Healthcare workers including physicians, nurses, medical technicians and administrative staff experience high levels of occupational stress as a result of heavy workloads, extended working hours and time-related pressure. The aims of this study were to investigate factors associated with work stress among hospital staff members and to evaluate their health-promoting lifestyle behaviors.We conducted a cross-sectional study from May 1, 2010 to July 30, 2010 and recruited 775 professional staff from two regional hospitals in Taiwan using purposive sampling. Demographic data and self-reported symptoms related to work-related stress were collected. Each subject completed the Chinese versions of the Job Content Questionnaire (C-JCQ) and The Health-Promoting Lifestyle Profile (HPLSP). Linear and binary regression analyses were applied to identify associations between these two measurements and subjects’ characteristics, and associations between the two measurements and stress symptoms.Self-reported symptoms of work-related stress included 64.4% of subjects reporting nervousness, 33.7% nightmares, 44.1% irritability, 40.8% headaches, 35.0% insomnia, and 41.4% gastrointestinal upset. C-JCQ scores for psychological demands of the job and discretion to utilize skills had a positive correlation with stress-related symptoms; however, the C-JCQ scores for decision-making authority and social support correlated negatively with stress-related symptoms except for nightmares and irritability. All items on the HPLSP correlated negatively with stress-related symptoms except for irritability, indicating an association between subjects’ symptoms and a poor quality of health-promoting lifestyle behaviors.We found that high demands, little decision-making authority, and low levels of social support were associated with the development of stress-related symptoms. The results also suggested that better performance on or a higher frequency of health-promoting life-style behaviors might reduce the chances of hospital staff developing stress-related symptoms. Our report may contribute to the development of educational programs designed to encourage members of high stress groups among the hospital staff to increase their health-promoting behaviors. Healthcare workers in hospitals are exposed to high levels of occupational stress resulting from heavy workloads, extended working hours and high levels of time pressure. Hospital staff members, including physicians and nurses, are at a higher risk of suffering from depressive disorders than is the general population. The hazRecently, considerable concern about job stress has given rise to a theoretical approach that focuses on a demand-control-support model of job strain, as proposed by Karasek et al. This model predicts that job strain will occur when psychological work demands are high and the worker’s job control is low, while a low level of workplace social support will increase the risk of negative health outcomes. The psychological demand dimension relates to "how hard workers work" , organizational constraints on task completion, and conflicting demands. Job control, discretion in utilizing ones’ skills, and decision-making authority are measured by a set of questions that assess the level of skill and creativity required on the job and the flexibility permitted the worker in deciding what skills to employ.. A Job CA study of nurses in Taiwan, found that occupational stress was associated with young age, marital status (widowed/divorced/separated), high psychological demand, low workplace support, and threat of assault at work. A lower score for general health was associated with low job control, high psychological demand, and perceived occupational stress. A lower mental health score was associated with low job control, high psychological demand, low workplace support, and perceived occupational stress.While the JCQ is able to evaluate psychosocial aspects of workplace stress, it does not consider individual personalities or lifestyle factors that may influence responses to those stressors. Job stress has been linked to a range of adverse physical and mental health outcomes, such as cardiovascular disease, insomnia, depression, and anxiety. IncreasHealth-promoting behaviors were described by Walker et al. as behaviors that were directed toward sustaining or increasing the individual’s level of well-being, self-actualization and personal fulfillment. A HealtThe present study proposed that, for the professional staff in a hospital, the extent of job stress (measured by the JCQ) and performance in health-promoting lifestyle (measured by HPLSP) may correlate with stress-related symptoms. To the best of our knowledge, no previous study has examined the correlations among the factors related to stress in a cross section of hospital staff professionals.st, 2010 to July 30th, 2010. The retrieval rate was 72.5% (775/1069) and 467 subjects were in Chia-Yi and 308 subjects in Hsin-Chu. After the study was explained to participants, all subjects provided written informed consent. The institutional review boards of the two hospitals approved the study protocol.In this cross-sectional study, a total of 1069 subjects who worked in regional hospitals in Chia-Yi and Hsin-Chu in Taiwan, were selected based on purposively sampling  from May 1The participants were asked to complete a self-reported questionnaire about basic characteristics including job, marriage, education, location of hospital, length of work experience, average number of hours worked per day and symptoms related to work-related stress. These symptoms were chosen based on related articles in the literature-13 and dThe C-JCQ is a modA short form of the Chinese version of the HPLSP scale was developed by Wei & Lu in 2005 as a modp < 0.05. Statistical analyses were performed using SPSS 15.0 statistical software .Subjects’ characteristics were summarized as mean ± standard deviation (SD) for continuous variables and count (n) with percentage (%) for categorical variables. Measurements on the JCQ and HPLSP were represented as mean ± SD and range (min. - max.) Spearman’s correlation analysis, point biserial correlation analysis, and point multiserial correlation analysis were utilized to show the coefficients of correlation. Binary logistic regression analysis was also utilized to identify symptoms of work-related stress while considering subjects’ characteristics, JCQ, and HPLSP. All statistical assessments were considered significant at Among the 775 subjects, 107 were male and 668 were female. Table Table Table Longer work experience was positively correlated with discretion in use of skills and decision-making authority but showed a negative correlation with coworker social support and supervisor social support. Table  Daily woThe correlation of subjects’ characteristics with HPLSP categories is shown in Table Among the subcategories of HPLSP, most  were positively correlated with job position. Physicians had less self-actualization, fewer chances to exercise, cared less about nutrition, and did not manage stress well. They were followed by nurses, medical technician staff, and administrative staff in that order. Table  Health rTable For C-JCQ items, scores on psychological demands of the job and decisions to utilize skills had a positive correlation with stress-related symptoms, except for irritability; however, decision-making authority scores had a negative correlation with stress-related symptoms, except for irritability. Both the scores for coworker social support and supervisor social support had negative correlations with stress-related symptoms except for nightmares and irritability. All items on the health-promoting life-style profiles had a negative correlation with stress-related symptoms, except for irritability.High job demands, little decision-making authority, and low social support were associated with the development of stress-related symptoms. Relationships were also shown between job category and dimensions of the JCQ. Male workers had fewer psychological demands on the job than did females but had greater discretion in utilizing their skills. Hospital nursing staff, medical technicians and administrative staff had significantly less discretion in utilizing their skills and decision-making authority than did physicians. Longer work experience was associated with significantly higher discretion in utilizing skills and decision-making authority among all workers. Longer daily work times were associated with significantly higher psychological demands on the job, discretion in utilizing skills, and decision-making authority. Psychological demands on the job were somewhat associated with gender and daily work time. In terms of symptoms, being female, having a longer work experience, and working longer hours each day were associated with significantly greater stress-related symptoms, except for irritability. Nervousness, headache, and, to a lesser extent, gastrointestinal upset were reported more frequently.Staff responses to HPLSP categories revealed that nurses performed less well in self-actualization and nutrition categories when compared to other types of workers. Participants with longer work experience performed better in self-actualization, health responsibility and nutrition categories. Staff with longer daily work times performed less well in nutrition, indicating that time constraints on the job interfered with their ability to eat well. The total scores for health-promoting lifestyle indicated that hospital staff did have an interest in health-promoting measures but did not always perform them well. All items on the HPLSP correlated negatively with stress-related symptoms except for irritability, indicating an association between subjects’ symptoms and their self-reported, low-quality, health-promoting lifestyle behaviors.As in the study by Shen et al., lower gMcElligott et al. examinedIn the present study, nurses sensed a lack of social support from peers and supervisors and, in expressing a need for more social support, placed a high value on relationships at work as being an important aspect of the work environment. Work relationships were also cited as a direct source of stress by Hope et al. as hospital nurses who experienced high work stress were more apt to seek professional support and the support of family and friends or “having a good cry”. SeekingSolutions must fit the problem and different settings have produced different explanations for work-related stress. A recent study by Chen et al. explored job stress and specific stressors along with coping strategies and overall job satisfaction among nurses and found that the main stressors were related to the type of hospital, patient safety issues, and administrative feedback. They recommended implementation of standard operating procedures, security measures and increases in the quantity and quality of stress relief courses. Other sMany researchers in Taiwan have studied job stress, coping strategies and health promoting behavior among hospital staffs,18,20,21There are several limitations to our study. First, 48.5% of the subjects worked as nursing staff and only 4.5% as physicians; therefore, nursing staff responses may disproportionally affect the overall scores on the questionnaires, and, to a lesser extent, reflect the job content and life-style profile of male physicians. Second, our study population of 775 healthcare workers was recruited from only two regional hospitals, and this may preclude generalization of the results to larger and smaller institutions such as medical centers, local hospitals, and clinics. Third, odds ratios in logistic regression may not be appropriate for a cross-sectional study, and a prospective study should be conducted in the future. Finally, a future study will be needed to demonstrate whether a high quality of health-promoting lifestyle can really reduce the stress-related symptoms associated with high demand, low control and low social support.Little decision-making authority and a lack of social support from either coworkers or supervisors are associated with the development of stress-related symptoms. Better performance in or higher frequency of health-promoting life-style behaviors might reduce the chances of developing stress-related symptoms. We suggest that our results may be useful in the development of educational programs designed to encourage highly stressed hospital staff members to pay more attention to health-promoting lifestyles and to increase health-promoting behaviors as protection against the demands of the hospital work environment.The authors declare that they have no competing interests.YC Tsai designed the study, wrote the protocol, managed the literature searches, data acquisition and analysis, and wrote the manuscript. Dr. CH Liu was the supervisor for the project, was closely involved in creating the hypothesis and study design, and undertook the manuscript editing and review of the rough draft. All authors read and approved the final manuscript.The pre-publication history for this paper can be accessed here:http://www.biomedcentral.com/1472-6963/12/199/prepub


Pre-hospital airway management is a controversial subject, but there is general agreement that a small number of seriously ill or injured patients require urgent emergency tracheal intubation (ETI) and ventilation. Many European emergency medical services (EMS) systems provide physicians to care for these patients while other systems rely on paramedics . The ETI success rate is an important measure of provider and EMS system success and a marker of patient safety.We conducted a systematic search of Medline and EMBASE to identify all of the published original English-language articles reporting pre-hospital ETI in adult patients. We selected all of the studies that reported ETI success rates and extracted information on the number of attempted and successful ETIs, type of provider, level of ETI training and the availability of drugs on scene. We calculated the overall success rate using meta-analysis and assessed the relationships between the ETI success rate and type of provider and between the ETI success rate and the types of drugs available on the scene.P = 0.0345). In the non-physician group, the use of drug-assisted intubation significantly increased the success rates. All physicians had access to traditional rapid sequence induction (RSI) and, comparing these to non-physicians using muscle paralytics or a traditional RSI, there still was a significant difference in success rate in favour of physicians, 0.991 and 0.955, respectively (P = 0.047).From 1,070 studies initially retrieved, we identified 58 original studies meeting the selection criteria. Sixty-four per cent of the non-physician-manned services and 54% of the physician-manned services reported ETI success rates but the success rate reporting was incomplete in three studies from non-physician-manned services. Median success rate was 0.905 . In a weighted linear regression analysis, physicians as providers were significantly associated with increased success rates, 0.092 (This comprehensive meta-analysis suggests that physicians have significantly fewer pre-hospital ETI failures overall than non-physicians. This finding, which remains true when the non-physicians administer muscle paralytics or RSI, raises significant patient safety issues. In the absence of pre-hospital physicians, conducting basic or advanced airway techniques other than ETI should be strongly considered. Airway compromise has been identified as a preventable cause of poor outcomes and death in trauma and cardiac arrest patients for many years ,2. AfterRapid sequence induction (RSI) is generally accepted as the technique of choice for securing the airway in seriously ill or injured patients ,4. RSI cIn a pre-hospital setting, the situation is somewhat different. The first Medline- or EMBASE-indexed reports on pre-hospital ETI were published in the mid-to-late1960s -13. ReceAs a complex intervention performed by operators with different skill levels in different ways on different patient groups, the effect of pre-hospital ETI on patient outcome is difficult to assess. However, the rate of successful placement of a tracheal tube into the trachea after attempted intubation, particularly after the administration of a muscle paralytic, is recognized as a quality indicator for systems practicing ETI. Although muscle paralytics are administered to facilitate intubation they also render the patient apnoeic and, therefore, make the consequences of failed intubation much more serious.The aim of this project was to establish whether the published literature indicates a difference in ETI success rates between physician- and non-physician-manned EMS systems. We compared the success rates of non-physicians and physicians and those of non-physicians using different levels of drug assistance. Further, we wanted to explore whether there was a difference in ETI success rates between physicians and the sub-group of non-physicians using a muscle paralytic or a standard RSI.We conducted a systematic search of Medline and EMBASE according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines . We idenFrom the initial search, we selected all of the studies reporting ETI success rates. From these papers, we extracted information on the numbers of attempted ETIs and successful ETIs, type of provider, level of ETI training and drug availability on scene. The providers were categorized into two groups: physician and non-physician. The use of drugs was categorized into three groups: 1) no drugs available; 2) analgesics, anaesthetics, or a combination; and 3) muscle paralytics, with or without co-administration of analgesics and anaesthetics, or a standard RSI.The ETI success rates are reported as medians (range) unless stated otherwise. The individual and overall success rate is presented in a forest plot and the overall success rate was calculated using a random effects meta-analysis for proportions. The analysis did not consider the number of ETI attempts before success was achieved.P < 0.05.To assess the relationships between the ETI success rate and provider type, and between the ETI success rate and types of drugs available on the scene, we performed a weighted univariate linear regression analysis with the ETI success rate as the dependent variable and drug availability and provider type as categorical independent variables. The regression was weighted by the size of each study, that is, by the number of intubation attempts. As all physicians use RSI (drug group '3'), a multiple regression model would have been degenerate and was not performed. All the tests were two-tailed, and statistical significance was indicated by The data were analysed using R 2.12  .As a meta-analysis based on a systematic literature review, this study did not require approval from The Regional Committee for Research Ethics or the National Social Science Services.From 1,070 studies initially retrieved through the systematic search, we identified 58 original studies that met the inclusion criteria. Of these, 45 (78%) were studies of non-physician-manned services (paramedic- or paramedic/nurse-manned). Twenty-nine (64%) of the 45 non-physician-manned services and seven (54%) of the 13 physician-manned services reported ETI success rates. The success rate reporting was incomplete in three studies from non-physician-manned services, leaving 33 studies for the final analysis  reported success rate was 0.905   ETI success rates were 0.991  versus 0.849 .All seven physician-manned services reporting success rates also reported drugs available on the scene . Of the 26 non-physician-manned services reporting success rates, 19 (73%) reported drugs available on scene, leaving seven services reporting no use of drugs (drug group 1). Of the 19 services reporting use of drugs, six had analgesics, anaesthetics or a combination available (drug group 2), and 13 reported having muscle paralytics, with or without analgesics or anaesthetics, or standard RSI available (drug group 3). In drug groups 1, 2 and 3, the reported median (range) ETI success rates for non-physicians were 0.675 , 0.810  and 0.967 , respectively.P = 0.0345. Similarly, drug groups 2 and 3 were significantly associated with an increased success rate: 0.108 , P = 0.006 and 0.199 , P < 0.001, respectively.In weighted linear regression analysis, having physician providers was significantly associated with an increased success rate: 0.092 , P = 0.047).When comparing physician to drug group 3  non-physician success rates, there still was a significant difference in favour of physicians: 0.991  and 0.955 , respectively  is provided by both physicians and non-physicians, and the published studies report a wide range in success rates from different emergency medical service (EMS) systems.• EMS-physicians have ETI success rates close to 100% and significantly higher than non-physicians.• ETI is a potentially hazardous intervention, especially when conducted with muscle paralytics, and failed intubation increases the risk of severe adverse events and fatal outcome.• In the absence of pre-hospital physicians, conducting basic and advanced airway techniques other than ETI should be strongly considered.ETI: emergency tracheal intubation; EMS: emergency medical services; RSI: rapid sequence inductionThe authors declare that they have no competing interests.HML and DJL conceived and planned the study. HML performed the literature review and JR performed the meta-analysis. All authors contributed to writing a draft, and HML wrote the final manuscript, which was read and approved by all the authors.Overview of included studies. Aim of study, EMS manning, drugs available on scene, number of ETI attempts, number of ETI's successfully conducted, and reported success rate extracted from the 33 reviewed studies. EMS, emergency medical service; ETI, emergency tracheal intubation; RSI, rapid sequence induction.Click here for file


Signal processing is a long-established engineering field with broad applications in so different arenas such as multimedia , coding, communications, seismology, astronomy, biomedicine, artificial intelligence, and econometrics, to only name some of them. Signal processing stems from cross-fertilized grounds including mathematical analysis, algebra, numerical analysis, probability, statistics, information theory, discrete mathematics, cybernetics, and computer science. Advances in signal processing have frequently been pulled by needs in specific application domains, so that they are readily incorporated to the signal processing knowledge base for convenient use in distant areas of application. Signal and image processing is ubiquitous in modern biomedical imaging, as it provides essential techniques for image construction, enhancement, coding, storage, transmission, analysis, understanding, and visualization from any of an increasing number of different multidimensional sensing modalities. As biomedical imaging is rapidly evolving, new and more powerful signal and image processing algorithms are required to meet the challenges imposed by modern huge multidimensional multimodal biomedical data, particularly in real clinical settings.In this special issue, we present high-quality original research papers that address specific challenges for the biomedical imaging community and benefit of advanced and emerging methods in signal and image processing required for novel time-varying high-dimensional structural and functional biomedical imaging modalities. Interesting new ideas from other fields of application of signal and image processing have been highly welcome since their practical relevance for biomedical imaging is clearly motivated.In particular, this special issue features original research for different imaging modalities, such as generalized diffusion tensor imaging (GDTI), conventional diffusion weighted MRI (DW-MRI), dynamic contrast enhanced MRI (DCE-MRI), functional MRI (fMRI), X-ray mammography and time-frequency representations (TFR) of electrophysiological data such as electroencephalography (EEG), magnetoencephalography (MEG), or local field potentials (LFP). The medical application areas include central nervous system fiber tractography, analysis of episodic memory and motor brain activity, analysis of neural activity patterns, and breast cancer screening and detection. As for the signal and image processing methods, a brief list of topics addressed in this special issue include higher-order tensors, signal estimation and classification, clustering, and multivariate statistics, to name a few. Fast and analytical EAP approximation from a 4th-order tensor,” A. Ghosha and R. Deriche deal with the complicated problem of inferring the microstructure of tissue or fiber bundles from DW-MRI. To this extent they propose a modified GDTI approach, where the higher-Order tensor (HOT) representation of the apparent diffusivity coefficient (ADC) is estimated, from the DW-MRI data, in such a way that they provide a closed-form approximation, using Hermite polynomials, to the ensemble average propagator (EAP) that overcomes the computational overload of other EAP estimation methods from GDTI. The EAP describes the probability of the diffusing particles, and, hence, the geometry of the EAP is a direct indicator of the microstructure of the underlying tissue or fiber bundles. They provide experimental results on the fiber bundles estimated from real and synthetic brain datasets.In “DCE-MRI and DWI integration for breast lesions assessment and heterogeneity quantification,” C. A. Méndez et al. address the quantification of breast tumor heterogeneity using jointly DW-MRI and DCE-MRI, which provide a measure of cellularity and an indication of blood volume, flow, and vascular permeability, respectively. To that end, they first make an affine followed by an elastic registration of both datasets and approach the tissue segmentation by clustering using a dissimilarity-based representation (DBR) of the DCE curves and the ADC maps, followed by K-means. Statistical testing is carried out for the ADC maps of the resulting clusters. They provide experimental results from 21 patients with primary ductal carcinoma.In “The smoothing artifact of spatially constrained canonical correlation analysis in functional MRI,” D. Cordes et al. address the problem of the spatial specificity of the activation signal in fMRI due to smoothing artifacts that arise in an extension of the canonical correlation analysis (CCA) termed constrained CCA (cCCA), which is used as a statistic in fMRI to test for functional brain activation in a specific neighborhood. In particular, they investigate in detail the smoothing artifact that is associated with each spatial constraint in cCCA and provide a novel approach in order to correct the measure of activation for the smoothing artifact within a Bayesian testing framework. They also provide experimental results on six real cases with six normal subjects carrying out certain motor and episodic memory tasks.In “A new GLLD operator for mass detection in digital mammograms,” N. Gargouri et al. propose an extension to the local binary pattern (LBP) operator used for texture classification in order to overcome some limitations that arise from the fact that LBP uses local gray-level differences. In particular they introduce the gray level and local Difference (GLLD) representation that, in addition to differences, also uses gray levels and investigate the efficiency of the GLLD-based approach as a method of feature extraction. They tackle the detection of abnormal masses on breast X-ray images by performing a manual region of interest (ROI) delineation, followed by the GLLD representation and standard classification by k-NN, support vector machines, and multilayer perceptrons. Experimental results are from 1000 ROIs from the Digital Database for Screening Mammography.In “A flexible model for feature extraction from brain signals in the time-frequency domain,” R. Heideklang and G. Ivanova provide a different perspective since they deal with electrophysiological data. Images arise from the time-frequency representation (TFR) of these nonstationary signals that are obtained in the paper from the smoothed pseudo-Wigner-Ville distribution. A common problem of TFRs from electrophysiological data is inter- and intrasubject variability of the features to be extracted (curves in the TFR), which is here addressed by proposing the smooth natural Gaussian extension (snaGe) model, characterized by a sequence of multivariate Gaussians located on a parametric curve described by a cubic B-spline. By combining cubic B-splines with the Gaussian shape, they obtain a “sufficiently smooth model which inherits both the splines' flexibility and the Gaussian standard model's robustness.” In order to fit the model to the data, after subsampling, an initial estimation of the initial parameters of the curve is obtained by dynamic programming, which is refined through iteration, and using Fréchet and other metrics for curve difference. The authors present results on real and synthetic EEG data, and they discuss the robustness and the sensitivity of the method to noise.Last but not least, in “We hope that the readers enjoy this special issue.Juan Ruiz-AlzolaJuan Ruiz-AlzolaCarlos Alberola-LópezCarlos Alberola-LópezCarl-FredrikWestinCarl-FredrikWestin


This review introduces quantum dots (QDs) and explores their properties, synthesis, applications, delivery systems in biology, and their toxicity. QDs are one of the first nanotechnologies to be integrated with the biological sciences and are widely anticipated to eventually find application in a number of commercial consumer and clinical products. They exhibit unique luminescence characteristics and electronic properties such as wide and continuous absorption spectra, narrow emission spectra, and high light stability. The application of QDs, as a new technology for biosystems, has been typically studied on mammalian cells. Due to the small structures of QDs, some physical properties such as optical and electron transport characteristics are quite different from those of the bulk materials. In the past years, a new class of fluorescent particles emerged as a good candidate for single molecule and single particle tracking (SPT) in living cells and organisms, the semiconductor quantum dots . QuantumSeveral routes have been used to synthesize QDs  but, genIn the approaches of top-down, for making the QDs, a bulk semiconductor is thinned. For the achieve QDs of diameter approximately 30 nm, electron beam lithography, reactive-ion etching, and/or wet chemical etching are commonly used. For systematic experiments on quantum confinement effect, controlled shapes and sizes are achievable with the desired packing geometries. Alternatively, focused ion or laser beams have also been used to fabricate arrays of zero-dimension dots. Incorporation of impurities into the QDs and structural imperfections by patterning are major disadvantages with these processes .A number of different self-assembly techniques (bottom-up) have been used to synthesize the QDs, and they may be broadly subdivided into wet-chemical and vapor-phase methods : (a) wetIn this review, we evaluate few experiments that show the high potential of QDs in biological application, including tracking different macromolecules in the cell, tracking various cells in the tissue, labeling organelles and cells, clinical applications, and other applications -43.Because QDs have constant and unique optical properties, they are the best candidate for cell labeling, as compared with organic dyes.Use in plant bioimaging There is an increasing application of QD as markers for the cells or cell walls (CWs) in plant science. A first target location for external agents in a plant cell is the CW [Picea omorika branch. Respectively, binding to lignin and cellulose are achieved by interaction with the chains of C = C and C-C alternating bonds and interaction with the OH groups [s the CW . DjikanoH groups . Data shH groups .Use in animal bioimaging Goldman et al. used biotinylated CTxB in conjunction with QD-avidin conjugates [njugates  for labenjugates .In another study, they labeled live HeLa cells which were biotinylated using sulfo-NHS-SS biotinylating reagent and then incubated with the avidin-conjugated yellow-emitting QDs. It is shown in Figure 2-QD complexes which were uniformly internalized into the cells without being aggregated. Therefore, CHPNH2 nanogel has high potential for use in long-term live cell imaging. The interaction of QDs with cells was successfully controlled by the amino group content of the CHPNH2 nanogel [For long-term live cell imaging, Hasegawa et al. used the CHPNH nanogel .Use in prokaryote bioimaging Sensitive and selective staining of bacterial mutants using QD labels was demonstrated by Smith's group. This principle of detection is based on selective targeting affinity of Zn(II)-dipicolylamine coordination complex to phospholipids on the bacterial cell surface of specific strain as shown in Figure E.coli O157 antibodies and streptavidin-coated QDs for measuring the bacterial cell concentration [E. coli O157:H7 and Salmonella typhimurium[In another study, authors demonstrated the use of magnetic beads coated with anti-ntration . Yang anphimurium.With the application of new imaging methods and the use of brighter and more stable probes, such as QDs, single particle tracking has the potential to enter into a new era of high resolution and long timescale imaging -55. SPT For extracellular study Because QDs do not require intracellular delivery through the impermeable plasma membrane, membrane receptors or membrane-associated proteins are intuitive targets for QD imaging [P = 1.6 × 10−14) [ imaging . Howarth× 10−14) .In similar studies, recently, QDs used to target membrane proteins and investigate the mobility and entry-exit kinetics in several systems: (1) various transmembrane proteins, for example, integrins , channelFor intracellular study In one of the study, the advantages of the broad, continuous excitation spectrum were demonstrated in a dual-emission, single-excitation labeling experiment on mouse fibroblasts. These nanocrystal probes are, thus, complementary and, in some cases, may be superior to existing fluorophores [rophores . Nonspecrophores .This is shown as green color for nucleus and red color for actin filaments. Nonspecific labeling of the nucleus by both the red and the green probes resulted in a yellow color .Superior stability of QD fluorophores gives the possibility to improve quantitation of FISH analysis of human chromosomal changes. Xiao and Barker have investigated coated (CdSe)ZnS QDs as fluorescence labels for FISH of biotinylated DNA to human lymphocyte metaphase chromosomes under conditions that approximate those commonly found in clinical cytogenetics laboratories . They hain vitro and in-cell measurements of myosin V motors. Then, the complex myosin V/QD (MyoV::QD), using the pinocytic influx, was introduced into the cells.Pierobon et al.  and NelsYoo et al.  and CourImaging of the satellite cells in rat intact and injured soleus muscles using quantum dots The employment of satellite cells, which are located between the basement membrane and the plasma membrane in myofibers, is required for myofiber repair after muscle injury or disease. Using QDs conjugated to anti-M-cadherin antibody, Ishido and Kasuga attempted the visualization of satellite cells in both intact and injured skeletal muscle of rat in situ. They demonstrated in situ real-time imaging of satellite cells localized within the skeletal muscle  cells, a primary diagnostic target for Hodgkin's disease, which was not achievable using traditional immunohistochemistry assays ,85. 2. Yu et al. reported the use of GSH-TGA-QDs-ND-1 probes to label colorectal cancer cells CCL187. They prepared QDs, which were conjugated with monoclonal antibody ND-1 for specific reaction with antigen LEA . 3. In the United States, pancreatic cancer is the fourth leading cause of cancer death  in 2010) . Using sThere are evidences showing the application of QDs in micro- and nanoarrays for the detection of cancer biomarkers .Imaging and sensing of infectious diseases by QDs QDs have become one of the most hopeful and interesting materials for diagnostic applications of bioimaging, labeling, and sensing for infectious diseases such as respiratory syncytial virus (RSV)that isone of the families of Paramyxoviridae [. In Table oviridae . In Tabl 1. QDs for assessing axon growthA major health problem with injuries to the spinal cord and brain is traumatic central nervous system injury reporting of approximately 265,000 and 1.5 million new injuries each year -105. QDs 2. QD used as a probe in an anti-malarial drug-screening assayPlasmodium falciparum[P. falciparum-infected RBC using a QD-based probe and its applicability as an efficient probe for anti-malarial drug screening [Malaria is a major global health problem, threatening over 300 million people and causing nearly one million deaths annually ,115. Tokalciparum. Ku et aQDs as pH probes for the study of enzyme reaction kinetics[−[2+ by using CdSe/ZnS QDs modified with bovine serum albumin [ kinetics Lately, inetics[−,118. Xie albumin . QDs als albumin -125. The albumin . Water-s albumin .QDs use for protein micro- and nanoarrays to the detection of cancer biomarkers Protein microarrays are useful device as highthroughput screening tools in proteomics [oteomics -129, foroteomics , new druoteomics , and enaoteomics -135. Heroteomics . Kerman oteomics . Gokarnaoteomics .QD delivery Due to the unique properties of QDs, they are best tools for intracellular studies such as visualizing the cellular structure, studying the dynamic cellular processes, and tracking single molecules in the cell [in vivo unless their surface is modified. Thus, by surface modification, their hydrophilicity will increase but their toxicity will decrease.the cell ,138. To 2(15)-QD nanoparticles using other normal cells (TIG-3 and MRC-5) and cancer cells   relative to the oxidized glutathione (GSSG) in plants suggests that QDs caused oxidative stress on the plant at this condition .in vitro. Their results suggested that QDs could not only impair mitochondria but also exert endothelial toxicity through activation of mitochondrial death pathway and induction of endothelial apoptosis [Yan et al. investigated the potential vascular endothelial toxicity of mercaptosuccinic acid (2-sulfanylbutanedioic acid)-capped QDs poptosis .2+ ions but also intracellular distribution of QDs in cells and the associated nanoscale effects [More recently, Chen et al. have studied the cytotoxicity of CdTe/CdS (core-shell) structured and also CdTe/CdS/ZnS (core-shell-shell) structured aqueous synthesized QDs, and their results suggest that the cytotoxicity of CdTe QDs not only comes from the release of Cd effects . Table 4 effects -162.In this review, we summarize few experiments that illustrate the high potential of QDs used for/as: 1. labeling biomolecules and cells; 2. tracer to follow the intracellular/extracellular dynamic of a single biomolecule/cell;in vitro/in vivo; 3. localization of biomolecules in vitro/in vivo; 4. imaging of biomolecules or cells  5. assessing cell growth in damaged tissue; 6. pH probes for the study of enzyme reaction kinetics; 7. biomarker detection in various cancers; 8. imaging and sensing of infectious diseases; and 9. protein micro- and nanoarrays to the detection of cancer biomarkers.in vivo. Therefore, more experiments should be done, and much more data should be available, to be sure to do clinical trials on humans.These studies have been generated using QDs because of their small size, brightness, independence of emission on the excitation wavelength, and stability under relatively harsh environments which would be advantageous. In contrast, there are different opinions about the toxicity and fate of QDs In the future, QDs will be used for identifying various categories of cancer cells, the molecular mechanisms of disease, and new drug action mechanisms, applying them in the intracellular/extracellular studies, and making new methods for biochemical assaying.The authors declare that they have no competing interests.SD conceived of the study and participated in its design and coordination. AA participated in the sequence alignment and drafted the manuscript. All authors read and approved the final manuscript.


It is important to correctly and efficiently predict the interaction of substrate-enzyme and to predict their product in metabolic pathway. In this work, a novel approach was introduced to encode substrate/product and enzyme molecules with molecular descriptors and physicochemical properties, respectively. Based on this encoding method, KNN was adopted to build the substrate-enzyme-product interaction network. After selecting the optimal features that are able to represent the main factors of substrate-enzyme-product interaction in our prediction, totally 160 features out of 290 features were attained which can be clustered into ten categories: elemental analysis, geometry, chemistry, amino acid composition, predicted secondary structure, hydrophobicity, polarizability, solvent accessibility, normalized van der Waals volume, and polarity. As a result, our predicting model achieved an MCC of 0.423 and an overall prediction accuracy of 89.1% for 10-fold cross-validation test. With the completion of gene sequencing projects, scientific focus is shifting from the investigation of the proteomics to metabonomics which is of chemical processes involving metabolites. Metabolism consists of almost all of the chemical-chemical reactions or chemical-macromolecules reactions that generally take place within metabolic pathway . Above lDue to the complexity of metabolic pathways, it is both time-consuming and costly to determine the interaction of substrate-enzyme-product by experiments. It is in urgent to develop a quick, reliable, and effective approach to predict the interactions among substrate, enzyme, and product.In this study, we reported a computational approach for predicting the network of substrate-enzyme-product triads based on K-nearest neighbor (KNN) –6 algoriMinimum Redundancy Maximum Relevance (mRMR), proposed by Peng et al., is an effective feature-selection method for evaluating the worth of an attribute by considering the minimum redundancy between attributes and the maximum relevance between attributes and targets . More inK-nearest neighbors (KNN) is the most basic instance-based machine learning technique classifying objects based on cluster theory –6. KNN rN feature subset by incrementally adding features to D as follows:fi is the ith feature added into feature subset D).First, construct Di and evaluate the model by cross-validation. Then, a classification accuracy curve called IFS curve is attained.Second, use KNN method to build the prediction model based on subset http://www.genome.jp/kegg/) (release 42 in 2006) ), specificity (SP = TN/[TN + FP]), overall accuracy (ACC = [TP + TN]/[TP + TN + FP + FN]), and Matthew's correlation coefficient (MCC) to measure the prediction. The MCC can be represented asIn the recent years, many efforts have been made in feature selection –46. In tThen, IFS method is applied based on mRMR feature table. From Based on the 160 features, predicting model of network of substrate-enzyme-production interaction could be built.Ten folds cross-validation test, which is applied in many other applications , 47–52, To evaluate our feature selection method, we compared the prediction results generated by final optimal subset and the original data set with 10-folds cross validation test see .  Table The selected 160 features in the final subset can be clustered into the following ten categories: elemental analysis, geometry, chemistry, amino acid composition, predicted secondary structure, hydrophobicity, polarizability, solvent accessibility, normalized van der Waals volume, and polarity see . The forAccording to the distribution of features of compounds (substrate and product) and enzymes, it shows that enzymes contribute more to the interaction process. Further calculating the proposition of the selected features to the original features, it is found that the proposition of enzyme feature (92/132 = 0.70) is higher than the proposition of compound feature (70/158 = 0.44). From π-π stacking interaction to enzyme's functional site. The substrates and products are varied and diverse greatly in structure. And it is difficult to describe their structure with only one or two descriptors. Hence, more geometry features could better extract the information of compounds' structure. This is why though single geometry feature has no strong relevance to the interaction, the overall contribution of the forty-four geometry feature can often be crucial to the interaction.According to the distribution of features in In this paper, a feature selection method called mRMR combined with IFS was applied to dataset of substrate-enzyme-product interaction which is encoded with molecular descriptors of substrate/product and 132 physicochemical protein descriptors. As a result, we find that enzymes are essential in substrate-enzyme-product interaction; 160 important features were abstracted from 290 features. Based on the above findings, we also used KNN method to build a prediction model of substrate-enzyme product interaction. Based on the prediction results, it is expected that molecular descriptors and 132 physicochemical protein descriptors can be served as an efficient coding method for network of substrate-enzyme-product interaction.： The ID of 1326 compounds and 939 enzymes of metabolic pathway in Kegg database.Supplementary Material 1：14,592 networking triads of substrate-enzyme-product.Supplementary Material 2Supplementary Material 3: 729,600 non-networking triads of substrate-enzyme-product.Supplementary Material 4: Calculated value of molecular descriptors of 1326 compounds and the categories.Supplementary Material 5: The value of 132 physicochemical descriptors for 939 enzyme.Supplementary Material 6: The MaxRel and mRMR feature tables using mRMR method.Click here for additional data file.


By using animal sera as sentinels, natural TBEV foci could be identified and further analyses including investigations of ticks could be initiated. However, antibody response against TBEV-related flaviviruses might adversely affect the readout of such a monitoring. Therefore, the cross-reactivity of the applied TBEV serology test systems – enzyme linked immunosorbent assay (ELISA) and virus neutralization test (VNT) – as well as the longevity of TBEV antibody titres in sheep and goats were investigated in this study.Flaviviridae family  was observed for Louping-ill-positive sera only. In contrast, the commercial West Nile virus (WNV) competitive ELISA showed a high level of cross-reactivity with TBEV-specific positive sera.Cross-reactivity of the TBEV antibody test systems with defined antibody-positive samples against selected members of the To assess the longevity of TBEV antibody titres, sera from two sheep and two goats, which had been immunized four times with a commercially available TBEV vaccine, were tested routinely over 28 months. In three of the four animals, TBEV-specific antibody titres could be detected over the whole test period.In addition, sera from the years 2010 and 2011 were collected in flocks in different villages of Baden-Württemberg and Thuringia to allow re-examination two to four years after the initial analysis. Interestingly, in most cases the results of the former investigations were confirmed, which may be caused by steadily existing natural TBEV foci.Cross-reactivity must be taken into consideration, particularly for TBEV serology in regions with a prevalence of Louping ill virus and for serological testing of WNV by cross-reactive ELISAs. Furthermore, over-interpretation of single TBEV-positive serological results should be avoided, especially in areas without a TBEV history. Tick-borne encephalitis (TBE) is the most important viral tick-borne zoonosis in Europe. TBE virOvis ammon musimon) for example has been reported from Austria[In general, knowledge on TBE in animals is limited; however infections have been reported in dogs-15, monk Austria. However Austria-25. TBE  Austria-28.These grazing animals have been shown to be suitable sentinels for the detection of antibodies against TBEV, but somOne example of known cross-reactivity between members of the flavivirus genus comes from serological West Nile virus (WNV) diagnostics. WNV is Here we present results on cross-reactivity within the TBEV-specific serology, but also provide a strategy to identify TBEV antibodies as the cause of false positive reactions in serological tests for other flaviviruses using WNV as an example.To determine cross-reactivity, five Louping ill virus (LIV) antibody-positive reference sera from sheep  as well as WNV-positive sera from the National Reference Laboratory for WNV  were tested. The WNV sample panel included 15 equine sera (field sera or sera collected after vaccination), and 10 hyperimmune-sera from vaccinated ducks, chickens and rabbits. Additionally, two rabbit sera with antibodies against Usutu virus (USUV) and Japanese encephalitis virus (JEV), respectively, were analyzed.Furthermore, ascites liquid from mice immunized against TBEV-related viruses such as Russian-spring-summer-encephalitis virus (RSSEV), Powassan virus (POWV), Yellow fever virus (YFV), JEV and St. Louis encephalitis virus (SLEV) could be investigated . Each sample was diluted 1:10, 1:50, 1:100, 1:500, and 1:1000 before testing ”, and sera from the TBE non-risk area “Altenburger Land” which were collected in 2010 and 2011 Table . AlthougMacaca sylvanus)[In addition, in Salem, district Bodenseekreis, not only sera but also ticks were collected in 2011  in the vicinity of the monkey mountain, where in 2006 TBEV strain Salem had first been isolated from a monkey (ylvanus) and sheeylvanus), but TBEAll sera were examined by means of a two-step method,34, whicFor detection of WNV-specific antibodies, horse samples were investigated by a commercially available competition ELISA, which allows the species-independent recognition of WNV antibodies against the PrM- and E envelope protein . Additionally, all serum samples were tested for neutralizing WNV antibodies by VNT with the WNV strain NY 99  and/or strain Austria  as described previously[, such as WNV, JEV, USUV, YFV, SLEV or POWV, scored also clearly negative using the TBEV-ELISA. Nevertheless, four out of five LIV-antibody-positive sheep sera reacted positive in the TBEV-ELISA as well as in the TBEV-VNT. In addition, RSSEV reactive mouse ascites scored also positive in both, the TBEV-ELISA and the TBEV-VNT, but only at the lowest dilution of 1:10  horse sera scored positive in the commercial WNV-ELISA. Here it could be verified that TBEV-specific antibodies (ELISA and VNT) were the source of cross-reactivity. These results therefore indicate that TBEV-specific antibodies did interfere with WNV-specific ELISA diagnostics and have to be taken into account Table .The development of TBEV-specific antibody titres over a time span of more than two years is shown in Table In order to track the development of TBEV-antibodies in the field situation, selected flocks in Baden-Wuerttemberg and Thuringia Table  were repAll animal experiments in this study were conducted in strict accordance with a high standard of veterinary care. The protocols were approved by the competent authority of the Federal State of Thuringia, Thuringian State Office for Food Safety and Consumer Protection, Dept. of Health Protection, Veterinary Medicine and Pharmacy, Bad Langensalza, Thuringia, Germany (Reg. no. 04-104/10) and reviewed and approved by the competent authority of the Federal State of Mecklenburg-Western Pomerania, State Office for Agriculture, Food Safety and Fisheries, Rostock, Mecklenburg-Western Pomerania, Germany (LALLF M-V/TSD/7221.3-2.5.1-002/11).In addition to these serological results in Salem (Bodenseekreis) 1788 collected ticks in 208 pools were analyzed by TBEV-specific RT-qPCR and in one pool of 10 nymphs collected around the monkey mountain TBEV-RNA was detected. The nucleotide sequence  of the structure protein genes of TBEV were determined (GenBank KC292217) and compared with the TBEV sequences available in the NCBI GenBank database using BLAST. The highest homology with 99.55% was ascertained for TBEV strain Salem (GenBank FJ572210). Here 2853 nt of the compared 2866 nt were identical.Interestingly, the results from a flock in Thuringia surveyed in 2009 could not be confirmed: In 2009, surprisingly five out of 73 sera in this goat flock in “Altkirchen” in the district “Altenburger Land”, Thuringia, which is defined as a TBE non-risk area, tested TBEV-antibody-positive. In 2011A limited cross-reactivity of non-TBEV, but flavivirus-antibody-positive sera was observed in the TBEV-specific test strategy (ELISA and VNT) used for the selection of regions with a risk for TBEV infection. Four of five sera defined as LIV-antibody positive and ascites from a RSSEV-infected mouse reacted positive in the ELISA as well as in the VNT assay Table . TherefoFurthermore, no cross-reactivity was observed between our TBEV test system (ELISA and VNT) and defined WNV-positive horse sera Table .It is well-known, that the used commercial competitive WNV-ELISA cross-reacts with other flaviviruses,32, neceOn the other hand, testing of horses can even be used as an indicator to detect TBEV-affected areas and thus identify a TBEV focus.In summary, our TBEV antibody test system is well suited and, despite a partial cross-reactivity to LIV- and RSSEV-antibodies, cross-reactivity with other flaviviruses is not to be expected in countries like Germany. However, the number of samples tested so far has been low, so these findings should be verified in future studies.In our investigations on the longevity of TBEV antibody titres, only small differences were seen between the two immunized goats and sheep. TBEV-specific antibody titres were still detectable after 28 months with lower but specific titres in the two goats and two sheep Table . While tMacaca sylvanus) from the monkey mountain Salem with severe neurological clinical symptoms in 2006[In addition, in repeatedly tested goat and sheep flocks the detected sero-prevalences were in good accordance with the epidemiological TBEV situation in the surroundings. In the district “Bodenseekreis”, a defined TBE risk area with a very long TBEV history, 60 human cases were registered between 2001 and 2012, and the existence of a TBEV natural focus in Salem described in animals in 2006,17,34 wa in 2006,17. HoweThe districts “Breisgau-HS” and “Ortenaukreis” also have a well-known TBEV history with 64 (Breisgau-HS) and 246 (Ortenaukreis) human cases, respectively, between 2001 and 2012.In the goat flock in “Altkirchen”, district “Altenburger Land” (Thuringia), however, re-testing provided a different unexpected result. Surprisingly, in 2009, five of 73 sera from this TBE non-risk area with so far no human TBE cases had been found to be TBEV antibody-positive (7%). In 2011, 90 sera from new goats of this flock were re-tested and no TBEV antibody-positive results were detected Table . One reaTherefore, detection of a small number of TBEV antibody-positive sera in TBEV non-risk areas with no human TBE cases should be interpreted with care . However, the longevity data support the conclusion that sera from grazing animals are well suited as a valuable source of serological data supporting the TBEV status of an area.TBEV-specific sero-prevalences in animals are an additional valuable tool that can help identify natural TBEV foci which are in most cases spread in a patchwork-like pattern. Cross-reactivity is rare and does not play a significant role in countries without a prevalence of a broad range of TBEV-related flaviviruses. Furthermore, TBEV is a very important and relevant cause for false-positive WNV-ELISA results in horses and must be taken into consideration in monitoring or sentinel programs.Finally, all TBEV serology results should be interpreted in close cooperation between human and veterinary medicine, and recommendations for the vaccination of humans, based exclusively on the TBEV sero-prevalence in animals should be avoided.The authors declare that they have no competing interests nor did they have any competing financial interests in relation to the work described.CK collected sera from immunized animals, carried out ELISA, evaluated and interpreted data of TBEV, wrote the manuscript; UZ evaluated and interpreted data of WNV, wrote this part of manuscript; DK developed and carried out VNT; BH developed and carried out RT-qPCR; MB designed the study and drafted the manuscript. All authors revised the manuscript critically and approved the final version.


The database consists of selected high-quality microarray and RNA-sequencing experiments from ArrayExpress that have been manually curated, annotated with Experimental Factor Ontology terms and processed using standardized microarray and RNA-sequencing analysis methods. The new version of Expression Atlas introduces the concept of ‘baseline’ expression, i.e. gene and splice variant abundance levels in healthy or untreated conditions, such as tissues or cell types. Differential gene expression data benefit from an in-depth curation of experimental intent, resulting in biologically meaningful ‘contrasts’, i.e. instances of differential pairwise comparisons between two sets of biological replicates. Other novel aspects of Expression Atlas are its strict quality control of raw experimental data, up-to-date RNA-sequencing analysis methods, expression data at the level of gene sets, as well as genes and a more powerful search interface designed to maximize the biological value provided to the user.Expression Atlas ( Expression Atlas is a further development of our previous version of Gene Expression Atlas , launcheIn particular, Expression Atlas introduces the concept of baseline expression—the abundance of each gene and splice variant in healthy or untreated tissues, cell types or cellular components. Baseline expression is reported within a species-specific context of selected large RNA-sequencing experiments and provides a useful reference for the user when considering differential expression data.P-values and, (for microarray only) t-statistics, linking each gene to differential contrasts in each experiment.Expression Atlas continues to analyse and report statistically robust differential expression for both coding and non-coding transcripts. However, the biological relevance of these data has been vastly improved due to an in-depth manual curation of the experimental intent that for each differential experiment yields a set of ‘contrasts’, i.e. instances of differential pairwise comparisons between two sets of biological replicates—the ‘reference’  set and a ‘test’ set (e.g. ‘diseased’ or ‘mutant’). Each of these sets is typically described by a number of sample attributes and experimental factors. For example, all biological replicates treated with a test compound may be compared with untreated samples. Statistical analysis is then performed, providing Another novel aspect of Expression Atlas is its focus on quality control of raw experimental data and of experimental design. A minimum acceptable number of biological sample replicates (three) is also enforced to ensure sufficient statistical power to detect differential expression. Before submission into analysis pipelines, all experimental raw data undergo quality control. In the case of RNA-sequencing experiments, poor quality reads and those originating from contamination are excluded from further analysis. Outlier arrays in microarray experiments are also removed before manual contrast identification and statistical analysis.The focus on the quality of raw data and experimental design has led to exclusion of low-quality experiments. The manual curation of contrasts for all eligible experiments is also on-going, leading to a temporary reduction in the number of experiments in Expression Atlas.Support of reproducible analysis is provided for each experiment by listing analysis methods and versions used for processing its raw data, offering links to source code where possible, as well as showing the version of Ensembl genome reference used for mapping (for RNA-sequencing experiments), and the version of miRBase  release Expression Atlas search interface allows for querying gene, splice variant or protein attributes (including organism), at the level of individual genes or whole gene sets. The user can also search for sample attributes and experimental factors. Both baseline and differential components of Expression Atlas are queried by default. The experiments returned are those in which the queried sample attributes match either the studied healthy or untreated biological conditions, e.g. tissues or cell types (baseline expression), or match either a ‘test’ or a ‘reference’ side of a differential contrast . Finally, the set of queried experiments can be restricted by providing a list of accessions, keywords or the species of samples studied in them.The RNA-seq processing pipeline used to generate data for Expression Atlas is shown in Illumina Body Map (http://www.ebi.ac.uk/gxa/experiments/E-MTAB-513) and Encode Cell Lines (http://www.ebi.ac.uk/gxa/experiments/E-GEOD-26284). Differential experiments include 10 RNA-sequencing and 200 microarray experiments—mainly single-channel experiments performed on gene arrays. Finally, microarray experiments studying microRNAs are also available (e.g. http://www.ebi.ac.uk/gxa/experiments/E-TABM-713).As of 24 September 13, Expression Atlas contains highly curated data from 214 experiments, including four baseline RNA-sequencing experiments (nine species) and 210 differential experiments (13 species). Baseline experiments include Expression Atlas offers a separate page for each experiment, as well as pages presenting baseline and differential expression data for each gene, protein, gene set (e.g. REACTOME pathway) and experimental condition (e.g. ‘heart’) stored in Atlas.Users can search a baseline experiment with gene names, protein accessions, gene, protein or splice variant identifiers, keywords, biotypes (e.g. ‘protein coding’), GO and InterPro terms as well as Reactome pathway IDs. Optionally, each term (e.g. REACTOME pathway ID) can be interpreted as a gene set, offering the user an aggregated expression level across all genes in each queried gene set. Users may also search using studied experimental conditions  of interest and at the same time penalizing genes with low P-values in the remaining contrasts. Optionally, the user may perform a ‘non-specific’ search, in which genes with lowest P-values in the selected contrast(s) come first, irrespective of whether they are reported with low P-values in the remaining contrasts. The results of this analysis are presented to the user in a matrix, with genes (and design elements—for microarray only) as row labels, and contrasts as column labels. The results are sorted by P-value; the t-statistics and log2-fold changes are also available. As part of the differential analysis, ‘MA’ plots are shown for the default FDR of 0.05. The user is able to choose a different FDR and observe in the resulting matrix, what effect this has had on the results. The differential experiment page offers downloads of analytics data as well as raw counts (RNA-sequencing), normalized expression values (one-colour microarray) and log2-ratios (two-colour microarray), respectively. Finally, experimental conditions for each contrast can be viewed via mouse-over on contrast column headers, in the results matrix, and on the experiment design page, available via a button in the top-right corner of the experiment page.Users may search a differential experiment by the same gene properties and keywords as listed earlier in text for baseline experiments, additionally selecting the type of differential expression of interest (up/down by default). A differential contrast dropdown is also available—the default search is for differential expression in any contrast, but the user can also choose one or more contrast of interest. By default, the search returns first genes that are differentially expressed most specifically in the queried contrast(s). This is achieved by promoting to the top genes with lowest P-value, across all contrasts in experiments available in Expression Atlas. Mouse-over on a contrast description shows experimental conditions describing the test and the reference sides of that contrast , Expression Atlas provides a summary page that contains, at most, three separate panes . The tophttp://www.ebi.ac.uk/gxa/experiments) presents a sortable and searchable list of all experiments currently loaded in Expression Atlas, documenting, among other things, experiment type , the number of assays analysed for that experiment, the organisms and experimental conditions studied, the number of contrasts identified  and the array designs used in the experiment (microarray only).This page . The web services software will be released regularly, with appropriate release notes notifying users of functionality changes.Gene Expression Atlas, described in our previous update, released its data and software on a monthly basis. Expression Atlas will also release data regularly, providing individual experimental data and tar-gzip snapshots of all the data (for ease of download) on the EMBL-EBI FTP server  member states; the National Science Foundation ; the European Community's FP7 EurocanPlatform [260791]; and by GEUVADIS [261123]. Funding for open access charge: EMBL central publication budget.Conflict of interest statement. None declared.


Neck pain (NP) is a common condition in old age, leading to impaired functional ability and decreased independence. Spinal manipulation and exercise are common and effective treatments for the general NP population; however, their effectiveness among seniors is unknown. The primary aim of this randomized clinical trail was to assess the relative short- and long-term clinical effectiveness of spinal manipulative therapy (SMT) and supervised rehabilitative exercise (SRE), both in combination with and compared to home exercise (HE) alone, in NP patients 65 years and older.241 individuals age 65 and older with NP at least 12 weeks in duration were randomized to 12 weeks of treatment (above). The primary outcome was pain; secondary outcomes included disability, improvement, medication use, general health and satisfaction. Patient-rated outcome measures were collected via self-report questionnaires at baseline, 4, 12, 26, and 52 weeks post-randomization. Differences between the 3 groups were calculated for the short-term (weeks 4 and 12 data) and long-term  with a linear mixed model analysis.In the short-term, SMT+HE demonstrated significantly greater reduction in pain compared to the other two groups. SMT+HE also showed greater improvement compared to HE alone. Both combined treatment groups were more satisfied at all time points. In the long-term, significant between group differences in both pain and improvement persisted in favor of SMT+HE over HE, but not SRE+HE. Participants in the combination therapies continued to report greater satisfaction with care than HE alone. There was less medication use among SMT+HE group compared to SRE+HE in the long term.In a senior population with chronic NP, SMT combined with home exercise results in less pain and greater improvement than home exercise alone in both the short-and long-term, and greater pain reduction than rehabilitative exercise plus home exercise in the short-term.


Ultraviolet radiation (UVR) is known to be one of the most important environmental hazards acting on the skin. It was revealed that chronic exposure to UVR accelerates skin aging, induces immunosuppression and may lead to the development of skin cancers. On the other hand, UVR has been shown to be effective in the treatment of numerous skin diseases and thus, various phototherapy modalities have been developed to date. Narrow-band ultraviolet B (NB-UVB) emitting a light with a peak around 311 nm has been demonstrated to be effective in the treatment of various skin disorders; currently it is one of the most commonly used phototherapy devices. Despite NB-UVB has been developed more than 30 years ago, the exact mechanism of its therapeutic action remains poorly understood. To date, most of NB-UVB effects were attributed to its influence on immune cells; however, nearly 90% of NB-UVB irradiation is absorbed by epidermis and keratinocytes seem to be important players in mediating NB-UVB biological activity. Here, we have reviewed the current data about the influence of NB-UVB on epidermal cells, with a special emphasis on cell proliferation and death. Ultraviolet radiation (UVR) is known to be one of the most important environmental hazards acting on the skin. It was revealed that chronic exposure to UVR accelerates skin aging, induces local and systemic immunosuppression and may lead to the development of melanoma and non-melanoma skin cancers ,2. ImmunTo minimize the negative influence of UVR human skin possesses a number of protective mechanisms including cell-cycle arrest, DNA repair and programmed cell death for situation, when DNA damage cannot be repaired ,7–14. FaDespite the above mentioned hazardous properties, UVR was shown to be effective in the treatment of numerous skin diseases. In early 1980s, it was observed that the beneficial effect of UVB is mainly related to wavelengths between 295 and 313 nm, and a range between 310 and 313 nm seemed to have the best safety profile ,12. SincRemarkably, the exact mechanism of NB-UVB therapeutic action remains poorly understood; it is even unclear, whether local or systemic effect is more important ,15–18. Tin vitro and in vivo[et al.[2) in combination with retinoids (acitretin or tazarotene) inhibits the cell growth in vitro to significantly greater extent than therapy with these drugs alone. As suggested by the authors [in vivo, enabling epidermal cells to undergo apoptosis [Several studies have shown that NB-UVB inhibits proliferation and is able to induce apoptosis in human keratinocytes, both d in vivo–25. Luo vo[et al.,23 obser authors ,23 this  authors . Unlike  authors . Inhibit authors . GATA3 i authors . It is e authors ,30. The  authors . Standar authors . Further authors . GATA3 d authors . Importa authors . In addipoptosis .in vivo was observed after the dose equal or higher than at least 200 mJ/cm2[2, apoptosis of keratinocytes (HaCaT cell line) was observed.Regarding single NB-UVB irradiation, inhibition of epidermal cell growth 00 mJ/cm2,22. It set al.[2 of NB-UVB was required to obtain 50%–60% of cells positive for propidium iodide, which identifies cells with the loss of membrane integrity that is characteristic feature of later phases of cell death. However, a significant degree of apoptosis was already observed at the doses of about 800–1000 mJ/cm2 depending on studied cell types and conditions of irradiation [i.e., apoptotic cells) in native human epidermis. Broad-band UVB and NB-UVB at equivalent MED doses were equally potent in inducing p53 and p16 expression as well as apoptosis in healthy volunteers [et al.[in vitro. A recent study by Weatherhead et al.[in vivo during routine clinical therapy with NB-UVB and a computational model of psoriatic epidermis revealed that induction of keratinocyte apoptosis (but not inhibition of keratinocyte proliferation) in psoriatic lesions is sufficient for explanation of clearance of psoriatic plaques within the timeframes observed clinically during NB-UVB therapy [NB-UVB is able to evoke apoptosis in epidermal cells in a similar pattern as the broad-band UVB does. However, the required dose to induce the same amount of apoptosis and cell death as in the broad-band UVB treated cells is about five to ten times higher . As showet al., using hadiation ,22. Impoadiation  in Caucalunteers . As shows [et al. caspase ad et al. nicely dad et al.. They we therapy ,35. BaseIrradiation with apoptosis-inducing NB-UVB doses strongly altered cultured keratinocyte morphology, both on the cell surfaces as well as intracellulary. NB-UVB irradiation led to disintegration of nuclear and cell membranes as well as to severe cytoplasmic vacuolization ,22. Usini.e., lipid species which are considered to be signal transducers of a variety of cell stressors, including reactive oxygen species, cytokines, exposure to chemotherapeutic agents, irradiation or exogenous lipopolysaccharides [O-octadecyl-2-Omethyl-rac-glycero-3-phosphocholine) were able to induce apoptosis in a number of cell lines [2 of NB-UVB were found to accumulate triacylglycerols (TAG), which peaked at the later stages of apoptosis [et al.[et al.[Disruption of cellular membranes of cultured cells upon NB-UVB irradiation was accompanied by significant changes in the cellular lipid content . Irradiacharides . Increascharides , suggestcharides . Althougll lines ,42. In apoptosis . Severalpoptosis –48. Thiss [et al. suggestes [et al.,49,50. Is [et al.,47. Howes [et al.,52. In cl.[et al.. DespiteNB-UVB is also able to induce apoptosis of skin cells other than keratinocytes. Lymphocytes seems to be more sensitive to NB-UVB irradiation as compared to keratinocytes, as slightly lower doses were required to induce apoptosis of former cells . It was 2 increased proliferation rate of NCCmelan5 cells, a melanoblast cell line [i.e., cultured primary human melanocytes) studied [2) decreased the viability of NCCmelan5 cells by about 30% [NB-UVB also acts on the epidermal pigment cells. NB-UVB remains a gold standard in the treatment of vitiligo, an immune-driven disease with loss of melanocytes . It was ell line . Interes studied . However studied . On the  studied . NB-UVB  studied ,63. Remabout 30% .In summary, NB-UVB is able to inhibit cell proliferation as well as is able to induce apoptosis of various cell types. This action may be responsible for its therapeutic activity in diseases with a high proliferation rate, such as psoriasis. On the other hand, the induction of apoptosis upon NB-UVB irradiation may lead to the surface expression of nuclear antigens, which next may contribute to aggravation of autoimmune connective tissue diseases driven by antinuclear antibodies. Over the last decade, new data have arisen on the mechanism of action of NB-UVB, but still the exact mechanism of its therapeutic efficacy is far to be fully understood. It is e.g., not clear, why some patients with psoriasis respond to NB-UVB therapy, while others do not show any clinical improvement. It is also still not known which cells  are a primary target of NB-UVB action and whether NB-UVB is able to induce a systemic immunomodulatory effect or acts only within the irradiated skin area. In addition, to date most studies on NB-UVB mechanism concentrated mainly on psoriasis, but these data do not have to reflect the NB-UVB action in other diseases, which are successfully treated with NB-UVB. Therefore, future studies are needed to better understand the biological activity of NB-UVB irradiation.


Objective. To investigate whether advanced glycation endproducts (AGEs) in the skin are increased in patients with systemic sclerosis (SSc) and are related to the presence of disease-related and traditional cardiovascular risk factors. Methods. Skin autofluorescence, as a measure for the accumulation of AGEs, was assessed by measuring UV-A light excitation-emission matrices (AF-EEMS) in 41 SSc patients and 41 age- and sex-matched controls. Traditional cardiovascular risk factors and disease-related risk factors were recorded. Results. Skin AF-EEMS did not differ between SSc patients and controls . Skin AF-EEMS in SSc patients was associated with levels of CRP , Medsger's severity scale , and use of agents intervening in the renin-angiotensin system . When analysing SSc patients and controls together, in multivariate analysis, only age and use of agents intervening in the renin-angiotensin system were independently associated with AF-EEMS. Conclusion. These data demonstrate that skin AGEs are not increased in SSc patients.  Vascular involvement is a key factor in major manifestations of systemic sclerosis (SSc), such as Raynaud's phenomenon (RP), myocardial dysfunction, pulmonary hypertension, and renal involvement. Microvascular involvement, in which endothelial injury is present, is the main characteristic of SSc , 2 OxidaOxidative or carbonyl stress, leading to formation of so-called reactive carbonyl compounds, is an important source for the generation of so-called advanced glycation endproducts (AGEs) . AGE genTissue autofluorescence (AF) is a marker of the accumulation of AGEs, validated in different patient groups and healthy controls –18. TherForty-one patients with limited cutaneous SSc from our university medical center out-patient clinic, fulfilling the ACR criteria for SSc  were inc2 without evidence of fibrosis at the ventral site of the forearm, or other skin lesions. A series of measurements was obtained for each subject, and mean skin AF-EEMS was determined as described [Tissue AGEs accumulation can be assessed as skin autofluorescence (AF), following the principles of the AGE Reader, which is a validated and noninvasive technique , 25. Repescribed . Skin piLipid concentrations  and low-density lipoprotein (LDL) cholesterol and triglycerides), glucose, and creatinin were measured by routine techniques. CRP was measured using in-house enzyme-linked immunosorbent assays (ELISAs) as described . t-test or Mann-Whitney U tests, as appropriate. In case of categorical variables, the chi-square test was used. The univariate correlation between AF-EEMS values and other categorical variables was assessed by Pearson's correlation coefficient in case of normal distribution. Otherwise, Spearman's correlation coefficient was used. To assess the influence of tested parameters multiple regression analysis using the backward method was performed to assess the influence of demographic variables, outcome variables, and disease-related factors on skin autofluorescence (AF-EEMS). Variables which were significantly correlated in univariate analysis were used as independent variables in the multivariate analysis.Values are expressed as mean ± SD when variables were normally distributed. In case of a nonnormal distribution, values are reported as median (interquartile ranges). For comparison between groups, continuous variables were analysed by Student's P value < 0.05 was considered statistically significant.All analyses were performed using SPSS 14.0. A two-tailed P < 0.001). Immunosuppressive agents, such as prednisolone, methotrexate, azathioprine, and cyclophosphamide were used in 15 (37%) SSc patients.Characteristics of patients and controls are presented in Tables P = 0.684, n = 4) compared to those without a history of manifest CVD (n = 77) . In subjects using ACE inhibitors or ATII receptor blockers for hypertension or other reasons, AF-EEMS was significantly higher than in subjects not using these agents .No difference was found in AF-EEMS between patients and healthy controls , as well as MSS  and use of ACE inhibitors or ATII receptor blockers . Univariate analysis of all subjects, patients and controls together, resulted in an association between skin AF-EEMS and age , CRP , and use of ACE inhibitors or ATII receptor blockers . All other clinical and biochemical variables did not show significant correlations with skin AF-EEMS.Univariate analysis between skin AF-EEMS and traditional risk factors and disease-related factors for CVD in SSc patients resulted in a positive correlation between skin AF-EEMS and CRP lysine (CML), one of the AGEs which can be detected in vivo, in SSc patients and healthy controls by means of ELISA. They found increased CML levels in SSc patients regardless of subset, with highest the levels found in SSc patients with an “early” disease pattern in nailfold videocapillaroscopy, suggesting that AGEs are involved in SSc microangiopathy. This is in agreement with the observation that the highest values of markers of oxidative stress are seen in early stages of the disease [To our knowledge, only one study has been performed on the relation between AGEs and SSc. Kaloudi et al.  compared disease . Several factors may be responsible for this discrepancy. We used noninvasive skin autofluorescence measurements for the assessment of accumulation of AGEs. This technique is simple, rapid, and noninvasive. Results from this technique were found to correlate strongly with levels of AGEs measured from skin biopsies , 29, altWe expected to find more AGE accumulation in SSc patients with signs of inflammation and disease severity. Compared to controls, we found higher CRP levels in SSc patients, which might suggest a more active disease although absolute levels were not increased and EscSG activity index did not reflect active disease. We found a positive correlation between skin AF-EEMs levels and MSS, a measure of activity, severity, and damage in SSc patients, suggesting a relation between AGE accumulation and disease severity. Recently, doubts have been raised by Valentini and Cerinic on the weighting of the contribution of the different organ systems in the MSS . PerhapsWe found higher skin AF-EEMS levels in a substantial number of subjects using ACE inhibitors or ATII antagonists compared to subjects not using these agents, and their use was independently associated with skin AF-EEMS in multivariate analysis. This seems surprising because these agents have been found to reduce AGE accumulation in animal studies and in vitro studies –35. In oSkin fibrosis in SSc could be a possible explanation of the lack of increase in AF-EEMS values that we had expected to occur, although we only included patients with limited cutaneous SSc, who had no significant fibrosis of the forearm. AGE accumulation and skin autofluorescence are strongly related to collagen-linked fluorescence and, thereby, to the usually very long half-time (15–20 years) of collagen. Previously reported increases in both collagen synthesis but especially increased degradation of skin collagen in SSc suggest that our results in SSc patients may be explained by accelerated skin collagen turnover –40. In t In conclusion, although oxidative stress seems present in SSc and is an acknowledged important factor in the generation of AGEs, increased levels of AGEs, as determined by skin autofluorescence, were not found. We cannot rule out that accumulation of AGEs in SSc patients was prevented by the use of ACE inhibitors or ATII receptor blockers, and by accelerated skin collagen turnover in clinically unaffected areas.http://www.diagnoptics.com/). The other authors have nothing to declare.R. Graaff and A. J. Smit are both founders of DiagnOptics BV, the Netherlands, manufacturing autofluorescence readers (


Bacillus subtilis. This bacterium is both a paradigm for systems-level studies on gene expression and a highly appreciated biotechnological ‘cell factory’. We conclude that the temporal resolution of such analyses with TLM-Quant is only limited by the numbers of recorded images.Gene expression heterogeneity is a key driver for microbial adaptation to fluctuating environmental conditions, cell differentiation and the evolution of species. This phenomenon has therefore enormous implications, not only for life in general, but also for biotechnological applications where unwanted subpopulations of non-producing cells can emerge in large-scale fermentations. Only time-lapse fluorescence microscopy allows real-time measurements of gene expression heterogeneity. A major limitation in the analysis of time-lapse microscopy data is the lack of fast, cost-effective, open, simple and adaptable protocols. Here we describe TLM-Quant, a semi-automatic pipeline for the analysis of time-lapse fluorescence microscopy data that enables the user to visualize and quantify gene expression heterogeneity. Importantly, our pipeline builds on the open-source packages ImageJ and R. To validate TLM-Quant, we selected three possible scenarios, namely homogeneous expression, highly ‘noisy’ heterogeneous expression, and bistable heterogeneous expression in the Gram-positive bacterium  Bacillus subtilis. Individual B. subtilis cells within a population can, for example, differentiate into a motile state for migration to more favourable environments, a competent state to take up DNA from the environment, or a dormant state in the form of spores Microorganisms need to adapt to environmental changes by appropriately adjusting their gene expression B. subtilis strains producing GFP from promoters that direct either homogenous, heterogeneous, or bistable gene expression, as described by Botella et al.B. subtilis metabolism to nutritional shifts between the preferred carbon sources glucose and malate https://basysbio.ethz.ch/openbis/index.html?viewMode=SIMPLE#action=DOWNLOAD_ATTACHMENT&file=populationhomogeneity.pdf&&entity=PROJECT&code=BASYSBIO_BIG&space=BASYSBIO_PUBLIC or http://tinyurl.com/basysbiodata. A detailed description of TLM-Quant as presented here and in the Tutorial S1 was however not published thus far.The theoretical and practical ramifications of gene expression heterogeneity have led to a strong interest in effective tools to monitor and quantify this phenomenon. Most strategies involve the fusion of the promoter sequence of a gene of interest to a promoter-less copy of the gene encoding the Green Fluorescent Protein (GFP). Overall promoter activity and expression of the gene of interest can then be determined by fluorescence readings of culture samples. This is achieved in real time using suitable plate reader assays http://rsbweb.nih.gov/ij/) For image analysis by TLM-Quant, we will assume that, for each time point, a phase-contrast image and an overlapping fluorescent image are available, both encoded in 8-bits (intensity from 0 to 255). Downstream processing can be generalized to multiple channels (colours). To visualise and quantify gene expression heterogeneity, the fluorescence information in the recorded images is extracted using ImageJ software Click here for additional data file.