bluuebunny/crossref_metadata_2025 huggingface dataset:
CLORIFI: software vulnerability discovery using code clone verification
Authors: Li Hongzhe , Kwon Hyuckmin , Kwon Jonghoon , Lee Heejo
Published: June 2015

Software vulnerability has long been considered an important threat to the system safety. A vulnerability is often reproduced because of the frequent code reuse by programmers. Security patches are usually not propagated to all code clones; however, they could be leveraged to discover unknown vulnerabilities. Static code auditing approaches are frequently proposed to scan source codes for security flaws; unfortunately, these approaches generate too many false positives. While dynamic execution analysis methods can precisely report vulnerabilities, they are ineffective in path exploration, which limits them to scale to large programs. With the purpose of detecting vulnerability in a scalable way with more preciseness, in this paper, we propose a novel mechanism, called software vulnerability discovery using Code Clone Verification (CLORIFI), that scalably discovers vulnerabilities in real world programs using code clone verification. In the beginning, we use a fast and scalable syntax‐based way to find code clones in program source codes based on released security patches. Subsequently, code clones are being verified using concolic testing to dramatically decrease the false positives. In addition, we mitigate the path explosion problem by backward sensitive data tracing in concolic execution. Experiments have been conducted with real‐world open‐source projects (recent Linux OS distributions and program packages). As a result, we found 7 real vulnerabilities out of 63 code clones from Ubuntu 14.04 LTS (Canonical, London, UK) and 10 vulnerabilities out of 40 code clones from CentOS 7.0 (The CentOS Project(community contributed)). Furthermore, we confirmed more code clone vulnerabilities in various versions of programs including Rsyslog (Open Source(Original author: Rainer Gerhards)), Apache (Apache Software Foundation, Forest Hill, Maryland, USA) and Firefox (Mozilla Corporation, Mountain View, California, USA). In order to evaluate the effectiveness of vulnerability verification in a systematic way, we also utilized Juliet Test Suite as measurement objects. The results show that CLORIFI achieves 98% accuracy with 0 false positives. Copyright © 2015 John Wiley & Sons, Ltd.
A new certificateless signature with enhanced security and aggregation version
Authors: Deng Jiang , Xu Chunxiang , Wu Huai , Dong Liju
Published: June 2015

To satisfy the applications in certificateless environment, many researchers have been investigating certificateless aggregate signature schemes. Several schemes that are independent with the aggregated numbers are proposed to reduce the computation overhead. In these schemes, the pairing computations that in verification procedure needs are a constant value. Recently, Hou et al. proposed an improved certificateless aggregate signature scheme. They demonstrated the scheme is provably secure in the random oracle model. However, we find that their scheme is insecure in their security model by giving a concrete attack. Then, we propose an improved certificateless signature scheme and use it to construct a new certificateless signature scheme with enhanced security and aggregation. Furthermore, we provide formal security proof of our new scheme. Compared with other four schemes, our enhanced protocol is more suitable for realistic applications. Copyright © 2015 John Wiley & Sons, Ltd.
Parallel multi‐level 2D‐DWT on CUDA GPUs and its application in ring artifact removal
Authors: Zhu Leqing , Zhou Yadong , Zhang Daxing , Wang Dadong , Wang Huiyan , Wang Xun
Published: June 2015

This paper presented two schemes of parallel 2D discrete wavelet transform (DWT) on Compute Unified Device Architecture graphics processing units. For the first scheme, the image and filter are transformed to spectral domain by using Fast Fourier Transformation (FFT), multiplied and then transformed back to space domain by using inverse FFT. For the second scheme, the image pixels are convolved directly with filters. Because there is no data relevance, the convolution for data points on different positions could be executed concurrently. To reduce data transfer, the boundary extension and down‐sampling are processed during data loading stage, and transposing is completed implicitly during data storage. A similar skill is adopted when parallelizing inverse 2D DWT. To further speed up the data access, the filter coefficients are stored in the constant memory. We have parallelized the 2D DWT for dozens of wavelet types and achieved a speedup factor of over 380 times compared with that of its CPU version. We applied the parallel 2D DWT in a ring artifact removal procedure; the executing speed was accelerated near 200 times compared with its CPU version. The experimental results showed that the proposed parallel 2D DWT on graphics processing units can significantly improve the performance for a wide variety of wavelet types and is promising for various applications. Copyright © 2015 John Wiley & Sons, Ltd.
Worm propagation model in mobile network
Authors: Chen Zhide , Wang Meng , Xu Li , Wu Wei
Published: June 2015

With the popularity of mobile smart devices and functional diversification, the infection ways of mobile smartphones worm also become diverse. In mobile networks, mobile devices are suffering from the threat of worms all the time. Once the worm outbreaks, it will bring huge losses to mobile phone users and mobile network operators. Researches on mobile worm propagation model allow us to control and detect potential worm threat, according to the characteristics of worm's outbreak. In the paper, we put forward a worm propagation model based on the mobile network environment. After analyzing the model, we then give the simulation for controlling factors affecting worm propagation. This model allows us to have a certain understanding for the spread on the size and speed of the mobile worm and provide effective methods to control the spread of the mobile worm. Copyright © 2015 John Wiley & Sons, Ltd.
Receptor occupancy assessment by flow cytometry as a pharmacodynamic biomarker in biopharmaceutical development
Authors: Liang Meina , Schwickart Martin , Schneider Amy K. , Vainshtein Inna , Del Nagro Christopher , Standifer Nathan , Roskos Lorin K.
Published: June 2015

Receptor occupancy (RO) assays are designed to quantify the binding of therapeutics to their targets on the cell surface and are frequently used to generate pharmacodynamic (PD) biomarker data in nonclinical and clinical studies of biopharmaceuticals. When combined with the pharmacokinetic (PK) profile, RO data can establish PKPD relationships, which are crucial for informing dose decisions. RO is commonly measured by flow cytometry on fresh blood specimens and is subject to numerous technical and logistical challenges. To ensure that reliable and high quality results are generated from RO assays, careful assay design, key reagent characterization, data normalization/reporting, and thorough planning for implementation are of critical importance during development. In this article, the authors share their experiences and perspectives in these areas and discuss challenges and potential solutions when developing and implementing a flow cytometry‐based RO method in support of biopharmaceutical drug development. © 2015 The Authors Cytometry Part B: Clinical Cytometry Published by Wiley Periodicals, Inc.
Mindfulness‐based prevention for eating disorders: A school‐based cluster randomized controlled study
Authors: Atkinson Melissa J. , Wade Tracey D.
Published: June 2015

Objective

Successful prevention of eating disorders represents an important goal due to damaging long‐term impacts on health and well‐being, modest treatment outcomes, and low treatment seeking among individuals at risk. Mindfulness‐based approaches have received early support in the treatment of eating disorders, but have not been evaluated as a prevention strategy. This study aimed to assess the feasibility, acceptability, and efficacy of a novel mindfulness‐based intervention for reducing the risk of eating disorders among adolescent females, under both optimal (trained facilitator) and task‐shifted (non‐expert facilitator) conditions.

Method

A school‐based cluster randomized controlled trial was conducted in which 19 classes of adolescent girls (N = 347) were allocated to a three‐session mindfulness‐based intervention, dissonance‐based intervention, or classes as usual control. A subset of classes (N =156) receiving expert facilitation were analyzed separately as a proxy for delivery under optimal conditions.

Results

Task‐shifted facilitation showed no significant intervention effects across outcomes. Under optimal facilitation, students receiving mindfulness demonstrated significant reductions in weight and shape concern, dietary restraint, thin‐ideal internalization, eating disorder symptoms, and psychosocial impairment relative to control by 6‐month follow‐up. Students receiving dissonance showed significant reductions in socio‐cultural pressures. There were no statistically significant differences between the two interventions. Moderate intervention acceptability was reported by both students and teaching staff.

Discussion

Findings show promise for the application of mindfulness in the prevention of eating disorders; however, further work is required to increase both impact and acceptability, and to enable successful outcomes when delivered by less expert providers. © 2015 Wiley Periodicals, Inc. (Int J Eat Disord 2015; 48:1024–1037).
Synthesis of novel (Z)‐methyl‐12‐aminooctadec‐9‐enoate‐based phenolipids as potential antioxidants and chemotherapeutic agents
Authors: Yarra Mohini , Kaki Shiva Shanker , Prasad Rachapudi B. N. , Mallampalli Karuna S. L. , Yedla Poornachandra , Chityala Ganesh Kumar
Published: June 2015

A series of novel phenolipids were synthesized by coupling (Z)‐methyl‐12‐aminooctadec‐9‐enoate with substituted aromatic phenolic acids. The substrate (Z)‐methyl‐12‐aminooctadec‐9‐enoate was synthesized from methyl ricinoleate employing a four‐step procedure. The synthesized phenolipids were thoroughly characterized by FT‐IR, 1H NMR, 13C NMR, ESI‐MS, and HRMS spectral analysis. The in vitro antioxidant activities of synthesized compounds were evaluated by 2, 2‐diphenyl‐1‐picrylhydrazyl radical (DPPH•), superoxide free radical scavenging activity, and lipid peroxidation inhibitory activities. The novel phenolic compounds were compared in terms of antioxidant activity with the commercial antioxidants, namely butylated hydroxy toluene (BHT) and α‐tocopherol as reference compounds. The antioxidant screening data of all the synthesized compounds revealed that DPPH free radical scavenging activity, superoxide, and lipid peroxidation inhibitory activity of caffeic and gallic acid substituted phenolipids exhibited excellent activity as compared to commercial antioxidants, BHT, and α‐tocopherol. The synthesized phenolipids were also evaluated for anticancer activities against four different cancer cell lines namely DU145, HePG2, SKOV3, MDA‐MB‐231. Among these compounds, 7a, 7b, 7d, 7e which were derived from cinnamic acid‐based phenolic acids and 8b which is derived from vanillic acid exhibited good anticancer activity against the tested cell lines.

Practical applications: Lipophilization of phenolic acids improves their antioxidant and anticancer properties. The (Z)‐methyl‐12‐aminooctadec‐9‐enoate‐based phenolipids can be exploited in a number of lipophilic antioxidant and anticancer formulations.

A panel of (Z)‐methyl‐12‐aminooctadec‐9‐enoate‐based phenolipids are synthesized for the first time from methyl ricinoleate, an unusual fatty acid isolated from castor oil. These compounds were evaluated for antioxidant properties, and gallic and caffeic acid‐based phenolipids exhibited extraordinary properties compared to BHT and α‐tocopherol commercially available antioxidants used in food and pharmaceutical formulations. These compounds were evaluated for anticancer activity for the first time, where these have exhibited good to moderate activity. Hence, (Z)‐methyl‐12‐aminooctadec‐9‐enoate‐based phenolipids can be exploited in a number of lipophilic antioxidant and anticancer formulations.
Fate of polychlorinated biphenyls in a contaminated lake ecosystem: Combining equilibrium passive sampling of sediment and water with total concentration measurements of biota
Authors: Mäenpää Kimmo , Leppänen Matti T. , Figueiredo Kaisa , Mayer Philipp , Gilbert Dorothea , Jahnke Annika , Gil-Allué Carmen , Akkanen Jarkko , Nybom Inna , Herve Sirpa
Published: June 2015

Equilibrium sampling devices can be applied to study and monitor the exposure and fate of hydrophobic organic chemicals on a thermodynamic basis. They can be used to determine freely dissolved concentrations and chemical activity ratios and to predict equilibrium partitioning concentrations of hydrophobic organic chemicals in biota lipids. The authors' aim was to assess the equilibrium status of polychlorinated biphenyls (PCBs) in a contaminated lake ecosystem and along its discharge course using equilibrium sampling devices for measurements in sediment and water and by also analyzing biota. The authors used equilibrium sampling devices (silicone rubber and polyethylene [PE]) to determine freely dissolved concentrations and chemical activities of PCBs in the water column and sediment porewater and calculated for both phases the corresponding equilibrium concentrations and chemical activities in model lipids. Overall, the studied ecosystem appeared to be in disequilibrium for the studied phases: sediment, water, and biota. Chemical activities of PCBs were higher in sediment than in water, which implies that the sediment functioned as a partitioning source of PCBs and that net diffusion occurred from the sediment to the water column. Measured lipid-normalized PCB concentrations in biota were generally below equilibrium lipid concentrations relative to the sediment (CLip⇌Sed) or water (CLip⇌W), indicating that PCB levels in the organisms were below the maximum partitioning levels. The present study shows the application versatility of equilibrium sampling devices in the field and facilitates a thermodynamic understanding of exposure and fate of PCBs in a contaminated lake and its discharge course. Environ Toxicol Chem 2015;34:2463–2474. © 2015 SETAC
UVCB substances: Methodology for structural description and application to fate and hazard assessment
Authors: Dimitrov Sabcho D. , Georgieva Denitsa G. , Pavlov Todor S. , Karakolev Yordan H. , Karamertzanis Panagiotis G. , Rasenberg Mike , Mekenyan Ovanes G.
Published: June 2015

Substances of unknown or variable composition, complex reaction products, or biological materials (UVCBs) have been conventionally described in generic terms. Commonly used substance identifiers are generic names of chemical classes, generic structural formulas, reaction steps, physical–chemical properties, or spectral data. Lack of well-defined structural information has significantly restricted in silico fate and hazard assessment of UVCB substances. A methodology for the structural description of UVCB substances has been developed that allows use of known identifiers for coding, generation, and selection of representative constituents. The developed formats, Generic Simplified Molecular-Input Line-Entry System (G SMILES) and Generic Graph (G Graph), address the need to code, generate, and select representative UVCB constituents; G SMILES is a SMILES-based single line notation coding fixed and variable structural features of UVCBs, whereas G Graph is based on a workflow paradigm that allows generation of constituents coded in G SMILES and end point–specific or nonspecific selection of representative constituents. Structural description of UVCB substances as afforded by the developed methodology is essential for in silico fate and hazard assessment. Data gap filling approaches such as read-across, trend analysis, or quantitative structure–activity relationship modeling can be applied to the generated constituents, and the results can be used to assess the substance as a whole. The methodology also advances the application of category-based data gap filling approaches to UVCB substances. Environ Toxicol Chem 2015;34:2450–2462. © 2015 SETAC
Incompressible multiphase flow and encapsulation simulations using the moment‐of‐fluid method
Authors: Li Guibo , Lian Yongsheng , Guo Yisen , Jemison Matthew , Sussman Mark , Helms Trevor , Arienti Marco
Published: June 2015

A moment‐of‐fluid method is presented for computing solutions to incompressible multiphase flows in which the number of materials can be greater than two. In this work, the multimaterial moment‐of‐fluid interface representation technique is applied to simulating surface tension effects at points where three materials meet. The advection terms are solved using a directionally split cell integrated semi‐Lagrangian algorithm, and the projection method is used to evaluate the pressure gradient force term. The underlying computational grid is a dynamic block‐structured adaptive grid. The new method is applied to multiphase problems illustrating contact‐line dynamics, triple junctions, and encapsulation in order to demonstrate its capabilities. Examples are given in two‐dimensional, three‐dimensional axisymmetric (R–Z), and three‐dimensional (X–Y–Z) coordinate systems. Copyright © 2015 John Wiley & Sons, Ltd.
ADRM1‐amplified metastasis gene in gastric cancer
Authors: Fejzo Marlena S. , Anderson Lee , Chen Hsiao‐Wang , Anghel Adrian , Zhuo Jiaying , Anchoori Ravi , Roden Richard , Slamon Dennis J.
Published: June 2015

The proteasome ubiquitin receptor ADRM1 has been shown to be a driver for 20q13.3 amplification in epithelial cancers including ovarian and colon cancer. We performed array‐CGH on 16 gastric cancer cell lines and found 20q13.3 to be amplified in 19% with the minimal amplified region in gastric cancer cell line AGS spanning a 1 Mb region including ADRM1. Expression microarray analysis shows overexpression of only two genes in the minimal region, ADRM1 and OSBPL2. While RNAi knockdown of both ADRM1 and OSBPL2 led to a slight reduction in growth, only ADRM1 RNAi knockdown led to a significant reduction in migration and growth in soft‐agar. Treatment of AGS cells with the ADRM1 inhibitor RA190 resulted in proteasome inhibition, but RNAi knockdown of ADRM1 did not. However, RNAi knockdown of ADRM1 led to a significant reduction in specific proteins including MNAT1, HRS, and EGFR. We hypothesize that ADRM1 may act in ADRM1‐amplified gastric cancer to alter protein levels of specific oncogenes resulting in an increase in metastatic potential. Selective inhibition of ADRM1 independent of proteasome inhibition may result in a targeted therapy for ADRM1‐amplified gastric cancer. In vivo models are now warranted to validate these findings. © 2015 Wiley Periodicals, Inc.
Influence of strip thinning on nutrient outflow concentrations from plantation forested watersheds
Authors: Fukushima Takehiko , Tei Rai , Arai Hiroyuki , Onda Yuichi , Kato Hiroaki , Kawaguchi Shimpei , Gomi Takashi , Dung Bui X. , Nam Sooyoun
Published: June 2015

Nutrient concentrations in stream water, rainfall, throughfall, stemflow, surface flow and ground water were compared before, during and after strip thinning (intensive 50%) in plantation forested watersheds in Tochigi, Japan. Influences were evaluated comparing four thinning‐applied and two reference basins for 1 year before, 6 months during and 1 year after the thinning. Results show that this strip thinning significantly increased dissolved total phosphorus, total phosphorus and dissolved organic carbon (0.01, 0.04 and 0.53 mg l−1, respectively) during the thinning period and dissolved total nitrogen and total nitrogen (0.34 and 0.46 mg l−1, respectively) after the thinning in stream waters relative to the unthinned basins. The increased phosphorus during thinning indicated ground disturbances by the strip thinning, with a concomitant increase in dissolved organic carbon. Changes in biotic and abiotic conditions resulted in increased nitrogen after the thinning, particularly in the dissolved pool. Changes in hydrological processes due to thinning, for example, a change in flow distributions (less high nutrient stemflow and more low nutrient throughfall) and an increase in water discharge in stream water, possibly weakened the direct influences of thinning on nutrient concentrations. Copyright © 2015 John Wiley & Sons, Ltd.
Metabolic Suppression of a Drug‐Resistant Subpopulation in Cancer Spheroid Cells
Authors: Koshkin Vasilij , Ailles Laurie E. , Liu Geoffrey , Krylov Sergey N.
Published: June 2015

Inhibition of metabolic features which distinguish cancer cells from their non‐malignant counterparts is a promising approach to cancer treatment. Energy support for drug extrusion in multidrug resistance (MDR) is a potential target for metabolic inhibition. Two major sources of ATP‐based metabolic energy are partial (glycolysis) and complete (mitochondrial oxidative phosphorylation) oxidation of metabolic fuels. In cancer cells, the balance between them tends to be shifted toward glycolysis; this shift is considered to be characteristic of the cancer metabolic phenotype. Numerous earlier studies, conducted with cells cultured in a monolayer (2‐D model), suggested inhibition of glycolytic ATP production as an efficient tool to suppress MDR in cancer cells. Yet, more recent work challenged the appropriateness of the 2‐D model for such studies and suggested that a more clinically relevant approach would utilize a more advanced cellular model such as a 3‐D model. Here, we show that the transition from the 2‐D model (cultured monolayer) to a 3‐D model (cultured spheroids) introduces essential changes into the concept of energetic suppression of MDR. The 3‐D cell organization leads to the formation of a discrete cell subpopulation (not formed in the 2‐D model) with elevated MDR transport capacity. This subpopulation has a specific metabolic phenotype (mixed glycolytic/oxidative MDR support) different from that of cells cultured in the 2‐D model. Finally, the shift to the oxidative phenotype becomes greater when the spheroids are grown under conditions of lactic acidosis that are typical for solid tumors. The potential clinical significance of these findings is discussed. J. Cell. Biochem. 117: 59–65, 2016. © 2015 Wiley Periodicals, Inc.
Lentiviral Vector‐Mediated FoxO1 Overexpression Inhibits Extracellular Matrix Protein Secretion Under High Glucose Conditions in Mesangial Cells
Authors: Guo Feng , Wang Qingzhu , Zhou Yingni , Wu Lina , Ma Xiaojun , Liu Fei , Huang Fengjuan , Qin Guijun
Published: June 2015

Diabetic nephropathy is characterized by inordinate secretion of extracellular matrix (ECM) proteins from mesangial cells (MCs), which is tightly associated with excessive activation of TGF‐β signaling. The forkhead transcription factor O1 (FoxO1) protects mesangial cells from hyperglycemia‐induced oxidative stress, which may be involved in ameliorating the redundant secretion of ECM proteins under high glucose conditions. Here, we reported that high glucose elevated the level of p‐Akt to attenuate endogenous FoxO1 bioactivities in MCs, accompanied with decreases in the mRNA expressions of catalase (CAT) and superoxide dismutase 2 (SOD2). Meanwhile, the expressions of major ECM proteins‐FN and Col I‐increased under high glucose conditions, in consistent with the activation of TGF‐β/Smad signaling. By contrast, overexpression of nucleus‐localized FoxO1 (insensitive to Akt phosphorylation) directly up‐regulated the expressions of anti‐oxidative enzymes, accompanied with inactivation of TGF‐β/Smad3 pathway, as well as decreases of extracellular matrix proteins. Moreover, similar to those MCs overexpressed of nucleus‐localized FoxO1 in high glucose conditions, MCs with down‐regulation of FoxO1 by small interference‐RNA under normal glucose conditions showed increased FN level and activated TGF‐β/Smad3 pathway. Our findings link the anti‐oxidative activity of FoxO1 and the TGF‐β‐induced secretion of ECM proteins, indicating the novel role of FoxO1 in protecting MCs under high glucose conditions. J. Cell. Biochem. 117: 74–83, 2016. © 2015 Wiley Periodicals, Inc.
Simian Immunodeficiency Virus Impacts MicroRNA‐16 Mediated Post‐Transcriptional Regulation of mu Opioid Receptor in CEM ×174 Cells
Authors: Hou Wenting , Li Hui , Jiang Wei , Zhang Chao , McNutt Michael A , Li Gang
Published: June 2015

Although the mechanism which regulates transcription in the 5′‐UTR of the mu opioid receptor gene (OPRM1) in lymphocytes has been well‐studied, a question remains as to whether there is post‐transcriptional regulation of OPRM1 gene in lymphocytes. In this study, the authors describe both the role played by miRNAs and the impact of SIVmac239 infection on post‐transcriptional regulation of OPRM1 gene in CEM ×174 cells. Our results show that miR‐16 is able to bind the target site in the range of 8699–8719 nt from the stop codon in MOR‐1 mRNA 3′‐UTR and suppress the expression of OPRM1 gene. Mutation of this target site reduces the effect of miR‐16. Morphine (1 µM) inhibits the expression of miR‐16, and this effect is reversed by the antagonist naloxone. Thus, morphine may up‐regulate receptor level by both stimulating OPRM1 gene transcription and stabilizing its mRNA. SIVmac239 infection results in an apparent elevation of miR‐16 and gradual reduction of OPRM1 gene expression. The inverse correlation of elevated miR‐16 and reduced OPRM1 gene expression under viral loading confirmed the effect of SIVmac239 on post‐transcriptional regulation of OPRM1 gene in lymphocytes. The authors conclude that miR‐16 is a primary factor in post‐transcriptional regulation of OPRM1 gene. SIVmac239 upregulates miR‐16 levels and consequently suppresses OPRM1 gene expression. This finding will be helpful for full understanding of the regulatory mechanism of OPRM1 gene in lymphocytes, as well as the synergistic mechanism of HIV infection and morphine addiction in the pathogenesis of AIDS. J. Cell. Biochem. 117: 84–93, 2016. © 2015 Wiley Periodicals, Inc.
Dual polarization of microglia isolated from mixed glial cell cultures
Authors: Ju Lili , Zeng Hui , Chen Yun , Wu Yanhong , Wang Beibei , Xu Qunyuan
Published: June 2015

Microglia are versatile immune effector cells of the CNS and are sensitive to various stimuli. The different methods used to isolate microglia may affect some of their characteristics, such as their polarization state. The influence of cell sorting methods on the polarization state of microglia has never been studied. Mixed glial culture system (MGCS) and magnetic activated cell sorting (MACS) are two methods that are commonly used to purify microglia. This study compares the immunological states between microglia isolated by MGCS and microglia isolated by MACS. We show that microglia isolated by MGCS exhibit a stronger immune‐activated state than microglia isolated by MACS. They present an elevated phagocytic ability and high levels of markers associated with classical activation (M1) and alternative activation (M2). In addition, high levels of M1‐type and M2‐type chemokine (C‐C motif) ligand 2 and transforming growth factor‐β1 were detected in the culture medium of mixed glial cells. Our results show that microglia isolated by MGCS are in an immune‐activated state, whereas microglia isolated by MACS appear to be closer to their primary in vivo state. Therefore, the immune status of microglia, depending on the protocol used to purify them, should be carefully considered in neuropathology research. © 2015 Wiley Periodicals, Inc.
13C SPE MAS measurement of ligand concentration in compressible chromatographic beads
Authors: Elwinger Fredrik , Dvinskikh Sergey V. , Furó István
Published: June 2015

A method for measuring the ligand concentration in heterogeneous materials like chromatography media is described. In this method, 13C single pulse excitation magic angle spinning NMR experiment with broadband 1H decoupling is used to determine the peak integrals for a butyl ligand in the spectrum of a dried chromatography medium. Within a carefully controlled protocol, those integrals compared with that of the internal reference compound dimethyl sulfone provide the required volume concentration with an accuracy of ca 2%. The effects of temperature, degree of hydration, and other experimental parameters are discussed. Copyright © 2015 The Authors. Magnetic Resonance in Chemistry published by John Wiley & Sons Ltd.
Resolution‐enhanced 2D NMR of complex mixtures by non‐uniform sampling
Authors: Le Guennec Adrien , Dumez Jean‐Nicolas , Giraudeau Patrick , Caldarelli Stefano
Published: June 2015

NMR is a powerful tool for the analysis of complex mixtures and the identification of individual components. Two‐dimensional (2D) NMR potentially offers a wealth of information, but resolution is often sacrificed in order to contain experimental times. We explore the use of non‐uniform sampling (NUS) to increase substantially the resolution of 2D NMR spectra of complex mixtures of small molecules, with no increase in experimental time. Two common pulse sequences for metabolomics applications are analysed, HSQC and TOCSY. Specific attention is paid to sensitivity in resolution‐enhanced NUS spectra, using the signal‐to‐maximum‐noise ratio as a metric. With a careful choice of sampling schedule and reconstruction algorithm, resolution in the 13C dimension for HSQC is increased by a factor of at least 32, with no loss in sensitivity and no spurious peaks. For TOCSY, multiplets can be resolved in the indirect dimension in a reasonable experimental time. These properties should increase the usefulness of 2D NMR for metabolomics applications by, for example, increasing the chances of metabolite identification. Copyright © 2015 John Wiley & Sons, Ltd.
Fully automatic assignment of small molecules' NMR spectra without relying on chemical shift predictions
Authors: Castillo Andrés M. , Bernal Andrés , Patiny Luc , Wist Julien
Published: June 2015

We present a method for the automatic assignment of small molecules' NMR spectra. The method includes an automatic and novel self‐consistent peak‐picking routine that validates NMR peaks in each spectrum against peaks in the same or other spectra that are due to the same resonances. The auto‐assignment routine used is based on branch‐and‐bound optimization and relies predominantly on integration and correlation data; chemical shift information may be included when available to fasten the search and shorten the list of viable assignments, but in most cases tested, it is not required in order to find the correct assignment. This automatic assignment method is implemented as a web‐based tool that runs without any user input other than the acquired spectra. Copyright © 2015 John Wiley & Sons, Ltd.
A framework for machine‐learning‐augmented multiscale atomistic simulations on parallel supercomputers
Authors: Caccin Marco , Li Zhenwei , Kermode James R. , De Vita Alessandro
Published: June 2015

Recent advances in quantum mechanical (QM)‐based molecular dynamics (MD) simulations have used machine‐learning (ML) to predict, rather than recalculate, QM‐accurate forces in atomic configurations sufficiently similar to previously encountered ones. Here, we discuss how ML approaches can be deployed within large‐scale QM/MM materials simulations on massively parallel supercomputers, making QM zones ofatoms routinely attainable. We argue that the ML approach allows computational effort to be concentrated on the most chemically active subregions of the QM zone, significantly improving the overall efficiency of the simulation. We thus propose a novel method to partition large QM regions into multiple subregions, which can be computed in parallel to achieve optimal scaling. Then we review a recently proposed QM/ML MD scheme (Z. Li, J.R. Kermode, A. De Vita Phys. Rev. Lett., 2015, 114, 096405), discussing how this could be efficiently combined with QM‐zone partitioning. © 2015 Wiley Periodicals, Inc.
Addressing global economic inequalities in local ways in Senegal's artisanal workshops
Authors: Cochrane Laura L.
Published: June 2015

Central Senegal was once a thriving agricultural area, but over the past century, it has struggled with repeated droughts, rising temperatures, and land mismanagement. In addition, global inequalities, including colonialism, unequal energy use, and international trade inequities, have escalated both climate change and economic insecurities worldwide. These inequalities in turn have affected local environments and economies. Throughout these long‐term crises, in central Senegal, communities have relied on religious networks. Leaders of local economic development projects also work through these networks to rebuild their communities. This article focuses on the extent to which residents of two towns have used these participatory networks to address environmental and economic challenges. Their varied experiences show the importance of using a region's social foundations in communities' work toward financial viability. This article argues that local development projects that use these existing strengths as organizing principles are able to adapt to persistent challenges more successfully than those that do not. Existing networks that strengthen communities also strengthen their efforts to become sustainable.
Unequal sustainabilities: The role of social inequalities in conservation and development projects
Authors: Peterson Nicole D.
Published: June 2015

In this article, I examine the efforts of a national marine protected area in Loreto, Mexico, to create sustainable development through regulations and economic development programs. I argue that these kinds of efforts can ignore social aspects of sustainability, particularly the ways that existing economic, political, and social inequalities interact with sustainability efforts through flawed participatory processes, misunderstandings of community values, and the lack of attention to the impact of a larger socioeconomic context. Instead, we should focus on how inequalities are reproduced, altered, challenged, and constructed by the policies and practices of sustainability. I propose that greater commitment to an integrated social, environmental, and economic sustainability can provide the space needed for alternative visions and values as well as real progress toward sustainability.
Shifting social dynamics and economic inequality in the post‐Soviet space: Networking and participation in toi among the novyi Kyrgyz
Authors: Provis René
Published: June 2015

This article analyzes recent changes in the important social gatherings of feasting celebrations in Kyrgyzstan (toi in the Kyrgyz language) as markers of significant change in social networking practices over the post‐Soviet period. I argue that the observable increase in the number of these celebrations has been mistaken for a revitalization of kinship relations, when in fact the toi often reflect more pragmatic and strategic considerations vis‐à‐vis social networking. In the context of the attrition of state services and increasing economic and social inequality since the collapse of the Soviet Union and Kyrgyzstan's subsequent independence in 1991, the resultant patterns of association evident in toi I interpret as a mélange of custom and the assimilation of neoliberal rhetoric that was widely disseminated across the former Soviet Union during this period. This has significant consequences for well‐being among the poorest segments of society that might not be appreciated by considering numerical measures of inequality alone, such as Gini measures of income inequality preferred by international development organizations like the World Bank.
Postdisaster reciprocity and the development of inequality in personal networks
Authors: Jones Eric C. , Murphy Arthur D. , Faas A. J. , Tobin Graham A. , McCarty Christopher , Whiteford Linda M.
Published: June 2015

Within the context of major changes in economics, population distribution, and lifestyles around the world, people continue to rely on personal relationships for support. People also often create or find themselves in relationships that are alternatively asymmetrical or balanced. In this study, we are interested in how people face acute or chronic hazards and how asymmetrical or balanced exchange relationships are associated with different types of social support in these contexts. This study examines the degree to which populations in three disaster settings–flooding in Mexico and volcanic eruptions in Mexico and Ecuador–show variation in the degree and form of reciprocity. We found people on average to engage in giving and/or receiving with three to five people in their personal networks. Most of these relationships were reciprocal, but those that were not reciprocal suggested potential inequality in these rural communities.
The cranial endocast of the Middle Devonian dipnoan Dipterus valenciennesi and a fossilized dipnoan otoconial mass
Authors: Challands Thomas J.
Published: June 2015

The well known Middle Devonian (Eifelian–Givetian) lungfish Dipterus valenciennesi from Scotland, UK, has been studied for more than one hundred years though our understanding of the neurocranium and cranial cavity is incomplete. Micro‐CT scanning demonstrates that the internal cast of the cranial cavity, the endocast, possesses a mix of primitive and derived characters. The olfactory bulbs are sessile, as in the derived extant Lepidosirenidae. However, Dipterus valenciennesi possesses the primitive condition of a shallow telencephalon unlike Upper Devonian forms such as Rhinodipterus kimberleyensis and extant lungfish taxa. Further information revealed by micro‐CT scanning has allowed coding for characters pertaining to the neurocranial cristae, previously unobservable in Dipterus valenciennesi, allowing hypotheses of relationships between Devonian Dipnoi and the position of Dipterus valenciennesi to be reassessed. New analyses do not refine the phylogenetic position of Dipterus valenciennesi but do increase support for most recently established Devonian dipnoan phylogeny. The first record of a three‐dimensionally preserved fossilized otoconial mass from the utricular recess in a fossil dipnoan is also described. Comparison of morphometric data of the endosseous and soft tissue manifestations of the labyrinth system in extant dipnoan taxa demonstrates that there is largely good correspondence between the two. When compared to Dipterus valenciennesi, extant taxa exhibit semi‐circular canals that are reduced in length. Furthermore, compared to Dipterus, in extant dipnoan taxa the size of the otoconial mass has increased relative to the utricular and sacculolagenar pouches containing them. The functional implications for these observations suggest that the Dipnoi have evolved towards a more sedentary lifestyle and behaviour at least since the Middle Devonian.
Extracellular matrix biomimicry for the creation of investigational and therapeutic devices
Authors: Pellowe Amanda S. , Gonzalez Anjelica L.
Published: June 2015

The extracellular matrix (ECM) is a web of fibrous proteins that serves as a scaffold for tissues and organs, and is important for maintaining homeostasis and facilitating cellular adhesion. Integrin transmembrane receptors are the primary adhesion molecules that anchor cells to the ECM, thus integrating cells with their microenvironments. Integrins play a critical role in facilitating cell–matrix interactions and promoting signal transduction, both from the cell to the ECM and vice versa, ultimately mediating cell behavior. For this reason, many advanced biomaterials employ biomimicry by replicating the form and function of fibrous ECM proteins. The ECM also acts as a reservoir for small molecules and growth factors, wherein fibrous proteins directly bind and present these bioactive moieties that facilitate cell activity. Therefore biomimicry can be enhanced by incorporating small molecules into ECM‐like substrates. Biomimetic ECM materials have served as invaluable research tools for studying interactions between cells and the surrounding ECM, revealing that cell–matrix signaling is driven by mechanical forces, integrin engagement, and small molecules. Mimicking pathological ECMs has also elucidated disease specific cell behaviors. For example, biomimetic tumor microenvironments have been used to induce metastatic cell behaviors, and have thereby shown promise for in vitro cancer drug testing and targeting. Further, ECM‐like substrates have been successfully employed for autologous cell recolonization for tissue engineering and wound healing. As we continue to learn more about the mechanical and biochemical characteristics of the ECM, these properties can be harnessed to develop new biomaterials, biomedical devices, and therapeutics. WIREs Nanomed Nanobiotechnol 2015, 8:5–22. doi: 10.1002/wnan.1349

This article is categorized under:

Diagnostic Tools > Biosensing

Diagnostic Tools > Diagnostic Nanodevices

Implantable Materials and Surgical Technologies > Nanotechnology in Tissue Repair and Replacement
Image‐guided surgery using multimodality strategy and molecular probes
Authors: Xi Lei , Jiang Hubei
Published: June 2015

The ultimate goal of cancer surgery is to maximize the excision of tumorous tissue with minimal damage to the collateral normal tissues, reduce the postoperative recurrence, and improve the survival rate of patients. In order to locate tumor lesions, highlight tumor margins, visualize residual disease in the surgical wound, and map potential lymph node metastasis, various imaging techniques and molecular probes have been investigated to assist surgeons to perform more complete tumor resection. Combining imaging techniques with molecular probes is particularly promising as a new approach for image‐guided surgery. Considering inherent limitations of different imaging techniques and insufficient sensitivity of nonspecific molecular probes, image‐guided surgery with multimodality strategy and specific molecular probes appears to be an optimal choice. In this article, we briefly describe typical imaging techniques and molecular probes followed by a focused review on the current progress of multimodal image‐guided surgery with specific molecular navigation. We also discuss optimal strategy that covers all stages of image‐guided surgery including preoperative scanning of tumors, intraoperative inspection of surgical bed and postoperative care of patients. WIREs Nanomed Nanobiotechnol 2015, 8:46–60. doi: 10.1002/wnan.1352

This article is categorized under:

Diagnostic Tools > In Vivo Nanodiagnostics and Imaging
Cumulative experiences with life adversity: Identifying critical levels for targeting prevention efforts☆
Authors: Mitchell Kimberly J. , Tynes Brendesha , Umaña‐Taylor Adriana J. , Williams David
Published: June 2015

This paper aims to assess the role of individual types and cumulative life adversity for understanding depressive symptomatology and aggressive behavior. Data were collected in 2011 as part of the Teen Life Online and in Schools Study from 916 ethnically‐diverse students from 12 middle, K–8, 6–12 and high schools in the Midwest United States. Youth reported an average of 4.1 non‐victimization adversities and chronic stressors in their lifetimes. There was a linear relationship between number of adversities and depression and aggression scores. Youth reporting the highest number of adversities (7 or more) had significantly higher depression and aggression scores than youth reporting any other number of adversities suggesting exposure at this level is a critical tipping point for mental health concerns. Findings underscore an urgent need to support youth as they attempt to negotiate, manage, and cope with adversity in their social worlds.
Local behavior of fractional p-minimizers
Authors: Di Castro Agnese , Kuusi Tuomo , Palatucci Giampiero
Published: June 2015

We extend the De Giorgi–Nash–Moser theory to nonlocal, possibly degenerate integro-differential operators.
The Quick Dementia Rating System (QDRS): A rapid dementia staging tool
Authors: Galvin James E.
Published: June 2015

Introduction

Test the validity and reliability of the Quick Dementia Rating System (QDRS), a rapid dementia staging tool.

Methods

The QDRS was tested in 267 patient‐caregiver dyads compared with Clinical Dementia Ratings (CDR), neuropsychological testing, and gold standard measures of function, mood, and behavior. Psychometric properties including, item variability, floor and ceiling effects, concurrent and construct validity, and internal consistency were determined. The QDRS was used to derive an independent CDR and sum‐of‐boxes (SB). Interscale reliability between QDRS and CDR was tested using intraclass correlation coefficients (ICC). Area under the receiver operator characteristic curves (AUC) tested discrimination properties of QDRS across CDR stages.

Results

QDRS scores increased with higher CDR staging and poorer neuropsychological performance (Ps < .001). The QDRS demonstrated low floor and ceiling effects; excellent known‐groups validity across CDR stages (Ps < .001); construct validity against cognitive, behavioral, and functional measures (Ps 0.004 to <0.001); and reliability (Cronbach α: 0.86–0.93). The QDRS demonstrated differential scores across different dementia etiologies. The AUC for the QDRS was 0.911 (95% confidence interval or CI 0.86–0.96) and for the CDR‐SB was 0.996 (95% CI 0.99–1.0) demonstrating comparable ability to discriminate normal controls from dementia. The QDRS‐generated CDR demonstrated excellent correspondence with the CDR (ICC = 0.90) and SB (ICC = 0.92).

Discussion

The QDRS validly and reliably differentiates individuals with and without dementia and accurately stages dementia without extensive training or clinician input, and is highly correlated with our gold standard measures. The QDRS provides a rapid method to determine study eligibility, stage patients in clinical practice, and improve case ascertainment in population studies.
Diagnóstico ecológico y económico de la cadena de suministros para el reciclaje de plásticos en el contexto empresarial cubano
Authors: Feitó Cespón Michael , Cespón Castro Roberto , Martínez Curbelo Gretel , Covas Varela Daylí
Published: June 2015

La cadena de suministros para el reciclaje de plásticos en Cuba ha estado presentando un bajo desempeño durante varios años, por lo tanto el objetivo de este trabajo es realizar un diagnóstico estratégico de su gestión que integre las dimensiones económicas y medioambientales. Para conseguir este propósito se utilizan los procesos de pensamiento desarrollados dentro de la teoría de las restricciones los cuales se fortalecen con el análisis del ciclo de vida, técnicas estadísticas y métodos multicriterios discretos. Los resultados del diagnóstico demostraron la necesidad de rediseñar las decisiones estratégicas teniendo en cuenta los criterios económicos integrados con los medioambientales con el fin de lograr un desempeño sostenible de la cadena de suministros estudiada.
SIRT1 is a regulator of autophagy: Implications in gastric cancer progression and treatment
Authors: Qiu Guanglin , Li Xuqi , Che Xiangming , Wei Chao , He Shicai , Lu Jing , Jia Zongliang , Pang Ke , Fan Lin
Published: June 2015

Silent mating type information regulation 1 (SIRT1) is implicated in tumorigenesis through its effect on autophagy. In gastric cancer (GC), SIRT1 is a marker for prognosis and is involved in cell invasion, proliferation, epithelial‐mesenchymal transition (EMT) and drug resistance. Autophagy can function as a cell‐survival mechanism or lead to cell death during the genesis and treatment of GC. This functionality is determined by factors including the stage of the tumor, cellular context and stress levels. Interestingly, SIRT1 can regulate autophagy through the deacetylation of autophagy‐related genes (ATGs) and mediators of autophagy. Taken together, these findings support the need for continued research efforts to understand the mechanisms mediating the development of gastric cancer and unveil new strategies to eradicate this disease.