Een recent gestart onderzoek aan de groep Akoestiek heeft tot doel de tijdsevolutie van verschillende geluidskarakteristieken te introduceren in de studie van stedelijke geluidslandschappen. Een micro-modellering van verkeersstromen wordt hierbij als basis gebruikt voor een nauwkeurige, dynamische modellering van de geluidsemissie veroorzaakt door verkeersstromen in steden. Deze dynamische emissie, gekoppeld aan een state of the art propagatiemodel, in ontwikkeling aan de onderzoeksgroep, laat vervolgens toe de tijdsvariatie in de geluisimmissie te evalueren. Het genereren van dynamische geluidskaarten, het berekenen van statistische geluidsniveau's, of het evalueren van ruimtelijke structuuringrepen behoort hiermee tot de mogelijkheden. A.d.h.v. van een aantal typesituaties zal de stand van het onderzoek worden toegelicht.
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Medicine by Alexandros G.Sfakianakis,Anapafseos 5 Agios Nikolaos,Crete 72100,Greece,tel :00302841026182 & 00306932607174
Τρίτη 17 Μαΐου 2016
Onderzoek naar de dynamiek in het stedelijk geluidslandschap veroorzaakt door wegverkeer
Renal Compartment Segmentation in DCE-MRI Images
Publication date: Available online 16 May 2016
Source:Medical Image Analysis
Author(s): Xin Yang, Hung Le Minh, Kwang-Ting (Tim) Cheng, Kyung Hyun Sung, Wenyu Liu
Renal compartment segmentation from Dynamic Contrast-Enhanced MRI (DCE-MRI) images is an important task for functional kidney evaluation. Despite advancement in segmentation methods, most of them focus on segmenting an entire kidney on CT images, there still lacks effective and automatic solutions for accurate segmentation of internal renal structures (i.e. cortex, medulla and renal pelvis) from DCE-MRI images. In this paper, we introduce a method for renal compartment segmentation which can robustly achieve high segmentation accuracy for a wide range of DCE-MRI data, and meanwhile requires little manual operations and parameter settings. The proposed method consists of five main steps. First, we pre-process the image time series to reduce the motion artifacts caused by the movement of the patients during the scans and enhance the kidney regions. Second, the kidney is segmented as a whole based on the concept of Maximally Stable Temporal Volume (MSTV). The proposed MSTV detects anatomical structures that are homogeneous in the spatial domain and stable in terms of temporal dynamics. MSTV-based kidney segmentation is robust to noises and does not require a training phase. It can well adapt to kidney shape variations caused by renal dysfunction. Third, voxels in the segmented kidney are described by principal components (PCs) to remove temporal redundancy and noises. And then k-means clustering of PCs is applied to separate voxels into multiple clusters. Fourth, the clusters are automatically labeled as cortex, medulla and pelvis based on voxels' geometric locations and intensity distribution. Finally, an iterative refinement method is introduced to further remove noises in each segmented compartment. Experiments on 14 real clinical kidney datasets and 12 synthetic dataset demonstrate that results produced by our method match very well with those segmented manually and the performance of our method is superior to the other five existing methods.
Graphical abstract
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Estimation of Fiber Orientations Using Neighborhood Information
Publication date: Available online 16 May 2016
Source:Medical Image Analysis
Author(s): Chuyang Ye, Jiachen Zhuo, Rao P. Gullapalli, Jerry L. Prince
Data from diffusion magnetic resonance imaging (dMRI) can be used to reconstruct fiber tracts, for example, in muscle and white matter. Estimation of fiber orientations (FOs) is a crucial step in the reconstruction process and these estimates can be corrupted by noise. In this paper, a new method called Fiber Orientation Reconstruction using Neighborhood Information (FORNI) is described and shown to reduce the effects of noise and improve FO estimation performance by incorporating spatial consistency. FORNI uses a fixed tensor basis to model the diffusion weighted signals, which has the advantage of providing an explicit relationship between the basis vectors and the FOs. FO spatial coherence is encouraged using weighted ℓ1-norm regularization terms, which contain the interaction of directional information between neighbor voxels. Data fidelity is encouraged using a squared error between the observed and reconstructed diffusion weighted signals. After appropriate weighting of these competing objectives, the resulting objective function is minimized using a block coordinate descent algorithm, and a straightforward parallelization strategy is used to speed up processing. Experiments were performed on a digital crossing phantom, ex vivo tongue dMRI data, and in vivo brain dMRI data for both qualitative and quantitative evaluation. The results demonstrate that FORNI improves the quality of FO estimation over other state of the art algorithms.
Graphical abstract
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Play in juvenile mink: litter effects, stability over time, and motivational heterogeneity
Abstract
Mink are potentially ideal for investigating the functions of play: deleterious effects of early social isolation suggest a crucial developmental role for play; and huge numbers of highly playful juvenile subjects can be studied on farms. We collected descriptive data on 186 pairs from 93 litters, half provided with play-eliciting environmental enrichment objects in their home cages, to test three hypotheses: (1) play frequency is subject to litter effects; (2) relative playfulness is stable over time; (3) play sub-types share a single, common motivational basis. We found weak litter effects that were driven by stronger litter effects on general activity, and weakly stable individual differences in both total and rough-and-tumble play. Experimentally increasing object play did not inhibit rough-and-tumble play, showing these sub-types are not motivational substitutes. Frequencies of these sub-types were also uncorrelated, and changed differently with time of day and age, further supporting this conclusion.
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Stakeholders' reactions toward iodine biofortified foods: an application of protection motivation theory and technology acceptance model
This doctoral dissertation investigates stakeholders' reactions toward iodine biofortified foods. Iodine deficiency alone affects over 2 billion people worldwide, and is particularly prevalent in developing countries. Iodine is an essential trace element found in seafood and iodized salt, as well as certain vegetables and is important for growth and development throughout the body, as well as cognitive development. Given the critical role of iodine in human nutrition, various strategies have been implemented to reduce iodine deficiency and Iodine Deficiency Disorders (IDD). However, despite considerable progress through iodine fortification, the goal is still far from being achieved. Therefore, there is a need to explore the potential of new approaches, such as iodine biofortification. Biofortification is a strategy to enhance micronutrient concentrations in staple crops, either through conventional or transgenic breeding techniques. Given its status as an agriculture-based, micronutrient strategy, a thorough insight into stakeholder reactions is necessary, examining stakeholders from both the demand-side (consumers) and the supply-side (farmers). A conceptual framework bringing together behavioural change models, technology acceptance modelling and an economic valuation technique was developed and tested for use in stakeholder analysis. Six distinct studies were conducted, targeting locations drawn from three East African countries: Kenya; Uganda; and Tanzania, which have high levels of iodine deficiency disorders (IDD) as well as retarded mental and neurological development coupled with poor school performance. These locations meet the criteria for iodine deficiency endemic areas with a large at risk population that seldom benefits from the existing intervention programs. All model constructs in the framework are decisive in determining the uptake of iodine biofortification. Consistent with evaluation of food with nutritional benefits, stakeholders on both the demand (parents and school heads) and supply-side (small-scale farmers) had favourable reactions towards iodine biofortified food, the uptake of which could drastically change the trend in iodine intake in iodine deficiency endemic areas. These findings present a niche opportunity for producers to tap into the demand market created. In principle, the findings could shape the policy terrain for addressing iodine deficiency, as well as ameliorating the nutrition intervention campaign through agricultural-based interventions, such as biofortification.
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Vergoeding voor piraten: omgekeerde wereld of gerechtigheid?
Begin december 2014 besliste het Europees Hof voor de Rechten van de Mens dat Frankrijk de rechten van piraterijverdachten had geschonden en een vergoeding diende te betalen aan deze 'slachtoffers'. In elk van de gevallen ging het om gelijkaardige situaties, waarbij Somalische piraterijverdachten te lang in hechtenis werden gehouden alvorens ze formeel werden beschuldigd of voor een rechter werden gebracht. Het lijkt niet verwonderlijk dat er onmiddellijk grote kritiek werd geuit. Vervolging en bestraffing van piraterij betreft immers op zich al een moeilijk verhaal, waardoor additionele obstakels absoluut vermeden moeten worden.
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Reach out! Praktijkboek voor outreachend werken
Laagdrempelige hulpverlening voor mensen die buiten de mazen van het net dreigen te vallen. Outreachend werken kent vandaag een grote bloei. Steeds meer hulp-, diensten zorgverleners verlaten hun bureau om buiten de muren van hun eigen organisatie met de meest kwetsbare mensen aan de slag te gaan. Door te werken in hun leefwereld wordt de manier van werken beter afgestemd op de noden en behoeften van de doelgroep. Zo verkleint de drempel van de dienst-, hulp- en zorgverlening en kan er meer geboden worden dan alleen maar praktische hulp. Dit handboek wil een inspiratiebron en leidraad zijn voor elke beginnende én geroutineerde outreach werker
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Immunotherapy for genitourinary cancer: state of the art and new perspectives.
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The effectiveness of a self-management occupational therapy intervention on activity performance in individuals with multiple sclerosis-related fatigue: a randomized-controlled trial.
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System Review about Function Role of ESCC Driver Gene KDM6A by Network Biology Approach
Background. KDM6A (Lysine (K)-Specific Demethylase 6A) is the driver gene related to esophageal squamous cell carcinoma (ESCC). In order to provide more biological insights into KDM6A, in this paper, we treat PPI (protein-protein interaction) network derived from KDM6A as a conceptual framework and follow it to review its biological function. Method. We constructed a PPI network with Cytoscape software and performed clustering of network with Clust&See. Then, we evaluate the pathways, which are statistically involved in the network derived from KDM6A. Lastly, gene ontology analysis of clusters of genes in the network was conducted. Result. The network includes three clusters that consist of 74 nodes connected via 453 edges. Fifty-five pathways are statistically involved in the network and most of them are functionally related to the processes of cell cycle, gene expression, and carcinogenesis. The biology themes of clusters 1, 2, and 3 are chromatin modification, regulation of gene expression by transcription factor complex, and control of cell cycle, respectively. Conclusion. The PPI network presents a panoramic view which can facilitate for us to understand the function role of KDM6A. It is a helpful way by network approach to perform system review on a certain gene.
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Long-term leucine supplementation aggravates prolonged strenuous exercise-induced cardiovascular changes in trained rats
Observational studies have raised concerns that prolonged strenuous exercise training may be associated with increased risk of cardiac arrhythmia and even primary cardiac arrest or sudden death. It has been demonstrated that leucine can reduce prolonged exercise-induced muscle damage and accelerate the recovery process. The aim of this study was to investigate the effects of prolonged strenuous endurance exercise on cardiovascular parameters and biomarkers of cardiac injury in trained adult male rats and assess the use of leucine as an auxiliary substance to prevent the likely cardiac adverse effects caused by strenuous exercise. Twenty-four male Wistar rats were randomly allocated to receive a balanced control diet (18% protein) or a leucine-rich diet (15% protein plus 3% leucine) for 6 weeks. The rats were submitted to 1 hour of exercise, 5 d.wk−1 for 6 wk. Three days after the training period rats were submitted to swimming exercises until exhaustion and cardiac parameters were assessed. Exercising until exhaustion significantly increased cardiac biomarker levels and cytokines, glycogen content and inhibited protein synthesis signaling also led to cardiac electrical disturbances. When combined with exercise, leucine supplementation led to further increases in the aforementioned parameters and also significant increase in blood pressure and protein degradation signaling. We report, for the first time, that leucine supplementation not only does not prevent cardiac fatigue symptoms, but may also aggravate prolonged strenuous exercise-induced cardiovascular disturbances in trained rats. Furthermore, we find that exercising until exhaustion can cause cardiac electrical disturbances and cardiac myocyte damage.
This article is protected by copyright. All rights reserved
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Sensitive determination of As (III) and As (V) by magnetic solid phase extraction with Fe@polyethyleneimine in combination with hydride generation atomic fluorescence spectrometry
Publication date: 15 August 2016
Source:Talanta, Volumes 156–157
Author(s): Qingxiang Zhou, Zhenwen Zheng, Junping Xiao, Huili Fan
The magnetic nanomaterial Fe@polyethyleneimine (Fe@PEI) was successfully synthesized and used as an effective adsorbent material for magnetic solid phase extraction(MSPE) of As(III) and As(V) from water samples. Fe@SiO2 nanoparticles were prepared by one pot synthetic method using a borohydride reduction method, then modified with (3-chloropropyl)trimethoxysilane to obtain Fe@SiO2-Cl by chloropropylation, which was reacted with PEI to achieve Fe@polyethyleneimine (Fe@PEI). The microstructure and morphology of Fe@PEI were characterized by transmission electron microscoscopy (TEM), Fourier transform infrared spectroscopy (FT-IR), and X-ray diffraction (XRD). The experimental results showed that Fe@PEI demonstrated excellent adsorption for As(III) and As(V). Based on this fact, the determination method for these two arsenic species earned good limits of detection (LODs) of 0.002μgL−1 and wide calibration curves in the concentration range from 0.008 to 0.2μgL−1. The precisions of As (III) and As (V)were 1.95% and 2.55% (RSD, n=6), respectively. The proposed method was validated with real samples and the spiked recoveries were in the range of 82.7–98.3% and the accuracies were in the range of 2–13.3%. The results demonstrated that the developed MSPE method had good advantages such as simplicity, rapid separation, low cost, easy to reuse and high-quality analytical performances, which made it attractive for rapid and efficient extraction of inorganic arsenic species in the environmental water samples.
Graphical abstract
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Surface plasmon resonance biosensing: Approaches for screening and characterising antibodies for food diagnostics
Publication date: 15 August 2016
Source:Talanta, Volumes 156–157
Author(s): B.J. Yakes, J. Buijs, C.T. Elliott, K Campbell
Research in biosensing approaches as alternative techniques for food diagnostics for the detection of chemical contaminants and foodborne pathogens has increased over the last twenty years. The key component of such tests is the biorecognition element whereby polyclonal or monoclonal antibodies still dominate the market. Traditionally the screening of sera or cell culture media for the selection of polyclonal or monoclonal candidate antibodies respectively has been performed by enzyme immunoassays. For niche toxin compounds, enzyme immunoassays can be expensive and/or prohibitive methodologies for antibody production due to limitations in toxin supply for conjugate production. Automated, self-regenerating, chip-based biosensors proven in food diagnostics may be utilised as rapid screening tools for antibody candidate selection. This work describes the use of both single channel and multi-channel surface plasmon resonance (SPR) biosensors for the selection and characterisation of antibodies, and their evaluation in shellfish tissue as standard techniques for the detection of domoic acid, as a model toxin compound. The key advantages in the use of these biosensor techniques for screening hybridomas in monoclonal antibody production were the real time observation of molecular interaction and rapid turnaround time in analysis compared to enzyme immunoassays. The multichannel prototype instrument was superior with 96 analyses completed in 2h compared to 12h for the single channel and over 24h for the ELISA immunoassay. Antibodies of high sensitivity, IC50's ranging from 4.8 to 6.9ng/mL for monoclonal and 2.3–6.0ng/mL for polyclonal, for the detection of domoic acid in a 1min analysis time were selected. Although there is a progression for biosensor technology towards low cost, multiplexed portable diagnostics for the food industry, there remains a place for laboratory-based SPR instrumentation for antibody development for food diagnostics as shown herein.
Graphical abstract
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An automated flow injection system for metal determination by flame atomic absorption spectrometry involving on-line fabric disk sorptive extraction technique
Publication date: 15 August 2016
Source:Talanta, Volumes 156–157
Author(s): A. Anthemidis, V. Kazantzi, V. Samanidou, A. Kabir, K.G. Furton
A novel flow injection-fabric disk sorptive extraction (FI-FDSE) system was developed for automated determination of trace metals. The platform was based on a minicolumn packed with sol-gel coated fabric media in the form of disks, incorporated into an on-line solid-phase extraction system, coupled with flame atomic absorption spectrometry (FAAS). This configuration provides minor backpressure, resulting in high loading flow rates and shorter analytical cycles. The potentials of this technique were demonstrated for trace lead and cadmium determination in environmental water samples. The applicability of different sol-gel coated FPSE media was investigated. The on-line formed complex of metal with ammonium pyrrolidine dithiocarbamate (APDC) was retained onto the fabric surface and methyl isobutyl ketone (MIBK) was used to elute the analytes prior to atomization. For 90s preconcentration time, enrichment factors of 140 and 38 and detection limits (3σ) of 1.8 and 0.4μgL−1 were achieved for lead and cadmium determination, respectively, with a sampling frequency of 30h−1. The accuracy of the proposed method was estimated by analyzing standard reference materials and spiked water samples.
Graphical abstract
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Ultrasensitive detection of explosives and chemical warfare agents by low-pressure photoionization mass spectrometry
Publication date: 15 August 2016
Source:Talanta, Volumes 156–157
Author(s): Wanqi Sun, Miao Liang, Zhen Li, Jinian Shu, Bo Yang, Ce Xu, Yao Zou
On-spot monitoring of threat agents needs high sensitive instrument. In this study, a low-pressure photoionization mass spectrometer (LPPI-MS) was employed to detect trace amounts of vapor-phase explosives and chemical warfare agent mimetics under ambient conditions. Under 10-s detection time, the limits of detection of 2,4-dinitrotoluene, nitrotoluene, nitrobenzene, and dimethyl methyl phosphonate were 30, 0.5, 4, and 1 parts per trillion by volume, respectively. As compared to those obtained previously with PI mass spectrometric techniques, an improvement of 3–4 orders of magnitude was achieved. This study indicates that LPPI-MS will open new opportunities for the sensitive detection of explosives and chemical warfare agents.
Graphical abstract
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A novel procedure for phase separation in dispersive liquid-liquid microextraction based on solidification of the aqueous phase
Publication date: 15 August 2016
Source:Talanta, Volumes 156–157
Author(s): J.G. March, V. Cerdà
In this paper, an alternative for handling the organic phase after a dispersive liquid-liquid microextraction using organic solvents lighter than water is presented. It is based on solidification (at −18°C) of the aqueous phase obtained after centrifugation, and the decantation, collection and analysis of the liquid organic layer. The extraction of nicotine in toluene, and its determination in eggplant samples was conducted as a proof of concept. The study has been carried out using standards prepared in water and the formation of the dispersion was assisted by sonication. The organic extract was analysed using gas chromatography coupled to mass spectrometry. Satisfactory analytical figures of merit as: limit of detection (0.4µgL−1, 2ngg−1 wet sample), limit of quantification (1.2µgL−1, 6.5ngg−1 wet sample), within-day precision (RSD=7%), and linearity interval (up to 384µgL−1 nicotine) were achieved. It constituted a contribution to the handling of organic extracts after microextraction processes.
Graphical abstract
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Non-enzymatic detection of glucose using poly(azure A)-nickel modified glassy carbon electrode
Publication date: 15 August 2016
Source:Talanta, Volumes 156–157
Author(s): Tong Liu, Yiqun Luo, Jiaming Zhu, Liyan Kong, Wen Wang, Liang Tan
A simple, sensitive and selective non-enzymatic glucose sensor was constructed in this paper. The poly(azure A)-nickel modified glassy carbon electrode was successfully fabricated by the electropolymerization of azure A and the adsorption of Ni2+. The Ni modified electrode, which was characterized by scanning electron microscope, cyclic voltammetry, electrochemical impedance spectra and X-ray photoelectron spectroscopy measurements, respectively, displayed well-defined current responses of the Ni(III)/Ni(II) couple and showed a good activity for electrocatalytic oxidation of glucose in alkaline medium. Under the optimized conditions, the developed sensor exhibited a broad linear calibration range of 5 μM–12mM for quantification of glucose and a low detection limit of 0.64μM (3σ). The excellent analytical performance including simple structure, fast response time, good anti-interference ability, satisfying stability and reliable reproducibility were also found from the proposed amperometric sensor. The results were satisfactory for the determination of glucose in human serum samples as comparison to those from a local hospital.
Graphical abstract
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Thiazole orange as a fluorescent probe: Label-free and selective detection of silver ions based on the structural change of i-motif DNA at neutral pH
Publication date: 15 August 2016
Source:Talanta, Volumes 156–157
Author(s): Bei Hua Kang, Zhong Feng Gao, Na Li, Yan Shi, Nian Bing Li, Hong Qun Luo
Silver ions have been widely applied to many fields and have harmful effects on environments and human health. Herein, a label-free optical sensor for Ag+ detection is constructed based on thiazole orange (TO) as a fluorescent probe for the recognition of i-motif DNA structure change at neutral pH. Ag+ can fold a C-rich single stranded DNA sequence into i-motif DNA structure at neutral pH and that folding is reversible by chelation with cysteine (Cys). The DNA folding process can be indicated by the fluorescence change of TO, which is non-fluorescent in free molecule state and emits strong fluorescence after the incorporation with i-motif DNA. Thus, a rapid, sensitive, and selective method for the detection of Ag+ and Cys is developed with a detection limit of 17 and 280nM, respectively. It is worth noting that the mechanism underlying the increase of the fluorescence of thiazole orange in the presence of i-motif structure is explained. Moreover, a fluorescent DNA logic gate is successfully designed based on the Ag+/Cys-mediated reversible fluorescence changes. The proposed detection strategy is label-free and economical. In addition, this system shows a great promise for i-motif/TO complex to analyze Ag+ in the real samples.
Graphical abstract
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Polypyrrole nanowire as an excellent solid phase microextraction fiber for bisphenol A analysis in food samples followed by ion mobility spectrometry
Publication date: 15 August 2016
Source:Talanta, Volumes 156–157
Author(s): Mahdie Kamalabadi, Abdorreza Mohammadi, Naader Alizadeh
A polypyrrole nanowire coated fiber was prepared and used in head-space solid phase microextraction coupled with ion mobility spectrometry (HS-SPME-IMS) to the analysis of bisphenol A (BPA) in canned food samples, for the first time. This fiber was synthesized by electrochemical oxidation of the monomer in aqueous solution. The fiber characterization by scanning electron microscopy (SEM) revealed that the new fiber exhibited two-dimensional structures with a nanowire morphology. The effects of important extraction parameters on the efficiency of HS-SPME were investigated and optimized. Under the optimum conditions, the linearity of 10–150ngg−1 and limit of detection (based on S/N=3) of 1ngg−1 were obtained in BPA analysis. The repeatability (n=5) expressed as the relative standard deviation (RSD%) was 5.8%. At the end, the proposed method was successfully applied to determine BPA in various canned food samples (peas, corns, beans). Relative recoveries were obtained 93–96%. Method validation was conducted by comparing our results with those obtained through HPLC with fluorescence detection (FLD). Compatible results indicate that the proposed method can be successfully used in BPA analysis. This method is simple and cheaper than chromatographic methods, with no need of extra organic solvent consumption and derivatization prior to sample introduction.
Graphical abstract
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A sensitive and selective on-line amperometric sulfite biosensor using sulfite oxidase immobilized on a magnetite-gold-folate nanocomposite modified carbon-paste electrode
Publication date: 15 August 2016
Source:Talanta, Volumes 156–157
Author(s): Wongduan Sroysee, Kitayanan Ponlakhet, Sanoe Chairam, Purim Jarujamrus, Maliwan Amatatongchai
We describe a novel amperometric sulfite biosensor, comprising a carbon-paste electrode (Fe3O4@Au-Cys-FA/CPE) modified with immobilized sulfite oxidase (SOx) on a gold-coated magnetite nanoparticle core, encased within a conjugated folic acid (FA) cysteine (Cys) shell. The biosensor electrode was fabricated using a polydimethylsiloxane (PDMS) and mineral oil mixture as binder, which also enhances the physical stability and sensitivity of the electrode. The developed biosensor displays good electrocatalytic activity toward oxidation of H2O2, which occurs by an enzymatic reaction between SOx and sulfite. The Fe3O4@Au-Cys-FA electrode exhibits good electrocatalytic activity, and has good retention of chemisorbed SOx on the electrode because of its large surface area. Sulfite was quantified using amperometric measurements from the Fe3O4@Au-Cys-FA/CPE biosensor, and using an in-house assembled flow cell at +0.35V (vs. Ag/AgCl), with a phosphate buffer carrier (0.10M, pH 7.0) at a flow rate of 0.8mLmin−1. The system detects sulfite over the range 0.1–200mgL−1 (r2=0.998), with a detection limit of 10µgL−1 (3σ of blank). The system exhibits acceptable precision (%R.S.D.=3.1%), rapid sample throughput (109samplesh−1), and good stability (2w). The developed biosensor shows satisfactory tolerance to potential interferences, such as sugars, anions, ascorbic acid, and ethanol. We applied the developed method to the determination of sulfite content in wines and pickled food extracts, and our results are in good agreement with those obtained by the standard iodometric method.
Graphical abstract
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Establishment of local searching methods for orbitrap-based high throughput metabolomics analysis
Publication date: 15 August 2016
Source:Talanta, Volumes 156–157
Author(s): Haiping Tang, Xueying Wang, Lina Xu, Xiaorong Ran, Xiangjun Li, Ligong Chen, Xinbin Zhao, Haiteng Deng, Xiaohui Liu
Our method aims to establish local endogenous metabolite databases economically without purchasing chemical standards, giving strong bases for following orbitrap based high throughput untargeted metabolomics analysis. A new approach here is introduced to construct metabolite databases on the base of biological sample analysis and mathematic extrapolation. Building local metabolite databases traditionally requires expensive chemical standards, which is barely affordable for most research labs. As a result, most labs working on metabolomics analysis have to refer public libraries, which is time consuming and limited for high throughput analysis. Using this strategy, a high throughput orbitrap based metabolomics platform can be established at almost no cost within a couple of months. It enables to facilitate the application of high throughput metabolomics analysis to identify disease-related biomarkers or investigate biological functions using orbitrap.
Graphical abstract
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An electrochemical genosensor for Leishmania major detection based on dual effect of immobilization and electrocatalysis of cobalt-zinc ferrite quantum dots
Publication date: 15 August 2016
Source:Talanta, Volumes 156–157
Author(s): H. Heli, N. Sattarahmady, G.R. Hatam, F. Reisi, R. Dehdari Vais
Identification of Leishmania parasites is important in diagnosis and clinical studies of leishmaniasis. Although epidemiological and clinical methods are available, they are not sufficient for identification of causative agents of leishmaniasis. In the present study, quantum dots of magnetic cobalt-zinc ferrite (Co0.5Zn0.5Fe2O4) were synthesized and characterized by physicochemical methods. The quantum dots were then employed as an electrode modifier to immobilize a 24-mer specific single stranded DNA probe, and fabrication of a label-free, PCR-free and signal-on electrochemical genosensor for the detection of Leishmania major. Hybridization of the complementary single stranded DNA sequence with the probe under the selected conditions was explored using methylene blue as a redox marker, utilizing the electrocatalytic effect of the quantum dots on the methylene blue electroreduction process. The genosensor could detect a synthetic single stranded DNA target in a range of 1.0×10−11 to 1.0×10−18molL−1 with a limit of detection of 2.0×10−19molL−1, and genomic DNA in a range of 7.31×10−14 to 7.31×10−6ngμL−1 with a limit of detection of 1.80×10−14ngμL−1 with a high selectivity and sensitivity.
Graphical abstract
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Chemometric study of Andalusian extra virgin olive oils Raman spectra: Qualitative and quantitative information
Publication date: 15 August 2016
Source:Talanta, Volumes 156–157
Author(s): E. Sánchez-López, M.I. Sánchez-Rodríguez, A. Marinas, J.M. Marinas, F.J. Urbano, J.M. Caridad, M. Moalem
Authentication of extra virgin olive oil (EVOO) is an important topic for olive oil industry. The fraudulent practices in this sector are a major problem affecting both producers and consumers. This study analyzes the capability of FT-Raman combined with chemometric treatments of prediction of the fatty acid contents (quantitative information), using gas chromatography as the reference technique, and classification of diverse EVOOs as a function of the harvest year, olive variety, geographical origin and Andalusian PDO (qualitative information). The optimal number of PLS components that summarizes the spectral information was introduced progressively. For the estimation of the fatty acid composition, the lowest error (both in fitting and prediction) corresponded to MUFA, followed by SAFA and PUFA though such errors were close to zero in all cases. As regards the qualitative variables, discriminant analysis allowed a correct classification of 94.3%, 84.0%, 89.0% and 86.6% of samples for harvest year, olive variety, geographical origin and PDO, respectively.
Graphical abstract
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Flavonoid and lignan intake and pancreatic cancer risk in the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort
Abstract
Despite the potential cancer preventive effects of flavonoids and lignans, their ability to reduce pancreatic cancer risk has not been demonstrated in epidemiological studies. Our aim was to examine the association between dietary intakes of flavonoids and lignans and pancreatic cancer risk in the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort.
A total of 865 exocrine pancreatic cancer cases occurred after 11.3 years of follow-up of 477,309 cohort members. Dietary flavonoid and lignan intake was estimated through validated dietary questionnaires and the U.S. Department of Agriculture (USDA) and Phenol Explorer databases. Hazard ratios (HR) and 95% confidence intervals (CIs) were calculated using age, sex and center-stratified Cox proportional hazards models, adjusted for energy intake, body mass index (BMI), smoking, alcohol and diabetes status.
Our results showed that neither overall dietary intake of flavonoids nor of lignans were associated with pancreatic cancer risk (multivariable-adjusted HR for a doubling of intake = 1.03, 95% CI: 0.95-1.11 and 1.02; 95% CI: 0.89-1.17, respectively). Statistically significant associations were also not observed by flavonoid subclasses. An inverse association between intake of flavanones and pancreatic cancer risk was apparent, without reaching statistical significance, in microscopically confirmed cases (HR for a doubling of intake = 0.96, 95% CI: 0.91-1.00).
In conclusion, we did not observe an association between intake of flavonoids, flavonoid subclasses or lignans and pancreatic cancer risk in the EPIC cohort. This article is protected by copyright. All rights reserved.
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Reduction in squamous cell carcinomas in mouse skin by dietary zinc supplementation
Abstract
Inadequate dietary Zn consumption increases susceptibility to esophageal and other cancers in humans and model organisms. Since Zn supplementation can prevent cancers in rodent squamous cell carcinoma (SCC) models, we were interested in determining if it could have a preventive effect in a rodent skin cancer model, as a preclinical basis for considering a role for Zn in prevention of human nonmelanoma skin cancers, the most frequent cancers in humans. We used the 7,12-dimethyl benzanthracene carcinogen/phorbol myristate acetate tumor promoter treatment method to induce skin tumors in Zn-sufficient wild-type and Fhit (human or mouse protein) knockout mice. Fhit protein expression is lost in >50% of human cancers, including skin SCCs, and Fhit-deficient mice show increased sensitivity to carcinogen induction of tumors. We hypothesized that: (1) the skin cancer burdens would be reduced by Zn supplementation; (2) Fhit−/−(Fhit, murine fragile histidine triad gene) mice would show increased susceptibility to skin tumor induction versus wild-type mice. 30 weeks after initiating treatment, the tumor burden was increased ~2-fold in Fhit−/− versus wild-type mice (16.2 versus 7.6 tumors, P < 0.001); Zn supplementation significantly reduced tumor burdens in Fhit−/− mice (males and females combined, 16.2 unsupplemented versus 10.3 supplemented, P = 0.001). Most importantly, the SCC burden was reduced after Zn supplementation in both strains and genders of mice, most significantly in the wild-type males (P = 0.035). Although the mechanism(s) of action of Zn supplementation in skin tumor prevention is not known in detail, the Zn-supplemented tumors showed evidence of reduced DNA damage and some cohorts showed reduced inflammation scores. The results suggest that mild Zn supplementation should be tested for prevention of skin cancer in high-risk human cohorts.
Zn supplementation can suppress tumor formation in rodent models. To determine if it could suppress development of nonmelanoma skin cancers, the most common cancer in humans, occurring with high frequency and morbidity in patients, we induced skin papillomas and squamous cell carcinoma (SCCs) in mice by carcinogen treatment. Zn supplementation suppressed the frequency of SCCs in both sexes of two mouse strains, suggesting that Zn supplementation should be tested for prevention of SCCs in high-risk humans.
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An examination of racial differences in 5-year survival of cervical cancer among African American and white American women in the southeastern US from 1985 to 2010
Abstract
Disparities in Cervical Cancer (CC) mortality outcomes between African American (AA) and White women have been studied for decades. However, conclusions about the effect of race on CC survival differ across studies. This study assessed differences in CC survival between AA and White women diagnosed between 1985 and 2010 and treated at two major hospitals in the southeastern US. The study sample included 925 AA and 1192 White women diagnosed with cervical adenocarcinoma, adenosquamous cell carcinoma, or squamous cell carcinoma. Propensity score adjustment and matching were employed to compare 5-year survival between the two racial groups. Crude comparisons suggested relevant racial differences in survival. However, the racial differences became of small magnitude after propensity-score adjustment and in matched analyses. Nonlinear models identified age at diagnosis, cancer stage, mode of treatment, and histological subtype as the most salient characteristics predicting 5-year survival of CC, yet these characteristics were also associated with race. Crude racial differences in survival might be partly explained by underlying differences in the characteristics of racial groups, such as age at diagnosis, histological subtype, cancer stage, and the mode of treatment. The study results highlight the need to improve access to early screening and treatment opportunities for AA women to improve posttreatment survival from CC.
We did not observe strong evidence for racial differences in survival of cervical cancer. The study suggests that the age at diagnosis, cancer stage, mode of treatment, and histological subtype are the most salient characteristics predicting 5-year survival.
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Expressions of SH3BP5, LMO3, and SNAP25 in diffuse large B-cell lymphoma cells and their association with clinical features
Abstract
Diffuse large B-cell lymphoma (DLBCL) is clinicopathologically and genetically heterogeneous with variable clinical outcomes. We previously identified signature genes overexpressed in CD5-positive (CD5+) DLBCL, which is a poor prognostic subgroup of DLBCL. To elucidate the clinical significance of the protein expression of the signature genes overexpressed in CD5+ DLBCL with regard to all DLBCL, not otherwise specified (NOS), 10 genes (SH3BP5, LMO3, SNAP25, SYT5, SV2C, CABP1, FGF1, FGFR2, NEUROD1, and SYN2) were selected and examined immunohistochemically with samples from 28 patients with DLBCL, NOS. Only three protein expressions, SH3BP5, LMO3, and SNAP25, were detected in DLBCL cells and then analyzed further with samples from 187 patients with DLBCL, NOS. The SH3BP5, LMO3, and SNAP25 proteins were expressed in 60% (103/173), 34% (59/175), and 46% (77/168) of DLBCL patients, respectively. These protein expressions were associated with CD5 expression, and only SH3BP5 was frequently expressed in activated B-cell-like DLBCL (P = 0.046). Compared to the SH3BP5-negative group, the SH3BP5+ group was correlated with elderly onset (>60 years, P = 0.0096) and advanced-stage disease (stage III/IV, P = 0.037). The LMO3+ group showed a worse performance status (>1, P = 0.0004). The SH3BP5+ group and the LMO3+ group had significantly worse overall survival than the negative groups (P = 0.030, 0.034; respectively) for the entire group. In a subgroup analysis of patients treated with rituximab-containing chemotherapy, there was no significant difference between groups. To the best of our knowledge, this is the first report showing the protein expressions of SH3BP5, LMO3, and SNAP25 in DLBCL cells and their clinical significance in patients with DLBCL. The SH3BP5 and LMO3 protein expressions are associated with the baseline clinical characteristics of DLBCL.
DLBCL cells can express SH3BP5, LMO3, and SNAP25 proteins. The SH3BP5 and LMO3 protein expressions are associated with clinical features of DLBCL patients.
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High expression of integrin β6 in association with the Rho–Rac pathway identifies a poor prognostic subgroup within HER2 amplified breast cancers
Abstract
Integrin αvβ6 is involved in the transition from ductal carcinoma in situ (DCIS) to invasive ductal carcinoma (IDC) of the breast. In addition, integrin β6 (ITGB6) is of prognostic value in invasive breast cancers, particularly in HER2+ subtype. However, pathways mediating the activity of integrin αvβ6 in clinical progression of invasive breast cancers need further elucidation. We have examined human breast cancer specimens (N = 460) for the expression of integrin β6 (ITGB6) mRNA by qPCR. In addition, we have examined a subset (N = 147) for the expression of αvβ6 integrin by immunohistochemistry (IHC). The expression levels of members of Rho–Rac pathway including downstream genes (ACTR2, ACTR3) and effector proteinases (MMP9, MMP15) were estimated by qPCR in the HER2+ subset (N = 59). There is a significant increase in the mean expression of ITGB6 in HER2+ tumors compared to HR+HER2- and triple negative (TNBC) subtypes (P = 0.00). HER2+ tumors with the highest levels (top quartile) of ITGB6 have significantly elevated levels of all the genes of the Rho–Rac pathway (P-values from 0.01 to 0.0001). Patients in this group have a significantly shorter disease-free survival compared to the group with lower ITGB6 levels (HR = 2.9 (0.9–8.9), P = 0.05). The mean level of ITGB6 expression is increased further in lymph node-positive tumors. The increased regional and distant metastasis observed in HER2+ tumors with high levels of ITGB6 might be mediated by the canonical Rho–Rac pathway through increased expression of MMP9 and MMP15.
The evidence for the involvement of αvβ6 integrin in the progression of breast cancer rests on data from two large European cohorts of patients. However, the identity of the downstream pathways involved is unclear. We have used two independent case series (N = 460) and have confirmed the observations of Moore et al. More importantly, we have found supporting evidence for the activation of the Rho–Rac pathway in HER2+ patients with elevated levels of ITGB6 expression.
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Fascin-1 as a novel diagnostic marker of triple-negative breast cancer
Abstract
In some cases of breast cancer, diagnosis of triple-negative breast cancer (TNBC) requires further fluorescence in situ hybridization (FISH) for determining human epidermal growth factor receptor 2 (HER2) status. However, few cases undergo FISH in China, leading to difficulty regarding subsequent treatment decisions. Here, we used immunohistochemical analysis to explore expression of fascin-1, an actin-bundling protein, as a diagnostic marker of TNBC. A total of 457 cases of breast cancer were divided into four molecular subtypes, including 82 cases (17.9%) of TNBC, 81 (17.7%) of HER2-enriched, 185 (40.5%) of luminal A, and 109 (23.9%) of luminal B. Positive fascin-1 expression was seen in 144 cases (31.5%), including 77 (16.8%) strong positive cases. Rates of positive and strong positive expression of fascin-1 were significantly higher in cases of TNBC than in the other molecular subtypes. In all cases of breast cancer, the sensitivities and specificities of positive and strong positive fascin-1 expression for predicting TNBC were 87.8% and 80.8%, and 78.0% and 96.5%, respectively. In cases of hormone receptor–negative breast cancer, the sensitivities and specificities of positive and strong positive fascin-1 expression for predicting TNBC were 87.8% and 61.7%, and 78.0% and 92.6%, respectively. In 24 cases with estrogen receptor (ER)-, PR-, and HER2 2 + equivocal status who underwent FISH, the sensitivity and specificity of strong positive fascin-1 expression for predicting TNBC were 71.4% and 90.0%. These results suggest that strong positive fascin-1 expression can be used as a diagnostic marker of TNBC.
A new scoring criterion for strong positive fascin-1 expression is proposed. A comparison between strong positive fascin-1 expression and fluorescence in situ hybridization (FISH) analysis was carried out. Strong positive fascin-1 expression has high sensitivity and specificity for predicting triple-negative breast cancer (TNBC).
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Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient
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Isolation and characterization of eight microsatellite loci from Galeocerdo cuvier (tiger shark) and cross-amplification in Carcharhinus leucas, Carcharhinus brevipinna, Carcharhinus plumbeus and Sphyrna lewini
The tiger shark Galeocerdo cuvier (Carcharhinidae) is a large elasmobranch suspected to have, as other apex predators, a keystone function in marine ecosystems and is currently considered Near Threatened (Red list IUCN). Knowledge on its ecology, which is crucial to design proper conservation and management plans, is very scarce. Here we describe the isolation of eight polymorphic microsatellite loci using 454 GS-FLX Titanium pyrosequencing of enriched DNA libraries. Their characteristics were tested on a population of tiger shark (n = 101) from Reunion Island (South-Western Indian Ocean). All loci were polymorphic with a number of alleles ranging from two to eight. No null alleles were detected and no linkage disequilibrium was detected after Bonferroni correction. Observed and expected heterozygosities ranged from 0.03 to 0.76 and from 0.03 to 0.77, respectively. No locus deviated from Hardy-Weinberg equilibrium and the global FIS of the population was of 0.04NS. Some of the eight loci developed here successfully cross-amplified in the bull shark Carcharhinus leucas (one locus), the spinner shark Carcharhinus brevipinna (four loci), the sandbar shark Carcharhinus plumbeus (five loci) and the scalloped hammerhead shark Sphyrna lewini (two loci). We also designed primers to amplify and sequence a mitochondrial marker, the control region. We sequenced 862 bp and found a low genetic diversity, with four polymorphic sites, a haplotype diversity of 0.15 and a nucleotide diversity of 2 × 10−4.
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The ontogenetic transformation of the mesosaurid tarsus: a contribution to the origin of the primitive amniotic astragalus
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Count trends for migratory Bald Eagles reveal differences between two populations at a spring site along the Lake Ontario shoreline
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Investigating body patterning in aquarium-raised flamboyant cuttlefish (Metasepia pfefferi)
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Microsatellite loci discovery from next-generation sequencing data and loci characterization in the epizoic barnacle Chelonibia testudinaria (Linnaeus, 1758)
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Flower, fruit phenology and flower traits in Cordia boissieri (Boraginaceae) from northeastern Mexico
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Transcriptomic analysis reveals distinct resistant response by physcion and chrysophanol against cucumber powdery mildew
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Nest site selection and nutritional provision through excreta: a form of parental care in a tropical endogeic earthworm
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Phylogenetics and population genetics of Plotosus canius (Siluriformes: Plotosidae) from Malaysian coastal waters
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