Identification of Apolipoprotein AI as a serum biomarker of chronic kidney disease in liver transplant recipients, using proteomic techniques

Chronic kidney disease (CKD) is a common complication post‐orthotopic liver transplantation (OLT). Development of CKD is detected by monitoring serum urea and creatinine, however disease can occasionally be at an advanced stage before they become abnormal. Therefore, more accurate parameters are required. In order to identify novel biomarkers of CKD, serum was obtained from 47 OLT recipients with CKD (glomerular filtration rate <60 mL/min) and 23 with normal renal function (glomerular filtration rate >90 mL/min). Using the proteomic technique SELDI‐TOF‐MS, three protein biomarkers (55.6 kDa, 9.5 kDa and 11.4 kDa) were identified that, together, could stratify patients into cases or controls with a sensitivity and specificity of 93.6 and 91.3%, respectively. The area under the curve was 0.94. The primary splitter of the groups at 55.6 kDa was an alternative version of a molecule at 27.8 kDa, which was subsequently identified by 1‐D SDS‐PAGE and LC‐ESI‐MS/MS to be Apolipoprotein AI. Protein expression was shown to be reduced in CKD, by both ELISA (p = 0.057) and Western blot analysis (p = 0.003). Apolipoprotein AI is a novel, accurate marker of CKD post‐OLT. It does require further validation in a large, more diverse patient population but could potentially improve detection of CKD.     

An immunoproteomic approach for identification of clinical biomarkers of Whipple's disease

Whipple's disease (WD) is a chronic multisystemic infection, caused by the bacterium Tropheryma whipplei. The main clinical presentations are classic WD (CWD) with histologic lesions in the gastrointestinal tract, endocarditis, and isolated neurologic infection. The current strategy for diagnosis remains invasive.The present study aimed to select the protein candidates for serological diagnosis of WD. The first step was to identify candidate proteins by an immunoproteomic approach combining 2‐DE using a total extract of a T. whipplei, immunoblotting, and MS. The second step was to validate the discovered biomarkers using a recombinant protein‐based ELISA. Serum samples from 18 patients with WD and from 54 control individuals were tested. A sugar ABC transporter, TWT328 (sensitivity (Se) 61%, specificity (Sp) 87%, positive predictive value (PPV) 61%, negative predictive value (NPV) 87%, and positive likelihood ratio (PLR) 4.69) was the best marker for development of serodiagnosis for CWD. We also obtained a reproducible immunoreactive protein pattern for patients with isolated neurological infection due to T. whipplei (Se 100%, Sp 93%, PPV 55.5%, NPV 100%, and PLR 13.51) as an encouraging step towards noninvasive diagnosis of this particular manifestation. Nine recombinant candidates have been successfully screened with serum samples. Results from these ELISA assays skewed with those obtained with immunoblots.     

Proteomic analysis of sera of asymptomatic,early‐stage patients with Wilson's disease

Wilson's disease (WD) is characterized by excessive accumulation of intracellular copper in liver and extrahepatic tissues, leading to significant oxidative stress and tissue damage. To date, several diagnostic biomarkers for WD such as serum ceruloplasmin, serum or urine copper levels and copper content in liver have been identified. However, these biomarkers may not be convincing for the diagnosis in some WD patients. To identify additional novel diagnostic biomarkers, we compared the serum protein profiles of asymptomatic childhood WD patients (n=20), without neurologic manifestation or liver cirrhosis, with normal controls (n=13). Fourteen spots, five up‐regulated and nine down‐regulated (>2‐fold), were differentially expressed in WD patients in comparison to normal control on 2‐DE. Among them, three spots were down‐regulated in both male and female WD. MS/MS analysis revealed that the three spots were complement component C3, complement factor B and alpha‐2 macroglobulin. By comparative proteome analysis, complement component C3, complement factor B and alpha‐2 macroglobulin, which are related to oxidative stress and inflammation, turned out to be good candidates for novel diagnostic biomarkers for early stages of WD.     

Proteomics analysis of plasma for potential biomarkers in the diagnosis of Alzheimer's disease

The objective of this study was to search for biological markers associated with Alzheimer's disease (AD). Plasma specimens obtained from ten pathologically diagnosed AD patients and ten non-demented (ND) control subjects were analyzed by a combination of 2-DE and MS. This strategy allowed us to identify six plasma proteins (alpha-1-antitrypsin, vitamin D-binding protein, inter-alpha-trypsin inhibitor family heavy chain-related protein, apolipoprotein J precursor, cAMP-dependent protein kinase catalytic subunit alpha 1, and an orf) whose 2-DE spot densities were different between the AD and ND groups. Due to their involvements in AD amyloid plaque formation, the plasma concentrations of alpha-1-antitrypsin and apolipoprotein J were further validated using either ELISA or Western blot. The results revealed that the plasma levels of alpha-1-antitrypsin in AD were higher than those of controls, confirming the 2-DE findings. However, no difference in total apolipoprotein J concentration was observed between the AD and ND groups. Considering the difference in resolving power to differentially quantitate protein isoforms provided by 2-DE and Western blot, 2-DE analysis combined with MS protein identification offers distinctive advantages when a disease-related protein isoform-specific variance is investigated.     

Redox proteomics identification of 4‐hydroxynonenal‐modified brain proteins in Alzheimer's disease: Role of lipid peroxidation in Alzheimer's disease pathogenesis

Numerous studies have shown that neuronal lipids are highly susceptible to oxidative stress including in those brain areas directly involved in the neurodegenerative process of Alzheimer's disease (AD). Lipid peroxidation directly damages membranes and also generates a number of secondary biologically active products (toxic aldehydes)that are capable of easily attacking lipids, proteins, and DNA. Accumulating evidence has demonstrated regionally increased brain lipid peroxidation in patients with AD; however, extensive studies on specific targets of lipid peroxidation‐induced damage are still missing. The present study represents a further step in understanding the relationship between oxidative modification of protein and neuronal death associated with AD. We used a proteomics approach to determine specific targets of lipid peroxidation in AD brain, both in hippocampus and inferior parietal lobule, by coupling immunochemical detection of 4‐hydroxynonenal‐bound proteins with 2‐D polyacrylamide gel electrophoresis and MS analysis. We identified 4‐hydroxynonenal‐bound proteins in the hippocampus and inferior parietal lobule brain regions of subjects with AD. The identified proteins play different biological functions including energy metabolism, antioxidant system, and structural proteins, thus impairing multiple molecular pathways. Our results provide further evidence for the role of lipid peroxidation in the pathogenesis of AD.     

Thymosin β4 is differentially expressed in the cerebrospinal fluid of Creutzfeldt‐Jakob disease patients: a MALDI‐TOF MS protein profiling study

MALDI‐TOF protein profiling analysis permits the detection of peptides and small proteins in complex protein mixtures with great accuracy. We applied this analysis to cerebrospinal fluid (CSF) from 15 patients affected by Creutzfeldt‐Jakob disease (CJD). We compared the levels of the normalized ion signals of 11 sporadic and 4 genetic CJD forms with those from ten healthy control subjects and eight non‐CJD relapsing‐remitting multiple sclerosis patients. In so doing, we detected 61 differentially expressed ion signals in CJD samples compared to controls. Among the 61 signals, 3 signals had significantly increased levels with high statistical significance (p <0.0001) and were located at 3238.3 m/z, 4963.7 m/z, and 8565.3 m/z. We characterized the 5.0 and 8.6 kDa proteins as thymosin β4 N‐acetylated and free ubiquitin, respectively, while the 3.2‐kDa peptide remained uncharacterized. Although elevated ubiquitin levels have previously been described in CJD, we have demonstrated for the first time the involvement of thymosin β4 in a neurodegenerative disease. To support the validity of thymosin β4 levels obtained by MALDI‐TOF analysis, an independent enzyme immunoassay analysis was performed. Moreover, a validation cohort consisting of CSF from three CJD patients, five healthy subjects, and six non‐CJD relapsing‐remitting multiple sclerosis patients was analyzed in a similar way, yielding superimposable results. We propose that thymosin β4 is a potential new candidate marker for the ante mortem diagnosis of CJD disease.     

A novel method for the classification of Alzheimer's disease from normal controls using magnetic resonance imaging

Alzheimer's disease (AD) is the most prevalent form of dementia. Although fewer people, who suffer from AD are correctly and promptly diagnosed, due to a lack of knowledge of its cause and unavailability of treatment, AD is more manageable if the symptoms of mild cognitive impairment (MCI) are in an early stage. In recent years, computer‐aided diagnosis has been widely used for the diagnosis of AD. The main motive of this paper is to improve the classification and prediction accuracy of AD. In this paper, a novel approach is developed to classify MCI, normal control (NC), and AD using structural magnetic resonance imaging (sMRI) from the Alzheimer's disease Neuroimaging Initiative (ADNI) dataset (50 AD, 50 NC, 50 MCI subjects). FreeSurfer is used to process these MRI data and obtain cortical features such as volume, surface area, thickness, white matter (WM), and intrinsic curvature of the brain regions. These features are modified by normalizing each cortical region's features using the absolute maximum value of that region's features from all subjects in each group of MCI, NC, and AD independently. A total of 420 features are obtained. To address the curse of dimensionality, the obtained features are reduced to 30 features using a sequential feature selection technique. Three classifiers, namely the twin support vector machine (TSVM), least squares TSVM (LSTSVM), and robust energy‐based least squares TSVM (RELS‐TSVM), are used to evaluate the classification accuracy from the obtained features. Five‐fold and 10‐fold cross‐validation are used to validate the proposed method. Experimental results show an accuracy of 100% for the studied database. The proposed approach is innovative due to its higher classification accuracy compared to methods in the existing literature.     

Proteomic studies on receptor for advanced glycation end product variants in idiopathic pulmonary fibrosis and chronic obstructive pulmonary disease

Purpose: Proteomic screening revealed declined levels of the receptor for advanced glycation end products (RAGE) in human idiopathic pulmonary fibrosis (IPF). This study was undertaken to investigate the different RAGE isoforms in two lung diseases with destruction of the lung parenchyma, i.e. IPF and chronic obstructive pulmonary disease (COPD). Experimental design: RAGE was analyzed by 2‐DE, MS and Western blotting using lung tissues from non‐smokers, smokers, patients with IPF, COPD and α‐1‐antitrypsin deficiency (AAT) and by ELISA from the bronchoalveolar lavage fluid samples. Results: RAGE, detected by 2‐DE in the control lung, was confirmed to be glycosylated, soluble, C‐truncated RAGE with characteristics indicative of the presence of endogenous secretory RAGE (esRAGE). Further studies revealed a decrease of the full length‐RAGE (FL‐RAGE) and its C‐terminal processed variant (cRAGE) in the lung tissues of IPF and COPD patients but not in AAT. The esRAGE level was reduced in IPF but was unchanged in COPD. Conclusions and clinical relevance: This study shows an involvement of the three RAGE variants (FL‐RAGE, cRAGE, esRAGE) in IPF. The decline of FL‐RAGE and cRAGE, but not esRAGE, in COPD lungs is evidence of involvement of specific RAGE variants also in this disease.     

A mass spectrometric strategy for profiling glycoproteinoses, Pompe disease, and sialic acid storage diseases

Glycoproteinoses, Pompe disease, and sialic acid storage diseases are characterized by a massive accumulation of unprocessed oligosaccharides and/or glycoconjugates in urine. The identification of these glycocompounds is essential for a proper diagnosis. In this study, we investigated the potential of MALDI‐TOF‐MS to identify glycocompounds present in urine from patients with different inborn errors of glycan metabolism. Urinary glycocompounds were permethylated, and analyzed using GC‐MS and MALDI‐TOF‐MS. In order to confirm tentative assignments, a second aliquot of urine was purified on a C18 Sep‐Pak cartridge and glycocompounds were desalted on a column of nonporous graphitized carbon. The glycocompounds were then sequentially on‐plate digested using an array of exoglycosidases. A range of disease‐specific oligosaccharides as well as glycopeptides was identified for all oligosacchariduria models. In addition, free sialic acid accumulated in urine from a patient suffering from French‐type sialuria, has been detected by a GC‐MS approach, which could be applied to other sialic acid storage diseases. This procedure is simple, and can be performed in few simple steps in less than 24 h. This current method can be applied for newborn screening for other inherited metabolic diseases as well as for assessing treatments in clinical trials.     

Analysis of protein profiling studies of β‐thalassemia/Hb E disease

A number of studies have used global protein profiling technologies on a range of patient samples to detect proteins that are differentially expressed in β‐thalassemia/Hb E as an aid for understanding the physiopathology of this disease. Seven studies have identified a total of 111 unique, differentially expressed proteins. Seven proteins (prothrombin, alpha‐1‐antichymotrypsin, fibrinogen beta chain, hemoglobin beta, selenium‐binding protein, microtubule‐actin cross‐linking factor and adenomatous polyposis coli protein 2) have been identified in two independent studies, whereas two proteins (carbonic anhydrase 1 and peroxiredoxin‐2) have been identified in three independent studies. Both of these latter two proteins were consistently upregulated in the studies that identified them. Ontological analysis of all differentially regulated proteins identified “response to inorganic substances” as the most significant functional annotation cluster, which is consistent with iron overload being a major pathological consequence of this disease. Despite the range of samples investigated and the relatively small number of studies undertaken, a coherent picture of the mediators of the pathological consequences of β‐thalassemia/Hb E disease is starting to emerge.     

Optimal pricing decisions for an omni‐channel supply chain with retail service

Motivated by the emergence of dominant physical stores utilizing a buy‐online‐and‐pickup‐in‐store (BOPS) channel, we examine the interaction of such a stronger retailer and a manufacturer's strategies on the pricing and service value. The dominant retailer provides an added service value to end consumers by the traditional channel and BOPS option, which has a positive influence on the market demand. The manufacturer makes the channel selection decision between a dual channel and an omni‐channel. We formulate a retailer Stackelberg game and characterize the equilibrium pricing and service solutions under centralized and decentralized cases. Our results indicate that the service value of a physical store strongly influences the players' pricing strategies. The sensitivity analysis reveals that the total revenue of the supply chain increases with the market scale expansion coefficient of the BOPS option. Furthermore, the result suggests that offering the BOPS channel is always an effective initiative to boost supply chain performance, especially in the centralized structure.     

Compact quad‐band band‐pass filters using stepped‐impedance coupled‐line resonators

In this article, compact quad‐band band‐pass filters are realized by using stepped‐impedance coupled‐line quad‐mode resonators (SICLQMRs). The compactness of the quad‐mode resonator relies in its folded structure without extra space between the parallel lines. Unlike stepped‐impedance resonators, SICLQMRs provide more design freedoms for controlling the four resonating frequencies since the even‐ and odd‐mode equivalents can be separately assigned with characteristic impedances. Internal and external couplings are also parallel couplings, resulting in very compact dimensions of the filters. Simulated and measured S parameters are compared with good agreement, demonstrating the feasibility of the design.     

Ultra‐low‐power LTPS TFT‐LCD technology using a multi‐bit pixel memory circuit

Abstract— Two types of low‐temperature poly‐Si TFT LCDs, which integrate a multi‐bit memory circuit and a liquid‐crystal driver within a pixel, have been developed using two different TFT process technologies. Both a 1.3‐in. 116‐ppi LCD having a 2‐bit pixel memory and a 1.5‐in. 130‐ppi LCD having a 5‐bit pixel memory consume very little power, less than 100 μW, which indicates that this technology is promising for mobile displays.     

Dual‐mode resonator with modified dual‐square‐Loop for WLAN and WiMAX quad‐band filter design

We propose the improved configurations with dual‐mode dual‐square‐loop resonators (DMDSLR) for quad‐band bandpass filter (BPF) design. The modified DMDSLR filter employs two sets of the loops. The square loop is designed to operate at the first and third resonated frequencies (2.4/5.22 GHz) and the G‐shaped loop is employed at the second and fourth resonated frequencies (3.59/6.6 GHz). The resonant frequency equations of DMDSLR are introduced for simply designing quad‐band BPF. Resonant frequencies can be controlled by tuning the perimeter ratio of the square loops. A systematic design procedure with the design map is applied for accuracy design. To obtain lower insertion loss, higher out‐of‐band rejection level and wider bandwidth of quad‐band, the miniaturized DMDSLR with meander‐line technique is proposed. The proposed filters are successfully simulated and measured showing frequency responses and current distributions. It can be applied to WLAN and WiMAX quad‐band systems. © 2013 Wiley Periodicals, Inc. Int J RF and Microwave CAE 24:332–340, 2014.     

Model‐to‐model and model‐to‐text: looking for the automation of VigilAgent

VigilAgent is a methodology for the development of agent‐oriented monitoring applications that uses agents as the key abstraction elements of the involved models. It has not been developed from scratch, but it reuses fragments from Prometheus and INGENIAS methodologies for modelling tasks and the ICARO framework for implementation purposes. As VigilAgent intends to automate as much as possible the development process, it exploits. Model transformation techniques are one of the key aspects of the model‐driven development approach. A model‐to‐model transformation is used to facilitate the interoperability between Prometheus and INGENIAS methodologies. Also, a model‐to‐text transformation is performed to generate ICARO code from the INGENIAS model. A case study based on access control is used to illustrate the fundamentals of the model‐to‐model and model‐to‐text transformations implemented in VigilAgent.     

A 1‐to‐n way single‐ended‐to‐balanced substrate integrated waveguide filtering power splitter

An approach to 1‐to‐n (n = 3, 4…) way single‐ended‐to‐balanced filtering power splitter (SETBFPS) is proposed. The properly placed balanced ports with 0.5λ_g (λ_g is the substrate integrated waveguide [SIW] guided wavelength at f₀) space make the TE32nd 103 and TE32nd 105 modes of n 32nd‐mode SIW multimode resonators form differential‐mode (DM) passband of the SETBFPS. Compared with the state‐of‐art single‐ended‐to‐balanced power splitters, the proposed approach has all the functions of 1‐to‐n way, filtering, and common‐mode (CM) suppression. A 1‐to‐3 way prototype is exemplified at 3.5 GHz with the minimum insertion loss (IL) of 0.09 dB, a fractional bandwidth (FBW) for a 15‐dB return loss of 35%, and a FBW for 15‐dB CM suppression of 52%. Low IL and wide bandwidth can be observed.     

Low‐power‐consumption TFT‐LCD with dynamic memory embedded in the pixels

A low‐power‐consumption thin‐film‐transistor liquid‐crystal display (TFT‐LCD) with dynamic memory cells embedded in each pixel using low‐temperature poly‐Si technology has been developed. By holding data in the memory, the operating rate of the data driver can be dramatically reduced to 4 Hz. Eight levels of gray scale with low power consumption can be achieved by using the area‐ratio gray‐scale method. This TFT‐LCD can be used for displaying fine still images, with low power consumption.     

A novel compact self‐similar fractal UWB MIMO antenna

A novel compact self‐similar fractal ultra‐wideband (UWB) multiple‐input‐multiple‐output (MIMO) antenna is presented. This fractal geometry is designed by using iterated function system (IFS). Self‐similar fractal geometry is used here to achieve miniaturization and wideband performance. The self‐similarity dimension of proposed fractal geometry is 1.79, which is a fractional dimension. The antenna consists of two novel self‐similar fractal monopole‐antenna elements and their metallic area is minimized by 29.68% at second iteration. A ground stub of T‐shape with vertical slot enhances isolation and impedance bandwidth of proposed MIMO antenna. This antenna has a compact dimension of 24 × 32 mm² and impedance bandwidth (S₁₁ < ?10 dB) of 9.4 GHz ranging from 3.1 to 12.5 GHz with an isolation better than 16 dB. The various diversity performance parameters are also determined. There is good agreement between measured and simulated results, which confirms that the proposed antenna is acceptable for UWB applications.