeutic strategies.
Synthesis and biological evaluation of novel quinoxalinone-based HIV-1 reverse transcriptase inhibitors
Authors: Zhou Jie , Ba Mingyu , Wang Bo , Zhou Haibo , Bie Jianbo , Fu Decai , Cao Yingli , Xu Bailing , Guo Ying
Published: December 2013

A series of novel quinoxalinone derivatives were identified as potent anti-HIV-1 agents with IC50 values at 10−8 μmol L−1 level.
A novel 3D structured reduced graphene oxide/TiO2 composite: synthesis and photocatalytic performance
Authors: Yan Wang , He Fei , Gai Shili , Gao Peng , Chen Yujin , Yang Piaoping
Published: December 2013

3D structured rGO/TiO2 composite was synthesized by a simple solvothermal reaction using poly(l-lysine) (PLL) and ethylene glycol (EG) as coupling agents. The composite shows enhanced photocatalytic degradation of MB compared to simply a mixture of TiO2 and GO, TiO2, and commercial P25.
Betaine Reduces Serum Uric Acid Levels and Improves Kidney Function in Hyperuricemic Mice
Authors: Liu Yang-Liu , Pan Ying , Wang Xing , Fan Chen-Yu , Zhu Qin , Li Jian-Mei , Wang Shui-Juan , Kong Ling-Dong
Published: December 2013

Betaine as a dietary alkaloid has attracted the attention of patients with kidney diseases. This study aimed to investigate the effects of betaine on serum uric acid levels and kidney function, and explore their underlying mechanisms in potassium oxonate-induced hyperuricemic mice. Betaine at 5, 10, 20, and 40 mg/kg was orally administered to hyperuricemic mice for 7 days and found to significantly reduce serum uric acid levels and increase fractional excretion of uric acid in hyperuricemic mice in a dose-dependent manner. It effectively restored renal protein level alterations of urate transport-related molecular proteins urate transporter 1, glucose transporter 9, organic anion transporter 1, and ATP-binding cassette subfamily G member 2 in this model, possibly resulting in the enhancement of kidney urate excretion. Moreover, betaine reduced serum creatinine and blood urea nitrogen levels and affected urinary levels of beta-2-microglobulin and
N-acetyl-beta-D-glucosaminidase as well as upregulated renal protein levels of organic cation/carnitine transporters OCT1, OCTN1, and OCTN2, resulting in kidney function improvement in hyperuricemic mice. The findings from this study provide evidence that betaine has anti-hyperuricemic and nephroprotective actions by regulating protein levels of these renal organic ion transporters in hyperuricemic mice.
The R&D progress of 4 MW EAST-NBI high current ion source
Authors: Xie Yahong , Hu Chundong , Liu Sheng , Xu Yongjian , Liang Lizhen , Xie Yuanlai , Sheng Peng , Jiang Caichao , Liu Zhimin
Published: December 2013

A high current ion source, which consists of the multi-cusp bucket plasma generator and tetrode accelerator with multi-slot apertures, is developed and tested for the Experimental Advanced Superconducting Tokamak neutral beam injector. Three ion sources are tested on the test bed with arc power of 80 kW, beam voltage of 80 keV, and beam power of 4 MW. The arc regulation technology with Langmuir probes is employed for the long pulse operation of ion source, and the long pulse beam of 50 keV @ 15.5 A @ 100 s and 80 keV @ 52A @ 1s are extracted, respectively.
Direct and precise measurement of displacement and velocity of flexible web in roll-to-roll manufacturing systems
Authors: Kang Dongwoo , duk Kim Young , Lee Eonseok , Choi Young-Man , Lee Taik-Min , Kim Dongmin
Published: December 2013

Interest in the production of printed electronics using a roll-to-roll system has gradually increased due to its low mass-production costs and compatibility with flexible substrate. To improve the accuracy of roll-to-roll manufacturing systems, the movement of the web needs to be measured precisely in advance. In this paper, a novel measurement method is developed to measure the displacement and velocity of the web precisely and directly. The proposed algorithm is based on the traditional single field encoder principle, and the scale grating has been replaced with a printed grating on the web. Because a printed grating cannot be as accurate as a scale grating in a traditional encoder, there will inevitably be variations in pitch and line-width, and the motion of the web should be measured even though there are variations in pitch and line-width in the printed grating patterns. For this reason, the developed algorithm includes a precise method of estimating the variations in pitch. In addtion, a method of correcting the Lissajous curve is presented for precision phase interpolation to improve measurement accuracy by correcting Lissajous circle to unit circle. The performance of the developed method is evaluated by simulation and experiment. In the experiment, the displacement error was less than 2.5 μm and the velocity error of 1σ was about 0.25%, while the grating scale moved 30 mm.