Automatic detection of diabetic retinopathy using an artificial neural network: a screening tool.

PubMed

Gardner, G G; Keating, D; Williamson, T H; Elliott, A T

1996-11-01

To determine if neural networks can detect diabetic features in fundus images and compare the network against an ophthalmologist screening a set of fundus images. 147 diabetic and 32 normal images were captured from a fundus camera, stored on computer, and analysed using a back propagation neural network. The network was trained to recognise features in the retinal image. The effects of digital filtering techniques and different network variables were assessed. 200 diabetic and 101 normal images were then randomised and used to evaluate the network's performance for the detection of diabetic retinopathy against an ophthalmologist. Detection rates for the recognition of vessels, exudates, and haemorrhages were 91.7%, 93.1%, and 73.8% respectively. When compared with the results of the ophthalmologist, the network achieved a sensitivity of 88.4% and a specificity of 83.5% for the detection of diabetic retinopathy. Detection of vessels, exudates, and haemorrhages was possible, with success rates dependent upon preprocessing and the number of images used in training. When compared with the ophthalmologist, the network achieved good accuracy for the detection of diabetic retinopathy. The system could be used as an aid to the screening of diabetic patients for retinopathy.

Diabetic retinopathy screening using deep neural network.

PubMed

Ramachandran, Nishanthan; Hong, Sheng Chiong; Sime, Mary J; Wilson, Graham A

2017-09-07

There is a burgeoning interest in the use of deep neural network in diabetic retinal screening. To determine whether a deep neural network could satisfactorily detect diabetic retinopathy that requires referral to an ophthalmologist from a local diabetic retinal screening programme and an international database. Retrospective audit. Diabetic retinal photos from Otago database photographed during October 2016 (485 photos), and 1200 photos from Messidor international database. Receiver operating characteristic curve to illustrate the ability of a deep neural network to identify referable diabetic retinopathy (moderate or worse diabetic retinopathy or exudates within one disc diameter of the fovea). Area under the receiver operating characteristic curve, sensitivity and specificity. For detecting referable diabetic retinopathy, the deep neural network had an area under receiver operating characteristic curve of 0.901 (95% confidence interval 0.807-0.995), with 84.6% sensitivity and 79.7% specificity for Otago and 0.980 (95% confidence interval 0.973-0.986), with 96.0% sensitivity and 90.0% specificity for Messidor. This study has shown that a deep neural network can detect referable diabetic retinopathy with sensitivities and specificities close to or better than 80% from both an international and a domestic (New Zealand) database. We believe that deep neural networks can be integrated into community screening once they can successfully detect both diabetic retinopathy and diabetic macular oedema. © 2017 Royal Australian and New Zealand College of Ophthalmologists.

Network-based reading system for lung cancer screening CT

NASA Astrophysics Data System (ADS)

Fujino, Yuichi; Fujimura, Kaori; Nomura, Shin-ichiro; Kawashima, Harumi; Tsuchikawa, Megumu; Matsumoto, Toru; Nagao, Kei-ichi; Uruma, Takahiro; Yamamoto, Shinji; Takizawa, Hotaka; Kuroda, Chikazumi; Nakayama, Tomio

2006-03-01

This research aims to support chest computed tomography (CT) medical checkups to decrease the death rate by lung cancer. We have developed a remote cooperative reading system for lung cancer screening over the Internet, a secure transmission function, and a cooperative reading environment. It is called the Network-based Reading System. A telemedicine system involves many issues, such as network costs and data security if we use it over the Internet, which is an open network. In Japan, broadband access is widespread and its cost is the lowest in the world. We developed our system considering human machine interface and security. It consists of data entry terminals, a database server, a computer aided diagnosis (CAD) system, and some reading terminals. It uses a secure Digital Imaging and Communication in Medicine (DICOM) encrypting method and Public Key Infrastructure (PKI) based secure DICOM image data distribution. We carried out an experimental trial over the Japan Gigabit Network (JGN), which is the testbed for the Japanese next-generation network, and conducted verification experiments of secure screening image distribution, some kinds of data addition, and remote cooperative reading. We found that network bandwidth of about 1.5 Mbps enabled distribution of screening images and cooperative reading and that the encryption and image distribution methods we proposed were applicable to the encryption and distribution of general DICOM images via the Internet.

Video Games, Internet and Social Networks: A Study among French School students

PubMed

Dany, Lionel; Moreau, Laure; Guillet, Clémentine; Franchina, Carmelo

2016-11-25

Aim : Screen-based media use is gradually becoming a public health issue, especially among young people.Method : A local descriptive observational study was conducted in 11 colleges of the Bouches-du-Rhône department. All middle high school students were asked to fill in a questionnaire comprising questions about their demographic characteristics, their screen-based media use (Internet, video games, social networks), any problematic use (video games and social networks), self-esteem and quality of life.Results : A total of 950 college students (mean age : 12.96 years) participated in the research. The results show a high level and a very diverse screen-based media use. Boys more frequently played video games and girls go more frequently used social networks. The levels of problematic use were relatively low for all middle high school students. The level of problematic video game use was significantly higher in boys, and the level of problematic social network use was higher in girls.Conclusion : Differences in the use of video games or social networks raise the general issue of gender differences in society. This study indicates the need for more specific preventive interventions for screen-based media use. The addictive “nature” of certain practices needs to be studied in more detail.

Computer-aided diagnosis workstation and network system for chest diagnosis based on multislice CT images

NASA Astrophysics Data System (ADS)

Satoh, Hitoshi; Niki, Noboru; Eguchi, Kenji; Moriyama, Noriyuki; Ohmatsu, Hironobu; Masuda, Hideo; Machida, Suguru

2008-03-01

Mass screening based on multi-helical CT images requires a considerable number of images to be read. It is this time-consuming step that makes the use of helical CT for mass screening impractical at present. To overcome this problem, we have provided diagnostic assistance methods to medical screening specialists by developing a lung cancer screening algorithm that automatically detects suspected lung cancers in helical CT images, a coronary artery calcification screening algorithm that automatically detects suspected coronary artery calcification and a vertebra body analysis algorithm for quantitative evaluation of osteoporosis likelihood by using helical CT scanner for the lung cancer mass screening. The function to observe suspicious shadow in detail are provided in computer-aided diagnosis workstation with these screening algorithms. We also have developed the telemedicine network by using Web medical image conference system with the security improvement of images transmission, Biometric fingerprint authentication system and Biometric face authentication system. Biometric face authentication used on site of telemedicine makes "Encryption of file" and Success in login" effective. As a result, patients' private information is protected. Based on these diagnostic assistance methods, we have developed a new computer-aided workstation and a new telemedicine network that can display suspected lesions three-dimensionally in a short time. The results of this study indicate that our radiological information system without film by using computer-aided diagnosis workstation and our telemedicine network system can increase diagnostic speed, diagnostic accuracy and security improvement of medical information.

Automatic Screening for Perturbations in Boolean Networks.

PubMed

Schwab, Julian D; Kestler, Hans A

2018-01-01

A common approach to address biological questions in systems biology is to simulate regulatory mechanisms using dynamic models. Among others, Boolean networks can be used to model the dynamics of regulatory processes in biology. Boolean network models allow simulating the qualitative behavior of the modeled processes. A central objective in the simulation of Boolean networks is the computation of their long-term behavior-so-called attractors. These attractors are of special interest as they can often be linked to biologically relevant behaviors. Changing internal and external conditions can influence the long-term behavior of the Boolean network model. Perturbation of a Boolean network by stripping a component of the system or simulating a surplus of another element can lead to different attractors. Apparently, the number of possible perturbations and combinations of perturbations increases exponentially with the size of the network. Manually screening a set of possible components for combinations that have a desired effect on the long-term behavior can be very time consuming if not impossible. We developed a method to automatically screen for perturbations that lead to a user-specified change in the network's functioning. This method is implemented in the visual simulation framework ViSiBool utilizing satisfiability (SAT) solvers for fast exhaustive attractor search.

Network Solutions.

ERIC Educational Resources Information Center

Vietzke, Robert; And Others

1996-01-01

This special section explains the latest developments in networking technologies, profiles school districts benefiting from successful implementations, and reviews new products for building networks. Highlights include ATM (asynchronous transfer mode), cable modems, networking switches, Internet screening software, file servers, network management…

Integrated Model of Chemical Perturbations of a Biological PathwayUsing 18 In Vitro High Throughput Screening Assays for the Estrogen Receptor

EPA Science Inventory

We demonstrate a computational network model that integrates 18 in vitro, high-throughput screening assays measuring estrogen receptor (ER) binding, dimerization, chromatin binding, transcriptional activation and ER-dependent cell proliferation. The network model uses activity pa...

Friendship Network Characteristics Are Associated with Physical Activity and Sedentary Behavior in Early Adolescence.

PubMed

Marks, Jennifer; de la Haye, Kayla; Barnett, Lisa M; Allender, Steven

2015-01-01

There is limited understanding of the association between peer social networks and physical activity (PA), sedentary and screen-related behaviors. This study reports on associations between personal network characteristics and these important health behaviors for early adolescents. Participants were 310 students, aged 11-13 years, from fifteen randomly selected Victorian primary schools (43% response rate). PA and sedentary behaviors were collected via accelerometer and self-report questionnaire, and anthropometric measures via trained researchers. Participants nominated up to fifteen friends, and described the frequency of interaction and perceived activity intensity of these friends. Personal network predictors were examined using regression modelling for PA and sedentary/screen behavior. Perceived activity levels of friends, and friendships with very frequent interaction were associated with outside-of-school PA and/or sedentary/screen time. Differences according to sex were also observed in the association between network characteristics and PA and sedentary time. A higher number of friends and greater proportion of same sex friends were associated with boys engaging in more moderate-to-vigorous PA outside of school hours. PA intensity during school-day breaks was positively associated with having a greater proportion of friends who played sports for girls, and a greater proportion of male friends for boys. Friendship network characteristics are associated with PA and sedentary/screen time in late childhood/early adolescence, and these associations differ by sex. The positive influence of very active peers may be a promising avenue to strengthen traditional interventions for the promotion of PA and reduction in screen time.

Friendship Network Characteristics Are Associated with Physical Activity and Sedentary Behavior in Early Adolescence

PubMed Central

Marks, Jennifer; de la Haye, Kayla; Barnett, Lisa M; Allender, Steven

2015-01-01

Introduction There is limited understanding of the association between peer social networks and physical activity (PA), sedentary and screen-related behaviors. This study reports on associations between personal network characteristics and these important health behaviors for early adolescents. Methods Participants were 310 students, aged 11–13 years, from fifteen randomly selected Victorian primary schools (43% response rate). PA and sedentary behaviors were collected via accelerometer and self-report questionnaire, and anthropometric measures via trained researchers. Participants nominated up to fifteen friends, and described the frequency of interaction and perceived activity intensity of these friends. Personal network predictors were examined using regression modelling for PA and sedentary/screen behavior. Results Perceived activity levels of friends, and friendships with very frequent interaction were associated with outside-of-school PA and/or sedentary/screen time. Differences according to sex were also observed in the association between network characteristics and PA and sedentary time. A higher number of friends and greater proportion of same sex friends were associated with boys engaging in more moderate-to-vigorous PA outside of school hours. PA intensity during school-day breaks was positively associated with having a greater proportion of friends who played sports for girls, and a greater proportion of male friends for boys. Conclusion Friendship network characteristics are associated with PA and sedentary/screen time in late childhood/early adolescence, and these associations differ by sex. The positive influence of very active peers may be a promising avenue to strengthen traditional interventions for the promotion of PA and reduction in screen time. PMID:26709924

Using deep recurrent neural network for direct beam solar irradiance cloud screening

NASA Astrophysics Data System (ADS)

Chen, Maosi; Davis, John M.; Liu, Chaoshun; Sun, Zhibin; Zempila, Melina Maria; Gao, Wei

2017-09-01

Cloud screening is an essential procedure for in-situ calibration and atmospheric properties retrieval on (UV-)MultiFilter Rotating Shadowband Radiometer [(UV-)MFRSR]. Previous study has explored a cloud screening algorithm for direct-beam (UV-)MFRSR voltage measurements based on the stability assumption on a long time period (typically a half day or a whole day). To design such an algorithm requires in-depth understanding of radiative transfer and delicate data manipulation. Recent rapid developments on deep neural network and computation hardware have opened a window for modeling complicated End-to-End systems with a standardized strategy. In this study, a multi-layer dynamic bidirectional recurrent neural network is built for determining the cloudiness on each time point with a 17-year training dataset and tested with another 1-year dataset. The dataset is the daily 3-minute cosine corrected voltages, airmasses, and the corresponding cloud/clear-sky labels at two stations of the USDA UV-B Monitoring and Research Program. The results show that the optimized neural network model (3-layer, 250 hidden units, and 80 epochs of training) has an overall test accuracy of 97.87% (97.56% for the Oklahoma site and 98.16% for the Hawaii site). Generally, the neural network model grasps the key concept of the original model to use data in the entire day rather than short nearby measurements to perform cloud screening. A scrutiny of the logits layer suggests that the neural network model automatically learns a way to calculate a quantity similar to total optical depth and finds an appropriate threshold for cloud screening.

Computer-aided diagnosis workstation and telemedicine network system for chest diagnosis based on multislice CT images

NASA Astrophysics Data System (ADS)

Satoh, Hitoshi; Niki, Noboru; Eguchi, Kenji; Ohmatsu, Hironobu; Kakinuma, Ryutaru; Moriyama, Noriyuki

2009-02-01

Mass screening based on multi-helical CT images requires a considerable number of images to be read. It is this time-consuming step that makes the use of helical CT for mass screening impractical at present. Moreover, the doctor who diagnoses a medical image is insufficient in Japan. To overcome these problems, we have provided diagnostic assistance methods to medical screening specialists by developing a lung cancer screening algorithm that automatically detects suspected lung cancers in helical CT images, a coronary artery calcification screening algorithm that automatically detects suspected coronary artery calcification and a vertebra body analysis algorithm for quantitative evaluation of osteoporosis likelihood by using helical CT scanner for the lung cancer mass screening. The functions to observe suspicious shadow in detail are provided in computer-aided diagnosis workstation with these screening algorithms. We also have developed the telemedicine network by using Web medical image conference system with the security improvement of images transmission, Biometric fingerprint authentication system and Biometric face authentication system. Biometric face authentication used on site of telemedicine makes "Encryption of file" and "Success in login" effective. As a result, patients' private information is protected. We can share the screen of Web medical image conference system from two or more web conference terminals at the same time. An opinion can be exchanged mutually by using a camera and a microphone that are connected with workstation. Based on these diagnostic assistance methods, we have developed a new computer-aided workstation and a new telemedicine network that can display suspected lesions three-dimensionally in a short time. The results of this study indicate that our radiological information system without film by using computer-aided diagnosis workstation and our telemedicine network system can increase diagnostic speed, diagnostic accuracy and security improvement of medical information.

Comfortably engaging: which approach to alcohol screening should we use?

PubMed

Vinson, Daniel C; Galliher, James M; Reidinger, Carol; Kappus, Jennifer A

2004-01-01

We wanted to compare 2 screening instruments for problem drinking, the CAGE and a single question, assessing frequency of use, patient and clinician comfort, and patient engagement in change. The study was a crossover, cluster-randomized clinical trial with 31 clinicians in Missouri and 13 in the American Academy of Family Physicians (AAFP) National Network for Family Practice and Primary Care Research; 2,800 patients provided data. The clinician was the unit of randomization. Clinicians decided whether to screen each patient; if they chose to screen, they used the screening approach assigned for that block of patients. The clinician and patient separately completed questionnaires immediately after the office visit to assess each one's comfort with screening (and any ensuing discussion) and the patient's engagement in change. Missouri clinicians screened more patients when assigned the single question (81%) than the CAGE (69%, P = .001 in weighted analysis). There was no difference among AAFP network clinicians (96% of patients screened with the CAGE, 97% with the single question). Eighty percent to 90% of clinicians and 70% of patients reported being comfortable with screening and the ensuing discussion, with no difference between approaches in either network. About one third of patients who were identified as problem drinkers reported thinking about or planning to change their drinking behavior, with no difference in engagement between screening approaches. Clinicians and patients reported similar comfort with the CAGE questions and the single-question screening tools for problem drinking, and the 2 instruments were equal in their ability to engage the patient. In Missouri, the single question was more likely to be used.

Factors that influence mammography screening behaviour: a qualitative study of Greek women's experiences.

PubMed

Kaltsa, Aikaterina; Holloway, Aisha; Cox, Karen

2013-06-01

To identify the factors that influence mammography screening behaviour in a sample of Greek women. Data were collected in Athens-Greece, from individuals who were members of six women's associations. A subset of 33 women were interviewed about their screening behaviour and experiences out of the 186 women who completed an initial questionnaire. This paper focuses on the findings revealed from the interviews. Women's associations were approached for the recruitment of the interviewees. Influences arising from women's immediate networks, such as family and close friends, appeared to be of essential importance in relation to their screening behaviour, while influences from their broader networks were of moderate impact. Fear acted as a motivator but also as a barrier in relation to mammography screening participation. Experiences that arose from engagement with the mammography screening processes were mostly characterized by having to overcome a variety of obstacles, such as long bureaucratic procedures and distrust in doctors. The interpersonal relationships between women and their social networks appeared to have an important and influential role in relation to breast screening behaviour. The quality of these relationships appeared to determine women's participation in mammography screening. It would appear that future practice needs to focus on these relationships in order to utilize them in a positive way. Future research is needed to explore this further. Copyright © 2012 Elsevier Ltd. All rights reserved.

Antituberculosis activity of the molecular libraries screening center network library.

PubMed

Maddry, Joseph A; Ananthan, Subramaniam; Goldman, Robert C; Hobrath, Judith V; Kwong, Cecil D; Maddox, Clinton; Rasmussen, Lynn; Reynolds, Robert C; Secrist, John A; Sosa, Melinda I; White, E Lucile; Zhang, Wei

2009-09-01

There is an urgent need for the discovery and development of new antitubercular agents that target novel biochemical pathways and treat drug-resistant forms of the disease. One approach to addressing this need is through high-throughput screening of drug-like small molecule libraries against the whole bacterium in order to identify a variety of new, active scaffolds that will stimulate additional biological research and drug discovery. Through the Molecular Libraries Screening Center Network, the NIAID Tuberculosis Antimicrobial Acquisition and Coordinating Facility tested a 215,110-compound library against Mycobacterium tuberculosis strain H37Rv. A medicinal chemistry survey of the results from the screening campaign is reported herein.

[Small compounds libraries: a research tool for chemical biology].

PubMed

Florent, Jean-Claude

2013-01-01

Obtaining and screening collections of small molecules remain a challenge for biologists. Recent advances in analytical techniques and instrumentation now make screening possible in academia. The history of the creation of such public or commercial collections and their accessibility is related. It shows that there is interest for an academic laboratory involved in medicinal chemistry, chemogenomics or "chemical biology" to organize its own collection and make it available through existing networks such as the French National chimiothèque or the European partner network "European Infrastructure of open screening platforms for Chemical Biology" EU-OpenScreen under construction. © Société de Biologie, 2013.

Establishment of apoptotic regulatory network for genetic markers of colorectal cancer and optimal selection of traditional Chinese medicine target.

PubMed

Tian, Tongde; Chen, Chuanliang; Yang, Feng; Tang, Jingwen; Pei, Junwen; Shi, Bian; Zhang, Ning; Zhang, Jianhua

2017-03-01

The paper aimed to screen out genetic markers applicable to early diagnosis for colorectal cancer and establish apoptotic regulatory network model for colorectal cancer, and to analyze the current situation of traditional Chinese medicine (TCM) target, thereby providing theoretical evidence for early diagnosis and targeted therapy of colorectal cancer. Taking databases including CNKI, VIP, Wanfang data, Pub Med, and MEDLINE as main sources of literature retrieval, literatures associated with genetic markers that are applied to early diagnosis of colorectal cancer were searched and performed comprehensive and quantitative analysis by Meta analysis, hence screening genetic markers used in early diagnosis of colorectal cancer. KEGG analysis was employed to establish apoptotic regulatory network model based on screened genetic markers, and optimization was conducted on TCM targets. Through Meta analysis, seven genetic markers were screened out, including WWOX, K-ras, COX-2, P53, APC, DCC and PTEN, among which DCC has the highest diagnostic efficiency. Apoptotic regulatory network was built by KEGG analysis. Currently, it was reported that TCM has regulatory function on gene locus in apoptotic regulatory network. The apoptotic regulatory model of colorectal cancer established in this study provides theoretical evidence for early diagnosis and TCM targeted therapy of colorectal cancer in clinic.

Hypothesis generation using network structures on community health center cancer-screening performance.

PubMed

Carney, Timothy Jay; Morgan, Geoffrey P; Jones, Josette; McDaniel, Anna M; Weaver, Michael T; Weiner, Bryan; Haggstrom, David A

2015-10-01

Nationally sponsored cancer-care quality-improvement efforts have been deployed in community health centers to increase breast, cervical, and colorectal cancer-screening rates among vulnerable populations. Despite several immediate and short-term gains, screening rates remain below national benchmark objectives. Overall improvement has been both difficult to sustain over time in some organizational settings and/or challenging to diffuse to other settings as repeatable best practices. Reasons for this include facility-level changes, which typically occur in dynamic organizational environments that are complex, adaptive, and unpredictable. This study seeks to understand the factors that shape community health center facility-level cancer-screening performance over time. This study applies a computational-modeling approach, combining principles of health-services research, health informatics, network theory, and systems science. To investigate the roles of knowledge acquisition, retention, and sharing within the setting of the community health center and to examine their effects on the relationship between clinical decision support capabilities and improvement in cancer-screening rate improvement, we employed Construct-TM to create simulated community health centers using previously collected point-in-time survey data. Construct-TM is a multi-agent model of network evolution. Because social, knowledge, and belief networks co-evolve, groups and organizations are treated as complex systems to capture the variability of human and organizational factors. In Construct-TM, individuals and groups interact by communicating, learning, and making decisions in a continuous cycle. Data from the survey was used to differentiate high-performing simulated community health centers from low-performing ones based on computer-based decision support usage and self-reported cancer-screening improvement. This virtual experiment revealed that patterns of overall network symmetry, agent cohesion, and connectedness varied by community health center performance level. Visual assessment of both the agent-to-agent knowledge sharing network and agent-to-resource knowledge use network diagrams demonstrated that community health centers labeled as high performers typically showed higher levels of collaboration and cohesiveness among agent classes, faster knowledge-absorption rates, and fewer agents that were unconnected to key knowledge resources. Conclusions and research implications: Using the point-in-time survey data outlining community health center cancer-screening practices, our computational model successfully distinguished between high and low performers. Results indicated that high-performance environments displayed distinctive network characteristics in patterns of interaction among agents, as well as in the access and utilization of key knowledge resources. Our study demonstrated how non-network-specific data obtained from a point-in-time survey can be employed to forecast community health center performance over time, thereby enhancing the sustainability of long-term strategic-improvement efforts. Our results revealed a strategic profile for community health center cancer-screening improvement via simulation over a projected 10-year period. The use of computational modeling allows additional inferential knowledge to be drawn from existing data when examining organizational performance in increasingly complex environments. Copyright © 2015 Elsevier Inc. All rights reserved.

Characterization of ToxCast Phase II compounds disruption of spontaneous network activity in cortical networks grown on multi-well microelectrode array (mwMEA) plates.

EPA Science Inventory

The development of multi-well microelectrode array (mwMEA) systems has increased in vitro screening throughput making them an effective method to screen and prioritize large sets of compounds for potential neurotoxicity. In the present experiments, a multiplexed approach was used...

Quality control methodology for high-throughput protein-protein interaction screening.

PubMed

Vazquez, Alexei; Rual, Jean-François; Venkatesan, Kavitha

2011-01-01

Protein-protein interactions are key to many aspects of the cell, including its cytoskeletal structure, the signaling processes in which it is involved, or its metabolism. Failure to form protein complexes or signaling cascades may sometimes translate into pathologic conditions such as cancer or neurodegenerative diseases. The set of all protein interactions between the proteins encoded by an organism constitutes its protein interaction network, representing a scaffold for biological function. Knowing the protein interaction network of an organism, combined with other sources of biological information, can unravel fundamental biological circuits and may help better understand the molecular basics of human diseases. The protein interaction network of an organism can be mapped by combining data obtained from both low-throughput screens, i.e., "one gene at a time" experiments and high-throughput screens, i.e., screens designed to interrogate large sets of proteins at once. In either case, quality controls are required to deal with the inherent imperfect nature of experimental assays. In this chapter, we discuss experimental and statistical methodologies to quantify error rates in high-throughput protein-protein interactions screens.

HTS-Net: An integrated regulome-interactome approach for establishing network regulation models in high-throughput screenings

PubMed Central

Rioualen, Claire; Da Costa, Quentin; Chetrit, Bernard; Charafe-Jauffret, Emmanuelle; Ginestier, Christophe

2017-01-01

High-throughput RNAi screenings (HTS) allow quantifying the impact of the deletion of each gene in any particular function, from virus-host interactions to cell differentiation. However, there has been less development for functional analysis tools dedicated to RNAi analyses. HTS-Net, a network-based analysis program, was developed to identify gene regulatory modules impacted in high-throughput screenings, by integrating transcription factors-target genes interaction data (regulome) and protein-protein interaction networks (interactome) on top of screening z-scores. HTS-Net produces exhaustive HTML reports for results navigation and exploration. HTS-Net is a new pipeline for RNA interference screening analyses that proves better performance than simple gene rankings by z-scores, by re-prioritizing genes and replacing them in their biological context, as shown by the three studies that we reanalyzed. Formatted input data for the three studied datasets, source code and web site for testing the system are available from the companion web site at http://htsnet.marseille.inserm.fr/. We also compared our program with existing algorithms (CARD and hotnet2). PMID:28949986

Using an Ocean of Data, Researchers Model Real-Life Benefits of Cancer Screening

Cancer.gov

Using the results of screening trials, the NCI Cancer Intervention and Surveillance Modeling Network is trying to estimate the true benefit of cancer screening in the general population and identify the optimal way to implement screening within the health care system.

Current levels of gonorrhoea screening in MSM in Belgium may have little effect on prevalence: a modelling study.

PubMed

Buyze, J; Vanden Berghe, W; Hens, N; Kenyon, C

2018-02-01

There is considerable uncertainty as to the effectiveness of Neisseria gonorrhoeae (NG) screening in men who have sex with men. It is important to ensure that screening has benefits that outweigh the risks of increased antibiotics resistance. We develop a mathematical model to estimate the effectiveness of screening on prevalence. Separable Temporal Exponential family Random Graph Models are used to model the sexual relationships network, both with main and casual partners. Next, the transmission of Gonorrhoea is simulated on this network. The models are implemented using the R package 'statnet', which we adapted among other things to incorporate infection status at the pharynx, urethra and rectum separately and to distinguish between anal sex, oral sex and rimming. The different screening programmes compared are no screening, 3.5% of the population screened, 32% screened and 50% screened. The model simulates day-by-day evolution for 10 years of a population of 10 000. If half of the population would be screened, the prevalence in the pharynx decreases from 11.9% to 10.2%. We conclude that the limited impact of screening on NG prevalence may not outweigh the increased risk of antibiotic resistance.

A private-sector preferred provider network model for public health screening of newly resettled refugees.

PubMed

Geltman, Paul L; Cochran, Jennifer

2005-02-01

US law and regulations stipulate a process for the health screening of refugees. The responsibility of caring for refugees resettled in the United States rests, in part, with public health or welfare departments. Massachusetts has met its screening responsibilities through the innovative creation of a network of private preferred providers. We explore the Massachusetts model of public-private collaboration within the context of federal refugee health priorities and current state fiscal restraints affecting public health programs, and demonstrate the model's accomplishments.

Pilot Integration of HIV Screening and Healthcare Settings with Multi- Component Social Network and Partner Testing for HIV Detection.

PubMed

Rentz, Michael F; Ruffner, Andrew H; Ancona, Rachel M; Hart, Kimberly W; Kues, John R; Barczak, Christopher M; Lindsell, Christopher J; Fichtenbaum, Carl J; Lyons, Michael S

2017-11-23

Healthcare settings screen broadly for HIV. Public health settings use social network and partner testing ("Transmission Network Targeting (TNT)") to select high-risk individuals based on their contacts. HIV screening and TNT systems are not integrated, and healthcare settings have not implemented TNT. The study aimed to evaluate pilot implementation of multi-component, multi-venue TNT in conjunction with HIV screening by a healthcare setting. Our urban, academic health center implemented a TNT program in collaboration with the local health department for five months during 2011. High-risk or HIV positive patients of the infectious diseases clinic and emergency department HIV screening program were recruited to access social and partner networks via compensated peer-referral, testing of companions present with them, and partner notification services. Contacts became the next-generation index cases in a snowball recruitment strategy. The pilot TNT program yielded 485 HIV tests for 482 individuals through eight generations of recruitment with five (1.0%; 95% CI = 0.4%, 2.3%) new diagnoses. Of these, 246 (51.0%; 95% CI = 46.6%, 55.5%) reported that they had not been tested for HIV within the last 12 months and 383 (79.5%; 95% CI = 75.7%, 82.9%) had not been tested by the existing ED screening program within the last five years. TNT complements population screening by more directly targeting high-risk individuals and by expanding the population receiving testing. Information from existing healthcare services could be used to seed TNT programs, or TNT could be implemented within healthcare settings. Research evaluating multi-component, multi-venue HIV detection is necessary to maximize complementary approaches while minimizing redundancy. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Apparel Research Network (ARN) Apparel Order Processing Module (AOPM). Application Program for Management of Special Measurement Clothing Orders

DTIC Science & Technology

1997-09-30

Screen, abandoning changes. APPAREL ORDER PROCESSING MODULE FIELD USER MANUAL Ordering Official Screens The Ordering Official Screens are provided for...currendy selected Ordering Official will appear on the Ordering Official Information Screen. APPAREL ORDER PROCESSING MODULE FIELD USER MANUAL Ordering Official

Bias in groundwater samples caused by wellbore flow

USGS Publications Warehouse

Reilly, Thomas E.; Franke, O. Lehn; Bennett, Gordon D.

1989-01-01

Proper design of physical installations and sampling procedures for groundwater monitoring networks is critical for the detection and analysis of possible contaminants. Monitoring networks associated with known contaminant sources sometimes include an array of monitoring wells with long well screens. The purpose of this paper is: (a) to report the results of a numerical experiment indicating that significant borehole flow can occur within long well screens installed in homogeneous aquifers with very small head differences in the aquifer (less than 0.01 feet between the top and bottom of the screen); (b) to demonstrate that contaminant monitoring wells with long screens may completely fail to fulfill their purpose in many groundwater environments.

The Study of Learners' Preference for Visual Complexity on Small Screens of Mobile Computers Using Neural Networks

ERIC Educational Resources Information Center

Wang, Lan-Ting; Lee, Kun-Chou

2014-01-01

The vision plays an important role in educational technologies because it can produce and communicate quite important functions in teaching and learning. In this paper, learners' preference for the visual complexity on small screens of mobile computers is studied by neural networks. The visual complexity in this study is divided into five…

E-mail to Promote Colorectal Cancer Screening Within Social Networks: Acceptability and Content

PubMed Central

CUTRONA, SARAH L.; WAGNER, JOANN; ROBLIN, DOUGLAS W.; GAGLIO, BRIDGET; WILLIAMS, ANDREW; TORRES-STONE, ROSALIE; MAZOR, KATHLEEN M.

2016-01-01

Effective techniques to encourage colorectal cancer (CRC) screening in underscreened populations have included social support interventions and email reminders from physicians. Personalized email messages to promote CRC screening within social networks could be even more effective, but have not been studied. We interviewed 387 email users, aged 42-73 years in Massachusetts, Hawaii, and Georgia. Participants were asked to edit a sample message in which the sender shares a recent colonoscopy experience and urges the recipient to discuss CRC screening with a doctor. For those reporting willingness to send this message, changes to the message and suggested subject lines were recorded. Edited text was analyzed for content and concordance with original message. The majority of participants (74.4%) were willing to email a modifiable message. Of those willing, 63.5% edited the message. Common edits included deletion (17.7%) or modification (17.4%) of a negatively framed sentence on colon cancer risks and addition or modification of personalizing words (15.6%). Few edits changed the meaning of the message (5.6%) and even fewer introduced factual inaccuracies (1.7%). Modifiable email messages offer a way for screened individuals to promote CRC screening to social network members. Accuracy and impact of such messages should be further studied. PMID:25839968

A convolutional neural network-based screening tool for X-ray serial crystallography

PubMed Central

Ke, Tsung-Wei; Brewster, Aaron S.; Yu, Stella X.; Ushizima, Daniela; Yang, Chao; Sauter, Nicholas K.

2018-01-01

A new tool is introduced for screening macromolecular X-ray crystallography diffraction images produced at an X-ray free-electron laser light source. Based on a data-driven deep learning approach, the proposed tool executes a convolutional neural network to detect Bragg spots. Automatic image processing algorithms described can enable the classification of large data sets, acquired under realistic conditions consisting of noisy data with experimental artifacts. Outcomes are compared for different data regimes, including samples from multiple instruments and differing amounts of training data for neural network optimization. PMID:29714177

A convolutional neural network-based screening tool for X-ray serial crystallography.

PubMed

Ke, Tsung Wei; Brewster, Aaron S; Yu, Stella X; Ushizima, Daniela; Yang, Chao; Sauter, Nicholas K

2018-05-01

A new tool is introduced for screening macromolecular X-ray crystallography diffraction images produced at an X-ray free-electron laser light source. Based on a data-driven deep learning approach, the proposed tool executes a convolutional neural network to detect Bragg spots. Automatic image processing algorithms described can enable the classification of large data sets, acquired under realistic conditions consisting of noisy data with experimental artifacts. Outcomes are compared for different data regimes, including samples from multiple instruments and differing amounts of training data for neural network optimization. open access.

A convolutional neural network-based screening tool for X-ray serial crystallography

DOE PAGES

Ke, Tsung-Wei; Brewster, Aaron S.; Yu, Stella X.; ...

2018-04-24

A new tool is introduced for screening macromolecular X-ray crystallography diffraction images produced at an X-ray free-electron laser light source. Based on a data-driven deep learning approach, the proposed tool executes a convolutional neural network to detect Bragg spots. Automatic image processing algorithms described can enable the classification of large data sets, acquired under realistic conditions consisting of noisy data with experimental artifacts. Outcomes are compared for different data regimes, including samples from multiple instruments and differing amounts of training data for neural network optimization.

A convolutional neural network-based screening tool for X-ray serial crystallography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ke, Tsung-Wei; Brewster, Aaron S.; Yu, Stella X.

A new tool is introduced for screening macromolecular X-ray crystallography diffraction images produced at an X-ray free-electron laser light source. Based on a data-driven deep learning approach, the proposed tool executes a convolutional neural network to detect Bragg spots. Automatic image processing algorithms described can enable the classification of large data sets, acquired under realistic conditions consisting of noisy data with experimental artifacts. Outcomes are compared for different data regimes, including samples from multiple instruments and differing amounts of training data for neural network optimization.

Large-Area Cross-Aligned Silver Nanowire Electrodes for Flexible, Transparent, and Force-Sensitive Mechanochromic Touch Screens.

PubMed

Cho, Seungse; Kang, Saewon; Pandya, Ashish; Shanker, Ravi; Khan, Ziyauddin; Lee, Youngsu; Park, Jonghwa; Craig, Stephen L; Ko, Hyunhyub

2017-04-25

Silver nanowire (AgNW) networks are considered to be promising structures for use as flexible transparent electrodes for various optoelectronic devices. One important application of AgNW transparent electrodes is the flexible touch screens. However, the performances of flexible touch screens are still limited by the large surface roughness and low electrical to optical conductivity ratio of random network AgNW electrodes. In addition, although the perception of writing force on the touch screen enables a variety of different functions, the current technology still relies on the complicated capacitive force touch sensors. This paper demonstrates a simple and high-throughput bar-coating assembly technique for the fabrication of large-area (>20 × 20 cm 2 ), highly cross-aligned AgNW networks for transparent electrodes with the sheet resistance of 21.0 Ω sq -1 at 95.0% of optical transmittance, which compares favorably with that of random AgNW networks (sheet resistance of 21.0 Ω sq -1 at 90.4% of optical transmittance). As a proof of concept demonstration, we fabricate flexible, transparent, and force-sensitive touch screens using cross-aligned AgNW electrodes integrated with mechanochromic spiropyran-polydimethylsiloxane composite film. Our force-sensitive touch screens enable the precise monitoring of dynamic writings, tracing and drawing of underneath pictures, and perception of handwriting patterns with locally different writing forces. The suggested technique provides a robust and powerful platform for the controllable assembly of nanowires beyond the scale of conventional fabrication techniques, which can find diverse applications in multifunctional flexible electronic and optoelectronic devices.

Applications of self-organizing neural networks in virtual screening and diversity selection.

PubMed

Selzer, Paul; Ertl, Peter

2006-01-01

Artificial neural networks provide a powerful technique for the analysis and modeling of nonlinear relationships between molecular structures and pharmacological activity. Many network types, including Kohonen and counterpropagation, also provide an intuitive method for the visual assessment of correspondence between the input and output data. This work shows how a combination of neural networks and radial distribution function molecular descriptors can be applied in various areas of industrial pharmaceutical research. These applications include the prediction of biological activity, the selection of screening candidates (cherry picking), and the extraction of representative subsets from large compound collections such as combinatorial libraries. The methods described have also been implemented as an easy-to-use Web tool, allowing chemists to perform interactive neural network experiments on the Novartis intranet.

Apparel Research Network (ARN); Apparel Order Processing Module (AOPM): Field User Manual, Version 1

DTIC Science & Technology

1997-09-30

changes. Cancel Button Closes the Site Information Screen, abandoning changes. APPAREL ORDER PROCESSING MODULE FIELD USER MANUAL Ordering Official...on the Ordering Official Information Screen. APPAREL ORDER PROCESSING MODULE FIELD USER MANUAL Ordering Official Information Screen (Jjj

Attitudes to Chlamydia screening elicited using the social networking site Facebook for subject recruitment.

PubMed

Ahmed, Navera; Jayasinghe, Yasmin; Wark, John D; Fenner, Yeshe; Moore, Elya E; Tabrizi, Sepehr N; Fletcher, Ashley; Garland, Suzanne M

2013-07-01

Chlamydia (Chlamydia trachomatis) is the commonest bacterial sexually transmissible infection worldwide and contributes to significant morbidity in females. We examined potential barriers and facilitating factors for screening in young Victorian women, using the social networking site, Facebook to recruit participants. This was part of a larger study on young women's health that assessed the feasibility of using social networking sites for recruitment. An advertisement was placed on Facebook between May and September 2010, and was visible to eligible women. Women who clicked on the advertisement and expressed their interest in participating were invited to complete a questionnaire either at a study site or online. In total, 278 participants completed the survey, with 76% reporting willingness to participate in chlamydia screening by recruitment via an online system. Overall, 73% of participants indicated they were comfortable providing a urine sample collected at home for chlamydia screening, with older participants less comfortable with this method (P=0.02, odds ratio (OR)=0.09, 95% confidence interval (CI)=0.01-0.7). Participants expressed comfort with their Pap smear and chlamydia screening being performed together (92.7%), especially those who were aware of human papillomavirus (P<0.01, OR=2.5, 95% CI=1.3-4.7). This study demonstrated willingness by young Victorian women using Facebook to participate in screening for chlamydia. There was strong acceptance of self-collected sampling, and of combined chlamydia and cervical cytology screening. Facebook may therefore be a feasible way for improving screening coverage at a population level.

["Local" or "mobile" screening for diabetic retinopathy in general practice by non-mydriatic digital cameras? about the Diabetes Midi-Pyrénées network activity between 2005 and 2010].

PubMed

Bismuth, Pierre; Bismuth, Michel; Dupouy, Julie; Rougé-Bugat, Marie-Eve; Poutrain, Jean-Christophe; Escourrou, Brigitte; Hanaire, Hélène; Oustric, Stéphane

2012-12-01

Fundus photographs using non-mydriatic digital cameras for diabetic retinopathy screening have been studied in France during the past 10 years. Nevertheless, the different screening modalities have not been compared. The main goal of this study was to compare patient recruitment with two different screening modalities, and secondarily to compare diagnostic effectiveness and cost. A retrospective study analyzed data from the Diabetes Midi Pyrenees Network in 2005 and between 2006 and 2010. In 2005, a vehicle with digital camera traveled through a rural department in order to screen diabetic patients whose last fundus examination was performed greater than 1 year previously. Between 2006 and 2010, general practitioners sent their diabetic patients whose last fundus examination was performed greater than 1 year previously to a "local" screening site. In the two cases, fundus photographs were made by trained operator at screening site and analyzed by an ophthalmologist. The "mobile" screening recruited 698 patients, and the "local" screening 345 patients. Patients recruited by "mobile" screening were older than those recruited by "local" screening. They were preferentially men and suffered from diabetes from far longer The diagnostic performance of "local" screening was 26.8%, and it was 28.6% for "mobile" screening (p = 0.47). The cost of screening was higher for "mobile" screening: 116 Euro against 61 Euro for "local" screening. "Mobile" screening could allow more patient recruitment than "local" screening when geographic and demographic constraints are more important.

Study of an overload truck screening system for a sustainable highway bridge network.

DOT National Transportation Integrated Search

2009-01-01

he objective of this project was to study the use and implementation of an overload truck screening system for bridge structures. This screening system combines two advanced technologies, namely a weigh-in-motion (WIM) system and a bridge strain sens...

Comparative economic evaluation of data from the ACRIN National CT Colonography Trial with three cancer intervention and surveillance modeling network microsimulations.

PubMed

Vanness, David J; Knudsen, Amy B; Lansdorp-Vogelaar, Iris; Rutter, Carolyn M; Gareen, Ilana F; Herman, Benjamin A; Kuntz, Karen M; Zauber, Ann G; van Ballegooijen, Marjolein; Feuer, Eric J; Chen, Mei-Hsiu; Johnson, C Daniel

2011-11-01

To estimate the cost-effectiveness of computed tomographic (CT) colonography for colorectal cancer (CRC) screening in average-risk asymptomatic subjects in the United States aged 50 years. Enrollees in the American College of Radiology Imaging Network National CT Colonography Trial provided informed consent, and approval was obtained from the institutional review board at each site. CT colonography performance estimates from the trial were incorporated into three Cancer Intervention and Surveillance Modeling Network CRC microsimulations. Simulated survival and lifetime costs for screening 50-year-old subjects in the United States with CT colonography every 5 or 10 years were compared with those for guideline-concordant screening with colonoscopy, flexible sigmoidoscopy plus either sensitive unrehydrated fecal occult blood testing (FOBT) or fecal immunochemical testing (FIT), and no screening. Perfect and reduced screening adherence scenarios were considered. Incremental cost-effectiveness and net health benefits were estimated from the U.S. health care sector perspective, assuming a 3% discount rate. CT colonography at 5- and 10-year screening intervals was more costly and less effective than FOBT plus flexible sigmoidoscopy in all three models in both 100% and 50% adherence scenarios. Colonoscopy also was more costly and less effective than FOBT plus flexible sigmoidoscopy, except in the CRC-SPIN model assuming 100% adherence (incremental cost-effectiveness ratio: $26,300 per life-year gained). CT colonography at 5- and 10-year screening intervals and colonoscopy were net beneficial compared with no screening in all model scenarios. The 5-year screening interval was net beneficial over the 10-year interval except in the MISCAN model when assuming 100% adherence and willingness to pay $50,000 per life-year gained. All three models predict CT colonography to be more costly and less effective than non-CT colonographic screening but net beneficial compared with no screening given model assumptions. RSNA, 2011

FRET and BRET-based biosensors in live cell compound screens.

PubMed

Robinson, Katie Herbst; Yang, Jessica R; Zhang, Jin

2014-01-01

Live cell compound screening with genetically encoded fluorescence or bioluminescence-based biosensors offers a potentially powerful approach to identify novel regulators of a signaling event of interest. In particular, compound screening in living cells has the added benefit that the entire signaling network remains intact, and thus the screen is not just against a single molecule of interest but against any molecule within the signaling network that may modulate the distinct signaling event reported by the biosensor in use. Furthermore, only molecules that are cell permeable or act at cell surface receptors will be identified as "hits," thus reducing further optimization of the compound in terms of cell penetration. Here we discuss a detailed protocol for using genetically encoded biosensors in living cells in a 96-well format for the execution of high throughput compound screens and the identification of small molecules which modulate a signaling event of interest.

Automated screening of propulsion system test data by neural networks, phase 1

NASA Technical Reports Server (NTRS)

Hoyt, W. Andes; Whitehead, Bruce A.

1992-01-01

The evaluation of propulsion system test and flight performance data involves reviewing an extremely large volume of sensor data generated by each test. An automated system that screens large volumes of data and identifies propulsion system parameters which appear unusual or anomalous will increase the productivity of data analysis. Data analysts may then focus on a smaller subset of anomalous data for further evaluation of propulsion system tests. Such an automated data screening system would give NASA the benefit of a reduction in the manpower and time required to complete a propulsion system data evaluation. A phase 1 effort to develop a prototype data screening system is reported. Neural networks will detect anomalies based on nominal propulsion system data only. It appears that a reasonable goal for an operational system would be to screen out 95 pct. of the nominal data, leaving less than 5 pct. needing further analysis by human experts.

Rule extraction from minimal neural networks for credit card screening.

PubMed

Setiono, Rudy; Baesens, Bart; Mues, Christophe

2011-08-01

While feedforward neural networks have been widely accepted as effective tools for solving classification problems, the issue of finding the best network architecture remains unresolved, particularly so in real-world problem settings. We address this issue in the context of credit card screening, where it is important to not only find a neural network with good predictive performance but also one that facilitates a clear explanation of how it produces its predictions. We show that minimal neural networks with as few as one hidden unit provide good predictive accuracy, while having the added advantage of making it easier to generate concise and comprehensible classification rules for the user. To further reduce model size, a novel approach is suggested in which network connections from the input units to this hidden unit are removed by a very straightaway pruning procedure. In terms of predictive accuracy, both the minimized neural networks and the rule sets generated from them are shown to compare favorably with other neural network based classifiers. The rules generated from the minimized neural networks are concise and thus easier to validate in a real-life setting.

A holistic framework for design of cost-effective minimum water utilization network.

PubMed

Wan Alwi, S R; Manan, Z A; Samingin, M H; Misran, N

2008-07-01

Water pinch analysis (WPA) is a well-established tool for the design of a maximum water recovery (MWR) network. MWR, which is primarily concerned with water recovery and regeneration, only partly addresses water minimization problem. Strictly speaking, WPA can only lead to maximum water recovery targets as opposed to the minimum water targets as widely claimed by researchers over the years. The minimum water targets can be achieved when all water minimization options including elimination, reduction, reuse/recycling, outsourcing and regeneration have been holistically applied. Even though WPA has been well established for synthesis of MWR network, research towards holistic water minimization has lagged behind. This paper describes a new holistic framework for designing a cost-effective minimum water network (CEMWN) for industry and urban systems. The framework consists of five key steps, i.e. (1) Specify the limiting water data, (2) Determine MWR targets, (3) Screen process changes using water management hierarchy (WMH), (4) Apply Systematic Hierarchical Approach for Resilient Process Screening (SHARPS) strategy, and (5) Design water network. Three key contributions have emerged from this work. First is a hierarchical approach for systematic screening of process changes guided by the WMH. Second is a set of four new heuristics for implementing process changes that considers the interactions among process changes options as well as among equipment and the implications of applying each process change on utility targets. Third is the SHARPS cost-screening technique to customize process changes and ultimately generate a minimum water utilization network that is cost-effective and affordable. The CEMWN holistic framework has been successfully implemented on semiconductor and mosque case studies and yielded results within the designer payback period criterion.

University of California San Francisco (UCSF-1): Construction of Directional Regulatory Networks Using Orthogonal CRISPR/Cas Screens | Office of Cancer Genomics

Cancer.gov

UCSF investigators developed an orthogonal CRISPR/Cas system which can be used to quantify gene regulation and construct directional regulatory networks. They combined two orthogonal Cas9 proteins from Streptococcus pyogenes and Staphylococcus aureus to carry out a dual screen in which one gene is activated while a second gene is deleted in the same cell. Read the abstract.

Feasibility of telemammography as biomedical application for breast imaging

NASA Astrophysics Data System (ADS)

Beckerman, Barbara G.; Batsell, Stephen G.; MacIntyre, Lawrence P.; Sarraf, Hamed S.; Gleason, Shaun S.; Schnall, Mitchell D.

1999-07-01

Mammographic screening is an important tool in the early detection of breast cancer. The migration of mammography from the current mode of x-ray mammography using a film screen image detector and display to a digital technology provides an opportunity to improve access and performance of breast cancer screening. The sheer size and volume of the typical screening exam, the need to have previous screening data readily available, and the need to view other breast imaging data together to provide a common consensus and to plan treatment, make telemammography an ideal application for breast imaging. For telemammography to be a viable option, it must overcome the technical challenges related to transmission, archiving, management, processing and retrieval of large data sets. Researchers from the University of Pennsylvania, the University of Chicago and Lockheed Martin Energy Systems/Oak Ridge National Laboratory have developed a framework for transmission of large-scale medical images over high-speed networks, leveraged existing high-speed networks between research and medical facilities; tested the feasibility of point-to-point transmission of mammographic images in a near-real time environment; evaluated network performance and transmission scenarios; and investigated the impact of image preprocessing on an experimental computer-aided diagnosis system. Results of the initial study are reported here.

Computer-aided diagnosis workstation and teleradiology network system for chest diagnosis using the web medical image conference system with a new information security solution

NASA Astrophysics Data System (ADS)

Satoh, Hitoshi; Niki, Noboru; Eguchi, Kenji; Ohmatsu, Hironobu; Kaneko, Masahiro; Kakinuma, Ryutaro; Moriyama, Noriyuki

2010-03-01

Diagnostic MDCT imaging requires a considerable number of images to be read. Moreover, the doctor who diagnoses a medical image is insufficient in Japan. Because of such a background, we have provided diagnostic assistance methods to medical screening specialists by developing a lung cancer screening algorithm that automatically detects suspected lung cancers in helical CT images, a coronary artery calcification screening algorithm that automatically detects suspected coronary artery calcification and a vertebra body analysis algorithm for quantitative evaluation of osteoporosis. We also have developed the teleradiology network system by using web medical image conference system. In the teleradiology network system, the security of information network is very important subjects. Our teleradiology network system can perform Web medical image conference in the medical institutions of a remote place using the web medical image conference system. We completed the basic proof experiment of the web medical image conference system with information security solution. We can share the screen of web medical image conference system from two or more web conference terminals at the same time. An opinion can be exchanged mutually by using a camera and a microphone that are connected with the workstation that builds in some diagnostic assistance methods. Biometric face authentication used on site of teleradiology makes "Encryption of file" and "Success in login" effective. Our Privacy and information security technology of information security solution ensures compliance with Japanese regulations. As a result, patients' private information is protected. Based on these diagnostic assistance methods, we have developed a new computer-aided workstation and a new teleradiology network that can display suspected lesions three-dimensionally in a short time. The results of this study indicate that our radiological information system without film by using computer-aided diagnosis workstation and our teleradiology network system can increase diagnostic speed, diagnostic accuracy and security improvement of medical information.

An Evolutionarily Conserved Innate Immunity Protein Interaction Network*

PubMed Central

De Arras, Lesly; Seng, Amara; Lackford, Brad; Keikhaee, Mohammad R.; Bowerman, Bruce; Freedman, Jonathan H.; Schwartz, David A.; Alper, Scott

2013-01-01

The innate immune response plays a critical role in fighting infection; however, innate immunity also can affect the pathogenesis of a variety of diseases, including sepsis, asthma, cancer, and atherosclerosis. To identify novel regulators of innate immunity, we performed comparative genomics RNA interference screens in the nematode Caenorhabditis elegans and mouse macrophages. These screens have uncovered many candidate regulators of the response to lipopolysaccharide (LPS), several of which interact physically in multiple species to form an innate immunity protein interaction network. This protein interaction network contains several proteins in the canonical LPS-responsive TLR4 pathway as well as many novel interacting proteins. Using RNAi and overexpression studies, we show that almost every gene in this network can modulate the innate immune response in mouse cell lines. We validate the importance of this network in innate immunity regulation in vivo using available mutants in C. elegans and mice. PMID:23209288

Establishment of apoptotic regulatory network for genetic markers of colorectal cancer.

PubMed

Hao, Yibin; Shan, Guoyong; Nan, Kejun

2017-03-01

Our purpose is to screen out genetic markers applicable to early diagnosis for colorectal cancer and to establish apoptotic regulatory network model for colorectal cancer, thereby providing theoretical evidence and targeted therapy for early diagnosis of colorectal cancer. Taking databases including CNKI, VIP, Wanfang data, Pub Med, and MEDLINE as main sources of literature retrieval, literatures associated with genetic markers applied to early diagnosis of colorectal cancer were searched to perform comprehensive and quantitative analysis by Meta analysis, hence screening genetic markers used in early diagnosis of colorectal cancer. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were employed to establish apoptotic regulatory network model based on screened genetic markers, and then verification experiment was conducted. Through Meta analysis, seven genetic markers were screened out, including WWOX, K-ras, COX-2, p53, APC, DCC and PTEN, among which DCC shows highest diagnostic efficiency. GO analysis of genetic markers found that six genetic markers played role in biological process, molecular function and cellular component. It was indicated in apoptotic regulatory network built by KEGG analysis and verification experiment that WWOX could promote tumor cell apoptotic in colorectal cancer and elevate expression level of p53. The apoptotic regulatory model of colorectal cancer established in this study provides clinically theoretical evidence and targeted therapy for early diagnosis of colorectal cancer.

An actor-based model of social network influence on adolescent body size, screen time, and playing sports.

PubMed

Shoham, David A; Tong, Liping; Lamberson, Peter J; Auchincloss, Amy H; Zhang, Jun; Dugas, Lara; Kaufman, Jay S; Cooper, Richard S; Luke, Amy

2012-01-01

Recent studies suggest that obesity may be "contagious" between individuals in social networks. Social contagion (influence), however, may not be identifiable using traditional statistical approaches because they cannot distinguish contagion from homophily (the propensity for individuals to select friends who are similar to themselves) or from shared environmental influences. In this paper, we apply the stochastic actor-based model (SABM) framework developed by Snijders and colleagues to data on adolescent body mass index (BMI), screen time, and playing active sports. Our primary hypothesis was that social influences on adolescent body size and related behaviors are independent of friend selection. Employing the SABM, we simultaneously modeled network dynamics (friendship selection based on homophily and structural characteristics of the network) and social influence. We focused on the 2 largest schools in the National Longitudinal Study of Adolescent Health (Add Health) and held the school environment constant by examining the 2 school networks separately (N = 624 and 1151). Results show support in both schools for homophily on BMI, but also for social influence on BMI. There was no evidence of homophily on screen time in either school, while only one of the schools showed homophily on playing active sports. There was, however, evidence of social influence on screen time in one of the schools, and playing active sports in both schools. These results suggest that both homophily and social influence are important in understanding patterns of adolescent obesity. Intervention efforts should take into consideration peers' influence on one another, rather than treating "high risk" adolescents in isolation.

Interdisciplinary care in disorders/differences of sex development (DSD): The psychosocial component of the DSD-Translational research network.

PubMed

Sandberg, David E; Gardner, Melissa; Callens, Nina; Mazur, Tom

2017-06-01

Scientific discovery and clinical management strategies for Disorders/Differences of Sex Development (DSD) have advanced in recent years. The 2006 Consensus Statement on Management of Intersex Disorders stated that a mental health component to care is integral to promote positive adaptation, yet the parameters of this element have not been described. The objective of this paper is threefold: to describe the psychosocial screening protocol adopted by the clinical centers of the DSD-Translational Research Network; to summarize psychosocial data collected at 1 of the 10 network sites; and to suggest how systematic behavioral health screenings can be employed to tailor care in DSD that results in better health and quality of life outcomes. Steps taken in developing the largely "noncategorical" screening protocol are described. These preliminary findings suggest that DSD, as one category of pediatric chronic conditions, is not associated with marked disturbances of psychosocial adaptation, either for the family or the child; however, screening frequently uncovered "risk factors" for individual families or patients that can potentially be addressed in the context of ongoing clinical care. Administration of the DSD-TRN psychosocial screening protocol was demonstrated to be feasible in the context of interdisciplinary team care and was acceptable to families on a longitudinal basis. The ultimate value of systematic screening will be demonstrated through a tailoring of psychosocial, medical and surgical services, based on this information that enhances the quality of patient and family-centered care and subsequent outcomes. © 2017 Wiley Periodicals, Inc.

Upper Washita River experimental watersheds: Data screening procedure for data quality assurance

USDA-ARS?s Scientific Manuscript database

The presence of non-stationary condition in long term hydrologic observation networks are associated with natural and anthropogenic stressors or network operation problems. Detection and identification of network operation drivers is fundamental in hydrologic investigation due to changes in systemat...

Transcriptome profiling analysis reveals biomarkers in colon cancer samples of various differentiation

PubMed Central

Yu, Tonghu; Zhang, Huaping; Qi, Hong

2018-01-01

The aim of the present study was to investigate more colon cancer-related genes in different stages. Gene expression profile E-GEOD-62932 was extracted for differentially expressed gene (DEG) screening. Series test of cluster analysis was used to obtain significant trending models. Based on the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases, functional and pathway enrichment analysis were processed and a pathway relation network was constructed. Gene co-expression network and gene signal network were constructed for common DEGs. The DEGs with the same trend were clustered and in total, 16 clusters with statistical significance were obtained. The screened DEGs were enriched into small molecule metabolic process and metabolic pathways. The pathway relation network was constructed with 57 nodes. A total of 328 common DEGs were obtained. Gene signal network was constructed with 71 nodes. Gene co-expression network was constructed with 161 nodes and 211 edges. ABCD3, CPT2, AGL and JAM2 are potential biomarkers for the diagnosis of colon cancer. PMID:29928385

Evaluating predictive modeling’s potential to improve teleretinal screening participation in urban safety net clinics

PubMed Central

Ogunyemi, Omolola; Teklehaimanot, Senait; Patty, Lauren; Moran, Erin; George, Sheba

2013-01-01

Introduction Screening guidelines for diabetic patients recommend yearly eye examinations to detect diabetic retinopathy and other forms of diabetic eye disease. However, annual screening rates for retinopathy in US urban safety net settings remain low. Methods Using data gathered from a study of teleretinal screening in six urban safety net clinics, we assessed whether predictive modeling could be of value in identifying patients at risk of developing retinopathy. We developed and examined the accuracy of two predictive modeling approaches for diabetic retinopathy in a sample of 513 diabetic individuals, using routinely available clinical variables from retrospective medical record reviews. Bayesian networks and radial basis function (neural) networks were learned using ten-fold cross-validation. Results The predictive models were modestly predictive with the best model having an AUC of 0.71. Discussion Using routinely available clinical variables to predict patients at risk of developing retinopathy and to target them for annual eye screenings may be of some usefulness to safety net clinics. PMID:23920536

Evaluating predictive modeling's potential to improve teleretinal screening participation in urban safety net clinics.

PubMed

Ogunyemi, Omolola; Teklehaimanot, Senait; Patty, Lauren; Moran, Erin; George, Sheba

2013-01-01

Screening guidelines for diabetic patients recommend yearly eye examinations to detect diabetic retinopathy and other forms of diabetic eye disease. However, annual screening rates for retinopathy in US urban safety net settings remain low. Using data gathered from a study of teleretinal screening in six urban safety net clinics, we assessed whether predictive modeling could be of value in identifying patients at risk of developing retinopathy. We developed and examined the accuracy of two predictive modeling approaches for diabetic retinopathy in a sample of 513 diabetic individuals, using routinely available clinical variables from retrospective medical record reviews. Bayesian networks and radial basis function (neural) networks were learned using ten-fold cross-validation. The predictive models were modestly predictive with the best model having an AUC of 0.71. Using routinely available clinical variables to predict patients at risk of developing retinopathy and to target them for annual eye screenings may be of some usefulness to safety net clinics.

The Use of Social Networking Websites as a Recruiting Tool for Employers

ERIC Educational Resources Information Center

Vicknair, Jamie; Elkersh, Dalia; Yancey, Katie; Budden, Michael C.

2010-01-01

The use of online social networking is a commonplace occurrence. A recent trend is for employers and recruiters to utilize social networking sites to screen candidates as part of the hiring process. This study examines student attitudes and awareness of these practices.

Computer-aided diagnosis workstation and network system for chest diagnosis based on multislice CT images

NASA Astrophysics Data System (ADS)

Satoh, Hitoshi; Niki, Noboru; Mori, Kiyoshi; Eguchi, Kenji; Kaneko, Masahiro; Kakinuma, Ryutarou; Moriyama, Noriyuki; Ohmatsu, Hironobu; Masuda, Hideo; Machida, Suguru

2007-03-01

Multislice CT scanner advanced remarkably at the speed at which the chest CT images were acquired for mass screening. Mass screening based on multislice CT images requires a considerable number of images to be read. It is this time-consuming step that makes the use of helical CT for mass screening impractical at present. To overcome this problem, we have provided diagnostic assistance methods to medical screening specialists by developing a lung cancer screening algorithm that automatically detects suspected lung cancers in helical CT images and a coronary artery calcification screening algorithm that automatically detects suspected coronary artery calcification. Moreover, we have provided diagnostic assistance methods to medical screening specialists by using a lung cancer screening algorithm built into mobile helical CT scanner for the lung cancer mass screening done in the region without the hospital. We also have developed electronic medical recording system and prototype internet system for the community health in two or more regions by using the Virtual Private Network router and Biometric fingerprint authentication system and Biometric face authentication system for safety of medical information. Based on these diagnostic assistance methods, we have now developed a new computer-aided workstation and database that can display suspected lesions three-dimensionally in a short time. This paper describes basic studies that have been conducted to evaluate this new system.

Road screening and distribution route multi-objective robust optimization for hazardous materials based on neural network and genetic algorithm.

PubMed

Ma, Changxi; Hao, Wei; Pan, Fuquan; Xiang, Wang

2018-01-01

Route optimization of hazardous materials transportation is one of the basic steps in ensuring the safety of hazardous materials transportation. The optimization scheme may be a security risk if road screening is not completed before the distribution route is optimized. For road screening issues of hazardous materials transportation, a road screening algorithm of hazardous materials transportation is built based on genetic algorithm and Levenberg-Marquardt neural network (GA-LM-NN) by analyzing 15 attributes data of each road network section. A multi-objective robust optimization model with adjustable robustness is constructed for the hazardous materials transportation problem of single distribution center to minimize transportation risk and time. A multi-objective genetic algorithm is designed to solve the problem according to the characteristics of the model. The algorithm uses an improved strategy to complete the selection operation, applies partial matching cross shift and single ortho swap methods to complete the crossover and mutation operation, and employs an exclusive method to construct Pareto optimal solutions. Studies show that the sets of hazardous materials transportation road can be found quickly through the proposed road screening algorithm based on GA-LM-NN, whereas the distribution route Pareto solutions with different levels of robustness can be found rapidly through the proposed multi-objective robust optimization model and algorithm.

A Community Capacity-Enhancement Approach to Breast and Cervical Cancer Screening among Older Women of Color

ERIC Educational Resources Information Center

Bullock, Karen; McGraw, Sarah A.

2006-01-01

In the Screening Older Minority Women project, the authors applied a community capacity-enhancement approach to promoting breast and cervical cancer screening among older women of color. Members of informal support networks were recruited for this health promotion intervention to empower Latina and African American women to engage in positive…

Protein-protein interaction network of gene expression in the hydrocortisone-treated keloid.

PubMed

Chen, Rui; Zhang, Zhiliang; Xue, Zhujia; Wang, Lin; Fu, Mingang; Lu, Yi; Bai, Ling; Zhang, Ping; Fan, Zhihong

2015-01-01

In order to explore the molecular mechanism of hydrocortisone in keloid tissue, the gene expression profiles of keloid samples treated with hydrocortisone were subjected to bioinformatics analysis. Firstly, the gene expression profiles (GSE7890) of five samples of keloid treated with hydrocortisone and five untreated keloid samples were downloaded from the Gene Expression Omnibus (GEO) database. Secondly, data were preprocessed using packages in R language and differentially expressed genes (DEGs) were screened using a significance analysis of microarrays (SAM) protocol. Thirdly, the DEGs were subjected to gene ontology (GO) function and KEGG pathway enrichment analysis. Finally, the interactions of DEGs in samples of keloid treated with hydrocortisone were explored in a human protein-protein interaction (PPI) network, and sub-modules of the DEGs interaction network were analyzed using Cytoscape software. Based on the analysis, 572 DEGs in the hydrocortisone-treated samples were screened; most of these were involved in the signal transduction and cell cycle. Furthermore, three critical genes in the module, including COL1A1, NID1, and PRELP, were screened in the PPI network analysis. These findings enhance understanding of the pathogenesis of the keloid and provide references for keloid therapy. © 2015 The International Society of Dermatology.

A network pharmacology-integrated metabolomics strategy for clarifying the difference between effective compounds of raw and processed Farfarae flos by ultra high-performance liquid chromatography-quadrupole-time of flight mass spectrometry.

PubMed

Ding, Mingya; Li, Zhen; Yu, Xie-An; Zhang, Dong; Li, Jin; Wang, Hui; He, Jun; Gao, Xiu-Mei; Chang, Yan-Xu

2018-07-15

This study aimed to clarify the difference between the effective compounds of raw and processed Farfarae flos using a network pharmacology-integrated metabolomics strategy. First, metabolomics data were obtained by ultra high-performance liquid chromatography-quadrupole-time of flight mass spectrometry (UHPLC-Q-TOF/MS). Then, metabolomics analysis was developed to screen for the influential compounds that were different between raw and processed Farfarae flos. Finally, a network pharmacology approach was applied to verify the activity of the screened compounds. As a result, 4 compounds (chlorogenic acid, caffeic acid, rutin and isoquercitrin) were successfully screened, identified, quantified and verified as the most influential effective compounds. They may synergistically inhibit the p38, JNK and ERK-mediated pathways, which would induce the inhibition of the expression of the IFA virus. The results revealed that the proposed network pharmacology-integrated metabolomics strategy was a powerful tool for discovering the effective compounds that were responsible for the difference between raw and processed Chinese herbs. Copyright © 2018 Elsevier B.V. All rights reserved.

The importance of older family members in providing social resources and promoting cancer screening in families with a hereditary cancer syndrome.

PubMed

Ashida, Sato; Hadley, Donald W; Goergen, Andrea F; Skapinsky, Kaley F; Devlin, Hillary C; Koehly, Laura M

2011-12-01

This study evaluates the role of older family members as providers of social resources within familial network systems affected by an inherited cancer susceptibility syndrome.  Respondents who previously participated in a study that involved genetic counseling and testing for Lynch syndrome and their family network members were invited to participate in a onetime telephone interview about family communication. A total of 206 respondents from 33 families identified 2,051 social relationships (dyads). Nineteen percent of the respondents and 25% of the network members were older (≥60 years). Younger respondents (≤59 years) were more likely to nominate older network members as providers of social resources than younger members: instrumental support (odds ratio [OR] = 1.68), emotional support (OR = 1.71), help in crisis situation (OR = 2.04), and dependability when needed (OR = 2.15). Compared with younger network members, older members were more likely to be listed as encouragers of colon cancer screening by both younger (OR = 3.40) and older respondents (OR = 1.90) independent of whether support exchange occurred in the relationship. Engaging older network members in health interventions to facilitate screening behaviors and emotional well-being of younger members within families affected by inherited conditions may be beneficial. Findings can be used to empower older individuals about their important social roles in enhancing the well-being of their family members and to inform younger individuals about their older relatives' resourcefulness to facilitate positive social interactions.

Localizing Global Medicine: Challenges and Opportunities in Cervical Screening in an Indigenous Community in Ecuador.

PubMed

Nugus, Peter; Désalliers, Julie; Morales, Juana; Graves, Lisa; Evans, Andrea; Macaulay, Ann C

2018-04-01

This participatory research study examines the tensions and opportunities in accessing allopathic medicine, or biomedicine, in the context of a cervical cancer screening program in a rural indigenous community of Northern Ecuador. Focusing on the influence of social networks, the article extends research on "re-appropriation" of biomedicine. It does so by recognizing two competing tensions expressed through social interactions: suspicion of allopathic medicine and the desire to maximize one's health. Semistructured individual interviews and focus groups were conducted with 28 women who had previously participated in a government-sponsored cervical screening program. From inductive thematic analysis, the article traces these women's active agency in navigating coherent paths of health. Despite drawing on social networks to overcome formidable challenges, the participants faced enduring system obstacles-the organizational effects of the networks of allopathic medicine. Such obstacles need to be understood to reconcile competing knowledge systems and improve health care access in underresourced communities.

Interdisciplinary Care in Disorders/Differences of Sex Development (DSD): The Psychosocial Component of the DSD – Translational Research Network

PubMed Central

Sandberg, David E.; Gardner, Melissa; Callens, Nina; Mazur, Tom

2017-01-01

Scientific discovery and clinical management strategies for Disorders/Differences of Sex Development (DSD) have advanced in recent years. The 2006 Consensus Statement on Management of Intersex Disorders stated that a mental health component to care is integral to promote positive adaptation, yet the parameters of this element have not been described. The objective of this paper is three-fold: to describe the psychosocial screening protocol adopted by the clinical centers of the DSD-Translational Research Network; to summarize psychosocial data collected at one of the 10 network sites; and to suggest how systematic behavioral health screenings can be employed to tailor care in DSD that results in better health and quality of life outcomes. Steps taken in developing the largely “noncategorical” screening protocol are described. These preliminary findings suggest that DSD, as one category of pediatric chronic conditions, is not associated with marked disturbances of psychosocial adaptation, either for the family or the child; however, screening frequently uncovered “risk factors” for individual families or patients that can potentially be addressed in the context of ongoing clinical care. Administration of the DSD-TRN psychosocial screening protocol was demonstrated to be feasible in the context of interdisciplinary team care and was acceptable to families on a longitudinal basis. The ultimate value of systematic screening will be demonstrated through a tailoring of psychosocial, medical and surgical services, based on this information that enhances the quality of patient and family-centered care and subsequent outcomes. PMID:28574671

Health IT-assisted population-based preventive cancer screening: a cost analysis.

PubMed

Levy, Douglas E; Munshi, Vidit N; Ashburner, Jeffrey M; Zai, Adrian H; Grant, Richard W; Atlas, Steven J

2015-12-01

Novel health information technology (IT)-based strategies harnessing patient registry data seek to improve care at a population level. We analyzed costs from a randomized trial of 2 health IT strategies to improve cancer screening compared with usual care from the perspective of a primary care network. Monte Carlo simulations were used to compare costs across management strategies. We assessed the cost of the software, materials, and personnel for baseline usual care (BUC) compared with augmented usual care (AUC [ie, automated patient outreach]) and augmented usual care with physician input (AUCPI [ie, outreach mediated by physicians' knowledge of their patient panels]) over 1 year. AUC and AUCPI each reduced the time physicians spent on cancer screening by 6.5 minutes per half-day clinical session compared with BUC without changing cancer screening rates. Assuming the value of this time accrues to the network, total costs of cancer screening efforts over the study year were $3.83 million for AUC, $3.88 million for AUCPI, and $4.10 million for BUC. AUC was cost-saving relative to BUC in 87.1% of simulations. AUCPI was cost-saving relative to BUC in 82.5% of simulations. Ongoing per patient costs were lower for both AUC ($35.63) and AUCPI ($35.58) relative to BUC ($39.51). Over the course of the study year, the value of reduced physician time devoted to preventive cancer screening outweighed the costs of the interventions. Primary care networks considering similar interventions will need to capture adequate physician time savings to offset the costs of expanding IT infrastructure.

Inference of RhoGAP/GTPase regulation using single-cell morphological data from a combinatorial RNAi screen.

PubMed

Nir, Oaz; Bakal, Chris; Perrimon, Norbert; Berger, Bonnie

2010-03-01

Biological networks are highly complex systems, consisting largely of enzymes that act as molecular switches to activate/inhibit downstream targets via post-translational modification. Computational techniques have been developed to perform signaling network inference using some high-throughput data sources, such as those generated from transcriptional and proteomic studies, but comparable methods have not been developed to use high-content morphological data, which are emerging principally from large-scale RNAi screens, to these ends. Here, we describe a systematic computational framework based on a classification model for identifying genetic interactions using high-dimensional single-cell morphological data from genetic screens, apply it to RhoGAP/GTPase regulation in Drosophila, and evaluate its efficacy. Augmented by knowledge of the basic structure of RhoGAP/GTPase signaling, namely, that GAPs act directly upstream of GTPases, we apply our framework for identifying genetic interactions to predict signaling relationships between these proteins. We find that our method makes mediocre predictions using only RhoGAP single-knockdown morphological data, yet achieves vastly improved accuracy by including original data from a double-knockdown RhoGAP genetic screen, which likely reflects the redundant network structure of RhoGAP/GTPase signaling. We consider other possible methods for inference and show that our primary model outperforms the alternatives. This work demonstrates the fundamental fact that high-throughput morphological data can be used in a systematic, successful fashion to identify genetic interactions and, using additional elementary knowledge of network structure, to infer signaling relations.

Polymer-Based Dense Fluidic Networks for High Throughput Screening with Ultrasensitive Fluorescence Detection

PubMed Central

Okagbare, Paul I.; Soper, Steven A.

2011-01-01

Microfluidics represents a viable platform for performing High Throughput Screening (HTS) due to its ability to automate fluid handling and generate fluidic networks with high number densities over small footprints appropriate for the simultaneous optical interrogation of many screening assays. While most HTS campaigns depend on fluorescence, readers typically use point detection and serially address the assay results significantly lowering throughput or detection sensitivity due to a low duty cycle. To address this challenge, we present here the fabrication of a high density microfluidic network packed into the imaging area of a large field-of-view (FoV) ultrasensitive fluorescence detection system. The fluidic channels were 1, 5 or 10 μm (width), 1 μm (depth) with a pitch of 1–10 μm and each fluidic processor was individually addressable. The fluidic chip was produced from a molding tool using hot embossing and thermal fusion bonding to enclose the fluidic channels. A 40X microscope objective (numerical aperture = 0.75) created a FoV of 200 μm, providing the ability to interrogate ~25 channels using the current fluidic configuration. An ultrasensitive fluorescence detection system with a large FoV was used to transduce fluorescence signals simultaneously from each fluidic processor onto the active area of an electron multiplying charge-coupled device (EMCCD). The utility of these multichannel networks for HTS was demonstrated by carrying out the high throughput monitoring of the activity of an enzyme, APE1, used as a model screening assay. PMID:20872611

Use of NCCN Guidelines, Other Guidelines, and Biomarkers for Colorectal Cancer Screening.

PubMed

Williams, Christina D; Grady, William M; Zullig, Leah L

2016-11-01

Colorectal cancer (CRC) remains a common cancer and significant public health burden. CRC-related mortality is declining, partly due to the early detection of CRC through robust screening. NCCN has established the NCCN Guidelines for CRC Screening to help healthcare providers make appropriate screening recommendations according to the patient's risk of developing CRC. This review describes the evolution of CRC screening guidelines for average-risk individuals, discusses the role of NCCN Guidelines for CRC Screening in cancer prevention, and comments on the current and emerging use of biomarkers for CRC screening. Copyright © 2016 by the National Comprehensive Cancer Network.

Building synthetic gene circuits from combinatorial libraries: screening and selection strategies.

PubMed

Schaerli, Yolanda; Isalan, Mark

2013-07-01

The promise of wide-ranging biotechnology applications inspires synthetic biologists to design novel genetic circuits. However, building such circuits rationally is still not straightforward and often involves painstaking trial-and-error. Mimicking the process of natural selection can help us to bridge the gap between our incomplete understanding of nature's design rules and our desire to build functional networks. By adopting the powerful method of directed evolution, which is usually applied to protein engineering, functional networks can be obtained through screening or selecting from randomised combinatorial libraries. This review first highlights the practical options to introduce combinatorial diversity into gene circuits and then examines strategies for identifying the potentially rare library members with desired functions, either by screening or selection.

Two level approach to safety planning incorporating the Highway Safety Manual (HSM) network screening.

DOT National Transportation Integrated Search

2014-04-01

Compared to microscopic safety studies, macroscopic-focused research is more efficient at integrating zonal-level features into crash prediction models and identifying hot zones. However, macroscopic screening has accuracy limitations. Thus, this stu...

Recommendations From the International Colorectal Cancer Screening Network on the Evaluation of the Cost of Screening Programs.

PubMed

Subramanian, Sujha; Tangka, Florence K L; Hoover, Sonja; Nadel, Marion; Smith, Robert; Atkin, Wendy; Patnick, Julietta

2016-01-01

Worldwide, colorectal cancer is the fourth leading cause of death from cancer and the incidence is projected to increase. Many countries are exploring the introduction of organized screening programs, but there is limited information on the resources required and guidance for cost-effective implementation. To facilitate the generating of the economics evidence base for program implementation, we collected and analyzed detailed program cost data from 5 European members of the International Colorectal Cancer Screening Network. The cost per person screened estimates, often used to compare across programs as an overall measure, varied significantly across the programs. In addition, there were substantial differences in the programmatic and clinical cost incurred, even when the same type of screening test was used. Based on these findings, several recommendations are provided to enhance the underlying methodology and validity of the comparative economic assessments. The recommendations include the need for detailed activity-based cost information, the use of a comprehensive set of effectiveness measures to adequately capture differences between programs, and the incorporation of data from multiple programs in cost-effectiveness models to increase generalizability. Economic evaluation of real-world colorectal cancer-screening programs is essential to derive valuable insights to improve program operations and ensure optimal use of available resources.

The Sheffield RNAi Screening Facility (SRSF): portfolio growth and technology development.

PubMed

Brown, Stephen

2014-05-01

The Sheffield RNAi Screening Facility (SRSF) (www.rnai.group.shef.ac.uk) was established in 2008 with Wellcome Trust and University of Sheffield funding, with the task to provide the first UK RNAi screening resource for academic groups interested in identifying genes required in a diverse range of biological processes using Drosophila cell culture. The SRSF has carried out a wide range of screens varying in sizes from bespoke small-scale libraries, targeting a few hundred genes, to high-throughput, genome-wide studies. The SRSF has grown and improved with a dedicated partnership of its academic customers based mainly in the UK. We are part of the UK Academics Functional Genomics Network, participating in organizing an annual meeting in London and are part of the University of Sheffield's D3N (www.d3n.org.uk), connecting academics, biotech and pharmaceutical companies with a multidisciplinary network in Drug Discovery and Development. Recently, the SRSF has been funded by the Yorkshire Cancer Research Fund to perform genome-wide RNAi screens using human cells as part of a core facility for regional Yorkshire Universities and screens are now underway. Overall the SRSF has carried out more than 40 screens from Drosophila and human cell culture experiments.

Computationally assisted screening and design of cell-interactive peptides by a cell-based assay using peptide arrays and a fuzzy neural network algorithm.

PubMed

Kaga, Chiaki; Okochi, Mina; Tomita, Yasuyuki; Kato, Ryuji; Honda, Hiroyuki

2008-03-01

We developed a method of effective peptide screening that combines experiments and computational analysis. The method is based on the concept that screening efficiency can be enhanced from even limited data by use of a model derived from computational analysis that serves as a guide to screening and combining the model with subsequent repeated experiments. Here we focus on cell-adhesion peptides as a model application of this peptide-screening strategy. Cell-adhesion peptides were screened by use of a cell-based assay of a peptide array. Starting with the screening data obtained from a limited, random 5-mer library (643 sequences), a rule regarding structural characteristics of cell-adhesion peptides was extracted by fuzzy neural network (FNN) analysis. According to this rule, peptides with unfavored residues in certain positions that led to inefficient binding were eliminated from the random sequences. In the restricted, second random library (273 sequences), the yield of cell-adhesion peptides having an adhesion rate more than 1.5-fold to that of the basal array support was significantly high (31%) compared with the unrestricted random library (20%). In the restricted third library (50 sequences), the yield of cell-adhesion peptides increased to 84%. We conclude that a repeated cycle of experiments screening limited numbers of peptides can be assisted by the rule-extracting feature of FNN.

A function approximation approach to anomaly detection in propulsion system test data

NASA Technical Reports Server (NTRS)

Whitehead, Bruce A.; Hoyt, W. A.

1993-01-01

Ground test data from propulsion systems such as the Space Shuttle Main Engine (SSME) can be automatically screened for anomalies by a neural network. The neural network screens data after being trained with nominal data only. Given the values of 14 measurements reflecting external influences on the SSME at a given time, the neural network predicts the expected nominal value of a desired engine parameter at that time. We compared the ability of three different function-approximation techniques to perform this nominal value prediction: a novel neural network architecture based on Gaussian bar basis functions, a conventional back propagation neural network, and linear regression. These three techniques were tested with real data from six SSME ground tests containing two anomalies. The basis function network trained more rapidly than back propagation. It yielded nominal predictions with, a tight enough confidence interval to distinguish anomalous deviations from the nominal fluctuations in an engine parameter. Since the function-approximation approach requires nominal training data only, it is capable of detecting unknown classes of anomalies for which training data is not available.

Segmentation of dermoscopy images using wavelet networks.

PubMed

Sadri, Amir Reza; Zekri, Maryam; Sadri, Saeed; Gheissari, Niloofar; Mokhtari, Mojgan; Kolahdouzan, Farzaneh

2013-04-01

This paper introduces a new approach for the segmentation of skin lesions in dermoscopic images based on wavelet network (WN). The WN presented here is a member of fixed-grid WNs that is formed with no need of training. In this WN, after formation of wavelet lattice, determining shift and scale parameters of wavelets with two screening stage and selecting effective wavelets, orthogonal least squares algorithm is used to calculate the network weights and to optimize the network structure. The existence of two stages of screening increases globality of the wavelet lattice and provides a better estimation of the function especially for larger scales. R, G, and B values of a dermoscopy image are considered as the network inputs and the network structure formation. Then, the image is segmented and the skin lesions exact boundary is determined accordingly. The segmentation algorithm were applied to 30 dermoscopic images and evaluated with 11 different metrics, using the segmentation result obtained by a skilled pathologist as the ground truth. Experimental results show that our method acts more effectively in comparison with some modern techniques that have been successfully used in many medical imaging problems.

Non-attendance in mammography screening and women's social network: a cohort study on the influence of family composition, social support, attitudes and cancer in close relations.

PubMed

Manjer, Åsa Ritenius; Emilsson, Ulla Melin; Zackrisson, Sophia

2015-06-28

Mammography screening can reduce breast cancer mortality. The aim of the present study was to investigate non-attendance in mammography screening in relation to different aspects of a women's social network, attitudes and cancer in close relations. Data from the Malmö Diet and Cancer Study baseline examination in 1991-1996 was used. A re-examination began in 2007, and 1452 women participated. Family composition, social support, sense of belonging, attitudes on screening and breast cancer risk and on previous cancer in close relations were investigated in relation to self-reported participation in mammography screening using logistic regression analysis, yielding odds ratios with 95 % confidence intervals. Both attendees (98.0 %) and non-attendees (95.2 %) considered mammography screening important. Non-attendance in mammography screening was associated with being unmarried vs. married (2.40:1.30-4.45) and with not having vs. having children (1.77:1.08-2.92). Non-attendees planned to abstain from mammography screening in the future more often than attendees (4.78:2.56-8.90), and they had often abstained from cervical cancer screening (1.69:1.04-2.75). No other statistically significant association was found. This study indicates that family composition, but not necessarily the presence or absence of social support, perceived cancer risk or cancer in close relations, may affect non-attendance in mammography screening. A positive attitude towards mammography screening was found among both attendees and non-attendees, although the latter group planned to a lesser degree to attend mammography screening in the future.

Variation in detection of ductal carcinoma in situ (DCIS) during screening mammography A survey within the International Cancer Screening Network (ICSN)

PubMed Central

Lynge, Elsebeth; Ponti, Antonio; James, Ted; Májek, Ondřej; von Euler-Chelpin, My; Anttila, Ahti; Fitzpatrick, Patricia; Frigerio, Alfonso; Kawai, Masaaki; Scharpantgen, Astrid; Broeders, Mireille; Hofvind, Solveig; Vidal, Carmen; Ederra, Maria; Salas, Dolores; Bulliard, Jean-Luc; Tomatis, Mariano; Kerlikowske, Karla; Taplin, Stephen

2013-01-01

Background There is concern about detection of Ductal Carcinoma in Situ (DCIS) in screening mammography. DCIS accounts for a substantial proportion of screen detected lesions but its effect on breast cancer mortality is debated. The International Cancer Screening Network conducted a comparative analysis to determine variation in DCIS detection. Patients and Methods Data were collected during 2004–2008 on number of screening examinations, detected breast cancers, DCIS cases, and Globocan 2008 breast cancer incidence rates derived from national or regional cancer registers. We calculated screen-detection rates for breast cancers and DCIS. Results Data were obtained from 15 screening settings in 12 countries; 7,176,050 screening examinations; 29,605 breast cancers; and 5,324 DCIS cases. The ratio between highest and lowest breast cancer incidence was 2.88 (95% confidence interval (CI) 2.76–3.00); 2.97 (95% CI 2.51–3.51) for detection of breast cancer; and 3.49 (95% CI 2.70–4.51) for detection of DCIS. Conclusions Considerable international variation was found in DCIS detection. This variation could not be fully explained by variation in incidence nor in breast cancer detection rates. It suggests the potential for wide discrepancies in management of DCIS resulting in overtreatment of indolent DCIS or undertreatment of potentially curable disease. Comprehensive cancer registration is needed to monitor DCIS detection. Efforts to understand discrepancies and standardize management may improve care. PMID:24041876

Dual gene activation and knockout screen reveals directional dependencies in genetic networks. | Office of Cancer Genomics

Cancer.gov

Understanding the direction of information flow is essential for characterizing how genetic networks affect phenotypes. However, methods to find genetic interactions largely fail to reveal directional dependencies. We combine two orthogonal Cas9 proteins from Streptococcus pyogenes and Staphylococcus aureus to carry out a dual screen in which one gene is activated while a second gene is deleted in the same cell. We analyze the quantitative effects of activation and knockout to calculate genetic interaction and directionality scores for each gene pair.

Social support and cancer screening among older black Americans.

PubMed

Kang, S H; Bloom, J R

1993-05-05

Age-adjusted cancer mortality is 27% higher for Black Americans than for the general U.S. population, which may result from inappropriate use of cancer detection tests. Social support has been shown to affect adjustment to breast cancer and survival, but it has not been studied as a predictor of use of preventive health care services in the older population. Our hypothesis is that larger social networks are associated with greater utilization of cancer-screening tests in the older population. The objective of this study was to examine the relationship between social support and use of cancer-screening tests among older Black Americans. Data for this study were obtained from a 1986 baseline survey evaluation of a community intervention program to increase cancer awareness and a 1991 end-point survey of use of cancer detection tests. Our study sample consisted of 617 Black Americans aged 55 years or older who lived in San Francisco (Calif.), the control community, and in Oakland (Calif.), the target community for intervention. The survey included measures of 1) social network characteristics, as determined by a modified version of Berkman and Syme's Social Network Index; 2) demographic characteristics; and 3) use of six cancer-screening tests--mammography, occult blood stool examination, cervical smear, clinical breast examination, digital rectal examination, and sigmoidoscopy. Multiple logistic regression analysis of the Social Network Index results indicated statistically significant positive associations of social support with the use of mammography and occult blood stool examination but not with the other cancer-screening tests. There were statistically significant associations between having HMO (Health Maintenance Organization) insurance and increased use of mammography and occult blood stool examination, compared with having Medi-Cal or other insurance. The interval between the surveys had a statistically significant positive association with use of mammography. These significant associations were not explained by differences in the other variables, which included health status, age, gender, education, type of health insurance, interval between the surveys, and a regular source of care. Social support seems to be associated with increased use of mammography and occult blood stool examinations among older Black Americans. Interventions designed to increase utilization of social networks may be an effective way to increase use of cancer screening, which may ultimately lead to reduced mortality from cancer.

Automatic classification of transiently evoked otoacoustic emissions using an artificial neural network.

PubMed

Buller, G; Lutman, M E

1998-08-01

The increasing use of transiently evoked otoacoustic emissions (TEOAE) in large neonatal hearing screening programmes makes a standardized method of response classification desirable. Until now methods have been either subjective or based on arbitrary response characteristics. This study takes an expert system approach to standardize the subjective judgements of an experienced scorer. The method that is developed comprises three stages. First, it transforms TEOAEs from waveforms in the time domain into a simplified parameter set. Second, the parameter set is classified by an artificial neural network that has been taught on a large database TEOAE waveforms and corresponding expert scores. Third, additional fuzzy logic rules automatically detect probable artefacts in the waveforms and synchronized spontaneous emission components. In this way, the knowledge of the experienced scorer is encapsulated in the expert system software and thereafter can be accessed by non-experts. Teaching and evaluation of the neural network was based on TEOAEs from a database totalling 2190 neonatal hearing screening tests. The database was divided into learning and test groups with 820 and 1370 waveforms respectively. From each recorded waveform a set of 12 parameters was calculated, representing signal static and dynamic properties. The artifical network was taught with parameter sets of only the learning groups. Reproduction of the human scorer classification by the neural net in the learning group showed a sensitivity for detecting screen fails of 99.3% (299 from 301 failed results on subjective scoring) and a specificity for detecting screen passes of 81.1% (421 of 519 pass results). To quantify the post hoc performance of the net (generalization), the test group was then presented to the network input. Sensitivity was 99.4% (474 from 477) and specificity was 87.3% (780 from 893). To check the efficiency of the classification method, a second learning group was selected out of the previous test group, and the previous learning group was used as the test group. Repeating learning and test procedures yielded 99.3% sensitivity and 80.7% specificity for reproduction, and 99.4% sensitivity and 86.7% specificity for generalization. In all respects, performance was better than for a previously optimized method based simply on cross-correlation between replicate non-linear waveforms. It is concluded that classification methods based on neural networks show promise for application to large neonatal screening programmes utilizing TEOAEs.

Cervical Cancer: paradigms at home and abroad

Cancer.gov

NCI funded a clinical trial that will have an impact on the treatment of late-stage cervical cancer, and also supported a screening trial in India using a network of community outreach workers offering low tech-screening by direct visualization of the cer

A new focus for the International Cancer Screening Network

Cancer.gov

The ICSN is thinking about how to take advantage of the nearly three decades of work in cancer screening program research and implementation and reach out more actively to low- and middle-income countries considering screening. For that purpose, ICSN is migrating from its historical place under NCI Division of Cancer Control and Population Sciences to assume its new role within the Center for Global Health.

Diverse microRNAs with convergent functions regulate tumorigenesis.

PubMed

Zhu, Min-Yan; Zhang, Wei; Yang, Tao

2016-02-01

MicroRNAs (miRNAs) regulate several biological processes, including tumorigenesis. In order to comprehend the roles of miRNAs in cancer, various screens were performed to investigate the changes in the expression levels of miRNAs that occur in different types of cancer. The present review focuses on the results of five recent screens, whereby a number of overlapping miRNAs were identified to be downregulated or differentially regulated, whereas no miRNAs were observed to be frequently upregulated. Furthermore, the majority of the miRNAs that were common to >1 screen were involved in signaling networks, including wingless-related integration site, receptor tyrosine kinase and transforming growth factor-β, or in cell cycle checkpoint control. The present review will discuss the aforementioned miRNAs implicated in cell cycle checkpoint control and signaling networks.

Acceptability of reminder letters for Papanicolaou tests: a survey of women from 23 Family Health Networks in Ontario.

PubMed

Karwalajtys, Tina; Kaczorowski, Janusz; Lohfeld, Lynne; Laryea, Stephanie; Anderson, Kelly; Roder, Stefanie; Sebaldt, Rolf J

2007-10-01

To explore women's perspectives on the acceptability and content of reminder letters from the family physician for Papanicolaou (Pap) test screening and the effect of reminder letters on compliance with screening recommendations. A population-based survey was conducted in 23 Family Health Networks and Primary Care Networks participating in a demonstration project to increase the delivery of preventive services in Ontario. Questionnaires were mailed to randomly selected women aged 35 to 69 years who had received a reminder letter for a Pap test from their family physician within the previous six months. Two focus groups were conducted with a volunteer sample of respondents. The usable response rate was 54.3% (406/748). Two-thirds (65.8%, 267/406) of women who completed the survey recalled receiving the reminder letter. Overall, 52.3% (212/405) reported having a Pap test in the past six months. Among women who recalled the reminder letter and scheduled or had a Pap test, 71.4% (125/175) reported that the letter influenced their decision to be screened. The majority of respondents (80.8%, 328/406) wanted to continue to receive reminder letters for Pap tests from their physician, and 34.5% (140/406) wanted to receive additional information about cervical screening. Focus group interviews indicated that women who have had a Pap test may still be unsure about screening recommendations, what the test detects, and the rationale for follow-up procedures. Reminder letters in family practice were viewed as useful and influenced women's decisions to undergo Pap test screening. Women who have had a Pap test may still need additional information about the test.

GABA-A receptor antagonists increase firing, bursting and synchrony of spontaneous activity in neuronal networks grown on microelectrode arrays: a step towards chemical "fingerprinting"

EPA Science Inventory

Assessment of effects on spontaneous network activity in neurons grown on MEAs is a proposed method to screen chemicals for potential neurotoxicity. In addition, differential effects on network activity (chemical "fingerprints") could be used to classify chemical modes of action....

Protein interaction network topology uncovers melanogenesis regulatory network components within functional genomics datasets.

PubMed

Ho, Hsiang; Milenković, Tijana; Memisević, Vesna; Aruri, Jayavani; Przulj, Natasa; Ganesan, Anand K

2010-06-15

RNA-mediated interference (RNAi)-based functional genomics is a systems-level approach to identify novel genes that control biological phenotypes. Existing computational approaches can identify individual genes from RNAi datasets that regulate a given biological process. However, currently available methods cannot identify which RNAi screen "hits" are novel components of well-characterized biological pathways known to regulate the interrogated phenotype. In this study, we describe a method to identify genes from RNAi datasets that are novel components of known biological pathways. We experimentally validate our approach in the context of a recently completed RNAi screen to identify novel regulators of melanogenesis. In this study, we utilize a PPI network topology-based approach to identify targets within our RNAi dataset that may be components of known melanogenesis regulatory pathways. Our computational approach identifies a set of screen targets that cluster topologically in a human PPI network with the known pigment regulator Endothelin receptor type B (EDNRB). Validation studies reveal that these genes impact pigment production and EDNRB signaling in pigmented melanoma cells (MNT-1) and normal melanocytes. We present an approach that identifies novel components of well-characterized biological pathways from functional genomics datasets that could not have been identified by existing statistical and computational approaches.

Protein interaction network topology uncovers melanogenesis regulatory network components within functional genomics datasets

PubMed Central

2010-01-01

Background RNA-mediated interference (RNAi)-based functional genomics is a systems-level approach to identify novel genes that control biological phenotypes. Existing computational approaches can identify individual genes from RNAi datasets that regulate a given biological process. However, currently available methods cannot identify which RNAi screen "hits" are novel components of well-characterized biological pathways known to regulate the interrogated phenotype. In this study, we describe a method to identify genes from RNAi datasets that are novel components of known biological pathways. We experimentally validate our approach in the context of a recently completed RNAi screen to identify novel regulators of melanogenesis. Results In this study, we utilize a PPI network topology-based approach to identify targets within our RNAi dataset that may be components of known melanogenesis regulatory pathways. Our computational approach identifies a set of screen targets that cluster topologically in a human PPI network with the known pigment regulator Endothelin receptor type B (EDNRB). Validation studies reveal that these genes impact pigment production and EDNRB signaling in pigmented melanoma cells (MNT-1) and normal melanocytes. Conclusions We present an approach that identifies novel components of well-characterized biological pathways from functional genomics datasets that could not have been identified by existing statistical and computational approaches. PMID:20550706

Optogenetic stimulation of multiwell MEA plates for neural and cardiac applications

NASA Astrophysics Data System (ADS)

Clements, Isaac P.; Millard, Daniel C.; Nicolini, Anthony M.; Preyer, Amanda J.; Grier, Robert; Heckerling, Andrew; Blum, Richard A.; Tyler, Phillip; McSweeney, K. M.; Lu, Yi-Fan; Hall, Diana; Ross, James D.

2016-03-01

Microelectrode array (MEA) technology enables advanced drug screening and "disease-in-a-dish" modeling by measuring the electrical activity of cultured networks of neural or cardiac cells. Recent developments in human stem cell technologies, advancements in genetic models, and regulatory initiatives for drug screening have increased the demand for MEA-based assays. In response, Axion Biosystems previously developed a multiwell MEA platform, providing up to 96 MEA culture wells arrayed into a standard microplate format. Multiwell MEA-based assays would be further enhanced by optogenetic stimulation, which enables selective excitation and inhibition of targeted cell types. This capability for selective control over cell culture states would allow finer pacing and probing of cell networks for more reliable and complete characterization of complex network dynamics. Here we describe a system for independent optogenetic stimulation of each well of a 48-well MEA plate. The system enables finely graded control of light delivery during simultaneous recording of network activity in each well. Using human induced pluripotent stem cell (hiPSC) derived cardiomyocytes and rodent primary neuronal cultures, we demonstrate high channel-count light-based excitation and suppression in several proof-of-concept experimental models. Our findings demonstrate advantages of combining multiwell optical stimulation and MEA recording for applications including cardiac safety screening, neural toxicity assessment, and advanced characterization of complex neuronal diseases.

Genetic Evaluation of Children with Global Developmental Delay--Current Status of Network Systems in Taiwan.

PubMed

Foo, Yong-Lin; Chow, Julie Chi; Lai, Ming-Chi; Tsai, Wen-Hui; Tung, Li-Chen; Kuo, Mei-Chin; Lin, Shio-Jean

2015-08-01

This review article aims to introduce the screening and referral network of genetic evaluation for children with developmental delay in Taiwan. For these children, integrated systems provide services from the medical, educational, and social welfare sectors. All cities and counties in Taiwan have established a network for screening, detection, referral, evaluation, and intervention services. Increased awareness improves early detection and intervention. There remains a gap between supply and demand, especially with regard to financial resources and professional manpower. Genetic etiology has a major role in prenatal causes of developmental delay. A summary of reports on some related genetic disorders in the Taiwanese population is included in this review. Genetic diagnosis allows counseling with regard to recurrence risk and prevention. Networking with neonatal screening, laboratory diagnosis, genetic counseling, and orphan drugs logistics systems can provide effective treatment for patients. In Taiwan, several laboratories provide genetic tests for clinical diagnosis. Accessibility to advanced expensive tests such as gene chips or whole exome sequencing is limited because of funding problems; however, the service system in Taiwan can still operate in a relatively cost-effective manner. This experience in Taiwan may serve as a reference for other countries. Copyright © 2014. Published by Elsevier B.V.

Improving maternal care with a continuous quality improvement strategy: a report from the Interventions to Minimize Preterm and Low Birth Weight Infants through Continuous Improvement Techniques (IMPLICIT) Network.

PubMed

Bennett, Ian M; Coco, Andrew; Anderson, Janice; Horst, Michael; Gambler, Angela S; Barr, Wendy Brooks; Ratcliffe, Stephen

2009-01-01

Maternal medical care (prenatal and postpartum) involves a set of clinical interventions addressing risk factors associated with important maternal and infant outcomes. Programs to increase the rate of delivery of these interventions in clinical practice have not been widely implemented. A practice-based research network focused on developing continuous quality improvement (CQI) processes for maternal care among 10 family medicine residency training sites in the northeastern United States (the IMPLICIT Network) from January 2003 through September 2007. Documented delivery of 5 standard maternal care interventions was assessed before and after initiating a program to increase their frequency. Proportion chart analyses were conducted comparing the period before and after implementation of the CQI interventions. Data were available for 3936 pregnancies during the course of the study period. Results varied across the clinical interventions. Significant improvement in care processes was seen for 3 screening activities: (1) prenatal depression symptomatology (by 15 weeks' gestation); (2) screening for smoking at 30 weeks' gestation; (3) and postpartum contraception planning. Screening for smoking by 15 weeks' gestation and testing for asymptomatic bacteriuria were already conducted >90% of the time during the baseline period and did not increase significantly after initiating the CQI program. Screening for postpartum depression symptomatology was recorded in 50% to 60% of women before the CQI program and did not increase significantly. A practice-based research network of family medicine residency practices focused on CQI outcomes was successful in increasing the delivery of some maternal care interventions.

Why hasn't this patient been screened for colon cancer? An Iowa Research Network study.

PubMed

Levy, Barcey T; Nordin, Terri; Sinift, Suzanne; Rosenbaum, Marcy; James, Paul A

2007-01-01

Less than half of eligible Americans have been screened for colorectal cancer (CRC). The objective of this study was to describe physicians' reasons for screening or not screening specific patients for CRC and their approach to CRC testing discussions. This study used mixed-methods. Physicians described their reasons for screening or not screening 6 randomly chosen patients who were eligible for CRC screening (3 screened and 3 not screened) whose CRC testing status was ascertained by medical record review. Verbatim transcripts from physicians responding to structured interview questions were used to identify themes. Specific elements of discussion were examined for their association with each physician's screening rate. Fifteen randomly chosen Iowa family physicians from the Iowa Research Network stratified by privileges to perform colonoscopy, flexible sigmoidoscopy, or neither procedure dictated the reasons why 43 patients were screened and 40 patients were not screened. Reasons patients were not up to date fell into 2 major categories: (1) no discussion by physician (50%) and (2) patient refusal (43%). Reasons for no discussion included lack of opportunity, assessment that cost would be prohibitive, distraction by other life issues/health problems, physician forgetfulness, and expected patient refusal. Patients declined because of cost, lack of interest, autonomy, other life issues, fear of screening, and lack of symptoms. Patients who were up to date received (1) diagnostic testing (for previous colon pathology or symptoms; 56%) or (2) asymptomatic screening (44%). Physicians who were more adamant about screening had higher screening rates (P<.05; Wilcoxon rank sum). Physicians framed their recommendations differently ("I recommend" vs "They recommend"), with lower screening rates among physicians who used "they recommend" (P=.05; Wilcoxon rank sum). Reasons many patients remain unscreened for CRC include (1) factors related to the health care system, patient, and physician that impede or prevent discussion; (2) patient refusal; and (3) the focus on diagnostic testing. Strategies to improve screening might include patient and physician education about the rationale for screening, universal coverage for health maintenance exams, and development of effective tracking and reminder systems. The words physicians choose to frame their recommendations are important and should be explored further.

Reconstruction of the metabolic network of Pseudomonas aeruginosa to interrogate virulence factor synthesis

NASA Astrophysics Data System (ADS)

Bartell, Jennifer A.; Blazier, Anna S.; Yen, Phillip; Thøgersen, Juliane C.; Jelsbak, Lars; Goldberg, Joanna B.; Papin, Jason A.

2017-03-01

Virulence-linked pathways in opportunistic pathogens are putative therapeutic targets that may be associated with less potential for resistance than targets in growth-essential pathways. However, efficacy of virulence-linked targets may be affected by the contribution of virulence-related genes to metabolism. We evaluate the complex interrelationships between growth and virulence-linked pathways using a genome-scale metabolic network reconstruction of Pseudomonas aeruginosa strain PA14 and an updated, expanded reconstruction of P. aeruginosa strain PAO1. The PA14 reconstruction accounts for the activity of 112 virulence-linked genes and virulence factor synthesis pathways that produce 17 unique compounds. We integrate eight published genome-scale mutant screens to validate gene essentiality predictions in rich media, contextualize intra-screen discrepancies and evaluate virulence-linked gene distribution across essentiality datasets. Computational screening further elucidates interconnectivity between inhibition of virulence factor synthesis and growth. Successful validation of selected gene perturbations using PA14 transposon mutants demonstrates the utility of model-driven screening of therapeutic targets.

Interrogation of Mammalian Protein Complex Structure, Function, and Membership Using Genome-Scale Fitness Screens.

PubMed

Pan, Joshua; Meyers, Robin M; Michel, Brittany C; Mashtalir, Nazar; Sizemore, Ann E; Wells, Jonathan N; Cassel, Seth H; Vazquez, Francisca; Weir, Barbara A; Hahn, William C; Marsh, Joseph A; Tsherniak, Aviad; Kadoch, Cigall

2018-05-23

Protein complexes are assemblies of subunits that have co-evolved to execute one or many coordinated functions in the cellular environment. Functional annotation of mammalian protein complexes is critical to understanding biological processes, as well as disease mechanisms. Here, we used genetic co-essentiality derived from genome-scale RNAi- and CRISPR-Cas9-based fitness screens performed across hundreds of human cancer cell lines to assign measures of functional similarity. From these measures, we systematically built and characterized functional similarity networks that recapitulate known structural and functional features of well-studied protein complexes and resolve novel functional modules within complexes lacking structural resolution, such as the mammalian SWI/SNF complex. Finally, by integrating functional networks with large protein-protein interaction networks, we discovered novel protein complexes involving recently evolved genes of unknown function. Taken together, these findings demonstrate the utility of genetic perturbation screens alone, and in combination with large-scale biophysical data, to enhance our understanding of mammalian protein complexes in normal and disease states. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Deep neural networks for direct, featureless learning through observation: The case of two-dimensional spin models

NASA Astrophysics Data System (ADS)

Mills, Kyle; Tamblyn, Isaac

2018-03-01

We demonstrate the capability of a convolutional deep neural network in predicting the nearest-neighbor energy of the 4 ×4 Ising model. Using its success at this task, we motivate the study of the larger 8 ×8 Ising model, showing that the deep neural network can learn the nearest-neighbor Ising Hamiltonian after only seeing a vanishingly small fraction of configuration space. Additionally, we show that the neural network has learned both the energy and magnetization operators with sufficient accuracy to replicate the low-temperature Ising phase transition. We then demonstrate the ability of the neural network to learn other spin models, teaching the convolutional deep neural network to accurately predict the long-range interaction of a screened Coulomb Hamiltonian, a sinusoidally attenuated screened Coulomb Hamiltonian, and a modified Potts model Hamiltonian. In the case of the long-range interaction, we demonstrate the ability of the neural network to recover the phase transition with equivalent accuracy to the numerically exact method. Furthermore, in the case of the long-range interaction, the benefits of the neural network become apparent; it is able to make predictions with a high degree of accuracy, and do so 1600 times faster than a CUDA-optimized exact calculation. Additionally, we demonstrate how the neural network succeeds at these tasks by looking at the weights learned in a simplified demonstration.

Investigation of candidate genes for osteoarthritis based on gene expression profiles.

PubMed

Dong, Shuanghai; Xia, Tian; Wang, Lei; Zhao, Qinghua; Tian, Jiwei

2016-12-01

To explore the mechanism of osteoarthritis (OA) and provide valid biological information for further investigation. Gene expression profile of GSE46750 was downloaded from Gene Expression Omnibus database. The Linear Models for Microarray Data (limma) package (Bioconductor project, http://www.bioconductor.org/packages/release/bioc/html/limma.html) was used to identify differentially expressed genes (DEGs) in inflamed OA samples. Gene Ontology function enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enrichment analysis of DEGs were performed based on Database for Annotation, Visualization and Integrated Discovery data, and protein-protein interaction (PPI) network was constructed based on the Search Tool for the Retrieval of Interacting Genes/Proteins database. Regulatory network was screened based on Encyclopedia of DNA Elements. Molecular Complex Detection was used for sub-network screening. Two sub-networks with highest node degree were integrated with transcriptional regulatory network and KEGG functional enrichment analysis was processed for 2 modules. In total, 401 up- and 196 down-regulated DEGs were obtained. Up-regulated DEGs were involved in inflammatory response, while down-regulated DEGs were involved in cell cycle. PPI network with 2392 protein interactions was constructed. Moreover, 10 genes including Interleukin 6 (IL6) and Aurora B kinase (AURKB) were found to be outstanding in PPI network. There are 214 up- and 8 down-regulated transcription factor (TF)-target pairs in the TF regulatory network. Module 1 had TFs including SPI1, PRDM1, and FOS, while module 2 contained FOSL1. The nodes in module 1 were enriched in chemokine signaling pathway, while the nodes in module 2 were mainly enriched in cell cycle. The screened DEGs including IL6, AGT, and AURKB might be potential biomarkers for gene therapy for OA by being regulated by TFs such as FOS and SPI1, and participating in the cell cycle and cytokine-cytokine receptor interaction pathway. Copyright © 2016 Turkish Association of Orthopaedics and Traumatology. Production and hosting by Elsevier B.V. All rights reserved.

Computer-aided diagnosis workstation and database system for chest diagnosis based on multi-helical CT images

NASA Astrophysics Data System (ADS)

Satoh, Hitoshi; Niki, Noboru; Mori, Kiyoshi; Eguchi, Kenji; Kaneko, Masahiro; Kakinuma, Ryutarou; Moriyama, Noriyuki; Ohmatsu, Hironobu; Masuda, Hideo; Machida, Suguru; Sasagawa, Michizou

2006-03-01

Multi-helical CT scanner advanced remarkably at the speed at which the chest CT images were acquired for mass screening. Mass screening based on multi-helical CT images requires a considerable number of images to be read. It is this time-consuming step that makes the use of helical CT for mass screening impractical at present. To overcome this problem, we have provided diagnostic assistance methods to medical screening specialists by developing a lung cancer screening algorithm that automatically detects suspected lung cancers in helical CT images and a coronary artery calcification screening algorithm that automatically detects suspected coronary artery calcification. We also have developed electronic medical recording system and prototype internet system for the community health in two or more regions by using the Virtual Private Network router and Biometric fingerprint authentication system and Biometric face authentication system for safety of medical information. Based on these diagnostic assistance methods, we have now developed a new computer-aided workstation and database that can display suspected lesions three-dimensionally in a short time. This paper describes basic studies that have been conducted to evaluate this new system. The results of this study indicate that our computer-aided diagnosis workstation and network system can increase diagnostic speed, diagnostic accuracy and safety of medical information.

From Cancer Screening to Treatment: Service Delivery and Referral in the National Breast and Cervical Cancer Early Detection Program

PubMed Central

Miller, Jacqueline W.; Hanson, Vivien; Johnson, Gale D.; Royalty, Janet E.; Richardson, Lisa C.

2015-01-01

The National Breast and Cervical Cancer Early Detection Program (NBCCEDP) provides breast and cervical cancer screening and diagnostic services to low-income and underserved women through a network of providers and health care organizations. Although the program serves women 40-64 years old for breast cancer screening and 21-64 years old for cervical cancer screening, the priority populations are women 50-64 years old for breast cancer and women who have never or rarely been screened for cervical cancer. From 1991 through 2011, the NBCCEDP provided screening and diagnostic services to more than 4.3 million women, diagnosing 54,276 breast cancers, 2554 cervical cancers, and 123,563 precancerous cervical lesions. A critical component of providing screening services is to ensure that all women with abnormal screening results receive appropriate and timely diagnostic evaluations. Case management is provided to assist women with overcoming barriers that would delay or prevent follow-up care. Women diagnosed with cancer receive treatment through the states' Breast and Cervical Cancer Treatment Programs (a special waiver for Medicaid) if they are eligible. The NBCCEDP has performance measures that serve as benchmarks to monitor the completeness and timeliness of care. More than 90% of the women receive complete diagnostic care and initiate treatment less than 30 days from the time of their diagnosis. Provision of effective screening and diagnostic services depends on effective program management, networks of providers throughout the community, and the use of evidence-based knowledge, procedures, and technologies. PMID:25099897

IN VITRO ASSESSMENT OF DEVELOPMENTAL NEUROTOXICITY: USE OF MICROELECTRODE ARRAYS TO MEASURE FUNCTIONAL CHANGES IN NEURONAL NETWORK ONTOGENY

EPA Science Inventory

Because the Developmental Neurotoxicity Testing Battery requires large numbers of animals and is expensive, development of in vitro approaches to screen chemicals for potential developmental neurotoxicity is a high priority. Many proposed approaches for screening are biochemical,...

In Vitro Assessment of Developmental Neurotoxicity: Use of Microelectrode Arrays to Measure Functional Changes in Neuronal Network Ontogeny*

EPA Science Inventory

Because the Developmental Neurotoxicity Testing Guidelines require large numbers of animals and is expensive, development of in vitro approaches to screen chemicals for potential developmental neurotoxicity is a high priority. Many proposed approaches for screening are biochemica...

DOE Office of Scientific and Technical Information (OSTI.GOV)

Burrage, Clare; Kuribayashi-Coleman, Andrew; Stevenson, James

We apply the new constraints from atom-interferometry searches for screening mechanisms to the symmetron model, finding that these experiments exclude a previously unexplored region of the parameter space. We discuss the possibility of networks of domain walls forming in the vacuum chamber, and how this could be used to discriminate between models of screening.

Investigation of Social Studies Teachers' Intended Uses of Social Networks in Terms of Various Variables

ERIC Educational Resources Information Center

Akgün, Ismail Hakan

2016-01-01

The aim of this research is to determine Social Studies teacher candidates' intended uses of social networks in terms of various variables. The research was carried out by using screening model of quantitative research methods. In the study, "The Social Network Intended Use Scale" was used as a data collection tool. As a result of the…

Heterogeneous information sharing of sensor information in contested environments

NASA Astrophysics Data System (ADS)

Wampler, Jason A.; Hsieh, Chien; Toth, Andrew; Sheatsley, Ryan

2017-05-01

The inherent nature of unattended sensors makes these devices most vulnerable to detection, exploitation, and denial in contested environments. Physical access is often cited as the easiest way to compromise any device or network. A new mechanism for mitigating these types of attacks developed under the Assistant Secretary of Defense for Research and Engineering, ASD(R and E) project, "Smoke Screen in Cyberspace", was demonstrated in a live, over-the-air experiment. Smoke Screen encrypts, slices up, and disburses redundant fragments of files throughout the network. Recovery is only possible after recovering all fragments and attacking/denying one or more nodes does not limit the availability of other fragment copies in the network. This experiment proved the feasibility of redundant file fragmentation, and is the foundation for developing sophisticated methods to blacklist compromised nodes, move data fragments from risks of compromise, and forward stored data fragments closer to the anticipated retrieval point. This paper outlines initial results in scalability of node members, fragment size, file size, and performance in a heterogeneous network consisting of the Wireless Network after Next (WNaN) radio and Common Sensor Radio (CSR).

Cardiac risk stratification in renal transplantation using a form of artificial intelligence.

PubMed

Heston, T F; Norman, D J; Barry, J M; Bennett, W M; Wilson, R A

1997-02-15

The purpose of this study was to determine if an expert network, a form of artificial intelligence, could effectively stratify cardiac risk in candidates for renal transplant. Input into the expert network consisted of clinical risk factors and thallium-201 stress test data. Clinical risk factor screening alone identified 95 of 189 patients as high risk. These 95 patients underwent thallium-201 stress testing, and 53 had either reversible or fixed defects. The other 42 patients were classified as low risk. This algorithm made up the "expert system," and during the 4-year follow-up period had a sensitivity of 82%, specificity of 77%, and accuracy of 78%. An artificial neural network was added to the expert system, creating an expert network. Input into the neural network consisted of both clinical variables and thallium-201 stress test data. There were 5 hidden nodes and the output (end point) was cardiac death. The expert network increased the specificity of the expert system alone from 77% to 90% (p < 0.001), the accuracy from 78% to 89% (p < 0.005), and maintained the overall sensitivity at 88%. An expert network based on clinical risk factor screening and thallium-201 stress testing had an accuracy of 89% in predicting the 4-year cardiac mortality among 189 renal transplant candidates.

A deep learning method for early screening of lung cancer

NASA Astrophysics Data System (ADS)

Zhang, Kunpeng; Jiang, Huiqin; Ma, Ling; Gao, Jianbo; Yang, Xiaopeng

2018-04-01

Lung cancer is the leading cause of cancer-related deaths among men. In this paper, we propose a pulmonary nodule detection method for early screening of lung cancer based on the improved AlexNet model. In order to maintain the same image quality as the existing B/S architecture PACS system, we convert the original CT image into JPEG format image by analyzing the DICOM file firstly. Secondly, in view of the large size and complex background of CT chest images, we design the convolution neural network on basis of AlexNet model and sparse convolution structure. At last we train our models on the software named DIGITS which is provided by NVIDIA. The main contribution of this paper is to apply the convolutional neural network for the early screening of lung cancer and improve the screening accuracy by combining the AlexNet model with the sparse convolution structure. We make a series of experiments on the chest CT images using the proposed method, of which the sensitivity and specificity indicates that the method presented in this paper can effectively improve the accuracy of early screening of lung cancer and it has certain clinical significance at the same time.

International Suspect Screening: NORMAN Suspect Exchange meets the US EPA CompTox Chemistry Dashboard (ICCE 2017 Oslo)

EPA Science Inventory

Members of the European NORMAN Network of Environmental Laboratories (www.norman-network.com) have many substance lists, including targets, suspects, surfactants, perfluorinated substances and regulated, partially confidential data sets of complex mixtures. The NORMAN Suspect Lis...

Reprogramming cell fate with a genome-scale library of artificial transcription factors.

PubMed

Eguchi, Asuka; Wleklinski, Matthew J; Spurgat, Mackenzie C; Heiderscheit, Evan A; Kropornicka, Anna S; Vu, Catherine K; Bhimsaria, Devesh; Swanson, Scott A; Stewart, Ron; Ramanathan, Parameswaran; Kamp, Timothy J; Slukvin, Igor; Thomson, James A; Dutton, James R; Ansari, Aseem Z

2016-12-20

Artificial transcription factors (ATFs) are precision-tailored molecules designed to bind DNA and regulate transcription in a preprogrammed manner. Libraries of ATFs enable the high-throughput screening of gene networks that trigger cell fate decisions or phenotypic changes. We developed a genome-scale library of ATFs that display an engineered interaction domain (ID) to enable cooperative assembly and synergistic gene expression at targeted sites. We used this ATF library to screen for key regulators of the pluripotency network and discovered three combinations of ATFs capable of inducing pluripotency without exogenous expression of Oct4 (POU domain, class 5, TF 1). Cognate site identification, global transcriptional profiling, and identification of ATF binding sites reveal that the ATFs do not directly target Oct4; instead, they target distinct nodes that converge to stimulate the endogenous pluripotency network. This forward genetic approach enables cell type conversions without a priori knowledge of potential key regulators and reveals unanticipated gene network dynamics that drive cell fate choices.

Back propagation artificial neural network for community Alzheimer's disease screening in China.

PubMed

Tang, Jun; Wu, Lei; Huang, Helang; Feng, Jiang; Yuan, Yefeng; Zhou, Yueping; Huang, Peng; Xu, Yan; Yu, Chao

2013-01-25

Alzheimer's disease patients diagnosed with the Chinese Classification of Mental Disorders diagnostic criteria were selected from the community through on-site sampling. Levels of macro and trace elements were measured in blood samples using an atomic absorption method, and neurotransmitters were measured using a radioimmunoassay method. SPSS 13.0 was used to establish a database, and a back propagation artificial neural network for Alzheimer's disease prediction was simulated using Clementine 12.0 software. With scores of activities of daily living, creatinine, 5-hydroxytryptamine, age, dopamine and aluminum as input variables, the results revealed that the area under the curve in our back propagation artificial neural network was 0.929 (95% confidence interval: 0.868-0.968), sensitivity was 90.00%, specificity was 95.00%, and accuracy was 92.50%. The findings indicated that the results of back propagation artificial neural network established based on the above six variables were satisfactory for screening and diagnosis of Alzheimer's disease in patients selected from the community.

Back propagation artificial neural network for community Alzheimer's disease screening in China★

PubMed Central

Tang, Jun; Wu, Lei; Huang, Helang; Feng, Jiang; Yuan, Yefeng; Zhou, Yueping; Huang, Peng; Xu, Yan; Yu, Chao

2013-01-01

Alzheimer's disease patients diagnosed with the Chinese Classification of Mental Disorders diagnostic criteria were selected from the community through on-site sampling. Levels of macro and trace elements were measured in blood samples using an atomic absorption method, and neurotransmitters were measured using a radioimmunoassay method. SPSS 13.0 was used to establish a database, and a back propagation artificial neural network for Alzheimer's disease prediction was simulated using Clementine 12.0 software. With scores of activities of daily living, creatinine, 5-hydroxytryptamine, age, dopamine and aluminum as input variables, the results revealed that the area under the curve in our back propagation artificial neural network was 0.929 (95% confidence interval: 0.868–0.968), sensitivity was 90.00%, specificity was 95.00%, and accuracy was 92.50%. The findings indicated that the results of back propagation artificial neural network established based on the above six variables were satisfactory for screening and diagnosis of Alzheimer's disease in patients selected from the community. PMID:25206598

Reprogramming cell fate with a genome-scale library of artificial transcription factors

PubMed Central

Eguchi, Asuka; Wleklinski, Matthew J.; Spurgat, Mackenzie C.; Heiderscheit, Evan A.; Kropornicka, Anna S.; Vu, Catherine K.; Bhimsaria, Devesh; Swanson, Scott A.; Stewart, Ron; Ramanathan, Parameswaran; Kamp, Timothy J.; Slukvin, Igor; Thomson, James A.; Dutton, James R.; Ansari, Aseem Z.

2016-01-01

Artificial transcription factors (ATFs) are precision-tailored molecules designed to bind DNA and regulate transcription in a preprogrammed manner. Libraries of ATFs enable the high-throughput screening of gene networks that trigger cell fate decisions or phenotypic changes. We developed a genome-scale library of ATFs that display an engineered interaction domain (ID) to enable cooperative assembly and synergistic gene expression at targeted sites. We used this ATF library to screen for key regulators of the pluripotency network and discovered three combinations of ATFs capable of inducing pluripotency without exogenous expression of Oct4 (POU domain, class 5, TF 1). Cognate site identification, global transcriptional profiling, and identification of ATF binding sites reveal that the ATFs do not directly target Oct4; instead, they target distinct nodes that converge to stimulate the endogenous pluripotency network. This forward genetic approach enables cell type conversions without a priori knowledge of potential key regulators and reveals unanticipated gene network dynamics that drive cell fate choices. PMID:27930301

An integrated approach to uncover quality marker underlying the effects of Alisma orientale on lipid metabolism, using chemical analysis and network pharmacology.

PubMed

Liao, Maoliang; Shang, Haihua; Li, Yazhuo; Li, Tian; Wang, Miao; Zheng, Yanan; Hou, Wenbin; Liu, Changxiao

2018-06-01

Quality control of traditional Chinese medicines is currently a great concern, due to the correlation between the quality control indicators and clinic effect is often questionable. According to the "multi-components and multi-targets" property of TCMs, a new special quality and bioactivity evaluation system is urgently needed. Present study adopted an integrated approach to provide new insights relating to uncover quality marker underlying the effects of Alisma orientale (AO) on lipid metabolism. In this paper, guided by the concept of the quality marker (Q-marker), an integrated strategies "effect-compound-target-fingerprint" was established to discovery and screen the potential quality marker of AO based on network pharmacology and chemical analysis. Firstly, a bioactivity evaluation was performed to screen the main active fractions. Then the chemical compositions were rapidly identified by chemical analysis. Next, networks were constructed to illuminate the interactions between these component and their targets for lipid metabolism, and the potential Q-marker of AO was initially screened. Finally, the activity of the Q-markers was validated in vitro. 50% ethanol extract fraction was found to have the strongest lipid-lowering activity. Then, the network pharmacology was used to clarify the unique relationship between the Q-markers and their integral pharmacological action. Combined with the results obtained, five active ingredients in the 50% ethanol extract fraction were given special considerations to be representative Q-markers: Alisol A, Alisol B, Alisol A 23-acetate, Alisol B 23-acetate and Alisol A 24-acetate, respectively. The chromatographic fingerprints based Q-marker was establishment. The integrated Q-marker screen may offer an alternative quality assessment of herbal medicines. Copyright © 2018. Published by Elsevier GmbH.

A Network-Based Method to Assess the Statistical Significance of Mild Co-Regulation Effects

PubMed Central

Horvát, Emőke-Ágnes; Zhang, Jitao David; Uhlmann, Stefan; Sahin, Özgür; Zweig, Katharina Anna

2013-01-01

Recent development of high-throughput, multiplexing technology has initiated projects that systematically investigate interactions between two types of components in biological networks, for instance transcription factors and promoter sequences, or microRNAs (miRNAs) and mRNAs. In terms of network biology, such screening approaches primarily attempt to elucidate relations between biological components of two distinct types, which can be represented as edges between nodes in a bipartite graph. However, it is often desirable not only to determine regulatory relationships between nodes of different types, but also to understand the connection patterns of nodes of the same type. Especially interesting is the co-occurrence of two nodes of the same type, i.e., the number of their common neighbours, which current high-throughput screening analysis fails to address. The co-occurrence gives the number of circumstances under which both of the biological components are influenced in the same way. Here we present SICORE, a novel network-based method to detect pairs of nodes with a statistically significant co-occurrence. We first show the stability of the proposed method on artificial data sets: when randomly adding and deleting observations we obtain reliable results even with noise exceeding the expected level in large-scale experiments. Subsequently, we illustrate the viability of the method based on the analysis of a proteomic screening data set to reveal regulatory patterns of human microRNAs targeting proteins in the EGFR-driven cell cycle signalling system. Since statistically significant co-occurrence may indicate functional synergy and the mechanisms underlying canalization, and thus hold promise in drug target identification and therapeutic development, we provide a platform-independent implementation of SICORE with a graphical user interface as a novel tool in the arsenal of high-throughput screening analysis. PMID:24039936

Detection of Significant Pneumococcal Meningitis Biomarkers by Ego Network.

PubMed

Wang, Qian; Lou, Zhifeng; Zhai, Liansuo; Zhao, Haibin

2017-06-01

To identify significant biomarkers for detection of pneumococcal meningitis based on ego network. Based on the gene expression data of pneumococcal meningitis and global protein-protein interactions (PPIs) data recruited from open access databases, the authors constructed a differential co-expression network (DCN) to identify pneumococcal meningitis biomarkers in a network view. Here EgoNet algorithm was employed to screen the significant ego networks that could accurately distinguish pneumococcal meningitis from healthy controls, by sequentially seeking ego genes, searching candidate ego networks, refinement of candidate ego networks and significance analysis to identify ego networks. Finally, the functional inference of the ego networks was performed to identify significant pathways for pneumococcal meningitis. By differential co-expression analysis, the authors constructed the DCN that covered 1809 genes and 3689 interactions. From the DCN, a total of 90 ego genes were identified. Starting from these ego genes, three significant ego networks (Module 19, Module 70 and Module 71) that could predict clinical outcomes for pneumococcal meningitis were identified by EgoNet algorithm, and the corresponding ego genes were GMNN, MAD2L1 and TPX2, respectively. Pathway analysis showed that these three ego networks were related to CDT1 association with the CDC6:ORC:origin complex, inactivation of APC/C via direct inhibition of the APC/C complex pathway, and DNA strand elongation, respectively. The authors successfully screened three significant ego modules which could accurately predict the clinical outcomes for pneumococcal meningitis and might play important roles in host response to pathogen infection in pneumococcal meningitis.

Network modeling of kinase inhibitor polypharmacology reveals pathways targeted in chemical screens

PubMed Central

Ursu, Oana; Gosline, Sara J. C.; Beeharry, Neil; Fink, Lauren; Bhattacharjee, Vikram; Huang, Shao-shan Carol; Zhou, Yan; Yen, Tim; Fraenkel, Ernest

2017-01-01

Small molecule screens are widely used to prioritize pharmaceutical development. However, determining the pathways targeted by these molecules is challenging, since the compounds are often promiscuous. We present a network strategy that takes into account the polypharmacology of small molecules in order to generate hypotheses for their broader mode of action. We report a screen for kinase inhibitors that increase the efficacy of gemcitabine, the first-line chemotherapy for pancreatic cancer. Eight kinase inhibitors emerge that are known to affect 201 kinases, of which only three kinases have been previously identified as modifiers of gemcitabine toxicity. In this work, we use the SAMNet algorithm to identify pathways linking these kinases and genetic modifiers of gemcitabine toxicity with transcriptional and epigenetic changes induced by gemcitabine that we measure using DNaseI-seq and RNA-seq. SAMNet uses a constrained optimization algorithm to connect genes from these complementary datasets through a small set of protein-protein and protein-DNA interactions. The resulting network recapitulates known pathways including DNA repair, cell proliferation and the epithelial-to-mesenchymal transition. We use the network to predict genes with important roles in the gemcitabine response, including six that have already been shown to modify gemcitabine efficacy in pancreatic cancer and ten novel candidates. Our work reveals the important role of polypharmacology in the activity of these chemosensitizing agents. PMID:29023490

A New Screening Methodology for Improved Oil Recovery Processes Using Soft-Computing Techniques

NASA Astrophysics Data System (ADS)

Parada, Claudia; Ertekin, Turgay

2010-05-01

The first stage of production of any oil reservoir involves oil displacement by natural drive mechanisms such as solution gas drive, gas cap drive and gravity drainage. Typically, improved oil recovery (IOR) methods are applied to oil reservoirs that have been depleted naturally. In more recent years, IOR techniques are applied to reservoirs even before their natural energy drive is exhausted by primary depletion. Descriptive screening criteria for IOR methods are used to select the appropriate recovery technique according to the fluid and rock properties. This methodology helps in assessing the most suitable recovery process for field deployment of a candidate reservoir. However, the already published screening guidelines neither provide information about the expected reservoir performance nor suggest a set of project design parameters, which can be used towards the optimization of the process. In this study, artificial neural networks (ANN) are used to build a high-performance neuro-simulation tool for screening different improved oil recovery techniques: miscible injection (CO2 and N2), waterflooding and steam injection processes. The simulation tool consists of proxy models that implement a multilayer cascade feedforward back propagation network algorithm. The tool is intended to narrow the ranges of possible scenarios to be modeled using conventional simulation, reducing the extensive time and energy spent in dynamic reservoir modeling. A commercial reservoir simulator is used to generate the data to train and validate the artificial neural networks. The proxy models are built considering four different well patterns with different well operating conditions as the field design parameters. Different expert systems are developed for each well pattern. The screening networks predict oil production rate and cumulative oil production profiles for a given set of rock and fluid properties, and design parameters. The results of this study show that the networks are able to recognize the strong correlation between the displacement mechanism and the reservoir characteristics as they effectively forecast hydrocarbon production for different types of reservoir undergoing diverse recovery processes. The artificial neuron networks are able to capture the similarities between different displacement mechanisms as same network architecture is successfully applied in both CO2 and N2 injection. The neuro-simulation application tool is built within a graphical user interface to facilitate the display of the results. The developed soft-computing tool offers an innovative approach to design a variety of efficient and feasible IOR processes by using artificial intelligence. The tool provides appropriate guidelines to the reservoir engineer, it facilitates the appraisal of diverse field development strategies for oil reservoirs, and it helps to reduce the number of scenarios evaluated with conventional reservoir simulation.

Novel High-Fidelity Screening of Environmental Chemicals and Carcinogens and Mechanisms in Colorectal Cancer.

DTIC Science & Technology

2016-09-01

Chemical Promiscuity, Pharmacokinetics, Colorectal Cancer, N , N ’-disalicylidene-1,2-diaminopropane, Pyraclostrobin, Paclobutrazol, Vitamin D Receptor, Wnt...Environmental Chemicals, TOX-TMFS, CPTM, Cancer Cellular Network Model, Chemical Reactivity, Chemical Promiscuity, Pharmacokinetics, Colorectal Cancer, N , N ...network models were further enriched with oncologic disease OMIM profiles to create cancer-specific networks. The ECs N , N ’-disalicylidene- 1,2

Competing endogenous RNA regulatory network in papillary thyroid carcinoma.

PubMed

Chen, Shouhua; Fan, Xiaobin; Gu, He; Zhang, Lili; Zhao, Wenhua

2018-05-11

The present study aimed to screen all types of RNAs involved in the development of papillary thyroid carcinoma (PTC). RNA‑sequencing data of PTC and normal samples were used for screening differentially expressed (DE) microRNAs (DE‑miRNAs), long non‑coding RNAs (DE‑lncRNAs) and genes (DEGs). Subsequently, lncRNA‑miRNA, miRNA‑gene (that is, miRNA‑mRNA) and gene‑gene interaction pairs were extracted and used to construct regulatory networks. Feature genes in the miRNA‑mRNA network were identified by topological analysis and recursive feature elimination analysis. A support vector machine (SVM) classifier was built using 15 feature genes, and its classification effect was validated using two microarray data sets that were downloaded from the Gene Expression Omnibus (GEO) database. In addition, Gene Ontology function and Kyoto Encyclopedia Genes and Genomes pathway enrichment analyses were conducted for genes identified in the ceRNA network. A total of 506 samples, including 447 tumor samples and 59 normal samples, were obtained from The Cancer Genome Atlas (TCGA); 16 DE‑lncRNAs, 917 DEGs and 30 DE‑miRNAs were screened. The miRNA‑mRNA regulatory network comprised 353 nodes and 577 interactions. From these data, 15 feature genes with high predictive precision (>95%) were extracted from the network and were used to form an SVM classifier with an accuracy of 96.05% (486/506) for PTC samples downloaded from TCGA, and accuracies of 96.81 and 98.46% for GEO downloaded data sets. The ceRNA regulatory network comprised 596 lines (or interactions) and 365 nodes. Genes in the ceRNA network were significantly enriched in 'neuron development', 'differentiation', 'neuroactive ligand‑receptor interaction', 'metabolism of xenobiotics by cytochrome P450', 'drug metabolism' and 'cytokine‑cytokine receptor interaction' pathways. Hox transcript antisense RNA, miRNA‑206 and kallikrein‑related peptidase 10 were nodes in the ceRNA regulatory network of the selected feature gene, and they may serve import roles in the development of PTC.

Application of Neural Networks for classification of Patau, Edwards, Down, Turner and Klinefelter Syndrome based on first trimester maternal serum screening data, ultrasonographic findings and patient demographics.

PubMed

Catic, Aida; Gurbeta, Lejla; Kurtovic-Kozaric, Amina; Mehmedbasic, Senad; Badnjevic, Almir

2018-02-13

The usage of Artificial Neural Networks (ANNs) for genome-enabled classifications and establishing genome-phenotype correlations have been investigated more extensively over the past few years. The reason for this is that ANNs are good approximates of complex functions, so classification can be performed without the need for explicitly defined input-output model. This engineering tool can be applied for optimization of existing methods for disease/syndrome classification. Cytogenetic and molecular analyses are the most frequent tests used in prenatal diagnostic for the early detection of Turner, Klinefelter, Patau, Edwards and Down syndrome. These procedures can be lengthy, repetitive; and often employ invasive techniques so a robust automated method for classifying and reporting prenatal diagnostics would greatly help the clinicians with their routine work. The database consisted of data collected from 2500 pregnant woman that came to the Institute of Gynecology, Infertility and Perinatology "Mehmedbasic" for routine antenatal care between January 2000 and December 2016. During first trimester all women were subject to screening test where values of maternal serum pregnancy-associated plasma protein A (PAPP-A) and free beta human chorionic gonadotropin (β-hCG) were measured. Also, fetal nuchal translucency thickness and the presence or absence of the nasal bone was observed using ultrasound. The architectures of linear feedforward and feedback neural networks were investigated for various training data distributions and number of neurons in hidden layer. Feedback neural network architecture out performed feedforward neural network architecture in predictive ability for all five aneuploidy prenatal syndrome classes. Feedforward neural network with 15 neurons in hidden layer achieved classification sensitivity of 92.00%. Classification sensitivity of feedback (Elman's) neural network was 99.00%. Average accuracy of feedforward neural network was 89.6% and for feedback was 98.8%. The results presented in this paper prove that an expert diagnostic system based on neural networks can be efficiently used for classification of five aneuploidy syndromes, covered with this study, based on first trimester maternal serum screening data, ultrasonographic findings and patient demographics. Developed Expert System proved to be simple, robust, and powerful in properly classifying prenatal aneuploidy syndromes.

Personal Network Characteristics as Predictors of Change in Obesity Risk Behaviors in Early Adolescence.

PubMed

Marks, Jennifer; de la Haye, Kayla; Barnett, Lisa M; Allender, Steven

2018-05-17

The potential for peers to influence obesity risk behavior increases in adolescence, yet there are knowledge gaps of how behaviors are modified in response to peers over time. This study examined how personal friendship network characteristics were associated with obesity-related behaviors from late childhood to early adolescence. Two waves of friendship, physical activity, screen time, and dietary recall data were collected from 11- to 13-year-old students (99% retention) in Australia (n = 308) over a five- to eight-month period. Regression models identified friendship network characteristics that predicted later health behaviors which varied by gender and behavior type, such as the number of friends positively associated with physical activity intensity (males) and screen time (females). The need for considering context to influence behavior change is discussed. © 2018 Society for Research on Adolescence.

A qualitative study of lung cancer risk perceptions and smoking beliefs among national lung screening trial participants.

PubMed

Park, Elyse R; Streck, Joanna M; Gareen, Ilana F; Ostroff, Jamie S; Hyland, Kelly A; Rigotti, Nancy A; Pajolek, Hannah; Nichter, Mark

2014-02-01

The National Comprehensive Cancer Network and the American Cancer Society recently released lung screening guidelines that include smoking cessation counseling for smokers undergoing screening. Previous work indicates that smoking behaviors and risk perceptions of the National Lung Screening Trial (NLST) participants were relatively unchanged. We explored American College of Radiology Imaging Network (ACRIN)/NLST former and current smokers' risk perceptions specifically to (a) determine whether lung screening is a cue for behavior change, (b) elucidate risk perceptions for lung cancer and smoking-related diseases, and (c) explore postscreening behavioral intentions and changes. A random sample of 35 participants from 4 ACRIN sites were qualitatively interviewed 1-2 years postscreen. We used a structured interview guide based on Health Belief Model and Self-Regulation Model constructs. Content analyses were conducted with NVivo 8. Most participants endorsed high-risk perceptions for lung cancer and smoking-related diseases, but heightened concern about these risks did not appear to motivate participants to seek screening. Risk perceptions were mostly attributed to participants' heavy smoking histories; former smokers expressed greatly reduced risk. Lung cancer and smoking-related diseases were perceived as very severe although participants endorsed low worry. Current smokers had low confidence in their ability to quit, and none reported quitting following their initial screen. Lung screening did not appear to be a behavior change cue to action, and high-risk perceptions did not translate into quitting behaviors. Cognitive and emotional dissonance and avoidance strategies may deter engagement in smoking behavior change. Smoking cessation and prevention interventions during lung screening should explore risk perceptions, emotions, and quit confidence.

A Qualitative Study of Lung Cancer Risk Perceptions and Smoking Beliefs Among National Lung Screening Trial Participants

PubMed Central

2014-01-01

Introduction: The National Comprehensive Cancer Network and the American Cancer Society recently released lung screening guidelines that include smoking cessation counseling for smokers undergoing screening. Previous work indicates that smoking behaviors and risk perceptions of the National Lung Screening Trial (NLST) participants were relatively unchanged. We explored American College of Radiology Imaging Network (ACRIN)/NLST former and current smokers’ risk perceptions specifically to (a) determine whether lung screening is a cue for behavior change, (b) elucidate risk perceptions for lung cancer and smoking-related diseases, and (c) explore postscreening behavioral intentions and changes. Methods: A random sample of 35 participants from 4 ACRIN sites were qualitatively interviewed 1–2 years postscreen. We used a structured interview guide based on Health Belief Model and Self-Regulation Model constructs. Content analyses were conducted with NVivo 8. Results: Most participants endorsed high-risk perceptions for lung cancer and smoking-related diseases, but heightened concern about these risks did not appear to motivate participants to seek screening. Risk perceptions were mostly attributed to participants’ heavy smoking histories; former smokers expressed greatly reduced risk. Lung cancer and smoking-related diseases were perceived as very severe although participants endorsed low worry. Current smokers had low confidence in their ability to quit, and none reported quitting following their initial screen. Conclusions: Lung screening did not appear to be a behavior change cue to action, and high-risk perceptions did not translate into quitting behaviors. Cognitive and emotional dissonance and avoidance strategies may deter engagement in smoking behavior change. Smoking cessation and prevention interventions during lung screening should explore risk perceptions, emotions, and quit confidence. PMID:23999653

Hydraulics of sprinkler and microirrigation systems

USDA-ARS?s Scientific Manuscript database

The fluid dynamics of sprinkler and microirrigation systems are complex. Water moves dynamically from the water source through the pump into the pipe network. Water often goes through a series of screens and filters depending on the source and type of irrigation system. From the pipe network, water ...

[Screening of diseases associated with asbestos. On-going activities, synthesis].

PubMed

Frimat, P; Paris, C; Letourneux, M; Catilina, P; Sobaszek, A

1999-12-01

Medical screening requires always assessment. On the basis of ongoing studies on occupational health asbestos programs, we suggest some recommendations for asbestos screening after occupational exposure. The proposal for asbestos workers post-exposure surveillance should take into account the medical but also the social aspects of the problem. Post-exposure screening of asbestos workers includes an evaluation of occupational exposure, compulsory basis medical check-up, the characteristics of the radiological investigations and schedule of the medical surveillance. In conclusion, we suggest some general recommendations for asbestos screening after occupational exposure, particularly the necessity to obtain a concerted approach of asbestos screening with regional and national networks, the concern of their assessment and the implementation of specific research studies.

Screening for Vision Problems, Including Usher's Syndrome, among Hearing Impaired Students.

ERIC Educational Resources Information Center

Fillman, Robyn D.; And Others

1987-01-01

A screening program for vision problems and Usher's Syndrome (a common cause of deaf-blindness) among 210 hearing-impaired students found 44 percent had significant vision problems and 1 percent had Usher's Syndrome. The program involved an interagency network of school, health care, and support personnel and utilized a dilated ophathalmological…

Further Evaluation of DNT Hazard Screening using Neural Networks from Rat Cortical Neurons on Multi-well Microelectrode Arrays

EPA Science Inventory

Thousands of chemicals have not been characterized for their DNT potential. Due to the need for DNT hazard identification, efforts to develop screening assays for DNT potential is a high priority. Multi-well microelectrode arrays (MEA) measure the spontaneous activity of electr...

OPTIMAL WELL LOCATOR (OWL): A SCREENING TOOL FOR EVALUATING LOCATIONS OF MONITORING WELLS

EPA Science Inventory

The Optimal Well Locator ( OWL) program was designed and developed by USEPA to be a screening tool to evaluate and optimize the placement of wells in long term monitoring networks at small sites. The first objective of the OWL program is to allow the user to visualize the change ...

A fast stimulability screening protocol for neuronal cultures on microelectrode arrays.

PubMed

Kapucu, Fikret E; Tanskanen, Jarno M A; Yuan, Yuting; Hyttinen, Jari A K

2015-01-01

Microelectrode arrays (MEAs) are used to study the electrical activity in brain slices and neuronal cultures. MEA experiments for the analysis of electrical stimulation responses require the tissue or culture to be prone to stimulation. For brain slices, potential stimulation sites may be directly visible in microscope, in which case the determination of stimulability at those locations is sufficient. In unstructured neuronal cultures, potential stimulation sites may not be known a priori, and spatial stimulability screening should be performed. Considering, e.g., 59 microelectrode sites, each to be stimulated several times, may result in long screening times, unacceptable with a MEA system without an integrated CO2 incubator, or in high stimulation effects on the networks. Here, we describe an implementation of a fast stimulation protocol employing pseudorandom stimulation site switching aiming at alleviating the network effects of the stimulability screening. In this paper, we show the usability of the proposed protocol by first detecting stimulable locations and subsequently apply repeated stimulation on the identified potentially stimulable locations to observe an exemplary neuronal pathway.

Development and application of a recombination-based library versus library high- throughput yeast two-hybrid (RLL-Y2H) screening system.

PubMed

Yang, Fang; Lei, Yingying; Zhou, Meiling; Yao, Qili; Han, Yichao; Wu, Xiang; Zhong, Wanshun; Zhu, Chenghang; Xu, Weize; Tao, Ran; Chen, Xi; Lin, Da; Rahman, Khaista; Tyagi, Rohit; Habib, Zeshan; Xiao, Shaobo; Wang, Dang; Yu, Yang; Chen, Huanchun; Fu, Zhenfang; Cao, Gang

2018-02-16

Protein-protein interaction (PPI) network maintains proper function of all organisms. Simple high-throughput technologies are desperately needed to delineate the landscape of PPI networks. While recent state-of-the-art yeast two-hybrid (Y2H) systems improved screening efficiency, either individual colony isolation, library preparation arrays, gene barcoding or massive sequencing are still required. Here, we developed a recombination-based 'library vs library' Y2H system (RLL-Y2H), by which multi-library screening can be accomplished in a single pool without any individual treatment. This system is based on the phiC31 integrase-mediated integration between bait and prey plasmids. The integrated fragments were digested by MmeI and subjected to deep sequencing to decode the interaction matrix. We applied this system to decipher the trans-kingdom interactome between Mycobacterium tuberculosis and host cells and further identified Rv2427c interfering with the phagosome-lysosome fusion. This concept can also be applied to other systems to screen protein-RNA and protein-DNA interactions and delineate signaling landscape in cells.

Independence screening for high dimensional nonlinear additive ODE models with applications to dynamic gene regulatory networks.

PubMed

Xue, Hongqi; Wu, Shuang; Wu, Yichao; Ramirez Idarraga, Juan C; Wu, Hulin

2018-05-02

Mechanism-driven low-dimensional ordinary differential equation (ODE) models are often used to model viral dynamics at cellular levels and epidemics of infectious diseases. However, low-dimensional mechanism-based ODE models are limited for modeling infectious diseases at molecular levels such as transcriptomic or proteomic levels, which is critical to understand pathogenesis of diseases. Although linear ODE models have been proposed for gene regulatory networks (GRNs), nonlinear regulations are common in GRNs. The reconstruction of large-scale nonlinear networks from time-course gene expression data remains an unresolved issue. Here, we use high-dimensional nonlinear additive ODEs to model GRNs and propose a 4-step procedure to efficiently perform variable selection for nonlinear ODEs. To tackle the challenge of high dimensionality, we couple the 2-stage smoothing-based estimation method for ODEs and a nonlinear independence screening method to perform variable selection for the nonlinear ODE models. We have shown that our method possesses the sure screening property and it can handle problems with non-polynomial dimensionality. Numerical performance of the proposed method is illustrated with simulated data and a real data example for identifying the dynamic GRN of Saccharomyces cerevisiae. Copyright © 2018 John Wiley & Sons, Ltd.

Defining toxicological tipping points in neuronal network development.

PubMed

Frank, Christopher L; Brown, Jasmine P; Wallace, Kathleen; Wambaugh, John F; Shah, Imran; Shafer, Timothy J

2018-02-02

Measuring electrical activity of neural networks by microelectrode array (MEA) has recently shown promise for screening level assessments of chemical toxicity on network development and function. Important aspects of interneuronal communication can be quantified from a single MEA recording, including individual firing rates, coordinated bursting, and measures of network synchrony, providing rich datasets to evaluate chemical effects. Further, multiple recordings can be made from the same network, including during the formation of these networks in vitro. The ability to perform multiple recording sessions over the in vitro development of network activity may provide further insight into developmental effects of neurotoxicants. In the current study, a recently described MEA-based screen of 86 compounds in primary rat cortical cultures over 12 days in vitro was revisited to establish a framework that integrates all available primary measures of electrical activity from MEA recordings into a composite metric for deviation from normal activity (total scalar perturbation). Examining scalar perturbations over time and increasing concentration of compound allowed for definition of critical concentrations or "tipping points" at which the neural networks switched from recovery to non-recovery trajectories for 42 compounds. These tipping point concentrations occurred at predominantly lower concentrations than those causing overt cell viability loss or disrupting individual network parameters, suggesting tipping points may be a more sensitive measure of network functional loss. Comparing tipping points for six compounds with plasma concentrations known to cause developmental neurotoxicity in vivo demonstrated strong concordance and suggests there is potential for using tipping points for chemical prioritization. Published by Elsevier Inc.

Low Frequency Activity of Cortical Networks on Microelectrode Arrays is Differentially Altered by Bicuculline and Carbaryl

EPA Science Inventory

Thousands of chemicals need to be characterized for their neurotoxicity potential. Neurons grown on microelectrode arrays (MEAs) are an in vitro model used to screen chemicals for functional effects on neuronal networks. Typically, after removal of low frequency components, effec...

Women's views on reminder letters for screening mammography: Mixed methods study of women from 23 family health networks.

PubMed

Kaczorowski, Janusz; Karwalajtys, Tina; Lohfeld, Lynne; Laryea, Stephanie; Anderson, Kelly; Roder, Stefanie; Sebaldt, Rolf J

2009-06-01

To explore women's perspectives on the acceptability and content of reminder letters for screening mammography from their family physicians, as well as such letters' effect on screening intentions. Cross-sectional mailed survey followed by focus groups with a subgroup of respondents. Ontario. One family physician was randomly selected from each of 23 family health networks and primary care networks participating in a demonstration project to increase the delivery of preventive services. From the practice roster of each physician, up to 35 randomly selected women aged 50 to 69 years who were due or overdue for screening mammograms and who had received reminder letters from their family physicians within the past 6 months were surveyed. Recall of having received reminder letters and of their content, influence of the letters on decisions to have mammograms, and interest in receiving future reminder letters. Focus group interviews with survey respondents explored the survey findings in greater depth using a standardized interview guide. The response rate to the survey was 55.7% (384 of 689), and 45.1% (173 of 384) of responding women reported having mammograms in the past 6 months. Among women who recalled receiving letters and either making appointments for or having mammograms, 74.8% (122 of 163) indicated that the letters substantially influenced their decisions. Most respondents (77.1% [296 of 384]) indicated that they would like to continue to receive reminders, and 28.9% (111 of 384) indicated that they would like to receive additional information about mammograms. Participants in 2 focus groups (n = 3 and n = 5) indicated that they thought letters reflected a positive attitude of physicians toward mammography screening. They also commented that newly eligible women had different information needs than women who had had mammograms done in the past. Reminder letters were considered by participants to be useful and appeared to influence women's decisions to undergo mammography screening.

Automatic detection of anomalies in screening mammograms

PubMed Central

2013-01-01

Background Diagnostic performance in breast screening programs may be influenced by the prior probability of disease. Since breast cancer incidence is roughly half a percent in the general population there is a large probability that the screening exam will be normal. That factor may contribute to false negatives. Screening programs typically exhibit about 83% sensitivity and 91% specificity. This investigation was undertaken to determine if a system could be developed to pre-sort screening-images into normal and suspicious bins based on their likelihood to contain disease. Wavelets were investigated as a method to parse the image data, potentially removing confounding information. The development of a classification system based on features extracted from wavelet transformed mammograms is reported. Methods In the multi-step procedure images were processed using 2D discrete wavelet transforms to create a set of maps at different size scales. Next, statistical features were computed from each map, and a subset of these features was the input for a concerted-effort set of naïve Bayesian classifiers. The classifier network was constructed to calculate the probability that the parent mammography image contained an abnormality. The abnormalities were not identified, nor were they regionalized. The algorithm was tested on two publicly available databases: the Digital Database for Screening Mammography (DDSM) and the Mammographic Images Analysis Society’s database (MIAS). These databases contain radiologist-verified images and feature common abnormalities including: spiculations, masses, geometric deformations and fibroid tissues. Results The classifier-network designs tested achieved sensitivities and specificities sufficient to be potentially useful in a clinical setting. This first series of tests identified networks with 100% sensitivity and up to 79% specificity for abnormalities. This performance significantly exceeds the mean sensitivity reported in literature for the unaided human expert. Conclusions Classifiers based on wavelet-derived features proved to be highly sensitive to a range of pathologies, as a result Type II errors were nearly eliminated. Pre-sorting the images changed the prior probability in the sorted database from 37% to 74%. PMID:24330643

Performance of an Abbreviated Version of the Lubben Social Network Scale among Three European Community-Dwelling Older Adult Populations

ERIC Educational Resources Information Center

Lubben, James; Blozik, Eva; Gillmann, Gerhard; Iliffe, Steve; von Renteln-Kruse, Wolfgang; Beck, John C.; Stuck, Andreas E.

2006-01-01

Purpose: There is a need for valid and reliable short scales that can be used to assess social networks and social supports and to screen for social isolation in older persons. Design and Methods: The present study is a cross-national and cross-cultural evaluation of the performance of an abbreviated version of the Lubben Social Network Scale…

Exploring the Ligand-Protein Networks in Traditional Chinese Medicine: Current Databases, Methods, and Applications

PubMed Central

Zhao, Mingzhu; Wei, Dong-Qing

2013-01-01

The traditional Chinese medicine (TCM), which has thousands of years of clinical application among China and other Asian countries, is the pioneer of the “multicomponent-multitarget” and network pharmacology. Although there is no doubt of the efficacy, it is difficult to elucidate convincing underlying mechanism of TCM due to its complex composition and unclear pharmacology. The use of ligand-protein networks has been gaining significant value in the history of drug discovery while its application in TCM is still in its early stage. This paper firstly surveys TCM databases for virtual screening that have been greatly expanded in size and data diversity in recent years. On that basis, different screening methods and strategies for identifying active ingredients and targets of TCM are outlined based on the amount of network information available, both on sides of ligand bioactivity and the protein structures. Furthermore, applications of successful in silico target identification attempts are discussed in detail along with experiments in exploring the ligand-protein networks of TCM. Finally, it will be concluded that the prospective application of ligand-protein networks can be used not only to predict protein targets of a small molecule, but also to explore the mode of action of TCM. PMID:23818932

Scottish Stroke Research Network: the first three years.

PubMed

McCormick, K; Langhorne, P; Graham, F E J; McFarlane, C

2010-08-01

Research networks were introduced in the UK to facilitate and improve clinical research and stroke was seen as a priority topic for local research network development. The Scottish Stroke Research Network (SSRN) is one of 11 stroke research networks in the UK. In this article we review the progress of the Scottish Stroke Research Network in the three years since inception. Between 2006-2009 the number of active hospital research sites has increased from 10 to 22 expanding to involve 20 stroke research nurses. There was a corresponding 58% increase in recruitment of participants into stroke studies, from 376 in 2006/07 to 594 in 2008/09. The majority (17/20) of our current studies are interventional. Data from one of these, the CLOTs trial (Clots in Legs Or sTocking after Stroke), demonstrates that the annual recruitment in Scotland increased from a median of 94 (range 6-122) patients per year in the six years before the SSRN, to 140 (135-158) patients per year after SSRN involvement. We currently screen about 50% of Scottish stroke patients and approximately 5% of Scottish stroke patients are participating in research studies that we support. The SSRN has made good progress in the first three years. Increasing the recruitment of screened patients remains a challenge.

RNAi screening comes of age: improved techniques and complementary approaches

PubMed Central

Mohr, Stephanie E.; Smith, Jennifer A.; Shamu, Caroline E.; Neumüller, Ralph A.; Perrimon, Norbert

2014-01-01

Gene silencing through sequence-specific targeting of mRNAs by RNAi has enabled genome-wide functional screens in cultured cells and in vivo in model organisms. These screens have resulted in the identification of new cellular pathways and potential drug targets. Considerable progress has been made to improve the quality of RNAi screen data through the development of new experimental and bioinformatics approaches. The recent availability of genome-editing strategies, such as the CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 system, when combined with RNAi, could lead to further improvements in screen data quality and follow-up experiments, thus promoting our understanding of gene function and gene regulatory networks. PMID:25145850

Factors influencing breast cancer screening in low-income African Americans in Tennessee.

PubMed

Patel, Kushal; Kanu, Mohamed; Liu, Jianguo; Bond, Brea; Brown, Elizabeth; Williams, Elizabeth; Theriot, Rosemary; Bailey, Stephanie; Sanderson, Maureen; Hargreaves, Margaret

2014-10-01

This study examined demographic and lifestyle factors that influenced decisions and obstacles to being screened for breast cancer in low-income African Americans in three urban Tennessee cities. As part of the Meharry Community Networks Program (CNP) needs assessment, a 123-item community survey was administered to assess demographic characteristics, health care access and utilization, and screening practices for various cancers in low-income African Americans. For this study, only African American women 40 years and older (n = 334) were selected from the Meharry CNP community survey database. There were several predictors of breast cancer screening such as marital status and having health insurance (P < .05). Additionally, there were associations between obstacles to screening and geographic region such as transportation and not having enough information about screenings (P < .05). Educational interventions aimed at improving breast cancer knowledge and screening rates should incorporate information about obstacles and predictors to screening.

Factors influencing Breast Cancer Screening in Low-Income African Americans in Tennessee

PubMed Central

Patel, Kushal; Kanu, Mohamed; Liu, Jianguo; Bond, Brea; Brown, Elizabeth; Williams, Elizabeth; Theriot, Rosemary; Bailey, Stephanie; Sanderson, Maureen; Hargreaves, Margaret

2014-01-01

This study examined demographic and lifestyle factors that influenced decisions and obstacles to being screened for breast cancer in low-income African Americans in three urban Tennessee cities. As part of the Meharry Community Networks Program (CNP) needs assessment, a 123-item community survey was administered to assess demographic characteristics, health care access and utilization, and screening practices for various cancers in low-income African Americans. For this study, only African American women 40 years and older (n=334) were selected from the Meharry CNP community survey database. There were several predictors of breast cancer screening such as marital status and having health insurance (P< .05). Additionally, there were associations between obstacles to screening and geographic region such as transportation and not having enough information about screenings (P< .05). Educational interventions aimed at improving breast cancer knowledge and screening rates should incorporate information about obstacles and predictors to screening. PMID:24554393

A comparison of network-based strategies for screening at-risk Hispanic/Latino adolescents and young adults for undiagnosed asymptomatic HIV infection.

PubMed

Boyer, Cherrie B; Robles-Schrader, Grisel M; Li, Su X; Miller, Robin L; Korelitz, James; Price, Georgine N; Rivera Torres, Carmen M; Chutuape, Kate S; Stines, Stephanie J; Straub, Diane M; Peralta, Ligia; Febo, Irma; Hightow-Weidman, Lisa; Gonin, René; Kapogiannis, Bill G; Ellen, Jonathan M

2014-12-01

Hispanic/Latino adolescents and young adults are disproportionately impacted by the HIV/AIDS epidemic; yet little is known about the best strategies to increase HIV testing in this group. Network-based approaches are feasible and acceptable means for screening at-risk adults for HIV infection, but it is unknown whether these approaches are appropriate for at-risk young Hispanics/Latinos. Thus, we compared an alternative venue-based testing (AVT) strategy with a social and sexual network-based interviewing and HIV testing (SSNIT) strategy. All participants were Hispanics/Latinos aged 13-24 years with self-reported HIV risk; they were recruited from 11 cities in the United States and Puerto Rico and completed an audio computer-assisted self-interview and underwent HIV screening. A total of 1,596 participants (94.5% of those approached) were enrolled: 784 (49.1%) through AVT and 812 (50.9%) through SSNIT. HIV infection was identified in three SSNIT (.37%) and four AVT (.51%) participants (p = .7213). Despite high levels of HIV risk, a low prevalence of HIV infection was identified with no differences by recruitment strategy. We found overwhelming support for the acceptability and feasibility of AVT and SSNIT for engaging and screening at-risk young Hispanics/Latinos. Further research is needed to better understand how to strategically implement such strategies to improve identification of undiagnosed HIV infection. Copyright © 2014 Society for Adolescent Health and Medicine. All rights reserved.

Towards automatic pulmonary nodule management in lung cancer screening with deep learning

NASA Astrophysics Data System (ADS)

Ciompi, Francesco; Chung, Kaman; van Riel, Sarah J.; Setio, Arnaud Arindra Adiyoso; Gerke, Paul K.; Jacobs, Colin; Th. Scholten, Ernst; Schaefer-Prokop, Cornelia; Wille, Mathilde M. W.; Marchianò, Alfonso; Pastorino, Ugo; Prokop, Mathias; van Ginneken, Bram

2017-04-01

The introduction of lung cancer screening programs will produce an unprecedented amount of chest CT scans in the near future, which radiologists will have to read in order to decide on a patient follow-up strategy. According to the current guidelines, the workup of screen-detected nodules strongly relies on nodule size and nodule type. In this paper, we present a deep learning system based on multi-stream multi-scale convolutional networks, which automatically classifies all nodule types relevant for nodule workup. The system processes raw CT data containing a nodule without the need for any additional information such as nodule segmentation or nodule size and learns a representation of 3D data by analyzing an arbitrary number of 2D views of a given nodule. The deep learning system was trained with data from the Italian MILD screening trial and validated on an independent set of data from the Danish DLCST screening trial. We analyze the advantage of processing nodules at multiple scales with a multi-stream convolutional network architecture, and we show that the proposed deep learning system achieves performance at classifying nodule type that surpasses the one of classical machine learning approaches and is within the inter-observer variability among four experienced human observers.

Towards automatic pulmonary nodule management in lung cancer screening with deep learning.

PubMed

Ciompi, Francesco; Chung, Kaman; van Riel, Sarah J; Setio, Arnaud Arindra Adiyoso; Gerke, Paul K; Jacobs, Colin; Scholten, Ernst Th; Schaefer-Prokop, Cornelia; Wille, Mathilde M W; Marchianò, Alfonso; Pastorino, Ugo; Prokop, Mathias; van Ginneken, Bram

2017-04-19

The introduction of lung cancer screening programs will produce an unprecedented amount of chest CT scans in the near future, which radiologists will have to read in order to decide on a patient follow-up strategy. According to the current guidelines, the workup of screen-detected nodules strongly relies on nodule size and nodule type. In this paper, we present a deep learning system based on multi-stream multi-scale convolutional networks, which automatically classifies all nodule types relevant for nodule workup. The system processes raw CT data containing a nodule without the need for any additional information such as nodule segmentation or nodule size and learns a representation of 3D data by analyzing an arbitrary number of 2D views of a given nodule. The deep learning system was trained with data from the Italian MILD screening trial and validated on an independent set of data from the Danish DLCST screening trial. We analyze the advantage of processing nodules at multiple scales with a multi-stream convolutional network architecture, and we show that the proposed deep learning system achieves performance at classifying nodule type that surpasses the one of classical machine learning approaches and is within the inter-observer variability among four experienced human observers.

Towards automatic pulmonary nodule management in lung cancer screening with deep learning

PubMed Central

Ciompi, Francesco; Chung, Kaman; van Riel, Sarah J.; Setio, Arnaud Arindra Adiyoso; Gerke, Paul K.; Jacobs, Colin; Th. Scholten, Ernst; Schaefer-Prokop, Cornelia; Wille, Mathilde M. W.; Marchianò, Alfonso; Pastorino, Ugo; Prokop, Mathias; van Ginneken, Bram

2017-01-01

The introduction of lung cancer screening programs will produce an unprecedented amount of chest CT scans in the near future, which radiologists will have to read in order to decide on a patient follow-up strategy. According to the current guidelines, the workup of screen-detected nodules strongly relies on nodule size and nodule type. In this paper, we present a deep learning system based on multi-stream multi-scale convolutional networks, which automatically classifies all nodule types relevant for nodule workup. The system processes raw CT data containing a nodule without the need for any additional information such as nodule segmentation or nodule size and learns a representation of 3D data by analyzing an arbitrary number of 2D views of a given nodule. The deep learning system was trained with data from the Italian MILD screening trial and validated on an independent set of data from the Danish DLCST screening trial. We analyze the advantage of processing nodules at multiple scales with a multi-stream convolutional network architecture, and we show that the proposed deep learning system achieves performance at classifying nodule type that surpasses the one of classical machine learning approaches and is within the inter-observer variability among four experienced human observers. PMID:28422152

Inferring Regulatory Networks by Combining Perturbation Screens and Steady State Gene Expression Profiles

PubMed Central

Michailidis, George

2014-01-01

Reconstructing transcriptional regulatory networks is an important task in functional genomics. Data obtained from experiments that perturb genes by knockouts or RNA interference contain useful information for addressing this reconstruction problem. However, such data can be limited in size and/or are expensive to acquire. On the other hand, observational data of the organism in steady state (e.g., wild-type) are more readily available, but their informational content is inadequate for the task at hand. We develop a computational approach to appropriately utilize both data sources for estimating a regulatory network. The proposed approach is based on a three-step algorithm to estimate the underlying directed but cyclic network, that uses as input both perturbation screens and steady state gene expression data. In the first step, the algorithm determines causal orderings of the genes that are consistent with the perturbation data, by combining an exhaustive search method with a fast heuristic that in turn couples a Monte Carlo technique with a fast search algorithm. In the second step, for each obtained causal ordering, a regulatory network is estimated using a penalized likelihood based method, while in the third step a consensus network is constructed from the highest scored ones. Extensive computational experiments show that the algorithm performs well in reconstructing the underlying network and clearly outperforms competing approaches that rely only on a single data source. Further, it is established that the algorithm produces a consistent estimate of the regulatory network. PMID:24586224

OPTIMAL WELL LOCATOR (OWL): A SCREENING TOOL FOR EVALUATING LOCATIONS OF MONITORING WELLS: USER'S GUIDE VERSION 1.2

EPA Science Inventory

The Optimal Well Locator ( OWL) program was designed and developed by USEPA to be a screening tool to evaluate and optimize the placement of wells in long term monitoring networks at small sites. The first objective of the OWL program is to allow the user to visualize the change ...

In vitro screening of metal oxide nanoparticles for effects on neural function using cortical networks on microelectrode arrays

EPA Science Inventory

Nanoparticles (NPs) may translocate to the brain following inhalation or oral exposures, yet higher throughput methods to screen NPs for potential neurotoxicity are lacking. The present study examined effects of 5 Ce02 (5- 1288 nm), and 4 Ti02 (6-142 nm) NPs and microparticles (M...

Adherence to Radiology Recommendations in a Clinical CT Lung Screening Program.

PubMed

Alshora, Sama; McKee, Brady J; Regis, Shawn M; Borondy Kitts, Andrea K; Bolus, Christopher C; McKee, Andrea B; French, Robert J; Flacke, Sebastian; Wald, Christoph

2018-02-01

Assess patient adherence to radiologist recommendations in a clinical CT lung cancer screening program. Patients undergoing CT lung cancer screening between January 12, 2012, and June 12, 2013, were included in this institutional review board-approved retrospective review. Patients referred from outside our institution were excluded. All patients met National Comprehensive Cancer Network Guidelines Lung Cancer Screening high-risk criteria. Full-time program navigators used a CT lung screening program management system to schedule patient appointments, generate patient result notification letters detailing the radiologist follow-up recommendation, and track patient and referring physician notification of missed appointments at 30, 60, and 90 days. To be considered adherent, patients could be no more than 90 days past due for their next recommended examination as of September 12, 2014. Patients who died, were diagnosed with cancer, or otherwise became ineligible for screening were considered adherent. Adherence rates were assessed across multiple variables. During the study interval, 1,162 high-risk patients were screened, and 261 of 1,162 (22.5%) outside referrals were excluded. Of the remaining 901 patients, 503 (55.8%) were male, 414 (45.9%) were active smokers, 377 (41.8%) were aged 65 to 73, and >95% were white. Of the 901 patients, 772 (85.7%) were adherent. Most common reasons for nonadherence were patient refusal of follow-up exam (66.7%), inability to successfully contact the patient (20.9%), and inability to obtain the follow-up order from the referring provider (7.8%); 23 of 901 (2.6%) were discharged for other reasons. High rates of adherence to radiologist recommendations are achievable for in-network patients enrolled in a clinical CT lung screening program. Copyright © 2017 American College of Radiology. Published by Elsevier Inc. All rights reserved.

The Pittsburgh Cervical Cancer Screening Model: a risk assessment tool.

PubMed

Austin, R Marshall; Onisko, Agnieszka; Druzdzel, Marek J

2010-05-01

Evaluation of cervical cancer screening has grown increasingly complex with the introduction of human papillomavirus (HPV) vaccination and newer screening technologies approved by the US Food and Drug Administration. To create a unique Pittsburgh Cervical Cancer Screening Model (PCCSM) that quantifies risk for histopathologic cervical precancer (cervical intraepithelial neoplasia [CIN] 2, CIN3, and adenocarcinoma in situ) and cervical cancer in an environment predominantly using newer screening technologies. The PCCSM is a dynamic Bayesian network consisting of 19 variables available in the laboratory information system, including patient history data (most recent HPV vaccination data), Papanicolaou test results, high-risk HPV results, procedure data, and histopathologic results. The model's graphic structure was based on the published literature. Results from 375 441 patient records from 2005 through 2008 were used to build and train the model. Additional data from 45 930 patients were used to test the model. The PCCSM compares risk quantitatively over time for histopathologically verifiable CIN2, CIN3, adenocarcinoma in situ, and cervical cancer in screened patients for each current cytology result category and for each HPV result. For each current cytology result, HPV test results affect risk; however, the degree of cytologic abnormality remains the largest positive predictor of risk. Prior history also alters the CIN2, CIN3, adenocarcinoma in situ, and cervical cancer risk for patients with common current cytology and HPV test results. The PCCSM can also generate negative risk projections, estimating the likelihood of the absence of histopathologic CIN2, CIN3, adenocarcinoma in situ, and cervical cancer in screened patients. The PCCSM is a dynamic Bayesian network that computes quantitative cervical disease risk estimates for patients undergoing cervical screening. Continuously updatable with current system data, the PCCSM provides a new tool to monitor cervical disease risk in the evolving postvaccination era.

Army Networks: Opportunities Exist to Better Utilize Results from Network Integration Evaluations

DTIC Science & Technology

2013-08-01

monitor operations; a touch screen-based mission command planning tool; and an antenna mast . The Army will field only one of these systems in capability...Office JTRS Joint Tactical Radio System NIE Network Integration Evaluation OSD Office of the Secretary of Defense SUE System under Evaluation...command systems . A robust transport layer capable of delivering voice, data, imagery, and video to the tactical edge (i.e., the forward battle lines

Basic Lessons in ORA and AutoMap 2011

DTIC Science & Technology

2011-06-13

A small legend also appears. Below is a screen capture showing the visualization of the agent x event graph from the Stargate Summit Meta-Network...4 The visualization displays the connections between all items in the Stargate Summit Meta-Network. The red circles represent the agents, the...It takes the examples I used for the Stargate dataset. 5 lessons - 201-207 A step by step run through of creating the Meta-Network from

Basic Lessons in *ORA and Automap 2009

DTIC Science & Technology

2009-06-01

screen capture showing the visualization of the agent x event graph from the Stargate Summit Meta-Network. The visualization displays the connections...for the Stargate dataset. 25.2 lessons - 201-207 A step by step run through of creating the Meta-Network from working with Excel, exporting data to...For the purpose of creating the Stargate MetaNetwork the two-episode story arc (Summit / Last Stand) was choosen as the basis for all the nodes

Identification of crucial genes related to postmenopausal osteoporosis using gene expression profiling.

PubMed

Ma, Min; Chen, Xiaofei; Lu, Liangyu; Yuan, Feng; Zeng, Wen; Luo, Shulin; Yin, Feng; Cai, Junfeng

2016-12-01

Postmenopausal osteoporosis is a common bone disease and characterized by low bone mineral density. This study aimed to reveal key genes associated with postmenopausal osteoporosis (PMO), and provide a theoretical basis for subsequent experiments. The dataset GSE7429 was obtained from Gene Expression Omnibus. A total of 20 B cell samples (ten ones, respectively from postmenopausal women with low or high bone mineral density (BMD) were included in this dataset. Following screening of differentially expressed genes (DEGs), coexpression analysis of all genes was performed, and key genes in the coexpression network were screened using the random walk algorithm. Afterwards, functional and pathway analyses were conducted. Additionally, protein-protein interactions (PPIs) between DEGs and key genes were analyzed. A set of 308 DEGs (170 up-regulated ones and 138 down-regulated ones) between low BMD and high BMD samples were identified, and 101 key genes in the coexpression network were screened out. In the coexpression network, some genes had a higher score and degree, such as CSTA. The key genes in the coexpression network were mainly enriched in GO terms of the defense response (e.g., SERPINA1 and CST3), immune response (e.g., IL32 and CLEC7A); while, the DEGs were mainly enriched in structural constituent of cytoskeleton (e.g., CYLC2 and TUBA1B) and membrane-enclosed lumen (e.g., CCNE1 and INTS5). In the PPI network, CCNE1 interacted with REL; and TUBA1B interacted with ESR1. A series of interactions, such as CSTA/TYROBP, CCNE1/REL and TUBA1B/ESR1 might play pivotal roles in the occurrence and development of PMO.

Chemical Genetic Screens for TDP-43 Modifiers and ALS Drug Discovery

DTIC Science & Technology

2015-03-01

Blackstone , 2012). Recently, a large network including many of these genes have been identify and this network is highly similar to Parkinson’s, ALS and...10.1186/1750- 1326-8-30 Blackstone , C. (2012). Cellular pathways of hereditary spastic paraplegia. Annu. Rev. Neurosci. 35, 25–47. doi: 10.1146/annurev

Screening for cardiovascular risk in asymptomatic users of the primary health care network in Lebanon, 2012-2013.

PubMed

Yamout, Rouham; Adib, Salim M; Hamadeh, Randa; Freidi, Alia; Ammar, Walid

2014-07-17

In 2012, the Ministry of Public Health in Lebanon piloted a service of multifactorial cardiovascular screening in the publicly subsidized Primary Health Care (PHC) Network. We present an epidemiological analysis of data produced during this pilot to justify the inclusion of this service in the package of essential services offered through PHC and to present a preliminary cardiovascular risk profile in an asymptomatic population. A total of 4,205 participants (two-thirds of which were women) aged at least 40 years and reportedly free from diabetes, hypertension, dyslipidemia, and cardiovascular disease (CVD) were screened. The screening protocol used a questionnaire and direct measurements to assess 5 modifiable cardiovascular risk factors; total cardiovascular risk score was calculated according to a paper-based algorithm developed by the World Health Organization and the International Society of Hypertension. Approximately 25% of the sample displayed metabolic impairments (11% for impaired blood glucose metabolism and 17% for impaired systolic blood pressure), and 6.6% were classified at total cardiovascular risk of 10% or more. Just over one-quarter of the sample was obese, almost half had a substantially elevated waist circumference, and 41% were smokers. Men were significantly more likely to screen positive for metabolic impairment than women, and women were more likely to be obese. The implementation of a multifactorial screening for CVD among asymptomatic subjects detected a substantial proportion of previously undiagnosed cases of high metabolic risk, people who could now be referred to optimal medical follow-up.

Audit feedback on reading performance of screening mammograms: An international comparison.

PubMed

Hofvind, S; Bennett, R L; Brisson, J; Lee, W; Pelletier, E; Flugelman, A; Geller, B

2016-09-01

Providing feedback to mammography radiologists and facilities may improve interpretive performance. We conducted a web-based survey to investigate how and why such feedback is undertaken and used in mammographic screening programmes. The survey was sent to representatives in 30 International Cancer Screening Network member countries where mammographic screening is offered. Seventeen programmes in 14 countries responded to the survey. Audit feedback was aimed at readers in 14 programmes, and facilities in 12 programmes. Monitoring quality assurance was the most common purpose of audit feedback. Screening volume, recall rate, and rate of screen-detected cancers were typically reported performance measures. Audit reports were commonly provided annually, but more frequently when target guidelines were not reached. The purpose, target audience, performance measures included, form and frequency of the audit feedback varied amongst mammographic screening programmes. These variations may provide a basis for those developing and improving such programmes. © The Author(s) 2016.

Effects of television weather broadcasters on viewers during severe weather: To be or not to be on-screen

NASA Astrophysics Data System (ADS)

Lea, Amanda Marie

An association was tested between the presence of a television weather broadcaster on-screen and viewers' likelihood to seek shelter, measured via risk perception and preventative behavior. Social networking websites were used to recruit respondents. Four clips of archived severe weather videos, one pair (on-screen and off-screen broadcaster) using the reflectivity product and another pair (on-screen and off-screen broadcaster) using velocity product, were presented to participants. Viewers' trust and weather salience were also quantified for additional interactions. A relationship between viewers' risk perception (preflectivity = 0.821, pvelocity = 0.625) and preventative behavior (preflectivity = 0.217, p velocity = 0.236) and the presence of the broadcaster on-screen was not found. The reflectivity product was associated with higher risk perception and preventative behavior scores than the velocity product (prp = 0.000, ppb = 0.000).

A Learning Collaborative Approach to Improve Primary Care STI Screening.

PubMed

McKee, M Diane; Alderman, Elizabeth; York, Deborah V; Blank, Arthur E; Briggs, Rahil D; Hoidal, Kelsey E S; Kus, Christopher; Lechuga, Claudia; Mann, Marie; Meissner, Paul; Patel, Nisha; Racine, Andrew D

2017-10-01

The Bronx Ongoing Pediatric Screening (BOPS) project sought to improve screening for sexual activity and sexually transmitted infections (gonorrhea and chlamydia [GCC] and HIV) in a primary care network, employing a modified learning collaborative, real-time clinical data feedback to practices, improvement coaching, and a pay-for-quality monetary incentive. Outcomes are compared for 11 BOPS-participating sites and 10 non-participating sites. The quarterly median rate for documenting sexual activity status increased from 55% to 88% (BOPS sites) and from 13% to 74% (non-BOPS sites). GCC screening of sexually active youth increased at BOPS and non-BOPS sites. Screening at non-health care maintenance visits improved more at BOPS than non-BOPS sites. Data from nonparticipating sites suggests that introduction of an adolescent EMR template or other factors improved screening rates regardless of BOPS participation; BOPS activities appear to promote additional improvement of screening during non-health maintenance visits.

Improved Classification of Lung Cancer Using Radial Basis Function Neural Network with Affine Transforms of Voss Representation.

PubMed

Adetiba, Emmanuel; Olugbara, Oludayo O

2015-01-01

Lung cancer is one of the diseases responsible for a large number of cancer related death cases worldwide. The recommended standard for screening and early detection of lung cancer is the low dose computed tomography. However, many patients diagnosed die within one year, which makes it essential to find alternative approaches for screening and early detection of lung cancer. We present computational methods that can be implemented in a functional multi-genomic system for classification, screening and early detection of lung cancer victims. Samples of top ten biomarker genes previously reported to have the highest frequency of lung cancer mutations and sequences of normal biomarker genes were respectively collected from the COSMIC and NCBI databases to validate the computational methods. Experiments were performed based on the combinations of Z-curve and tetrahedron affine transforms, Histogram of Oriented Gradient (HOG), Multilayer perceptron and Gaussian Radial Basis Function (RBF) neural networks to obtain an appropriate combination of computational methods to achieve improved classification of lung cancer biomarker genes. Results show that a combination of affine transforms of Voss representation, HOG genomic features and Gaussian RBF neural network perceptibly improves classification accuracy, specificity and sensitivity of lung cancer biomarker genes as well as achieving low mean square error.

Synthetic Tumor Networks for Screening Drug Delivery Systems

PubMed Central

Prabhakarpandian, Balabhaskar; Shen, Ming-Che; Nichols, Joseph B.; Garson, Charles J.; Mills, Ivy R.; Matar, Majed M.; Fewell, Jason G.; Pant, Kapil

2015-01-01

Tumor drug delivery is a complex phenomenon affected by several elements in addition to drug or delivery vehicle’s physico-chemical properties. A key factor is tumor microvasculature with complex effects including convective transport, high interstitial pressure and enhanced vascular permeability due to the presence of “leaky vessels”. Current in vitro models of the tumor microenvironment for evaluating drug delivery are oversimplified and, as a result, show poor correlation with in vivo performance. In this study, we report on the development of a novel microfluidic platform that models the tumor microenvironment more accurately, with physiologically and morphologically realistic microvasculature including endothelial cell lined leaky capillary vessels along with 3D solid tumors. Endothelial cells and 3D spheroids of cervical tumor cells were co-cultured in the networks. Drug vehicle screening was demonstrated using GFP gene delivery by different formulations of nanopolymers. The synthetic tumor network was successful in predicting in vivo delivery efficiencies of the drug vehicles. The developed assay will have critical applications both in basic research, where it can be used to develop next generation delivery vehicles, and in drug discovery where it can be used to study drug transport and delivery efficacy in realistic tumor microenvironment, thereby enabling drug compound and/or delivery vehicle screening. PMID:25599856

Predictors of Colorectal Screening in Rural Colorado: Testing to Prevent Colon Cancer in the High Plains Research Network

ERIC Educational Resources Information Center

Young, Walter F.; McGloin, Joe; Zittleman, Linda; West, David R.; Westfall, John M.

2007-01-01

Context: Colorectal cancer is the second leading cause of cancer death in the United States, yet screening rates are well below target levels. Rural communities may face common and unique barriers to health care, particularly preventive health care. Purpose: To establish baseline attitudinal, knowledge, belief, and behavior measures on colorectal…

Knowledge, Attitudes, Beliefs, and Personal Practices regarding Colorectal Cancer Screening among Health Care Professionals in Rural Colorado: A Pilot Survey

ERIC Educational Resources Information Center

Rim, Sun Hee; Zittleman, Linda; Westfall, John M.; Overholser, Linda; Froshaug, Desiree; Coughlin, Steven S.

2009-01-01

Purpose: This study reports the baseline knowledge, attitudes, beliefs, and personal practices of health care professionals regarding colorectal cancer (CRC) screening in the High Plains Research Network (HPRN) of rural Colorado prior to a community-based educational intervention. It also examines the association between health care staff members'…

Louisiana State University Health Sciences Center Katrina Inspired Disaster Screenings (KIDS): Psychometric Testing of the National Child Traumatic Stress Network Hurricane Assessment and Referral Tool

ERIC Educational Resources Information Center

Hansel, Tonya Cross; Osofsky, Joy D.; Osofsky, Howard J.

2015-01-01

Background: Post disaster psychosocial surveillance procedures are important for guiding effective and efficient recovery. The Louisiana State University Health Sciences Center Katrina Inspired Disaster Screenings (KIDS) is a model designed with the goal of assisting recovering communities in understanding the needs of and targeting services…

Evaluations of Thin Cirrus Contamination and Screening in Ground Aerosol Observations Using Collocated Lidar Systems

NASA Technical Reports Server (NTRS)

Huang, Jingfeng; Hsu, N. Christina; Tsay, Si-Chee; Holben, Brent N.; Welton, Ellsworth J.; Smirnov, Alexander; Jeong, Myeong-Jae; Hansell, Richard A.; Berkoff, Timothy A.

2012-01-01

Cirrus clouds, particularly sub visual high thin cirrus with low optical thickness, are difficult to be screened in operational aerosol retrieval algorithms. Collocated aerosol and cirrus observations from ground measurements, such as the Aerosol Robotic Network (AERONET) and the Micro-Pulse Lidar Network (MPLNET), provide us with an unprecedented opportunity to examine the susceptibility of operational aerosol products to thin cirrus contamination. Quality assured aerosol optical thickness (AOT) measurements were also tested against the CALIPSO vertical feature mask (VFM) and the MODIS-derived thin cirrus screening parameters for the purpose of evaluating thin cirrus contamination. Key results of this study include: (1) Quantitative evaluations of data uncertainties in AERONET AOT retrievals are conducted. Although AERONET cirrus screening schemes are successful in removing most cirrus contamination, strong residuals displaying strong spatial and seasonal variability still exist, particularly over thin cirrus prevalent regions during cirrus peak seasons, (2) Challenges in matching up different data for analysis are highlighted and corresponding solutions proposed, and (3) Estimation of the relative contributions from cirrus contamination to aerosol retrievals are discussed. The results are valuable for better understanding and further improving ground aerosol measurements that are critical for aerosol-related climate research.

Differentially Coexpressed Disease Gene Identification Based on Gene Coexpression Network.

PubMed

Jiang, Xue; Zhang, Han; Quan, Xiongwen

2016-01-01

Screening disease-related genes by analyzing gene expression data has become a popular theme. Traditional disease-related gene selection methods always focus on identifying differentially expressed gene between case samples and a control group. These traditional methods may not fully consider the changes of interactions between genes at different cell states and the dynamic processes of gene expression levels during the disease progression. However, in order to understand the mechanism of disease, it is important to explore the dynamic changes of interactions between genes in biological networks at different cell states. In this study, we designed a novel framework to identify disease-related genes and developed a differentially coexpressed disease-related gene identification method based on gene coexpression network (DCGN) to screen differentially coexpressed genes. We firstly constructed phase-specific gene coexpression network using time-series gene expression data and defined the conception of differential coexpression of genes in coexpression network. Then, we designed two metrics to measure the value of gene differential coexpression according to the change of local topological structures between different phase-specific networks. Finally, we conducted meta-analysis of gene differential coexpression based on the rank-product method. Experimental results demonstrated the feasibility and effectiveness of DCGN and the superior performance of DCGN over other popular disease-related gene selection methods through real-world gene expression data sets.

The Case for Lung Cancer Screening: What Nurses Need to Know.

PubMed

Sorrie, Kerrin; Cates, Lisa; Hill, Alethea

2016-06-01

Lung cancer screening with low-dose helical computed tomography (LDCT) can improve high-risk individuals' chances of being diagnosed at an earlier stage and increase survival. The aims of this article are to present the risk factors associated with the development of lung cancer, identify patients at high risk for lung cancer qualifying for LDCT screening, and understand the importance of early lung cancer detection through the use of LDCT screening. PubMed and CINAHL® databases were searched with key words lung cancer screening to identify full-text academic articles from 2004-2014. This resulted in 529 articles from PubMed and 195 from CINAHL. PubMed offered suggestions for additional relevant journal articles. The National Comprehensive Cancer Network guidelines also provided substantial evidence-based information. Nurses need to provide support, education, and resources for patients undergoing lung cancer screening.

The Healthy Connections project: a community-based participatory research project involving women at risk for diabetes and hypertension.

PubMed

Harvey, Idethia; Schulz, Amy; Israel, Barbara; Sand, Sharon; Myrie, Deanna; Lockett, Murlisa; Weir, Sheryl; Hill, Yolanda

2009-01-01

The Healthy Connections (HC) project was a community health worker (CHW) intervention that built upon existing social networks to encourage African American and Latina women to obtain screening for type 2 diabetes and hypertension. This community-based participatory research (CBPR) project involved identifying and training CHWs, known as HC Advocates (HCAs). The HCAs provided screening through House Parties and shared health information and practical support with members of their social networks and broader networks of individuals. Data collection methods included project documentation, participant observation, group interviews, closed-ended surveys, and written examinations to ensure HCAs had the required knowledge and skills to perform their roles. Data collection and analysis incorporated both qualitative and quantitative methods, and used a formative approach that integrated results from key aspects of the project into ongoing decision-making and project activities. Eight community residents completed training and the required exams to become HCAs. Together, they conducted 124 House Parties, screened 1,428 individuals for high blood pressure and glucose levels, and shared health information with those individuals as well as 218 additional members of HCAs informal social networks. Of those who attended the House Parties, 93% were African American, 4% Latina, 2% non-Hispanics whites, and 1% other racial and ethnic groups. The HC project demonstrated the potential for using a CBPR approach to develop, implement, and evaluate a CHW intervention designed to reach African American and Latina women at high risk for hypertension and type 2 diabetes. Participation from relevant communities in the design of the intervention and evaluation, with particular attention to recruitment and retention of representatives from communities who face challenges accessing health care, can help to increase involvement of community residents in screening and educational programs aimed at addressing disparities in type 2 diabetes and hypertension.

Structure-based manual screening and automatic networking for systematically exploring sansanmycin analogues using high performance liquid chromatography tandem mass spectroscopy.

PubMed

Jiang, Zhi-Bo; Ren, Wei-Cong; Shi, Yuan-Yuan; Li, Xing-Xing; Lei, Xuan; Fan, Jia-Hui; Zhang, Cong; Gu, Ren-Jie; Wang, Li-Fei; Xie, Yun-Ying; Hong, Bin

2018-05-18

Sansanmycins (SS), one of several known uridyl peptide antibiotics (UPAs) possessing a unique chemical scaffold, showed a good inhibitory effect on the highly refractory pathogens Pseudomonas aeruginosa and Mycobacterium tuberculosis, especially on the multi-drug resistant M. tuberculosis. This study employed high performance liquid chromatography-mass spectrometry detector (HPLC-MSD) ion trap and LTQ orbitrap tandem mass spectrometry (MS/MS) to explore sansanmycin analogues manually and automatically by re-analysis of the Streptomyces sp. SS fermentation broth. The structure-based manual screening method, based on analysis of the fragmentation pathway of known UPAs and on comparisons of the MS/MS spectra with that of sansanmycin A (SS-A), resulted in identifying twenty sansanmycin analogues, including twelve new structures (1-12). Furthermore, to deeply explore sansanmycin analogues, we utilized a GNPS based molecular networking workflow to re-analyze the HPLC-MS/MS data automatically. As a result, eight more new sansanmycins (13-20) were discovered. Compound 1 was discovered to lose two amino acids of residue 1 (AA 1 ) and (2S, 3S)-N 3 -methyl-2,3-diamino butyric acid (DABA) from the N-terminus, and compounds 6, 11 and 12 were found to contain a 2',3'-dehydrated 4',5'-enamine-3'-deoxyuridyl moiety, which have not been reported before. Interestingly, three trace components with novel 5,6-dihydro-5'-aminouridyl group (16-18) were detected for the first time in the sansanmycin-producing strain. Their structures were primarily determined by detail analysis of the data from MS/MS. Compounds 8 and 10 were further confirmed by nuclear magnetic resonance (NMR) data, which proved the efficiency and accuracy of the method of HPLC-MS/MS for exploration of novel UPAs. Comparing to manual screening, the networking method can provide systematic visualization results. Manual screening and networking method may complement with each other to facilitate the mining of novel UPAs. Copyright © 2018 Elsevier B.V. All rights reserved.

Exploring the Potential of a Global Emerging Contaminant Early Warning Network through the Use of Retrospective Suspect Screening with High-Resolution Mass Spectrometry.

PubMed

Alygizakis, Nikiforos A; Samanipour, Saer; Hollender, Juliane; Ibáñez, María; Kaserzon, Sarit; Kokkali, Varvara; van Leerdam, Jan A; Mueller, Jochen F; Pijnappels, Martijn; Reid, Malcolm J; Schymanski, Emma L; Slobodnik, Jaroslav; Thomaidis, Nikolaos S; Thomas, Kevin V

2018-05-01

A key challenge in the environmental and exposure sciences is to establish experimental evidence of the role of chemical exposure in human and environmental systems. High resolution and accurate tandem mass spectrometry (HRMS) is increasingly being used for the analysis of environmental samples. One lauded benefit of HRMS is the possibility to retrospectively process data for (previously omitted) compounds that has led to the archiving of HRMS data. Archived HRMS data affords the possibility of exploiting historical data to rapidly and effectively establish the temporal and spatial occurrence of newly identified contaminants through retrospective suspect screening. We propose to establish a global emerging contaminant early warning network to rapidly assess the spatial and temporal distribution of contaminants of emerging concern in environmental samples through performing retrospective analysis on HRMS data. The effectiveness of such a network is demonstrated through a pilot study, where eight reference laboratories with available archived HRMS data retrospectively screened data acquired from aqueous environmental samples collected in 14 countries on 3 different continents. The widespread spatial occurrence of several surfactants (e.g., polyethylene glycols ( PEGs ) and C12AEO-PEGs ), transformation products of selected drugs (e.g., gabapentin-lactam, metoprolol-acid, carbamazepine-10-hydroxy, omeprazole-4-hydroxy-sulfide, and 2-benzothiazole-sulfonic-acid), and industrial chemicals (3-nitrobenzenesulfonate and bisphenol-S) was revealed. Obtaining identifications of increased reliability through retrospective suspect screening is challenging, and recommendations for dealing with issues such as broad chromatographic peaks, data acquisition, and sensitivity are provided.

Space lab system analysis

NASA Technical Reports Server (NTRS)

Ingels, F. M.; Rives, T. B.

1987-01-01

An analytical analysis of the HOSC Generic Peripheral processing system was conducted. The results are summarized and they indicate that the maximum delay in performing screen change requests should be less than 2.5 sec., occurring for a slow VAX host to video screen I/O rate of 50 KBps. This delay is due to the average I/O rate from the video terminals to their host computer. Software structure of the main computers and the host computers will have greater impact on screen change or refresh response times. The HOSC data system model was updated by a newly coded PASCAL based simulation program which was installed on the HOSC VAX system. This model is described and documented. Suggestions are offered to fine tune the performance of the ETERNET interconnection network. Suggestions for using the Nutcracker by Excelan to trace itinerate packets which appear on the network from time to time were offered in discussions with the HOSC personnel. Several visits to the HOSC facility were to install and demonstrate the simulation model.

Practical Considerations for Optic Nerve Estimation in Telemedicine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Karnowski, Thomas Paul; Aykac, Deniz; Chaum, Edward

The projected increase in diabetes in the United States and worldwide has created a need for broad-based, inexpensive screening for diabetic retinopathy (DR), an eye disease which can lead to vision impairment. A telemedicine network with retina cameras and automated quality control, physiological feature location, and lesion / anomaly detection is a low-cost way of achieving broad-based screening. In this work we report on the effect of quality estimation on an optic nerve (ON) detection method with a confidence metric. We report on an improvement of the fusion technique using a data set from an ophthalmologists practice then show themore » results of the method as a function of image quality on a set of images from an on-line telemedicine network collected in Spring 2009 and another broad-based screening program. We show that the fusion method, combined with quality estimation processing, can improve detection performance and also provide a method for utilizing a physician-in-the-loop for images that may exceed the capabilities of automated processing.« less

Dynamic Reconfiguration and Link Fault Tolerance in a Transputer Network

DTIC Science & Technology

1989-06-01

linkO and link3 are connected to the C004s. LinkI and link2 are routed to the P2 edge connector, labelled ConfigUp and ConfiDown for access to...various commands recieved PROC handle.screen (VAL BYTE link.byte, SEQ -place the first byte on screen (source) I F1 linki < 16 -- a link 0 SEQ line.num l...determine characters used on screen for -- display of source & dest IF ((INT(bytel)) < 32) linki : to.slot[INT(bytel)] otherwise linki : 10 IF ((INT(byte2

Colleges Create Facebook-Style Social Networks to Reach Alumni

ERIC Educational Resources Information Center

Hermes, J.J.

2008-01-01

Trying to emulate the popularity of Web sites like Facebook and MySpace, hundreds of college alumni associations have begun to offer their own online social networks, seeking to stake a claim on the computer screens of current and former students, especially young alumni. Many of the sites have struggled to attract alumni and to keep them…

High content screening in neurodegenerative diseases.

PubMed

Jain, Shushant; van Kesteren, Ronald E; Heutink, Peter

2012-01-06

The functional annotation of genomes, construction of molecular networks and novel drug target identification, are important challenges that need to be addressed as a matter of great urgency. Multiple complementary 'omics' approaches have provided clues as to the genetic risk factors and pathogenic mechanisms underlying numerous neurodegenerative diseases, but most findings still require functional validation. For example, a recent genome wide association study for Parkinson's Disease (PD), identified many new loci as risk factors for the disease, but the underlying causative variant(s) or pathogenic mechanism is not known. As each associated region can contain several genes, the functional evaluation of each of the genes on phenotypes associated with the disease, using traditional cell biology techniques would take too long. There is also a need to understand the molecular networks that link genetic mutations to the phenotypes they cause. It is expected that disease phenotypes are the result of multiple interactions that have been disrupted. Reconstruction of these networks using traditional molecular methods would be time consuming. Moreover, network predictions from independent studies of individual components, the reductionism approach, will probably underestimate the network complexity. This underestimation could, in part, explain the low success rate of drug approval due to undesirable or toxic side effects. Gaining a network perspective of disease related pathways using HT/HC cellular screening approaches, and identifying key nodes within these pathways, could lead to the identification of targets that are more suited for therapeutic intervention. High-throughput screening (HTS) is an ideal methodology to address these issues. but traditional methods were one dimensional whole-well cell assays, that used simplistic readouts for complex biological processes. They were unable to simultaneously quantify the many phenotypes observed in neurodegenerative diseases such as axonal transport deficits or alterations in morphology properties. This approach could not be used to investigate the dynamic nature of cellular processes or pathogenic events that occur in a subset of cells. To quantify such features one has to move to multi-dimensional phenotypes termed high-content screening (HCS). HCS is the cell-based quantification of several processes simultaneously, which provides a more detailed representation of the cellular response to various perturbations compared to HTS. HCS has many advantages over HTS, but conducting a high-throughput (HT)-high-content (HC) screen in neuronal models is problematic due to high cost, environmental variation and human error. In order to detect cellular responses on a 'phenomics' scale using HC imaging one has to reduce variation and error, while increasing sensitivity and reproducibility. Herein we describe a method to accurately and reliably conduct shRNA screens using automated cell culturing and HC imaging in neuronal cellular models. We describe how we have used this methodology to identify modulators for one particular protein, DJ1, which when mutated causes autosomal recessive parkinsonism. Combining the versatility of HC imaging with HT methods, it is possible to accurately quantify a plethora of phenotypes. This could subsequently be utilized to advance our understanding of the genome, the pathways involved in disease pathogenesis as well as identify potential therapeutic targets. Copyright © 2012 Creative Commons Attribution License

HealthNavigator: a mobile application for chronic disease screening and linkage to services at an urban Primary Health Network.

PubMed

Seneviratne, Martin G; Hersch, Fred; Peiris, David P

2018-03-26

Mobile applications (apps) are promising tools to support chronic disease screening and linkage to health services. They have the potential to increase healthcare access for vulnerable populations. The HealthNavigator app was developed to provide chronic disease risk assessments, linkage to local general practitioners (GPs) and lifestyle programs, and a personalised health report for discussion with a GP. Assessments were either self-administered or facilitated by community health workers through a Primary Health Network (PHN) initiative targeting ethnically diverse communities. In total, 1492 assessments (80.4% self-administered, 19.6% facilitated) were conducted over a 12-month period in Queensland, Australia. Of these, 26% of people screened came from postcodes representing the lowest quartile of socioeconomic disadvantage. When compared against self-administered assessments, subjects screened by the facilitated program were more likely to be born outside Australia (80.5 v. 33.2%, P<0.001), and to fall within a high risk category based on cardiovascular risk scores (19.8 v. 13.7%, P<0.01) and type 2 diabetes mellitus risk scores (58.0 v. 40.1%, P<0.001). Mobile apps embedded into PHN programs may be a useful adjunct for the implementation of community screening programs. Further research is needed to determine their effect on health service access and health outcomes.

GHSI EMERGENCY RADIONUCLIDE BIOASSAY LABORATORY NETWORK: SUMMARY OF A RECENT EXERCISE.

PubMed

Li, Chunsheng; Ansari, Armin; Bartizel, Christine; Battisti, Paolo; Franck, Didier; Gerstmann, Udo; Giardina, Isabella; Guichet, Claude; Hammond, Derek; Hartmann, Martina; Jones, Robert L; Kim, Eunjoo; Ko, Raymond; Morhard, Ryan; Quayle, Deborah; Sadi, Baki; Saunders, David; Paquet, Francois

2016-11-01

The Global Health Security Initiative (GHSI) established a laboratory network within the GHSI community to develop their collective surge capacity for radionuclide bioassay in response to a radiological or nuclear emergency. A recent exercise was conducted to test the participating laboratories for their capabilities in screening and in vitro assay of biological samples, performing internal dose assessment and providing advice on medical intervention, if necessary, using a urine sample spiked with a single radionuclide, 241 Am. The laboratories were required to submit their reports according to the exercise schedule and using pre-formatted templates. Generally, the participating laboratories were found to be capable with respect to rapidly screening samples for radionuclide contamination, measuring the radionuclide in the samples, assessing the intake and radiation dose, and providing advice on medical intervention. However, gaps in bioassay measurement and dose assessment have been identified. The network may take steps to ensure that procedures and practices within this network be harmonised and a follow-up exercise be organised on a larger scale, with potential participation of laboratories from the networks coordinated by the International Atomic Energy Agency and the World Health Organization. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Remote observing with NASA's Deep Space Network

NASA Astrophysics Data System (ADS)

Kuiper, T. B. H.; Majid, W. A.; Martinez, S.; Garcia-Miro, C.; Rizzo, J. R.

2012-09-01

The Deep Space Network (DSN) communicates with spacecraft as far away as the boundary between the Solar System and the interstellar medium. To make this possible, large sensitive antennas at Canberra, Australia, Goldstone, California, and Madrid, Spain, provide for constant communication with interplanetary missions. We describe the procedures for radioastronomical observations using this network. Remote access to science monitor and control computers by authorized observers is provided by two-factor authentication through a gateway at the Jet Propulsion Laboratory (JPL) in Pasadena. To make such observations practical, we have devised schemes based on SSH tunnels and distributed computing. At the very minimum, one can use SSH tunnels and VNC (Virtual Network Computing, a remote desktop software suite) to control the science hosts within the DSN Flight Operations network. In this way we have controlled up to three telescopes simultaneously. However, X-window updates can be slow and there are issues involving incompatible screen sizes and multi-screen displays. Consequently, we are now developing SSH tunnel-based schemes in which instrument control and monitoring, and intense data processing, are done on-site by the remote DSN hosts while data manipulation and graphical display are done at the observer's host. We describe our approaches to various challenges, our experience with what worked well and lessons learned, and directions for future development.

How to develop a business case to establish a neonatal pulse oximetry programme for screening of congenital heart defects.

PubMed

Ewer, Andrew K

2012-12-01

Pulse oximetry screening for critical congenital heart defects (CCHDs) is a highly specific, moderately sensitive test which is cost effective, acceptable to both clinical staff and parents and meets the criteria for universal screening. Pulse oximetry screening is gaining considerable worldwide support and last year was added to the recommended uniform screening panel in the USA following endorsement by the Health and Human Services Secretary. There is significant heterogeneity in published screening protocols and it is important to consider all available evidence and also take local factors into account when developing a screening programme, whether it is within an individual hospital, neonatal network or even at a national level. This paper presents available options based both on the published evidence and personal practice experience which will aid those considering the introduction of screening to make the right decisions both from a clinical and financial perspective. Copyright © 2012 Elsevier Ltd. All rights reserved.

Network pharmacology-based prediction of active compounds and molecular targets in Yijin-Tang acting on hyperlipidaemia and atherosclerosis.

PubMed

Lee, A Yeong; Park, Won; Kang, Tae-Wook; Cha, Min Ho; Chun, Jin Mi

2018-07-15

Yijin-Tang (YJT) is a traditional prescription for the treatment of hyperlipidaemia, atherosclerosis and other ailments related to dampness phlegm, a typical pathological symptom of abnormal body fluid metabolism in Traditional Korean Medicine. However, a holistic network pharmacology approach to understanding the therapeutic mechanisms underlying hyperlipidaemia and atherosclerosis has not been pursued. To examine the network pharmacological potential effects of YJT on hyperlipidaemia and atherosclerosis, we analysed components, performed target prediction and network analysis, and investigated interacting pathways using a network pharmacology approach. Information on compounds in herbal medicines was obtained from public databases, and oral bioavailability and drug-likeness was screened using absorption, distribution, metabolism, and excretion (ADME) criteria. Correlations between compounds and genes were linked using the STITCH database, and genes related to hyperlipidaemia and atherosclerosis were gathered using the GeneCards database. Human genes were identified and subjected to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Network analysis identified 447 compounds in five herbal medicines that were subjected to ADME screening, and 21 compounds and 57 genes formed the main pathways linked to hyperlipidaemia and atherosclerosis. Among them, 10 compounds (naringenin, nobiletin, hesperidin, galangin, glycyrrhizin, homogentisic acid, stigmasterol, 6-gingerol, quercetin and glabridin) were linked to more than four genes, and are bioactive compounds and key chemicals. Core genes in this network were CASP3, CYP1A1, CYP1A2, MMP2 and MMP9. The compound-target gene network revealed close interactions between multiple components and multiple targets, and facilitates a better understanding of the potential therapeutic effects of YJT. Pharmacological network analysis can help to explain the potential effects of YJT for treating dampness phlegm-related diseases such as hyperlipidaemia and atherosclerosis. Copyright © 2018 Elsevier B.V. All rights reserved.

Consciousness, Functional Networks and Delirium Screening.

PubMed

Eeles, Eamonn; Burianova, Hana; Pandy, Shaun; Pinsker, Donna

2017-01-01

Consciousness, the medium of sentient thought, requires integrity of functional networks and their connectivity. In health, they function as a co-operative but mutually exclusive paradigm of introspection versus external awareness subserved via the Default Mode Network and Task Positive State, respectively. Higher thinking in the conscious state is then segregated according to need. There is research evidence to suggest that functional networks may be impacted in disorders of consciousness and conceptual support for a mechanistic role in delirium. This potentially central aspect of delirium manifestation is relatively unexplored. This article describes the role of disrupted functional networks in delirium. How this relates to current understanding of delirium neurobiology and the ramifications for clinical diagnosis is discussed. A review of the role of functional networks, particularly DMN and TPN, has been undertaken with respect to health and delirium. An exploration of how symptoms of delirium may be related to functional network aberrancy has been undertaken. Implications for research and clinical practice in delirium have been presented. In delirium, a disturbance of consciousness, the DMN is pathologically co-activated and functional cortical connectivity is compromised. The clinical correlate is of an experiential singularity where internal and external drivers become indistinguishable, reality and delusion merge and the notion of self is effaced. Our group propose that functional network disruption in conjunction with cortical disconnectivity is central to the mechanism of delirium. Clinical tools may exploit the neurobiology of delirium to improve its diagnosis and an example of such a simple screening instrument (SQeeC) is provided. Functional networks are critically disrupted in delirium and may be central to clinical features. A better understanding of the neurobiology of delirium will generate research opportunities with potential for therapeutic gains in detection, diagnosis, and management. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Insurance continuity and receipt of diabetes preventive care in a network of Federally Qualified Health Centers

PubMed Central

Gold, Rachel; DeVoe, Jennifer; Shah, Amit; Chauvie, Susan

2009-01-01

Background and Objectives Having health insurance is usually associated with better access to care and better health outcomes. For patients receiving care at Federally Qualified Health Centers (FQHCs), where care is provided regardless of insurance status, the role health insurance status plays in affecting receipt of services is less well understood. Research Design We used practice management data from a coalition of FQHCs in Oregon, and linked to Oregon’s electronic insurance data, to examine whether receipt of diabetes preventive care services was associated with continuity of insurance coverage among adult FQHC patients receiving diabetes care in 2005. Results About one-third (32%) of patients with diabetes received a flu vaccination in 2005, 36% an LDL screening, 54% at least one HbA1c screening, and 21% a nephropathy screening. Compared to the continuously insured, the continuously uninsured were less likely to receive an LDL screening, a flu vaccination, and/or a nephropathy screening; those with partial coverage were less likely than the continuously insured to receive a flu shot, at least one HbA1c screening, or an LDL screening. Conclusions Our results suggest that FQHCs do an excellent job in delivering most services to their uninsured and partially insured patients, but also underscore that for diabetic patients from underserved communities, having both an FQHC medical home and continuous health insurance plays a critical role in receiving optimal chronic disease management. Our study is one of the first to demonstrate how electronic administrative data from a network of FQHCs can be successfully used to gauge the state of healthcare delivery. PMID:19330890

ScreenPro FH: from the Czech MedPed to international collaboration. ScreenPro FH is a participating project of the EAS-FHCS.

PubMed

Ceska, R; Freiberger, T; Vaclova, M; Aleksicova, T; Votavova, L; Vrablik, M

2017-04-05

This article describes the evolution of our understanding of familial hypercholesterolemia (FH) in the Central, Eastern, and Southern Europe (CESE) region, and the dissemination of this understanding to other countries. Using the ScreenPro FH project as an example, we would like to illustrate the progression from national objectives, to regional networking and, finally, to international collaboration via the Familial Hypercholesterolemia Studies Collaboration (FHSC) project under the leadership of the European Atherosclerosis Society (EAS). It is essential to improve our ability to diagnose FH. In this regard, the EAS and its FHSC project must be commended for their educational and organizational activities which, above all, are dedicated to the creation of a global FH patient registry. In the CESE region, FH diagnostics and treatment situation are markedly different than in Western Europe or North America. Since the Czech MedPed project (Make Early Diagnoses to Prevent Early Deaths in Medical Pedigrees) has been so successful (with results not only comparable to, but, for some parameters, even surpassing the results of many Western countries) we decided to apply the Czech experience to the CESE region. Thus, the ScreenPro FH project was created. The aim of ScreenPro FH is to create a specialist network in the CESE region. The primary objective of the ScreenPro FH project was to dramatically reduce the number of premature deaths due to clinical complications of atherosclerosis in FH patients. At present, ScreenPro FH comprises 18 member countries with a total population of 500,000,000; which, in terms of the FH population, represents 1-2 million patients.

A new Information publishing system Based on Internet of things

NASA Astrophysics Data System (ADS)

Zhu, Li; Ma, Guoguang

2018-03-01

A new information publishing system based on Internet of things is proposed, which is composed of four level hierarchical structure, including the screen identification layer, the network transport layer, the service management layer and the publishing application layer. In the architecture, the screen identification layer has realized the internet of screens in which geographically dispersed independent screens are connected to the internet by the customized set-top boxes. The service management layer uses MQTT protocol to implement a lightweight broker-based publish/subscribe messaging mechanism in constrained environments such as internet of things to solve the bandwidth bottleneck. Meanwhile the cloud-based storage technique is used to storage and manage the promptly increasing multimedia publishing information. The paper has designed and realized a prototype SzIoScreen, and give some related test results.

Retina Image Screening and Analysis Software Version 2.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tobin, Jr., Kenneth W.; Karnowski, Thomas P.; Aykac, Deniz

2009-04-01

The software allows physicians or researchers to ground-truth images of retinas, identifying key physiological features and lesions that are indicative of disease. The software features methods to automatically detect the physiological features and lesions. The software contains code to measure the quality of images received from a telemedicine network; create and populate a database for a telemedicine network; review and report the diagnosis of a set of images; and also contains components to transmit images from a Zeiss camera to the network through SFTP.

Automated Age-related Macular Degeneration screening system using fundus images.

PubMed

Kunumpol, P; Umpaipant, W; Kanchanaranya, N; Charoenpong, T; Vongkittirux, S; Kupakanjana, T; Tantibundhit, C

2017-07-01

This work proposed an automated screening system for Age-related Macular Degeneration (AMD), and distinguishing between wet or dry types of AMD using fundus images to assist ophthalmologists in eye disease screening and management. The algorithm employs contrast-limited adaptive histogram equalization (CLAHE) in image enhancement. Subsequently, discrete wavelet transform (DWT) and locality sensitivity discrimination analysis (LSDA) were used to extract features for a neural network model to classify the results. The results showed that the proposed algorithm was able to distinguish between normal eyes, dry AMD, or wet AMD with 98.63% sensitivity, 99.15% specificity, and 98.94% accuracy, suggesting promising potential as a medical support system for faster eye disease screening at lower costs.

Deconstruction of the beaten Path-Sidestep interaction network provides insights into neuromuscular system development

PubMed Central

Li, Hanqing; Watson, Ash; Olechwier, Agnieszka; Anaya, Michael; Sorooshyari, Siamak K; Harnett, Dermott P; Lee, Hyung-Kook (Peter); Vielmetter, Jost; Fares, Mario A; Garcia, K Christopher; Özkan, Engin

2017-01-01

An ‘interactome’ screen of all Drosophila cell-surface and secreted proteins containing immunoglobulin superfamily (IgSF) domains discovered a network formed by paralogs of Beaten Path (Beat) and Sidestep (Side), a ligand-receptor pair that is central to motor axon guidance. Here we describe a new method for interactome screening, the Bio-Plex Interactome Assay (BPIA), which allows identification of many interactions in a single sample. Using the BPIA, we ‘deorphanized’ four more members of the Beat-Side network. We confirmed interactions using surface plasmon resonance. The expression patterns of beat and side genes suggest that Beats are neuronal receptors for Sides expressed on peripheral tissues. side-VI is expressed in muscle fibers targeted by the ISNb nerve, as well as at growth cone choice points and synaptic targets for the ISN and TN nerves. beat-V genes, encoding Side-VI receptors, are expressed in ISNb and ISN motor neurons. PMID:28829740

Integrating Routine HIV Screening in the New York City Community Health Center Collaborative.

PubMed

Rodriguez, Vanessa; Lester, Deborah; Connelly-Flores, Alison; Barsanti, Franco A; Hernandez, Paloma

2016-01-01

One in seven of the 1.1 million people living in the United States infected with HIV are not aware of their HIV status. At the same time, many clinical settings have not adopted routine HIV screening, which promotes linkage to specialist medical care. We sought to improve HIV screening in a large community health center network by using a data-driven, collaborative learning approach and system-wide modifications, where counselor-based HIV screening and testing were replaced by health-care providers and medical assistants. Urban Health Plan, Inc., a network of federally qualified health centers in the boroughs of the Bronx and Queens in New York City, provided HIV screening training for its health-care providers. In January 2011, it modified its electronic medical record system to incorporate HIV test offering. This study compared the 2010 baseline year with the three-year implementation follow-up period (January 2011 through December 2013) to determine the number of eligible individuals for HIV testing, HIV tests offered and performed, HIV-positive individuals, and HIV cases linked to specialty care. A total of 26,853 individuals at baseline and 100,369 individuals in the implementation period were eligible for HIV testing. HIV testing was performed on 2,079 (8%) of 26,853 eligible individuals in 2010 and 49,646 (50%) of 100,369 eligible individuals from 2011 through 2013. HIV-positive status was determined in 19 (0.9%) of 2,079 tested individuals in 2010 and 166 (0.3%) of 49,646 tested individuals from 2011 through 2013. Linkage to care was observed in all 19 eligible individuals and 127 (77%) of 166 eligible individuals who tested HIV positive in 2010 and 2011-2013, respectively. This study enabled routine HIV implementation testing at a community health center network, which resulted in enhanced HIV testing, an increased number of HIV-positive cases identified, and a rise in the number of patients linked to HIV specialist care.

Screening for Cardiovascular Risk in Asymptomatic Users of the Primary Health Care Network in Lebanon, 2012–2013

PubMed Central

Adib, Salim M.; Hamadeh, Randa; Freidi, Alia; Ammar, Walid

2014-01-01

Introduction In 2012, the Ministry of Public Health in Lebanon piloted a service of multifactorial cardiovascular screening in the publicly subsidized Primary Health Care (PHC) Network. We present an epidemiological analysis of data produced during this pilot to justify the inclusion of this service in the package of essential services offered through PHC and to present a preliminary cardiovascular risk profile in an asymptomatic population. Methods A total of 4,205 participants (two-thirds of which were women) aged at least 40 years and reportedly free from diabetes, hypertension, dyslipidemia, and cardiovascular disease (CVD) were screened. The screening protocol used a questionnaire and direct measurements to assess 5 modifiable cardiovascular risk factors; total cardiovascular risk score was calculated according to a paper-based algorithm developed by the World Health Organization and the International Society of Hypertension. Results Approximately 25% of the sample displayed metabolic impairments (11% for impaired blood glucose metabolism and 17% for impaired systolic blood pressure), and 6.6% were classified at total cardiovascular risk of 10% or more. Just over one-quarter of the sample was obese, almost half had a substantially elevated waist circumference, and 41% were smokers. Men were significantly more likely to screen positive for metabolic impairment than women, and women were more likely to be obese. Conclusion The implementation of a multifactorial screening for CVD among asymptomatic subjects detected a substantial proportion of previously undiagnosed cases of high metabolic risk, people who could now be referred to optimal medical follow-up. PMID:25032835

Automated Propulsion Data Screening demonstration system

NASA Technical Reports Server (NTRS)

Hoyt, W. Andes; Choate, Timothy D.; Whitehead, Bruce A.

1995-01-01

A fully-instrumented firing of a propulsion system typically generates a very large quantity of data. In the case of the Space Shuttle Main Engine (SSME), data analysis from ground tests and flights is currently a labor-intensive process. Human experts spend a great deal of time examining the large volume of sensor data generated by each engine firing. These experts look for any anomalies in the data which might indicate engine conditions warranting further investigation. The contract effort was to develop a 'first-cut' screening system for application to SSME engine firings that would identify the relatively small volume of data which is unusual or anomalous in some way. With such a system, limited and expensive human resources could focus on this small volume of unusual data for thorough analysis. The overall project objective was to develop a fully operational Automated Propulsion Data Screening (APDS) system with the capability of detecting significant trends and anomalies in transient and steady-state data. However, the effort limited screening of transient data to ground test data for throttle-down cases typical of the 3-g acceleration, and for engine throttling required to reach the maximum dynamic pressure limits imposed on the Space Shuttle. This APDS is based on neural networks designed to detect anomalies in propulsion system data that are not part of the data used for neural network training. The delivered system allows engineers to build their own screening sets for application to completed or planned firings of the SSME. ERC developers also built some generic screening sets that NASA engineers could apply immediately to their data analysis efforts.

ERLN Activities Details

EPA Pesticide Factsheets

Environmental Response Laboratory Network activities include the All Hazard Receipt Facility and Screening Protocol, standardizing chemical methods, Chemical Warfare Agent Fixed Laboratory Pilot Project, microbial efforts, and WLA response plan.

"Proceedings of the 22nd Aschauer Soiree on Growth and Health Screening", held at Altenhof, Germany, November 15th, 2014.

PubMed

Hermanussen, Michael; Anisimova, Anna; Abmann, Christian; Van Buuren, Stef; Camara, Antonio D; Elhusseini, Mona Abbas; Hassan, Mortada; El-Shabrawi, Mortada Hassan; Godina, Elena Zinovyevna; Gomula, Aleksandra; Groth, Detlef; Koziel, Slawomir; Lieberman, Leslie Sue; Meigen, Christof; Mumm, Rebekka; Nariyama, Koichi; Nowak-Szczepanska, Natalia; Novokmet, Natalija; Satake, Takashi; Scheffler, Christiane; Soderhall, Jani; Suchomlinov, Andrej; Tutkuviene, Janina; Wit, Jan M; Witwer-Backofen, Ursula; Yestrebsky, Cherie Lynn

2015-03-01

Twenty-five scientists met at Aschauhof, Altenhof, Germany, to discuss various aspects of the complex network of modern health screening, focusing on current scientific topics including medical sciences, human biology, and mathematics; on problems in implementing these results at the practical level of physicians, nurses, technicians, and engineers; and the level of administrative and political decisions. Whereas major scientific advancements have been published in the understanding and the bio-statistical evaluation of anthropometric screening parameters such as serial measurements of height and weight for preventive medical check-ups, BMI screening and surveillance in schools, etc., the implementation of these advancements into current health screening concepts, strategies and decision-making is poor. Fear of discrimination, misperception of body image, behavioural responses and political concerns, meanwhile dominate and negatively interfere with the implementation of recent scientific results into public health screening concepts and practices.

Newborn screening progress in developing countries--overcoming internal barriers.

PubMed

Padilla, Carmencita D; Krotoski, Danuta; Therrell, Bradford L

2010-04-01

Newborn screening is an important public health measure aimed at early identification and management of affected newborns thereby lowering infant morbidity and mortality. It is a comprehensive system of education, screening, follow-up, diagnosis, treatment/management, and evaluation that must be institutionalized and sustained within public health systems often challenged by economic, political, and cultural considerations. As a result, developing countries face unique challenges in implementing and expanding newborn screening that can be grouped into the following categories: (1) planning, (2) leadership, (3) medical support, (4) technical support, (5) logistical support, (6) education, (7) protocol and policy development, (8) administration, (9) evaluation, and (10) sustainability. We review some of the experiences in overcoming implementation challenges in developing newborn screening programs, and discuss recent efforts to encourage increased newborn screening through support networking and information exchange activities in 2 regions-the Asia Pacific and the Middle East/North Africa. Copyright 2010 Elsevier Inc. All rights reserved.

Improving outcomes for patients with type 2 diabetes using general practice networks: a quality improvement project in east London.

PubMed

Hull, Sally; Chowdhury, Tahseen A; Mathur, Rohini; Robson, John

2014-02-01

Structured diabetes care can improve outcomes and reduce risk of complications, but improving care in a deprived, ethnically diverse area can prove challenging. This report evaluates a system change to enhance diabetes care delivery in a primary care setting. All 35 practices in one inner London Primary Care Trust were geographically grouped into eight networks of four to five practices, each supported by a network manager, clerical staff and an educational budget. A multidisciplinary team developed a 'care package' for type 2 diabetes management, with financial incentives based on network achievement of targets. Monthly electronic performance dashboards enabled networks to track and improve performance. Network multidisciplinary team meetings including the diabetic specialist team supported case management and education. Key measures for improvement included the number of diabetes care plans completed, proportion of patients attending for digital retinal screen and proportions of patients achieving a number of biomedical indices (blood pressure, cholesterol, glycated haemoglobin). Between 2009 and 2012, completed care plans rose from 10% to 88%. The proportion of patients attending for digital retinal screen rose from 72% to 82.8%. The proportion of patients achieving a combination of blood pressure ≤ 140/80 mm Hg and cholesterol ≤ 4 mmol/L rose from 35.3% to 46.1%. Mean glycated haemoglobin dropped from 7.80% to 7.66% (62-60 mmol/mol). Investment of financial, organisational and education resources into primary care practice networks can achieve clinically important improvements in diabetes care in deprived, ethnically diverse communities. This success is predicated on collaborative working between practices, purposively designed high-quality information on network performance and engagement between primary and secondary care clinicians.

Tumor-induced perturbations of cytokines and immune cell networks.

PubMed

Burkholder, Brett; Huang, Ren-Yu; Burgess, Rob; Luo, Shuhong; Jones, Valerie Sloane; Zhang, Wenji; Lv, Zhi-Qiang; Gao, Chang-Yu; Wang, Bao-Ling; Zhang, Yu-Ming; Huang, Ruo-Pan

2014-04-01

Until recently, the intrinsically high level of cross-talk between immune cells, the complexity of immune cell development, and the pleiotropic nature of cytokine signaling have hampered progress in understanding the mechanisms of immunosuppression by which tumor cells circumvent native and adaptive immune responses. One technology that has helped to shed light on this complex signaling network is the cytokine antibody array, which facilitates simultaneous screening of dozens to hundreds of secreted signal proteins in complex biological samples. The combined applications of traditional methods of molecular and cell biology with the high-content, high-throughput screening capabilities of cytokine antibody arrays and other multiplexed immunoassays have revealed a complex mechanism that involves multiple cytokine signals contributed not just by tumor cells but by stromal cells and a wide spectrum of immune cell types. This review will summarize the interactions among cancerous and immune cell types, as well as the key cytokine signals that are required for tumors to survive immunoediting in a dormant state or to grow and spread by escaping it. Additionally, it will present examples of how probing secreted cell-cell signal networks in the tumor microenvironment (TME) with cytokine screens have contributed to our current understanding of these processes and discuss the implications of this understanding to antitumor therapies. Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.

Large-Scale Chemical Similarity Networks for Target Profiling of Compounds Identified in Cell-Based Chemical Screens

PubMed Central

Lo, Yu-Chen; Senese, Silvia; Li, Chien-Ming; Hu, Qiyang; Huang, Yong; Damoiseaux, Robert; Torres, Jorge Z.

2015-01-01

Target identification is one of the most critical steps following cell-based phenotypic chemical screens aimed at identifying compounds with potential uses in cell biology and for developing novel disease therapies. Current in silico target identification methods, including chemical similarity database searches, are limited to single or sequential ligand analysis that have limited capabilities for accurate deconvolution of a large number of compounds with diverse chemical structures. Here, we present CSNAP (Chemical Similarity Network Analysis Pulldown), a new computational target identification method that utilizes chemical similarity networks for large-scale chemotype (consensus chemical pattern) recognition and drug target profiling. Our benchmark study showed that CSNAP can achieve an overall higher accuracy (>80%) of target prediction with respect to representative chemotypes in large (>200) compound sets, in comparison to the SEA approach (60–70%). Additionally, CSNAP is capable of integrating with biological knowledge-based databases (Uniprot, GO) and high-throughput biology platforms (proteomic, genetic, etc) for system-wise drug target validation. To demonstrate the utility of the CSNAP approach, we combined CSNAP's target prediction with experimental ligand evaluation to identify the major mitotic targets of hit compounds from a cell-based chemical screen and we highlight novel compounds targeting microtubules, an important cancer therapeutic target. The CSNAP method is freely available and can be accessed from the CSNAP web server (http://services.mbi.ucla.edu/CSNAP/). PMID:25826798

NCG 4.0: the network of cancer genes in the era of massive mutational screenings of cancer genomes

PubMed Central

An, Omer; Pendino, Vera; D’Antonio, Matteo; Ratti, Emanuele; Gentilini, Marco; Ciccarelli, Francesca D.

2014-01-01

NCG 4.0 is the latest update of the Network of Cancer Genes, a web-based repository of systems-level properties of cancer genes. In its current version, the database collects information on 537 known (i.e. experimentally supported) and 1463 candidate (i.e. inferred using statistical methods) cancer genes. Candidate cancer genes derive from the manual revision of 67 original publications describing the mutational screening of 3460 human exomes and genomes in 23 different cancer types. For all 2000 cancer genes, duplicability, evolutionary origin, expression, functional annotation, interaction network with other human proteins and with microRNAs are reported. In addition to providing a substantial update of cancer-related information, NCG 4.0 also introduces two new features. The first is the annotation of possible false-positive cancer drivers, defined as candidate cancer genes inferred from large-scale screenings whose association with cancer is likely to be spurious. The second is the description of the systems-level properties of 64 human microRNAs that are causally involved in cancer progression (oncomiRs). Owing to the manual revision of all information, NCG 4.0 constitutes a complete and reliable resource on human coding and non-coding genes whose deregulation drives cancer onset and/or progression. NCG 4.0 can also be downloaded as a free application for Android smart phones. Database URL: http://bio.ieo.eu/ncg/ PMID:24608173

A Novel Malaria Pf/Pv Ab Rapid Diagnostic Test Using a Differential Diagnostic Marker Identified by Network Biology.

PubMed

Cho, Sung Jin; Lee, Jihoo; Lee, Hyun Jae; Jo, Hyun-Young; Sinniah, Mangalam; Kim, Hak-Yong; Chong, Chom-Kyu; Song, Hyun-Ok

2016-01-01

Rapid diagnostic tests (RDTs) can detect anti-malaria antibodies in human blood. As they can detect parasite infection at the low parasite density, they are useful in endemic areas where light infection and/or re-infection of parasites are common. Thus, malaria antibody tests can be used for screening bloods in blood banks to prevent transfusion-transmitted malaria (TTM), an emerging problem in malaria endemic areas. However, only a few malaria antibody tests are available in the microwell-based assay format and these are not suitable for field application. A novel malaria antibody (Ab)-based RDT using a differential diagnostic marker for falciparum and vivax malaria was developed as a suitable high-throughput assay that is sensitive and practical for blood screening. The marker, merozoite surface protein 1 (MSP1) was discovered by generation of a Plasmodium-specific network and the hierarchical organization of modularity in the network. Clinical evaluation revealed that the novel Malaria Pf/Pv Ab RDT shows improved sensitivity (98%) and specificity (99.7%) compared with the performance of a commercial kit, SD BioLine Malaria P.f/P.v (95.1% sensitivity and 99.1% specificity). The novel Malaria Pf/Pv Ab RDT has potential for use as a cost-effective blood-screening tool for malaria and in turn, reduces TTM risk in endemic areas.

Flavivirus NS3 and NS5 proteins interaction network: a high-throughput yeast two-hybrid screen

PubMed Central

2011-01-01

Background The genus Flavivirus encompasses more than 50 distinct species of arthropod-borne viruses, including several major human pathogens, such as West Nile virus, yellow fever virus, Japanese encephalitis virus and the four serotypes of dengue viruses (DENV type 1-4). Each year, flaviviruses cause more than 100 million infections worldwide, some of which lead to life-threatening conditions such as encephalitis or haemorrhagic fever. Among the viral proteins, NS3 and NS5 proteins constitute the major enzymatic components of the viral replication complex and are essential to the flavivirus life cycle. Results We report here the results of a high-throughput yeast two-hybrid screen to identify the interactions between human host proteins and the flavivirus NS3 and NS5 proteins. Using our screen results and literature curation, we performed a global analysis of the NS3 and NS5 cellular targets based on functional annotation with the Gene Ontology features. We finally created the first flavivirus NS3 and NS5 proteins interaction network and analysed the topological features of this network. Our proteome mapping screen identified 108 human proteins interacting with NS3 or NS5 proteins or both. The global analysis of the cellular targets revealed the enrichment of host proteins involved in RNA binding, transcription regulation, vesicular transport or innate immune response regulation. Conclusions We proposed that the selective disruption of these newly identified host/virus interactions could represent a novel and attractive therapeutic strategy in treating flavivirus infections. Our virus-host interaction map provides a basis to unravel fundamental processes about flavivirus subversion of the host replication machinery and/or immune defence strategy. PMID:22014111

Flavivirus NS3 and NS5 proteins interaction network: a high-throughput yeast two-hybrid screen.

PubMed

Le Breton, Marc; Meyniel-Schicklin, Laurène; Deloire, Alexandre; Coutard, Bruno; Canard, Bruno; de Lamballerie, Xavier; Andre, Patrice; Rabourdin-Combe, Chantal; Lotteau, Vincent; Davoust, Nathalie

2011-10-20

The genus Flavivirus encompasses more than 50 distinct species of arthropod-borne viruses, including several major human pathogens, such as West Nile virus, yellow fever virus, Japanese encephalitis virus and the four serotypes of dengue viruses (DENV type 1-4). Each year, flaviviruses cause more than 100 million infections worldwide, some of which lead to life-threatening conditions such as encephalitis or haemorrhagic fever. Among the viral proteins, NS3 and NS5 proteins constitute the major enzymatic components of the viral replication complex and are essential to the flavivirus life cycle. We report here the results of a high-throughput yeast two-hybrid screen to identify the interactions between human host proteins and the flavivirus NS3 and NS5 proteins. Using our screen results and literature curation, we performed a global analysis of the NS3 and NS5 cellular targets based on functional annotation with the Gene Ontology features. We finally created the first flavivirus NS3 and NS5 proteins interaction network and analysed the topological features of this network. Our proteome mapping screen identified 108 human proteins interacting with NS3 or NS5 proteins or both. The global analysis of the cellular targets revealed the enrichment of host proteins involved in RNA binding, transcription regulation, vesicular transport or innate immune response regulation. We proposed that the selective disruption of these newly identified host/virus interactions could represent a novel and attractive therapeutic strategy in treating flavivirus infections. Our virus-host interaction map provides a basis to unravel fundamental processes about flavivirus subversion of the host replication machinery and/or immune defence strategy.

An infectious disease/fever screening radar system which stratifies higher-risk patients within ten seconds using a neural network and the fuzzy grouping method.

PubMed

Sun, Guanghao; Matsui, Takemi; Hakozaki, Yukiya; Abe, Shigeto

2015-03-01

To classify higher-risk influenza patients within 10 s, we developed an infectious disease and fever screening radar system. The system screens infected patients based on vital signs, i.e., respiration rate measured by a radar, heart rate by a finger-tip photo-reflector, and facial temperature by a thermography. The system segregates subjects into higher-risk influenza (HR-I) group, lower-risk influenza (LR-I) group, and non-influenza (Non-I) group using a neural network and fuzzy clustering method (FCM). We conducted influenza screening for 35 seasonal influenza patients and 48 normal control subjects at the Japan Self-Defense Force Central Hospital. Pulse oximetry oxygen saturation (SpO2) was measured as a reference. The system classified 17 subjects into HR-I group, 26 into LR-I group, and 40 into Non-I group. Ten out of the 17 HR-I subjects indicated SpO2 <96%, whereas only two out of the 26 LR-I subjects showed SpO2 <96%. The chi-squared test revealed a significant difference in the ratio of subjects showed SpO2 <96% between HR-I and LR-I group (p < 0.001). There were zero and nine normal control subjects in HR-I and LR-I groups, respectively, and there was one influenza patient in Non-I group. The combination of neural network and FCM achieved efficient detection of higher-risk influenza patients who indicated SpO2 96% within 10 s. Copyright © 2014 The British Infection Association. Published by Elsevier Ltd. All rights reserved.

Common data elements for substance use disorders in electronic health records: the NIDA Clinical Trials Network experience.

PubMed

Ghitza, Udi E; Gore-Langton, Robert E; Lindblad, Robert; Shide, David; Subramaniam, Geetha; Tai, Betty

2013-01-01

Electronic health records (EHRs) are essential in improving quality and enhancing efficiency of health-care delivery. By 2015, medical care receiving service reimbursement from US Centers for Medicare and Medicaid Services (CMS) must show 'meaningful use' of EHRs. Substance use disorders (SUD) are grossly under-detected and under-treated in current US medical care settings. Hence, an urgent need exists for improved identification of and clinical intervention for SUD in medical settings. The National Institute on Drug Abuse Clinical Trials Network (NIDA CTN) has leveraged its infrastructure and expertise and brought relevant stakeholders together to develop consensus on brief screening and initial assessment tools for SUD in general medical settings, with the objective of incorporation into US EHRs. Stakeholders were identified and queried for input and consensus on validated screening and assessment for SUD in general medical settings to develop common data elements to serve as shared resources for EHRs on screening, brief intervention and referral to treatment (SBIRT), with the intent of supporting interoperability and data exchange in a developing Nationwide Health Information Network. Through consensus of input from stakeholders, a validated screening and brief assessment instrument, supported by Clinical Decision Support tools, was chosen to be used at out-patient general medical settings. The creation and adoption of a core set of validated common data elements and the inclusion of such consensus-based data elements for general medical settings will enable the integration of SUD treatment within mainstream health care, and support the adoption and 'meaningful use' of the US Office of the National Coordinator for Health Information Technology (ONC)-certified EHRs, as well as CMS reimbursement. Published 2012. This article is a U.S. Government work and is in the public domain in the USA.

Army Library Institute V: Product/Marketing/Service - Volume 2, Supplementary Data

DTIC Science & Technology

1981-11-01

Rinctlons OCLC for Beginners Performance Standards Screening Panel Session 4, Thursday, 21 May 1981 Task Force Group Meetings ADP/Networking...for Library Functions W OCLC for Beginners X Career Programs and Position Classification Standards Y Screening Panel...is non-DLC a librarian will examine it, assign a call number, and do any other editing. For a flowchart , see Appendix 6, but remember that this is a

Barriers to and factors facilitating breast cancer screening among Iranian women: a qualitative study.

PubMed

Lamyian, M; Hydarnia, A; Ahmadi, F; Faghihzadeh, S; Aguilar-Vafaie, M E

2007-01-01

This study used qualitative methodology to understand Iranian women's views about barriers to and factors facilitating screening for early detection of breast cancer. Using grounded theory with in-depth interviews of 31 participants, themes emerged from the data in 2 main categories (internal and external) with 3 sub-categories: women's attitudes, feelings and beliefs; women's social network experiences; and accessibility. Facilitating factors for screening were self-care, fear, proactive coping, state of mind and advocacy. Barriers were negligence, cancer-related fear, low self-efficacy, fatalism, misinformation, ineffective health communication and competing priorities.

N-Screen Aware Multicriteria Hybrid Recommender System Using Weight Based Subspace Clustering

PubMed Central

Ullah, Farman; Lee, Sungchang

2014-01-01

This paper presents a recommender system for N-screen services in which users have multiple devices with different capabilities. In N-screen services, a user can use various devices in different locations and time and can change a device while the service is running. N-screen aware recommendation seeks to improve the user experience with recommended content by considering the user N-screen device attributes such as screen resolution, media codec, remaining battery time, and access network and the user temporal usage pattern information that are not considered in existing recommender systems. For N-screen aware recommendation support, this work introduces a user device profile collaboration agent, manager, and N-screen control server to acquire and manage the user N-screen devices profile. Furthermore, a multicriteria hybrid framework is suggested that incorporates the N-screen devices information with user preferences and demographics. In addition, we propose an individual feature and subspace weight based clustering (IFSWC) to assign different weights to each subspace and each feature within a subspace in the hybrid framework. The proposed system improves the accuracy, precision, scalability, sparsity, and cold start issues. The simulation results demonstrate the effectiveness and prove the aforementioned statements. PMID:25152921

[How to assess and reduce social inequalities in cancer screening programmes].

PubMed

Binefa, Gemma; García, Montse; Peiró, Rosana; Molina-Barceló, Ana; Ibáñez, Raquel

2016-01-01

This field note presents the conclusions and recommendations made at the meeting 'How to reduce social inequalities in cancer screening programmes?' held at the XXVI School of Public Health of Mahon (Menorca, Spain). Participants developed recommendations based on experiences of population-based screening programmes (breast and colorectal) and opportunistic screening (cervical). The conclusions and recommendations focused on four main areas (information systems, evaluation and quality, research, and interventions): the inclusion of social variables at an individual level in health information systems; the establishment of minimum standards for gathering information regarding inequalities in access to preventive services; the performance of actions in vulnerable populations; and the promotion of the exchange of experiences and best practices through the Cancer Screening Programmes Network and working groups of the scientific societies. Copyright © 2016 SESPAS. Published by Elsevier Espana. All rights reserved.

Biomarker microRNAs for prostate cancer metastasis: screened with a network vulnerability analysis model.

PubMed

Lin, Yuxin; Chen, Feifei; Shen, Li; Tang, Xiaoyu; Du, Cui; Sun, Zhandong; Ding, Huijie; Chen, Jiajia; Shen, Bairong

2018-05-21

Prostate cancer (PCa) is a fatal malignant tumor among males in the world and the metastasis is a leading cause for PCa death. Biomarkers are therefore urgently needed to detect PCa metastatic signature at the early time. MicroRNAs are small non-coding RNAs with the potential to be biomarkers for disease prediction. In addition, computer-aided biomarker discovery is now becoming an attractive paradigm for precision diagnosis and prognosis of complex diseases. In this study, we identified key microRNAs as biomarkers for predicting PCa metastasis based on network vulnerability analysis. We first extracted microRNAs and mRNAs that were differentially expressed between primary PCa and metastatic PCa (MPCa) samples. Then we constructed the MPCa-specific microRNA-mRNA network and screened microRNA biomarkers by a novel bioinformatics model. The model emphasized the characterization of systems stability changes and the network vulnerability with three measurements, i.e. the structurally single-line regulation, the functional importance of microRNA targets and the percentage of transcription factor genes in microRNA unique targets. With this model, we identified five microRNAs as putative biomarkers for PCa metastasis. Among them, miR-101-3p and miR-145-5p have been previously reported as biomarkers for PCa metastasis and the remaining three, i.e. miR-204-5p, miR-198 and miR-152, were screened as novel biomarkers for PCa metastasis. The results were further confirmed by the assessment of their predictive power and biological function analysis. Five microRNAs were identified as candidate biomarkers for predicting PCa metastasis based on our network vulnerability analysis model. The prediction performance, literature exploration and functional enrichment analysis convinced our findings. This novel bioinformatics model could be applied to biomarker discovery for other complex diseases.

Targeting imported malaria through social networks: a potential strategy for malaria elimination in Swaziland.

PubMed

Koita, Kadiatou; Novotny, Joseph; Kunene, Simon; Zulu, Zulizile; Ntshalintshali, Nyasatu; Gandhi, Monica; Gosling, Roland

2013-06-27

Swaziland has made great progress towards its goal of malaria elimination by 2015. However, malaria importation from neighbouring high-endemic Mozambique through Swaziland's eastern border remains a major factor that could prevent elimination from being achieved. In order to reach elimination, Swaziland must rapidly identify and treat imported malaria cases before onward transmission occurs. A nationwide formative assessment was conducted over eight weeks to determine if the imported cases of malaria identified by the Swaziland National Malaria Control Programme could be linked to broader social networks and to explore methods to access these networks. Using a structured format, interviews were carried out with malaria surveillance agents (6), health providers (10), previously identified imported malaria cases (19) and people belonging to the networks identified through these interviews (25). Most imported malaria cases were Mozambicans (63%, 12/19) making a living in Swaziland and sustaining their families in Mozambique. The majority of imported cases (73%, 14/19) were labourers and self-employed contractors who travelled frequently to Mozambique to visit their families and conduct business. Social networks of imported cases with similar travel patterns were identified through these interviews. Nearly all imported cases (89%, 17/19) were willing to share contact information to enable network members to be interviewed. Interviews of network members and key informants revealed common congregation points, such as the urban market places in Manzini and Malkerns, as well as certain bus stations, where people with similar travel patterns and malaria risk behaviours could be located and tested for malaria. This study demonstrated that imported cases of malaria belonged to networks of people with similar travel patterns. This study may provide novel methods for screening high-risk groups of travellers using both snowball sampling and time-location sampling of networks to identify and treat additional malaria cases. Implementation of a proactive screening programme of importation networks may help Swaziland halt transmission and achieve malaria elimination by 2015.

A Druggable TCF4 and BRD4 dependent Transcriptional Network Sustains Malignancy in Blastic Plasmacytoid Dendritic Cell Neoplasm

PubMed Central

Ceribelli, Michele; Hou, Zhiying Esther; Kelly, Priscilla N.; Huang, Da Wei; Wright, George; Ganapathi, Karthik; Evbuomwan, Moses O.; Pittaluga, Stefania; Shaffer, Arthur L.; Marcucci, Guido; Forman, Stephen J.; Xiao, Wenming; Guha, Rajarshi; Zhang, Xiaohu; Ferrer, Marc; Chaperot, Laurence; Plumas, Joel; Jaffe, Elaine S.; Thomas, Craig J.; Reizis, Boris; Staudt, Louis M.

2016-01-01

SUMMARY Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is an aggressive and largely incurable hematologic malignancy originating from plasmacytoid dendritic cells (pDCs). Using RNA interference screening, we identified the E-box transcription factor TCF4 as a master regulator of the BPDCN oncogenic program. TCF4 served as a faithful diagnostic marker of BPDCN, and its downregulation caused the loss of the BPDCN-specific gene expression program and apoptosis. High-throughput drug screening revealed that bromodomain and extra-terminal domain inhibitors (BETi’s) induced BPDCN apoptosis, which was attributable to disruption of a BPDCN-specific transcriptional network controlled by TCF4-dependent super-enhancers. BETi’s retarded the growth of BPDCN xenografts, supporting their clinical evaluation in this recalcitrant malignancy. PMID:27846392

An exploration of motivations for two screen viewing, social interaction behaviors, and factors that influence viewing intentions.

PubMed

Shim, Hongjin; Oh, Poong; Song, Hyunjin; Lee, Yeonkyung

2015-03-01

This study explores whether, and how, motivations for two screen viewing predicted social interaction behaviors and subsequent viewing intention of TV programs. A total of 453 respondents who responded that they use social networking sites (SNSs) via smartphones and actively watch entertainment programs completed an online survey questionnaire. In agreement with uses and gratifications assumptions, motivations for TSV predicted distinctive sets of social interaction behaviors, which mediated the influence of motivations on viewing intentions. Respondents' two screen viewing was meaningfully related with social interaction, engagement with programs, information seeking, and passing time. Results suggest that two screen viewing could provide shared experiences nourishing social capital and reintegrate TV audiences by social adhesive resulting from TV with SNSs.

Construction of diagnosis system and gene regulatory networks based on microarray analysis.

PubMed

Hong, Chun-Fu; Chen, Ying-Chen; Chen, Wei-Chun; Tu, Keng-Chang; Tsai, Meng-Hsiun; Chan, Yung-Kuan; Yu, Shyr Shen

2018-05-01

A microarray analysis generally contains expression data of thousands of genes, but most of them are irrelevant to the disease of interest, making analyzing the genes concerning specific diseases complicated. Therefore, filtering out a few essential genes as well as their regulatory networks is critical, and a disease can be easily diagnosed just depending on the expression profiles of a few critical genes. In this study, a target gene screening (TGS) system, which is a microarray-based information system that integrates F-statistics, pattern recognition matching, a two-layer K-means classifier, a Parameter Detection Genetic Algorithm (PDGA), a genetic-based gene selector (GBG selector) and the association rule, was developed to screen out a small subset of genes that can discriminate malignant stages of cancers. During the first stage, F-statistic, pattern recognition matching, and a two-layer K-means classifier were applied in the system to filter out the 20 critical genes most relevant to ovarian cancer from 9600 genes, and the PDGA was used to decide the fittest values of the parameters for these critical genes. Among the 20 critical genes, 15 are associated with cancer progression. In the second stage, we further employed a GBG selector and the association rule to screen out seven target gene sets, each with only four to six genes, and each of which can precisely identify the malignancy stage of ovarian cancer based on their expression profiles. We further deduced the gene regulatory networks of the 20 critical genes by applying the Pearson correlation coefficient to evaluate the correlationship between the expression of each gene at the same stages and at different stages. Correlationships between gene pairs were calculated, and then, three regulatory networks were deduced. Their correlationships were further confirmed by the Ingenuity pathway analysis. The prognostic significances of the genes identified via regulatory networks were examined using online tools, and most represented biomarker candidates. In summary, our proposed system provides a new strategy to identify critical genes or biomarkers, as well as their regulatory networks, from microarray data. Copyright © 2018. Published by Elsevier Inc.

Modulation of molecular hybridization and charge screening in a carbon nanotube network channel using the electrical pulse method.

PubMed

Woo, Jun-Myung; Kim, Seok Hyang; Chun, Honnggu; Kim, Sung Jae; Ahn, Jinhong; Park, Young June

2013-09-21

In this paper, we investigate the effect of electrical pulse bias on DNA hybridization events in a biosensor platform, using a Carbon Nanotube Network (CNN) and Gold Nano Particles (GNP) as an electrical channel. The scheme provides both hybridization rate enhancement of bio molecules, and electrical measurement in a transient state to avoid the charge screening effect, thereby significantly improving the sensitivity. As an example, the probe DNA molecules oscillate with pulse trains, resulting in the enhancement of DNA hybridization efficiency, and accordingly of the sensor performances in Tris-EDTA (TE) buffer solution, by as much as over three times, compared to the non-biasing conditions. More importantly, a wide dynamic range of 10(6) (target-DNA concentration from 5 pM to 5 μM) is achieved in human serum. In addition, the pulse biasing method enables one to obtain the conductance change, before the ions within the Electrical Double Layer (EDL) are redistributed, to avoid the charge screening effect, leading to an additional sensitivity enhancement.

Integrating high-throughput genetic interaction mapping and high-content screening to explore yeast spindle morphogenesis

PubMed Central

Vizeacoumar, Franco J.; van Dyk, Nydia; S.Vizeacoumar, Frederick; Cheung, Vincent; Li, Jingjing; Sydorskyy, Yaroslav; Case, Nicolle; Li, Zhijian; Datti, Alessandro; Nislow, Corey; Raught, Brian; Zhang, Zhaolei; Frey, Brendan; Bloom, Kerry

2010-01-01

We describe the application of a novel screening approach that combines automated yeast genetics, synthetic genetic array (SGA) analysis, and a high-content screening (HCS) system to examine mitotic spindle morphogenesis. We measured numerous spindle and cellular morphological parameters in thousands of single mutants and corresponding sensitized double mutants lacking genes known to be involved in spindle function. We focused on a subset of genes that appear to define a highly conserved mitotic spindle disassembly pathway, which is known to involve Ipl1p, the yeast aurora B kinase, as well as the cell cycle regulatory networks mitotic exit network (MEN) and fourteen early anaphase release (FEAR). We also dissected the function of the kinetochore protein Mcm21p, showing that sumoylation of Mcm21p regulates the enrichment of Ipl1p and other chromosomal passenger proteins to the spindle midzone to mediate spindle disassembly. Although we focused on spindle disassembly in a proof-of-principle study, our integrated HCS-SGA method can be applied to virtually any pathway, making it a powerful means for identifying specific cellular functions. PMID:20065090

Colorimetric photonic hydrogel aptasensor for the screening of heavy metal ions.

PubMed

Ye, Bao-Fen; Zhao, Yuan-Jin; Cheng, Yao; Li, Ting-Ting; Xie, Zhuo-Ying; Zhao, Xiang-Wei; Gu, Zhong-Ze

2012-09-28

We have developed a robust method for the visual detection of heavy metal ions (such as Hg(2+) and Pb(2+)) by using aptamer-functionalized colloidal photonic crystal hydrogel (CPCH) films. The CPCHs were derived from a colloidal crystal array of monodisperse silica nanoparticles, which were polymerized within the polyacrylamide hydrogel. The heavy metal ion-responsive aptamers were then cross-linked in the hydrogel network. During detection, the specific binding of heavy metal ions and cross-linked single-stranded aptamers in the hydrogel network caused the hydrogel to shrink, which was detected as a corresponding blue shift in the Bragg diffraction peak position of the CPCHs. The shift value could be used to estimate, quantitatively, the amount of the target ion. It was demonstrated that our CPCH aptasensor could screen a wide concentration range of heavy metal ions with high selectivity and reversibility. In addition, these aptasensors could be rehydrated from dried gels for storage and aptamer protection. It is anticipated that our technology may also be used in the screening of a broad range of metal ions in food, drugs and the environment.

Integration and sustainability of alcohol screening, brief intervention, and pharmacotherapy in primary care settings.

PubMed

Ornstein, Steven M; Miller, Peter M; Wessell, Andrea M; Jenkins, Ruth G; Nemeth, Lynne S; Nietert, Paul J

2013-07-01

At-risk drinking and alcohol use disorders are common in primary care and may adversely affect the treatment of patients with diabetes and/or hypertension. The purpose of this article is to report the impact of dissemination of a practice-based quality improvement approach (Practice Partner Research Network-Translating Research into Practice [PPRNet-TRIP]) on alcohol screening, brief intervention for at-risk drinking and alcohol use disorders, and medications for alcohol use disorders in primary care practices. Nineteen primary care practices from 15 states representing 26,005 patients with diabetes and/or hypertension participated in a group-randomized trial (early intervention vs. delayed intervention). The 12-month intervention consisted of practice site visits for academic detailing and participatory planning and network meetings for "best practice" dissemination. At the end of Phase 1, eligible patients in early-intervention practices were significantly more likely than patients in delayed-intervention practices to have been screened (odds ratio [OR] = 3.30, 95% CI [1.15, 9.50]) and more likely to have been provided a brief intervention (OR = 6.58, 95% CI [1.69, 25.7]. At the end of Phase 2, patients in delayed-intervention practices were more likely than at the end of Phase 1 to have been screened (OR = 5.18, 95% CI [4.65, 5.76]) and provided a brief intervention (OR = 1.80, 95% CI [1.31, 2.47]). Early-intervention practices maintained their screening and brief intervention performance during Phase 2. Medication for alcohol use disorders was prescribed infrequently. PPRNet-TRIP is effective in improving and maintaining improvement in alcohol screening and brief intervention for patients with diabetes and/or hypertension in primary care settings.

Birth weight and prematurity in infants with single ventricle physiology: pediatric heart network infant single ventricle trial screened population.

PubMed

Williams, Richard V; Ravishankar, Chitra; Zak, Victor; Evans, Frank; Atz, Andrew M; Border, William L; Levine, Jami; Li, Jennifer S; Mahony, Lynn; Mital, Seema; Pearson, Gail D; Prakash, Ashwin; Hsu, Daphne T

2010-01-01

Although congenital heart disease is associated with low birth weight and prematurity, there is little information about these birth outcomes in infants with single ventricle physiology. We describe the birth outcomes (i.e., gestational age and birth weight) in neonates with single ventricle physiology screened for enrollment in the Pediatric Heart Network's Infant Single Ventricle Trial, compare these outcomes with US norms, and examine the association of birth outcomes with anatomic diagnosis and race. All neonates with single ventricle physiology presenting to Infant Single Ventricle Trial centers were screened for enrollment. Demographic data and anatomic diagnoses were obtained from medical records. A total of 1245 neonates with single ventricle physiology were screened at 10 centers (63 to 266 per center). Diagnoses included hypoplastic left heart syndrome in 49%, unbalanced atrioventricular septal defect in 12%, and tricuspid atresia in 9%. Preterm birth occurred in 16% of neonates with single ventricle physiology vs. 12% in normal neonates (P < .001), low birth weight (<2.5 kg) in 18% vs. 8% in normals (P < .001), and small for gestational age (<10th percentile by definition) in 22% vs. 10% in normals (P < .001). A genetic syndrome was reported in 8%. The percentage of preterm birth, low birth weight, and small for gestational age was similar between screened neonates with and without hypoplastic left heart syndrome. In this large, contemporary cohort of neonates with single ventricle physiology, rates of preterm birth, low birth weight, and small for gestational age were higher than in the general population, but similar between screened neonates with and without hypoplastic left heart syndrome.

Systematic review with meta-analysis: the comparative effectiveness of aspirin vs. screening for colorectal cancer prevention.

PubMed

Emilsson, L; Holme, Ø; Bretthauer, M; Cook, N R; Buring, J E; Løberg, M; Adami, H-O; Sesso, H D; Gaziano, M J; Kalager, M

2017-01-01

Both aspirin use and screening with flexible sigmoidoscopy or guaiac faecal occult blood testing (FOBT) may reduce mortality from colorectal cancer, but comparative effectiveness of these interventions is unknown. To compare aspirin to guaiac FOBT screening with regard to incidence and mortality of colorectal cancer in a network meta-analysis. We searched Medline, EMBASE and the COCHRANE central register (CENTRAL) for relevant randomised trials identified until 31 October 2015. Randomised trials in average-risk populations that reported colorectal cancer mortality, colorectal cancer incidence, or both, with a minimum follow-up of 2 years, and more than 100 randomised individuals were included. Three investigators independently extracted data. We calculated relative risks [RR with 95% predictive intervals (PrIs)] for the comparison of the interventions by frequentist network meta-analyses. The effect of aspirin on colorectal cancer mortality was similar to FOBT (RR 1.03; 95% PrI 0.76-1.39) and flexible sigmoidoscopy (RR 1.16; 95% PrI 0.84-1.60). Aspirin was more effective than FOBT (RR 0.36; 95% PrI 0.22-0.59) and flexible sigmoidoscopy (RR 0.37; 95% PrI 0.22-0.62) in preventing death from or cancer in the proximal colon. Aspirin was equally effective as screening in reducing colorectal cancer incidence, while flexible sigmoidoscopy was superior to FOBT (RR 0.84; 95% PrI 0.72-0.97). Low-dose aspirin seems to be equally effective as flexible sigmoidoscopy or guaiac FOBT screening to reduce colorectal cancer incidence and mortality, and more effective for cancers in the proximal colon. A randomised comparative effectiveness trial of aspirin vs. screening is warranted. © 2016 John Wiley & Sons Ltd.

The design of light pipe with microstructures for touch screen

NASA Astrophysics Data System (ADS)

Yang, Bo; Lu, Kan; Liu, Pengfei; Wei, Xiaona

2010-11-01

Touch screen has a very wide range of applications. Most of them are used in public information inquiries, for instance, service inquiries in telecommunication bureau, tax bureau, bank system, electric department, etc...Touch screen can also be used for entertainment and virtual reality applications too. Traditionally, touch screen was composed of pairs of infrared LED and correspondent receivers which were all installed in the screen frame. Arrays of LED were set in the adjacent sides of the frame of an infrared touch screen while arrays of the infrared receivers were fixed in each opposite side, so that the infrared detecting network was formed. While the infrared touch screen has some technical limitations nowadays such as the low resolution, limitations of touching methods and fault response due to environmental disturbances. The plastic material has a relatively high absorption rate for infrared light, which greatly limits the size of the touch screen. Our design uses laser diode as source and change the traditional inner structure of touch screen by using a light pipe with microstructures. The geometric parameters of the light pipe and the microstructures were obtained through equation solving. Simulation results prove that the design method for touch screen proposed in this paper could achieve high resolution and large size of touch screen.

Develop a solution for protecting and securing enterprise networks from malicious attacks

NASA Astrophysics Data System (ADS)

Kamuru, Harshitha; Nijim, Mais

2014-05-01

In the world of computer and network security, there are myriad ways to launch an attack, which, from the perspective of a network, can usually be defined as "traffic that has huge malicious intent." Firewall acts as one of the measure in order to secure the device from incoming unauthorized data. There are infinite number of computer attacks that no firewall can prevent, such as those executed locally on the machine by a malicious user. From the network's perspective, there are numerous types of attack. All the attacks that degrade the effectiveness of data can be grouped into two types: brute force and precision. The Firewall that belongs to Juniper has the capability to protect against both types of attack. Denial of Service (DoS) attacks are one of the most well-known network security threats under brute force attacks, which is largely due to the high-profile way in which they can affect networks. Over the years, some of the largest, most respected Internet sites have been effectively taken offline by Denial of Service (DOS) attacks. A DoS attack typically has a singular focus, namely, to cause the services running on a particular host or network to become unavailable. Some DoS attacks exploit vulnerabilities in an operating system and cause it to crash, such as the infamous Win nuke attack. Others submerge a network or device with traffic so that there are no more resources to handle legitimate traffic. Precision attacks typically involve multiple phases and often involves a bit more thought than brute force attacks, all the way from reconnaissance to machine ownership. Before a precision attack is launched, information about the victim needs to be gathered. This information gathering typically takes the form of various types of scans to determine available hosts, networks, and ports. The hosts available on a network can be determined by ping sweeps. The available ports on a machine can be located by port scans. Screens cover a wide variety of attack traffic as they are configured on a per-zone basis. Depending on the type of screen being configured, there may be additional settings beyond simply blocking the traffic. Attack prevention is also a native function of any firewall. Juniper Firewall handles traffic on a per-flow basis. We can use flows or sessions as a way to determine whether traffic attempting to traverse the firewall is legitimate. We control the state-checking components resident in Juniper Firewall by configuring "flow" settings. These settings allow you to configure state checking for various conditions on the device. You can use flow settings to protect against TCP hijacking, and to generally ensure that the fire-wall is performing full state processing when desired. We take a case study of attack on a network and perform study of the detection of the malicious packets on a Net screen Firewall. A new solution for securing enterprise networks will be developed here.

A Multilayer Network Approach for Guiding Drug Repositioning in Neglected Diseases

PubMed Central

Chernomoretz, Ariel; Agüero, Fernán

2016-01-01

Drug development for neglected diseases has been historically hampered due to lack of market incentives. The advent of public domain resources containing chemical information from high throughput screenings is changing the landscape of drug discovery for these diseases. In this work we took advantage of data from extensively studied organisms like human, mouse, E. coli and yeast, among others, to develop a novel integrative network model to prioritize and identify candidate drug targets in neglected pathogen proteomes, and bioactive drug-like molecules. We modeled genomic (proteins) and chemical (bioactive compounds) data as a multilayer weighted network graph that takes advantage of bioactivity data across 221 species, chemical similarities between 1.7 105 compounds and several functional relations among 1.67 105 proteins. These relations comprised orthology, sharing of protein domains, and shared participation in defined biochemical pathways. We showcase the application of this network graph to the problem of prioritization of new candidate targets, based on the information available in the graph for known compound-target associations. We validated this strategy by performing a cross validation procedure for known mouse and Trypanosoma cruzi targets and showed that our approach outperforms classic alignment-based approaches. Moreover, our model provides additional flexibility as two different network definitions could be considered, finding in both cases qualitatively different but sensible candidate targets. We also showcase the application of the network to suggest targets for orphan compounds that are active against Plasmodium falciparum in high-throughput screens. In this case our approach provided a reduced prioritization list of target proteins for the query molecules and showed the ability to propose new testable hypotheses for each compound. Moreover, we found that some predictions highlighted by our network model were supported by independent experimental validations as found post-facto in the literature. PMID:26735851

A Multilayer Network Approach for Guiding Drug Repositioning in Neglected Diseases.

PubMed

Berenstein, Ariel José; Magariños, María Paula; Chernomoretz, Ariel; Agüero, Fernán

2016-01-01

Drug development for neglected diseases has been historically hampered due to lack of market incentives. The advent of public domain resources containing chemical information from high throughput screenings is changing the landscape of drug discovery for these diseases. In this work we took advantage of data from extensively studied organisms like human, mouse, E. coli and yeast, among others, to develop a novel integrative network model to prioritize and identify candidate drug targets in neglected pathogen proteomes, and bioactive drug-like molecules. We modeled genomic (proteins) and chemical (bioactive compounds) data as a multilayer weighted network graph that takes advantage of bioactivity data across 221 species, chemical similarities between 1.7 105 compounds and several functional relations among 1.67 105 proteins. These relations comprised orthology, sharing of protein domains, and shared participation in defined biochemical pathways. We showcase the application of this network graph to the problem of prioritization of new candidate targets, based on the information available in the graph for known compound-target associations. We validated this strategy by performing a cross validation procedure for known mouse and Trypanosoma cruzi targets and showed that our approach outperforms classic alignment-based approaches. Moreover, our model provides additional flexibility as two different network definitions could be considered, finding in both cases qualitatively different but sensible candidate targets. We also showcase the application of the network to suggest targets for orphan compounds that are active against Plasmodium falciparum in high-throughput screens. In this case our approach provided a reduced prioritization list of target proteins for the query molecules and showed the ability to propose new testable hypotheses for each compound. Moreover, we found that some predictions highlighted by our network model were supported by independent experimental validations as found post-facto in the literature.

A network-based multi-target computational estimation scheme for anticoagulant activities of compounds.

PubMed

Li, Qian; Li, Xudong; Li, Canghai; Chen, Lirong; Song, Jun; Tang, Yalin; Xu, Xiaojie

2011-03-22

Traditional virtual screening method pays more attention on predicted binding affinity between drug molecule and target related to a certain disease instead of phenotypic data of drug molecule against disease system, as is often less effective on discovery of the drug which is used to treat many types of complex diseases. Virtual screening against a complex disease by general network estimation has become feasible with the development of network biology and system biology. More effective methods of computational estimation for the whole efficacy of a compound in a complex disease system are needed, given the distinct weightiness of the different target in a biological process and the standpoint that partial inhibition of several targets can be more efficient than the complete inhibition of a single target. We developed a novel approach by integrating the affinity predictions from multi-target docking studies with biological network efficiency analysis to estimate the anticoagulant activities of compounds. From results of network efficiency calculation for human clotting cascade, factor Xa and thrombin were identified as the two most fragile enzymes, while the catalytic reaction mediated by complex IXa:VIIIa and the formation of the complex VIIIa:IXa were recognized as the two most fragile biological matter in the human clotting cascade system. Furthermore, the method which combined network efficiency with molecular docking scores was applied to estimate the anticoagulant activities of a serial of argatroban intermediates and eight natural products respectively. The better correlation (r = 0.671) between the experimental data and the decrease of the network deficiency suggests that the approach could be a promising computational systems biology tool to aid identification of anticoagulant activities of compounds in drug discovery. This article proposes a network-based multi-target computational estimation method for anticoagulant activities of compounds by combining network efficiency analysis with scoring function from molecular docking.

A Network-Based Multi-Target Computational Estimation Scheme for Anticoagulant Activities of Compounds

PubMed Central

Li, Canghai; Chen, Lirong; Song, Jun; Tang, Yalin; Xu, Xiaojie

2011-01-01

Background Traditional virtual screening method pays more attention on predicted binding affinity between drug molecule and target related to a certain disease instead of phenotypic data of drug molecule against disease system, as is often less effective on discovery of the drug which is used to treat many types of complex diseases. Virtual screening against a complex disease by general network estimation has become feasible with the development of network biology and system biology. More effective methods of computational estimation for the whole efficacy of a compound in a complex disease system are needed, given the distinct weightiness of the different target in a biological process and the standpoint that partial inhibition of several targets can be more efficient than the complete inhibition of a single target. Methodology We developed a novel approach by integrating the affinity predictions from multi-target docking studies with biological network efficiency analysis to estimate the anticoagulant activities of compounds. From results of network efficiency calculation for human clotting cascade, factor Xa and thrombin were identified as the two most fragile enzymes, while the catalytic reaction mediated by complex IXa:VIIIa and the formation of the complex VIIIa:IXa were recognized as the two most fragile biological matter in the human clotting cascade system. Furthermore, the method which combined network efficiency with molecular docking scores was applied to estimate the anticoagulant activities of a serial of argatroban intermediates and eight natural products respectively. The better correlation (r = 0.671) between the experimental data and the decrease of the network deficiency suggests that the approach could be a promising computational systems biology tool to aid identification of anticoagulant activities of compounds in drug discovery. Conclusions This article proposes a network-based multi-target computational estimation method for anticoagulant activities of compounds by combining network efficiency analysis with scoring function from molecular docking. PMID:21445339

An interactive web-based application for Comprehensive Analysis of RNAi-screen Data.

PubMed

Dutta, Bhaskar; Azhir, Alaleh; Merino, Louis-Henri; Guo, Yongjian; Revanur, Swetha; Madhamshettiwar, Piyush B; Germain, Ronald N; Smith, Jennifer A; Simpson, Kaylene J; Martin, Scott E; Buehler, Eugen; Beuhler, Eugen; Fraser, Iain D C

2016-02-23

RNAi screens are widely used in functional genomics. Although the screen data can be susceptible to a number of experimental biases, many of these can be corrected by computational analysis. For this purpose, here we have developed a web-based platform for integrated analysis and visualization of RNAi screen data named CARD (for Comprehensive Analysis of RNAi Data; available at https://card.niaid.nih.gov). CARD allows the user to seamlessly carry out sequential steps in a rigorous data analysis workflow, including normalization, off-target analysis, integration of gene expression data, optimal thresholds for hit selection and network/pathway analysis. To evaluate the utility of CARD, we describe analysis of three genome-scale siRNA screens and demonstrate: (i) a significant increase both in selection of subsequently validated hits and in rejection of false positives, (ii) an increased overlap of hits from independent screens of the same biology and (iii) insight to microRNA (miRNA) activity based on siRNA seed enrichment.

An interactive web-based application for Comprehensive Analysis of RNAi-screen Data

PubMed Central

Dutta, Bhaskar; Azhir, Alaleh; Merino, Louis-Henri; Guo, Yongjian; Revanur, Swetha; Madhamshettiwar, Piyush B.; Germain, Ronald N.; Smith, Jennifer A.; Simpson, Kaylene J.; Martin, Scott E.; Beuhler, Eugen; Fraser, Iain D. C.

2016-01-01

RNAi screens are widely used in functional genomics. Although the screen data can be susceptible to a number of experimental biases, many of these can be corrected by computational analysis. For this purpose, here we have developed a web-based platform for integrated analysis and visualization of RNAi screen data named CARD (for Comprehensive Analysis of RNAi Data; available at https://card.niaid.nih.gov). CARD allows the user to seamlessly carry out sequential steps in a rigorous data analysis workflow, including normalization, off-target analysis, integration of gene expression data, optimal thresholds for hit selection and network/pathway analysis. To evaluate the utility of CARD, we describe analysis of three genome-scale siRNA screens and demonstrate: (i) a significant increase both in selection of subsequently validated hits and in rejection of false positives, (ii) an increased overlap of hits from independent screens of the same biology and (iii) insight to microRNA (miRNA) activity based on siRNA seed enrichment. PMID:26902267

A platform for rapid prototyping of synthetic gene networks in mammalian cells

PubMed Central

Duportet, Xavier; Wroblewska, Liliana; Guye, Patrick; Li, Yinqing; Eyquem, Justin; Rieders, Julianne; Rimchala, Tharathorn; Batt, Gregory; Weiss, Ron

2014-01-01

Mammalian synthetic biology may provide novel therapeutic strategies, help decipher new paths for drug discovery and facilitate synthesis of valuable molecules. Yet, our capacity to genetically program cells is currently hampered by the lack of efficient approaches to streamline the design, construction and screening of synthetic gene networks. To address this problem, here we present a framework for modular and combinatorial assembly of functional (multi)gene expression vectors and their efficient and specific targeted integration into a well-defined chromosomal context in mammalian cells. We demonstrate the potential of this framework by assembling and integrating different functional mammalian regulatory networks including the largest gene circuit built and chromosomally integrated to date (6 transcription units, 27kb) encoding an inducible memory device. Using a library of 18 different circuits as a proof of concept, we also demonstrate that our method enables one-pot/single-flask chromosomal integration and screening of circuit libraries. This rapid and powerful prototyping platform is well suited for comparative studies of genetic regulatory elements, genes and multi-gene circuits as well as facile development of libraries of isogenic engineered cell lines. PMID:25378321

Brain activation patterns elicited by the 'Faces Symbol Test' -- a pilot fMRI study.

PubMed

Grabner, Rh; Popotnig, F; Ropele, S; Neuper, C; Gorani, F; Petrovic, K; Ebner, F; Strasser-Fuchs, S; Fazekas, F; Enzinger, C

2008-04-01

The Faces Symbol Test (FST) has recently been proposed as a brief and patient-friendly screening instrument for the assessment of cognitive dysfunction in patients with multiple sclerosis (MS). However, in contrast to well-established MS screening tests such as the Paced Auditory Serial Addition Test, the neural correlates of the FST have not been investigated so far. In the present study, we developed a functional MRI (fMRI) version of the FST to provide first data on brain regions and networks involved in this test. A sample of 19 healthy participants completed a version of the FST adapted for fMRI, requiring matching of faces and symbols in a multiple choice test and two further experimental conditions drawing on cognitive subcomponents (face matching and symbol matching). Imaging data showed a differential involvement of a fronto-parieto-occipital network in the three conditions. The most demanding FST condition elicited brain activation patterns related with sustained attention and executive control. These results suggest that the FST recruits brain networks critical for higher-order cognitive functions often impaired in MS patients.

Identification of Linkages between EDCs in Personal Care Products and Breast Cancer through Data Integration Combined with Gene Network Analysis.

PubMed

Jeong, Hyeri; Kim, Jongwoon; Kim, Youngjun

2017-09-30

Approximately 1000 chemicals have been reported to possibly have endocrine disrupting effects, some of which are used in consumer products, such as personal care products (PCPs) and cosmetics. We conducted data integration combined with gene network analysis to: (i) identify causal molecular mechanisms between endocrine disrupting chemicals (EDCs) used in PCPs and breast cancer; and (ii) screen candidate EDCs associated with breast cancer. Among EDCs used in PCPs, four EDCs having correlation with breast cancer were selected, and we curated 27 common interacting genes between those EDCs and breast cancer to perform the gene network analysis. Based on the gene network analysis, ESR1, TP53, NCOA1, AKT1, and BCL6 were found to be key genes to demonstrate the molecular mechanisms of EDCs in the development of breast cancer. Using GeneMANIA, we additionally predicted 20 genes which could interact with the 27 common genes. In total, 47 genes combining the common and predicted genes were functionally grouped with the gene ontology and KEGG pathway terms. With those genes, we finally screened candidate EDCs for their potential to increase breast cancer risk. This study highlights that our approach can provide insights to understand mechanisms of breast cancer and identify potential EDCs which are in association with breast cancer.

Evaluating the Paper-to-Screen Translation of Participant-Aided Sociograms with High-Risk Participants

PubMed Central

Hogan, Bernie; Melville, Joshua R.; Philips, Gregory Lee; Janulis, Patrick; Contractor, Noshir; Mustanski, Brian S.; Birkett, Michelle

2016-01-01

While much social network data exists online, key network metrics for high-risk populations must still be captured through self-report. This practice has suffered from numerous limitations in workflow and response burden. However, advances in technology, network drawing libraries and databases are making interactive network drawing increasingly feasible. We describe the translation of an analog-based technique for capturing personal networks into a digital framework termed netCanvas that addresses many existing shortcomings such as: 1) complex data entry; 2) extensive interviewer intervention and field setup; 3) difficulties in data reuse; and 4) a lack of dynamic visualizations. We test this implementation within a health behavior study of a high-risk and difficult-to-reach population. We provide a within–subjects comparison between paper and touchscreens. We assert that touchscreen-based social network capture is now a viable alternative for highly sensitive data and social network data entry tasks. PMID:28018995

Evaluating the Paper-to-Screen Translation of Participant-Aided Sociograms with High-Risk Participants.

PubMed

Hogan, Bernie; Melville, Joshua R; Philips, Gregory Lee; Janulis, Patrick; Contractor, Noshir; Mustanski, Brian S; Birkett, Michelle

2016-05-01

While much social network data exists online, key network metrics for high-risk populations must still be captured through self-report. This practice has suffered from numerous limitations in workflow and response burden. However, advances in technology, network drawing libraries and databases are making interactive network drawing increasingly feasible. We describe the translation of an analog-based technique for capturing personal networks into a digital framework termed netCanvas that addresses many existing shortcomings such as: 1) complex data entry; 2) extensive interviewer intervention and field setup; 3) difficulties in data reuse; and 4) a lack of dynamic visualizations. We test this implementation within a health behavior study of a high-risk and difficult-to-reach population. We provide a within-subjects comparison between paper and touchscreens. We assert that touchscreen-based social network capture is now a viable alternative for highly sensitive data and social network data entry tasks.

Toward Joint Hypothesis-Tests Seismic Event Screening Analysis: Ms|mb and Event Depth

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anderson, Dale; Selby, Neil

2012-08-14

Well established theory can be used to combine single-phenomenology hypothesis tests into a multi-phenomenology event screening hypothesis test (Fisher's and Tippett's tests). Commonly used standard error in Ms:mb event screening hypothesis test is not fully consistent with physical basis. Improved standard error - Better agreement with physical basis, and correctly partitions error to include Model Error as a component of variance, correctly reduces station noise variance through network averaging. For 2009 DPRK test - Commonly used standard error 'rejects' H0 even with better scaling slope ({beta} = 1, Selby et al.), improved standard error 'fails to rejects' H0.

Novel strategy for protein exploration: high-throughput screening assisted with fuzzy neural network.

PubMed

Kato, Ryuji; Nakano, Hideo; Konishi, Hiroyuki; Kato, Katsuya; Koga, Yuchi; Yamane, Tsuneo; Kobayashi, Takeshi; Honda, Hiroyuki

2005-08-19

To engineer proteins with desirable characteristics from a naturally occurring protein, high-throughput screening (HTS) combined with directed evolutional approach is the essential technology. However, most HTS techniques are simple positive screenings. The information obtained from the positive candidates is used only as results but rarely as clues for understanding the structural rules, which may explain the protein activity. In here, we have attempted to establish a novel strategy for exploring functional proteins associated with computational analysis. As a model case, we explored lipases with inverted enantioselectivity for a substrate p-nitrophenyl 3-phenylbutyrate from the wild-type lipase of Burkhorderia cepacia KWI-56, which is originally selective for (S)-configuration of the substrate. Data from our previous work on (R)-enantioselective lipase screening were applied to fuzzy neural network (FNN), bioinformatic algorithm, to extract guidelines for screening and engineering processes to be followed. FNN has an advantageous feature of extracting hidden rules that lie between sequences of variants and their enzyme activity to gain high prediction accuracy. Without any prior knowledge, FNN predicted a rule indicating that "size at position L167," among four positions (L17, F119, L167, and L266) in the substrate binding core region, is the most influential factor for obtaining lipase with inverted (R)-enantioselectivity. Based on the guidelines obtained, newly engineered novel variants, which were not found in the actual screening, were experimentally proven to gain high (R)-enantioselectivity by engineering the size at position L167. We also designed and assayed two novel variants, namely FIGV (L17F, F119I, L167G, and L266V) and FFGI (L17F, L167G, and L266I), which were compatible with the guideline obtained from FNN analysis, and confirmed that these designed lipases could acquire high inverted enantioselectivity. The results have shown that with the aid of bioinformatic analysis, high-throughput screening can expand its potential for exploring vast combinatorial sequence spaces of proteins.

Identification of the active compounds and significant pathways of yinchenhao decoction based on network pharmacology

PubMed Central

Huang, Jihan; Cheung, Fan; Tan, Hor-Yue; Hong, Ming; Wang, Ning; Yang, Juan; Feng, Yibin; Zheng, Qingshan

2017-01-01

Yinchenhao decoction (YCHD) is a traditional Chinese medicine formulation, which has been widely used for the treatment of jaundice for 2,000 years. Currently, YCHD is used to treat various liver disorders and metabolic diseases, however its chemical/pharmacologic profiles remain to be elucidated. The present study identified the active compounds and significant pathways of YCHD based on network pharmacology. All of the chemical ingredients of YCHD were retrieved from the Traditional Chinese Medicine Systems Pharmacology database. Absorption, distribution, metabolism and excretion screening with oral bioavailability (OB) screening, drug-likeness (DL) and intestinal epithelial permeability (Caco-2) evaluation were applied to discover the bioactive compounds in YCHD. Following this, target prediction, pathway identification and network construction were employed to clarify the mechanism of action of YCHD. Following OB screening, and evaluation of DL and Caco-2, 34 compounds in YCHD were identified as potential active ingredients, of which 30 compounds were associated with 217 protein targets. A total of 31 significant pathways were obtained by performing enrichment analyses of 217 proteins using the JEPETTO 3.x plugin, and 16 classes of gene-associated diseases were revealed by performing enrichment analyses using Database for Annotation, Visualization and Integrated Discovery v6.7. The present study identified potential active compounds and significant pathways in YCHD. In addition, the mechanism of action of YCHD in the treatment of various diseases through multiple pathways was clarified. PMID:28791364

Implementing recommended screening for critical congenital heart disease.

PubMed

Martin, Gerard R; Beekman, Robert H; Mikula, Elizabeth Bradshaw; Fasules, James; Garg, Lorraine F; Kemper, Alex R; Morrow, W Robert; Pearson, Gail D; Mahle, William T

2013-07-01

Critical congenital heart disease (CCHD) is endorsed by the US Secretary of Health and Human Services as part of the recommended uniform screening panel for newborns. Although initial recommendations for implementation exist, as states and hospitals have moved forward with implementation of screening, new challenges and areas for additional focus have been identified. The objective of this study was to develop recommendations to address current challenges and areas of focus surrounding CCHD newborn screening. A workgroup of experts and stakeholders was convened in Washington, District of Columbia, for a 1-day meeting in February 2012. At the beginning of the meeting, the stakeholders held a brainstorming session to identify areas of main priority based on their experience. After this, stakeholders broke into small groups to refine recommendations, which were then finalized by consensus. Recommendations to address selection of screening equipment, standards for reporting of screening outcomes to stakeholders, training of health care providers and educating families, future research priorities, payment for screening, follow-up diagnostic testing, and public health oversight, and advocacy to facilitate effective and comprehensive screening were proposed. Suggestions for future work were developed. Screening for CCHD presents novel challenges and opportunities; however, addressing these will strengthen newborn screening and newborn care networks, and ultimately improve health outcomes.

Exploring the Perceptions of Anal Cancer Screening and Behaviors Among Gay and Bisexual Men Infected With HIV

PubMed Central

Koskan, Alexis M.; LeBlanc, Natalie; Rosa-Cunha, Isabella

2016-01-01

Background The incidence of anal cancer is on the rise among HIV-infected men who have sex with men (MSM). Given the increasing availability of screening, this study explored anal cancer screening awareness and behaviors among MSM infected with HIV. Methods In-depth interviews were conducted with 58 MSM infected with HIV. Results Other than 2 participants treated for anal cancer and 3 treated for precancerous anal lesions, the majority of participants had never heard of anal cancer. Men reported lack of awareness and recommendations from their health care professionals as the greatest barriers to screening. Upon learning about their risk for anal cancer and the availability of screening, the men were eager to discuss screening with their physicians. Participants provided numerous recommendations for future interventions, including training health care professionals to promote screening, disseminating information pertaining to anal cancer through social networks, and creating media campaigns to raise awareness about the need to screen for this type of cancer. Conclusions Future intervention work should focus on ensuring that health care professionals, particularly among HIV/primary care specialists, promote screening for anal dysplasia. It is critical that intervention methods use a community-based approach to raise awareness about the need to screen for anal cancer, especially among MSM infected with HIV. PMID:27009457

Reducing false negatives in clinical practice: the role of neural network technology.

PubMed

Mango, L J

1996-10-01

The fact that some cervical smears result in false-negative findings is an unavoidable and unpredictable consequence of the conventional (manual microscopic) method of screening. Errors in the detection and interpretation of abnormality are cited as leading causes of false-negative cytology findings; these are random errors that are not known to correlate with any patient risk factor, which makes the false-negative findings a "silent" threat that is difficult to prevent. Described by many as a labor-intensive procedure, the microscopic evaluation of a cervical smear involves a detailed search among hundreds of thousands of cells on each smear for a possible few that may indicate abnormality. Investigations into causes of false-negative findings preceding the discovery of high-grade lesions found that many smears had very few diagnostic cells that were often very small in size. These small cells were initially overlooked or misinterpreted and repeatedly missed on rescreening. PAPNET testing is designed to supplement conventional screening by detecting abnormal cells that initially may have been missed by microscopic examination. This interactive system uses neural networks, a type of artificial intelligence well suited for pattern recognition, to automate the arduous search for abnormality. The instrument focuses the review of suspicious cells by a trained cytologist. Clinical studies indicate that PAPNET testing is sensitive to abnormality typically missed by conventional screening and that its use as a supplemental test improves the accuracy of screening.

Assessing local capacity to expand rural breast cancer screening and patient navigation: An iterative mixed-method tool.

PubMed

Inrig, Stephen J; Higashi, Robin T; Tiro, Jasmin A; Argenbright, Keith E; Lee, Simon J Craddock

2017-04-01

Despite federal funding for breast cancer screening, fragmented infrastructure and limited organizational capacity hinder access to the full continuum of breast cancer screening and clinical follow-up procedures among rural-residing women. We proposed a regional hub-and-spoke model, partnering with local providers to expand access across North Texas. We describe development and application of an iterative, mixed-method tool to assess county capacity to conduct community outreach and/or patient navigation in a partnership model. Our tool combined publicly-available quantitative data with qualitative assessments during site visits and semi-structured interviews. Application of our tool resulted in shifts in capacity designation in 10 of 17 county partners: 8 implemented local outreach with hub navigation; 9 relied on the hub for both outreach and navigation. Key factors influencing capacity: (1) formal linkages between partner organizations; (2) inter-organizational relationships; (3) existing clinical service protocols; (4) underserved populations. Qualitative data elucidate how our tool captured these capacity changes. Our capacity assessment tool enabled the hub to establish partnerships with county organizations by tailoring support to local capacity and needs. Absent a vertically integrated provider network for preventive services in these rural counties, our tool facilitated a virtually integrated regional network to extend access to breast cancer screening to underserved women. Copyright © 2016 Elsevier Ltd. All rights reserved.

The BRIGHTEN program: implementation and evaluation of a program to bridge resources of an interdisciplinary geriatric health team via electronic networking.

PubMed

Emery, Erin E; Lapidos, Stan; Eisenstein, Amy R; Ivan, Iulia I; Golden, Robyn L

2012-12-01

To demonstrate the feasibility of the BRIGHTEN Program (Bridging Resources of an Interdisciplinary Geriatric Health Team via Electronic Networking), an interdisciplinary team intervention for assessing and treating older adults for depression in outpatient primary and specialty medical clinics. The BRIGHTEN team collaborates "virtually" to review patient assessment results, develop a treatment plan, and refer to appropriate team members for follow-up care. Older adults in 9 academic medical center clinics and 2 community-based clinics completed screening forms for symptoms of depression and anxiety. Those with positive screens engaged in comprehensive assessment with the BRIGHTEN Program Coordinator; the BRIGHTEN virtual team provided treatment recommendations based on the results of assessment. A collaborative treatment plan was developed with each participant, who was then connected to appropriate services. Two thousand four hundred twenty-two older adults were screened in participating clinics over a 40-month period. Eight hundred fifty-nine older adults screened positive, and 150 elected to enroll in BRIGHTEN. From baseline to 6 months, significant improvements were found in depression symptoms (Geriatric Depression Scale, p < .01) and general mental health (SF-12 Mental Component, p < .01). The BRIGHTEN Program demonstrated that an interdisciplinary virtual team linked with outpatient medical clinics can be an effective, nonthreatening, and seamless approach to enable older adults to access treatment for depression.

SUBSTANCE USE SCREENING AND INTERVENTIONS IN DENTAL CLINICS: SURVEY OF PRACTICE-BASED RESEARCH NETWORK DENTISTS ON CURRENT PRACTICES, POLICIES, AND BARRIERS

PubMed Central

Wright, Shana; Matthews, Abigail G.; Rotrosen, John; Shelley, Donna; Buchholz, Matthew P.; Curro, Frederick A.

2013-01-01

Background Dental visits represent an opportunity to identify and assist patients with substance use, but little is known about how dentists are addressing tobacco, alcohol and illicit drugs. We surveyed dentists to learn about the role their practices might play in providing substance use screening and interventions. Methods A 41-item, web-based survey was distributed to all 210 dentists active in the PEARL dental practice-based research network. The questionnaire assessed clinic policies and current practices, attitudes, and perceived barriers to providing services for tobacco, alcohol, and illicit drug use. Results 143 dentists completed the survey (68% response rate). While screening was common, fewer were providing follow-up counseling or referrals for substance use. Insufficient knowledge/training was the most frequently cited barrier to intervention. Many dentists said they would offer assistance for tobacco (67%) or alcohol or illicit drugs (52%) if reimbursed; an affirmative response was more likely among those who saw publicly insured patients. Conclusions Dentists recognize the importance of screening for substance use, but lack clinical training and systems that could facilitate intervention. Practice Implications If barriers were reduced through changes in reimbursement, education, and systems-level support, our findings indicate that dentists may be willing to address substance use, including use of alcohol and illicit drugs as well as tobacco. PMID:23729460

State transfer in highly connected networks and a quantum Babinet principle

NASA Astrophysics Data System (ADS)

Tsomokos, D. I.; Plenio, M. B.; de Vega, I.; Huelga, S. F.

2008-12-01

The transfer of a quantum state between distant nodes in two-dimensional networks is considered. The fidelity of state transfer is calculated as a function of the number of interactions in networks that are described by regular graphs. It is shown that perfect state transfer is achieved in a network of size N , whose structure is that of an (N/2) -cross polytope graph, if N is a multiple of 4 . The result is reminiscent of the Babinet principle of classical optics. A quantum Babinet principle is derived, which allows for the identification of complementary graphs leading to the same fidelity of state transfer, in analogy with complementary screens providing identical diffraction patterns.

[Clinical audit of screening for gestational diabetes among 848 pregnant women in 23 maternity units of the Pays de la Loire, 2014].

PubMed

Branger, B; Velupillai, C; François, S; Coutin, A S; Paumier, A; Gillard, P; Collin, R; Sentilhes, L; Winer, N

2016-10-01

Guidelines for screening for gestational diabetes mellitus (GDM) were published in 2010. An audit of the maternity units of the Pays de la Loire network sought to determine the adherence rate and to study the factors affecting it in order to propose corrective measures to improve it. The perinatal network in Pays de la Loire provided obstetricians of the 23 participating maternity units with a set of criteria to be collected from the files of women giving birth. The methodology of the audit was designed to enable calculation of the adherence rate overall and according to indications (risk factors, hyperglycemia, and macrosomia): adherence, non-adherence, and over-adherence (screening in the absence of an indication). To obtain around 900 pregnancies, the audit was planned to cover a week of deliveries in June 2014. The analysis included 848 pregnancies and 872 newborns. Risk factors were found for 46.6% of the women (43.2 to 49.9): 13.2% for maternal age≥35years and 30.8% for BMI≥25kg/m 2 . GDM was diagnosed for 14.6% (12.4 to 17.2). The adherence rate for screening was 45.5% (42.2 to 49.9), the non-adherence rate 27.6% (24.7 to 30.7), and the over-adherence rate 26.9% (24.0 to 30.0). Among the factors potentially associated with adherence, we observed only the second-trimester factor (macrosomia); there was no "professional" effect on adherence criteria. No evidence of overmanagement was observed for the pregnancies/deliveries/newborns with overdiagnosis. Oral glucose tolerance tests were performed in accordance with the guidelines (95.9%). Follow-up of women with GDM by specialists was satisfactory (84.6%). This audit showed that adherence to the guidelines was insufficient in the Pays de la Loire network. The reasons for this are numerous: ignorance of the guidelines, in part due to their relative recency, the change in the blood sugar levels defining GDM (perceived as too low), and the absence of strong evidence about these thresholds from publications and practices in other countries, the need to select women for risk factors, and sometimes the late onset of prenatal care at the maternity unit. In view of this audit, the Perinatal Network of Pays de la Loire must work to improve the knowledge and screening practices for GDM among its professionals, by the repeated dissemination of these guidelines and chart review sessions. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Deciphering metabonomics biomarkers-targets interactions for psoriasis vulgaris by network pharmacology.

PubMed

Gu, Jiangyong; Li, Li; Wang, Dongmei; Zhu, Wei; Han, Ling; Zhao, Ruizhi; Xu, Xiaojie; Lu, Chuanjian

2018-06-01

Psoriasis vulgaris is a chronic inflammatory and immune-mediated skin disease. 44 metabonomics biomarkers were identified by high-throughput liquid chromatography coupled to mass spectrometry in our previous work, but the roles of metabonomics biomarkers in the pathogenesis of psoriasis is unclear. The metabonomics biomarker-enzyme network was constructed. The key metabonomics biomarkers and enzymes were screened out by network analysis. The binding affinity between each metabonomics biomarker and target was calculated by molecular docking. A binding energy-weighted polypharmacological index was introduced to evaluate the importance of target-related pathways. Long-chain fatty acids, phospholipids, Estradiol and NADH were the most important metabonomics biomarkers. Most key enzymes belonged hydrolase, thioesterase and acyltransferase. Six proteins (TNF-alpha, MAPK3, iNOS, eNOS, COX2 and mTOR) were extensively involved in inflammatory reaction, immune response and cell proliferation, and might be drug targets for psoriasis. PI3K-Akt signaling pathway and five other pathways had close correlation with the pathogenesis of psoriasis and could deserve further research. The inflammatory reaction, immune response and cell proliferation are mainly involved in psoriasis. Network pharmacology provide a new insight into the relationships between metabonomics biomarkers and the pathogenesis of psoriasis. KEY MESSAGES   • Network pharmacology was adopted to identify key metabonomics biomarkers and enzymes.   • Six proteins were screened out as important drug targets for psoriasis.   • A binding energy-weighted polypharmacological index was introduced to evaluate the importance of target-related pathways.

Cancer diagnostics using neural network sorting of processed images

NASA Astrophysics Data System (ADS)

Wyman, Charles L.; Schreeder, Marshall; Grundy, Walt; Kinser, Jason M.

1996-03-01

A combination of image processing with neural network sorting was conducted to demonstrate feasibility of automated cervical smear screening. Nuclei were isolated to generate a series of data points relating to the density and size of individual nuclei. This was followed by segmentation to isolate entire cells for subsequent generation of data points to bound the size of the cytoplasm. Data points were taken on as many as ten cells per image frame and included correlation against a series of filters providing size and density readings on nuclei. Additional point data was taken on nuclei images to refine size information and on whole cells to bound the size of the cytoplasm, twenty data points per assessed cell were generated. These data point sets, designated as neural tensors, comprise the inputs for training and use of a unique neural network to sort the images and identify those indicating evidence of disease. The neural network, named the Fast Analog Associative Memory, accumulates data and establishes lookup tables for comparison against images to be assessed. Six networks were trained to differentiate normal cells from those evidencing various levels abnormality that may lead to cancer. A blind test was conducted on 77 images to evaluate system performance. The image set included 31 positives (diseased) and 46 negatives (normal). Our system correctly identified all 31 positives and 41 of the negatives with 5 false positives. We believe this technology can lead to more efficient automated screening of cervical smears.

Evaluating Developmental Neurotoxicity Hazard: Better than Before

EPA Pesticide Factsheets

EPA researchers grew neural networks in their laboratory that showed the promise of helping to screen thousands of chemicals in the environment that are yet to be characterized for developmental neurotoxicity hazard through traditional methods.

Cancer Intervention and Surveillance Modeling Network (CISNET)

Cancer.gov

CISNET is a consortium of NCI-sponsored investigators that use statistical modeling to improve our understanding of cancer control interventions in prevention, screening, and treatment and their effects on population trends in incidence and mortality.

National Child Traumatic Stress Network

MedlinePlus

... Información en Español Topics What is Child Traumatic Stress Trauma Types Finding Help Trauma-Informed Screening & Assessment ... Adolescence and Substance Abuse Culture and Trauma Economic Stress Military and Veteran Families and Children Secondary Traumatic ...

Alignment of breast cancer screening guidelines, accountability metrics, and practice patterns.

PubMed

Onega, Tracy; Haas, Jennifer S; Bitton, Asaf; Brackett, Charles; Weiss, Julie; Goodrich, Martha; Harris, Kimberly; Pyle, Steve; Tosteson, Anna N A

2017-01-01

Breast cancer screening guidelines and metrics are inconsistent with each other and may differ from breast screening practice patterns in primary care. This study measured breast cancer screening practice patterns in relation to common evidence-based guidelines and accountability metrics. Cohort study using primary data collected from a regional breast cancer screening research network between 2011 and 2014. Using information on women aged 30 to 89 years within 21 primary care practices of 2 large integrated health systems in New England, we measured the proportion of women screened overall and by age using 2 screening definition categories: any mammogram and screening mammogram. Of the 81,352 women in our cohort, 54,903 (67.5%) had at least 1 mammogram during the time period, 48,314 (59.4%) had a screening mammogram. Women aged 50 to 69 years were the highest proportion screened (82.4% any mammogram, 75% screening indication); 72.6% of women at age 40 had a screening mammogram with a median of 70% (range = 54.3%-84.8%) among the practices. Of women aged at least 75 years, 63.3% had a screening mammogram, with the median of 63.9% (range = 37.2%-78.3%) among the practices. Of women who had 2 or more mammograms, 79.5% were screened annually. Primary care practice patterns for breast cancer screening are not well aligned with some evidence-based guidelines and accountability metrics. Metrics and incentives should be designed with more uniformity and should also include shared decision making when the evidence does not clearly support one single conclusion.

The impact of overdiagnosis on the selection of efficient lung cancer screening strategies.

PubMed

Han, Summer S; Ten Haaf, Kevin; Hazelton, William D; Munshi, Vidit N; Jeon, Jihyoun; Erdogan, Saadet A; Johanson, Colden; McMahon, Pamela M; Meza, Rafael; Kong, Chung Yin; Feuer, Eric J; de Koning, Harry J; Plevritis, Sylvia K

2017-06-01

The U.S. Preventive Services Task Force (USPSTF) recently updated their national lung screening guidelines and recommended low-dose computed tomography (LDCT) for lung cancer (LC) screening through age 80. However, the risk of overdiagnosis among older populations is a concern. Using four comparative models from the Cancer Intervention and Surveillance Modeling Network, we evaluate the overdiagnosis of the screening program recommended by USPSTF in the U.S. 1950 birth cohort. We estimate the number of LC deaths averted by screening (D) per overdiagnosed case (O), yielding the ratio D/O, to quantify the trade-off between the harms and benefits of LDCT. We analyze 576 hypothetical screening strategies that vary by age, smoking, and screening frequency and evaluate efficient screening strategies that maximize the D/O ratio and other metrics including D and life-years gained (LYG) per overdiagnosed case. The estimated D/O ratio for the USPSTF screening program is 2.85 (model range: 1.5-4.5) in the 1950 birth cohort, implying LDCT can prevent ∼3 LC deaths per overdiagnosed case. This D/O ratio increases by 22% when the program stops screening at an earlier age 75 instead of 80. Efficiency frontier analysis shows that while the most efficient screening strategies that maximize the mortality reduction (D) irrespective of overdiagnosis screen through age 80, screening strategies that stop at age 75 versus 80 produce greater efficiency in increasing life-years gained per overdiagnosed case. Given the risk of overdiagnosis with LC screening, the stopping age of screening merits further consideration when balancing benefits and harms. © 2017 UICC.

Domestic violence screening practices of obstetrician-gynecologists.

PubMed

Horan, D L; Chapin, J; Klein, L; Schmidt, L A; Schulkin, J

1998-11-01

To ascertain the current knowledge base and screening practices of obstetrician-gynecologists in the area of domestic violence. We mailed a survey to 189 ACOG Fellows who are members of the Collaborative Ambulatory Research Network. Questionnaires were also mailed to a random sample of 1250 nonmember Fellows. Obstetrician-gynecologists are aware of the nature of domestic violence and are familiar with common symptomatology that may be associated with domestic violence. For pregnant patients, 39% of respondents routinely screen at the first prenatal visit; 27% of respondents routinely screen nonpregnant patients at the initial visit. Screening is most likely to occur when the obstetrician-gynecologist suspects a patient is being abused, both during pregnancy (68%) and when the patient is not pregnant (72%). Only 30% of obstetrician-gynecologists received training on domestic violence during medical school; 37% received such instruction during residency training. The majority (67%) have received continuing education on the subject. Years since training and personal experiences with intimate-partner violence were associated with increased screening practices. Routine screening of all women for domestic violence has been recommended by ACOG for more than a decade. The majority of obstetrician-gynecologists screen both pregnant and nonpregnant patients when they suspect abuse. However, with universal screening, more female victims of violence can be identified and can receive needed services.

Benchmarking Ligand-Based Virtual High-Throughput Screening with the PubChem Database

PubMed Central

Butkiewicz, Mariusz; Lowe, Edward W.; Mueller, Ralf; Mendenhall, Jeffrey L.; Teixeira, Pedro L.; Weaver, C. David; Meiler, Jens

2013-01-01

With the rapidly increasing availability of High-Throughput Screening (HTS) data in the public domain, such as the PubChem database, methods for ligand-based computer-aided drug discovery (LB-CADD) have the potential to accelerate and reduce the cost of probe development and drug discovery efforts in academia. We assemble nine data sets from realistic HTS campaigns representing major families of drug target proteins for benchmarking LB-CADD methods. Each data set is public domain through PubChem and carefully collated through confirmation screens validating active compounds. These data sets provide the foundation for benchmarking a new cheminformatics framework BCL::ChemInfo, which is freely available for non-commercial use. Quantitative structure activity relationship (QSAR) models are built using Artificial Neural Networks (ANNs), Support Vector Machines (SVMs), Decision Trees (DTs), and Kohonen networks (KNs). Problem-specific descriptor optimization protocols are assessed including Sequential Feature Forward Selection (SFFS) and various information content measures. Measures of predictive power and confidence are evaluated through cross-validation, and a consensus prediction scheme is tested that combines orthogonal machine learning algorithms into a single predictor. Enrichments ranging from 15 to 101 for a TPR cutoff of 25% are observed. PMID:23299552

A Stochastic Spiking Neural Network for Virtual Screening.

PubMed

Morro, A; Canals, V; Oliver, A; Alomar, M L; Galan-Prado, F; Ballester, P J; Rossello, J L

2018-04-01

Virtual screening (VS) has become a key computational tool in early drug design and screening performance is of high relevance due to the large volume of data that must be processed to identify molecules with the sought activity-related pattern. At the same time, the hardware implementations of spiking neural networks (SNNs) arise as an emerging computing technique that can be applied to parallelize processes that normally present a high cost in terms of computing time and power. Consequently, SNN represents an attractive alternative to perform time-consuming processing tasks, such as VS. In this brief, we present a smart stochastic spiking neural architecture that implements the ultrafast shape recognition (USR) algorithm achieving two order of magnitude of speed improvement with respect to USR software implementations. The neural system is implemented in hardware using field-programmable gate arrays allowing a highly parallelized USR implementation. The results show that, due to the high parallelization of the system, millions of compounds can be checked in reasonable times. From these results, we can state that the proposed architecture arises as a feasible methodology to efficiently enhance time-consuming data-mining processes such as 3-D molecular similarity search.

Echohydrology of a floodplain forest: relationships between vegetation and groundwater resources at Congaree National Park, South Carolina USA

Treesearch

Timothy Callahan; Lauren Senn

2016-01-01

The goal of this project was to investigate the relationship between the shallow, unconfined aquifer and woody vegetation at eight sites of the Congaree Observation Well Network at Congaree National Park near Hopkins, South Carolina. Eight piezometers with screens of 1.5-m length (top-of-screen depths ranging from 3.0 to 5.0 m below ground surface) along a 1.8-km cross...

Self-Organizing Maps for In Silico Screening and Data Visualization.

PubMed

Digles, Daniela; Ecker, Gerhard F

2011-10-01

Self-organizing maps, which are unsupervised artificial neural networks, have become a very useful tool in a wide area of disciplines, including medicinal chemistry. Here, we will focus on two applications of self-organizing maps: the use of self-organizing maps for in silico screening and for clustering and visualisation of large datasets. Additionally, the importance of parameter selection is discussed and some modifications to the original algorithm are summarised. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Internet Process Addiction Test: Screening for Addictions to Processes Facilitated by the Internet

PubMed Central

Northrup, Jason C.; Lapierre, Coady; Kirk, Jeffrey; Rae, Cosette

2015-01-01

The Internet Process Addiction Test (IPAT) was created to screen for potential addictive behaviors that could be facilitated by the internet. The IPAT was created with the mindset that the term “Internet addiction” is structurally problematic, as the Internet is simply the medium that one uses to access various addictive processes. The role of the internet in facilitating addictions, however, cannot be minimized. A new screening tool that effectively directed researchers and clinicians to the specific processes facilitated by the internet would therefore be useful. This study shows that the Internet Process Addiction Test (IPAT) demonstrates good validity and reliability. Four addictive processes were effectively screened for with the IPAT: Online video game playing, online social networking, online sexual activity, and web surfing. Implications for further research and limitations of the study are discussed. PMID:26226007

tcpl: the ToxCast pipeline for high-throughput screening data.

PubMed

Filer, Dayne L; Kothiya, Parth; Setzer, R Woodrow; Judson, Richard S; Martin, Matthew T

2017-02-15

Large high-throughput screening (HTS) efforts are widely used in drug development and chemical toxicity screening. Wide use and integration of these data can benefit from an efficient, transparent and reproducible data pipeline. Summary: The tcpl R package and its associated MySQL database provide a generalized platform for efficiently storing, normalizing and dose-response modeling of large high-throughput and high-content chemical screening data. The novel dose-response modeling algorithm has been tested against millions of diverse dose-response series, and robustly fits data with outliers and cytotoxicity-related signal loss. tcpl is freely available on the Comprehensive R Archive Network under the GPL-2 license. martin.matt@epa.gov. Published by Oxford University Press 2016. This work is written by US Government employees and is in the public domain in the US.

Effectiveness, efficiency, duration, and costs of recruiting for an African American women's lifestyle physical activity program.

PubMed

Wilbur, Joellen; Buchholz, Susan W; Ingram, Diana M; Braun, Lynne T; Johnson, Tricia J; Fogg, Louis; Miller, Arlene M; Volgman, Annabelle S; McDevitt, Judith

2013-10-01

In a 48-week lifestyle physical activity controlled trial in African American women, we analyzed recruitment effectiveness, efficiency, duration, and costs. Social networking was the most effective approach for inviting women to the trial. Of the 609 who responded to invitations, 514 completed telephone screening; of these, 409 (80%) were found eligible. The health assessment screening was completed by 337 women; of these, 297 (88%) were found eligible. The mean number of days from completion of the telephone and health assessment screenings to beginning the intervention was 23.01, and the mean cost was $74.57 per person. Results suggest that provision of health assessment screening by study staff as part of recruitment is effective for minimizing attrition and also might be cost-effective. © 2013 Wiley Periodicals, Inc.

The Internet Process Addiction Test: Screening for Addictions to Processes Facilitated by the Internet.

PubMed

Northrup, Jason C; Lapierre, Coady; Kirk, Jeffrey; Rae, Cosette

2015-07-28

The Internet Process Addiction Test (IPAT) was created to screen for potential addictive behaviors that could be facilitated by the internet. The IPAT was created with the mindset that the term "Internet addiction" is structurally problematic, as the Internet is simply the medium that one uses to access various addictive processes. The role of the internet in facilitating addictions, however, cannot be minimized. A new screening tool that effectively directed researchers and clinicians to the specific processes facilitated by the internet would therefore be useful. This study shows that the Internet Process Addiction Test (IPAT) demonstrates good validity and reliability. Four addictive processes were effectively screened for with the IPAT: Online video game playing, online social networking, online sexual activity, and web surfing. Implications for further research and limitations of the study are discussed.

Coronary Artery Dissection: Not Just a Heart Attack

MedlinePlus

... using an angiogram , but an intravascular ultrasound or optical coherence tomography screening, which allows doctors to see ... Changes Recovery FAQs • Heart Attack Tools & Resources • Support Network Watch, Learn and Live Our Interactive Cardiovascular Library ...

Statewide analysis of bicycle crashes : [project summary].

DOT National Transportation Integrated Search

2017-06-01

An extensive literature review was conducted to locate existing studies in four areas: (1) risk factors that affect the frequency and severity of bicycle crashes; (2) bicycle crash causes, patterns, and contributing factors; (3) network screening met...

Reduction of ZTD outliers through improved GNSS data processing and screening strategies

NASA Astrophysics Data System (ADS)

Stepniak, Katarzyna; Bock, Olivier; Wielgosz, Pawel

2018-03-01

Though Global Navigation Satellite System (GNSS) data processing has been significantly improved over the years, it is still commonly observed that zenith tropospheric delay (ZTD) estimates contain many outliers which are detrimental to meteorological and climatological applications. In this paper, we show that ZTD outliers in double-difference processing are mostly caused by sub-daily data gaps at reference stations, which cause disconnections of clusters of stations from the reference network and common mode biases due to the strong correlation between stations in short baselines. They can reach a few centimetres in ZTD and usually coincide with a jump in formal errors. The magnitude and sign of these biases are impossible to predict because they depend on different errors in the observations and on the geometry of the baselines. We elaborate and test a new baseline strategy which solves this problem and significantly reduces the number of outliers compared to the standard strategy commonly used for positioning (e.g. determination of national reference frame) in which the pre-defined network is composed of a skeleton of reference stations to which secondary stations are connected in a star-like structure. The new strategy is also shown to perform better than the widely used strategy maximizing the number of observations available in many GNSS programs. The reason is that observations are maximized before processing, whereas the final number of used observations can be dramatically lower because of data rejection (screening) during the processing. The study relies on the analysis of 1 year of GPS (Global Positioning System) data from a regional network of 136 GNSS stations processed using Bernese GNSS Software v.5.2. A post-processing screening procedure is also proposed to detect and remove a few outliers which may still remain due to short data gaps. It is based on a combination of range checks and outlier checks of ZTD and formal errors. The accuracy of the final screened GPS ZTD estimates is assessed by comparison to ERA-Interim reanalysis.

Applying operations research to optimize a novel population management system for cancer screening.

PubMed

Zai, Adrian H; Kim, Seokjin; Kamis, Arnold; Hung, Ken; Ronquillo, Jeremiah G; Chueh, Henry C; Atlas, Steven J

2014-02-01

To optimize a new visit-independent, population-based cancer screening system (TopCare) by using operations research techniques to simulate changes in patient outreach staffing levels (delegates, navigators), modifications to user workflow within the information technology (IT) system, and changes in cancer screening recommendations. TopCare was modeled as a multiserver, multiphase queueing system. Simulation experiments implemented the queueing network model following a next-event time-advance mechanism, in which systematic adjustments were made to staffing levels, IT workflow settings, and cancer screening frequency in order to assess their impact on overdue screenings per patient. TopCare reduced the average number of overdue screenings per patient from 1.17 at inception to 0.86 during simulation to 0.23 at steady state. Increases in the workforce improved the effectiveness of TopCare. In particular, increasing the delegate or navigator staff level by one person improved screening completion rates by 1.3% or 12.2%, respectively. In contrast, changes in the amount of time a patient entry stays on delegate and navigator lists had little impact on overdue screenings. Finally, lengthening the screening interval increased efficiency within TopCare by decreasing overdue screenings at the patient level, resulting in a smaller number of overdue patients needing delegates for screening and a higher fraction of screenings completed by delegates. Simulating the impact of changes in staffing, system parameters, and clinical inputs on the effectiveness and efficiency of care can inform the allocation of limited resources in population management.

Disrupted coupling of large-scale networks is associated with relapse behaviour in heroin-dependent men

PubMed Central

Li, Qiang; Liu, Jierong; Wang, Wei; Wang, Yarong; Li, Wei; Chen, Jiajie; Zhu, Jia; Yan, Xuejiao; Li, Yongbin; Li, Zhe; Ye, Jianjun; Wang, Wei

2018-01-01

Background It is unknown whether impaired coupling among 3 core large-scale brain networks (salience [SN], default mode [DMN] and executive control networks [ECN]) is associated with relapse behaviour in treated heroin-dependent patients. Methods We conducted a prospective resting-state functional MRI study comparing the functional connectivity strength among healthy controls and heroin-dependent men who had either relapsed or were in early remission. Men were considered to be either relapsed or in early remission based on urine drug screens during a 3-month follow-up period. We also examined how the coupling of large-scale networks correlated with relapse behaviour among heroin-dependent men. Results We included 20 controls and 50 heroin-dependent men (26 relapsed and 24 early remission) in our analyses. The relapsed men showed greater connectivity than the early remission and control groups between the dorsal anterior cingulate cortex (key node of the SN) and the dorsomedial prefrontal cortex (included in the DMN). The relapsed men and controls showed lower connectivity than the early remission group between the left dorsolateral prefrontal cortex (key node of the left ECN) and the dorsomedial prefrontal cortex. The percentage of positive urine drug screens positively correlated with the coupling between the dorsal anterior cingulate cortex and dorsomedial prefrontal cortex, but negatively correlated with the coupling between the left dorsolateral prefrontal cortex and dorsomedial prefrontal cortex. Limitations We examined deficits in only 3 core networks leading to relapse behaviour. Other networks may also contribute to relapse. Conclusion Greater coupling between the SN and DMN and lower coupling between the left ECN and DMN is associated with relapse behaviour. These findings may shed light on the development of new treatments for heroin addiction. PMID:29252165

Prediction of lung cancer incidence on the low-dose computed tomography arm of the National Lung Screening Trial: A dynamic Bayesian network

PubMed Central

Petousis, Panayiotis; Han, Simon X.; Aberle, Denise; Bui, Alex A.T.

2016-01-01

Introduction Identifying high-risk lung cancer individuals at an early disease stage is the most effective way of improving survival. The landmark National Lung Screening Trial (NLST) demonstrated the utility of low-dose computed tomography (LDCT) imaging to reduce mortality (relative to x-ray screening). As a result of the NLST and other studies, imaging-based lung cancer screening programs are now being implemented. However, LDCT interpretation results in a high number of false positives. A set of dynamic Bayesian networks (DBN) were designed and evaluated to provide insight into how longitudinal data can be used to help inform lung cancer screening decisions. Methods The LDCT arm of the NLST dataset was used to build and explore five DBNs for high-risk individuals. Three of these DBNs were built using a backward construction process, and two using structure learning methods. All models employ demographic, smoking status, cancer history, family lung cancer history, exposure risk factors, comorbidities related to lung cancer, and LDCT screening outcome information. Given the uncertainty arising from lung cancer screening, a cancer state-space model based on lung cancer staging was utilized to characterize the cancer status of an individual over time. The models were evaluated on balanced training and test sets of cancer and non-cancer cases to deal with data imbalance and overfitting. Results Results were comparable to expert decisions. The average area under the curve (AUC) of the receiver operating characteristic (ROC) for the three intervention points of the NLST trial was higher than 0.75 for all models. Evaluation of the models on the complete LDCT arm of the NLST dataset (N = 25, 486) demonstrated satisfactory generalization. Consensus of predictions over similar cases is reported in concordance statistics between the models’ and the physicians’ predictions. The models’ predictive ability with respect to missing data was also evaluated with the sample of cases that missed the second screening exam of the trial (N = 417). The DBNs outperformed comparison models such as logistic regression and naïve Bayes. Conclusion The lung cancer screening DBNs demonstrated high discrimination and predictive power with the majority of cancer and non-cancer cases. PMID:27664507

Practice Patterns in Hepatitis B Virus Screening Before Cancer Chemotherapy in a Major US Hospital Network.

PubMed

Kwak, Ye Eun; Stein, Stacy M; Lim, Joseph K

2018-01-01

Cancer patients receiving chemotherapy face an increased risk of reactivation of chronic hepatitis B virus infection. To determine the HBV screening rate in patients receiving cancer chemotherapy in various clinical settings. We identified 11,959 adult cancer patients (age ≥ 18 years) receiving parenteral chemotherapy between 2012 and 2015 within a major US hospital network, including a large university hospital, community teaching hospitals, and community oncology clinics. Two thousand and forty-five patients (17.1%) were screened for either HBV surface antigen (HBsAg) or HBV core antibody (HBcAb) before chemotherapy, and 1850 patients (15.5%) had both HBsAg and HBcAb tested before chemotherapy. 8.4% were exposed to HBV, and 0.9% had chronic HBV infection (both HBsAg/HBcAb positive). Patients with hematologic tumor were more often screened than with solid tumor (55.6 vs. 8.3%, p < 0.001). Patients receiving chemotherapy with higher HBV reactivation risk had higher yet suboptimal HBV screening rate (41.1% B-depleting agents, 21.5% anthracycline, 14.9% steroid, 64.7% anti-TNF alpha and 18.6% other chemotherapy, p < 0.001). Patients with age ≥ 50 years (old 16.2% vs. young 23.9%, p < 0.001) and Asian ethnicity (Asian 13.6 vs. Caucasian 16.6%, p < 0.001) were screened less for HBV despite higher prevalence of HBV exposure (old 9.3% vs. young 4.3%, p < 0.001 and Asian 27.8% vs. Caucasian 6.4%, p < 0.001). Patients receiving chemotherapy in community oncology clinics were less screened versus community teaching hospitals or university hospital (12.7 vs. 19.1 vs. 19.7%, p < 0.001), despite similar prevalence of HBV infection. On multivariate analysis, receiving chemotherapy at a community oncology clinic [odds ratio (OR) 0.57, 95% confidence interval (CI) 0.45-0.72, p < 0.001] was independently associated with less HBV screening compared to receiving chemotherapy at a university or community teaching hospital. HBV screening among patients undergoing cancer chemotherapy was suboptimal and less commonly performed in community oncology clinics compared to teaching hospitals.

Development of a Mobile Tool That Semiautomatically Screens Patients for Stroke Clinical Trials.

PubMed

Spokoyny, Ilana; Lansberg, Maarten; Thiessen, Rosita; Kemp, Stephanie M; Aksoy, Didem; Lee, YongJae; Mlynash, Michael; Hirsch, Karen G

2016-10-01

Despite several national coordinated research networks, enrollment in many cerebrovascular trials remains challenging. An electronic tool was needed that would improve the efficiency and efficacy of screening for multiple simultaneous acute clinical stroke trials by automating the evaluation of inclusion and exclusion criteria, improving screening procedures and streamlining the communication process between the stroke research coordinators and the stroke clinicians. A multidisciplinary group consisting of physicians, study coordinators, and biostatisticians designed and developed an electronic clinical trial screening tool on a HIPAA (Health Insurance Portability and Accountability Act)-compliant platform. A web-based tool was developed that uses branch logic to determine eligibility for simultaneously enrolling clinical trials and automatically notifies the study coordinator teams about eligible patients. After 12 weeks of use, 225 surveys were completed, and 51 patients were enrolled in acute stroke clinical trials. Compared with the 12 weeks before implementation of the tool, there was an increase in enrollment from 16.5% of patients screened to 23.4% of patients screened (P<0.05). Clinicians and coordinators reported increased satisfaction with the process and improved ease of screening. We created a semiautomated electronic screening tool that uses branch logic to screen patients for stroke clinical trials. The tool has improved efficiency and efficacy of screening, and it could be adapted for use at other sites and in other medical fields. © 2016 American Heart Association, Inc.

Components Necessary for High-Quality Lung Cancer Screening

PubMed Central

Powell, Charles A.; Arenberg, Douglas; Detterbeck, Frank; Gould, Michael K.; Jaklitsch, Michael T.; Jett, James; Naidich, David; Vachani, Anil; Wiener, Renda Soylemez; Silvestri, Gerard

2015-01-01

Lung cancer screening with a low-dose chest CT scan can result in more benefit than harm when performed in settings committed to developing and maintaining high-quality programs. This project aimed to identify the components of screening that should be a part of all lung cancer screening programs. To do so, committees with expertise in lung cancer screening were assembled by the Thoracic Oncology Network of the American College of Chest Physicians (CHEST) and the Thoracic Oncology Assembly of the American Thoracic Society (ATS). Lung cancer program components were derived from evidence-based reviews of lung cancer screening and supplemented by expert opinion. This statement was developed and modified based on iterative feedback of the committees. Nine essential components of a lung cancer screening program were identified. Within these components 21 Policy Statements were developed and translated into criteria that could be used to assess the qualification of a program as a screening facility. Two additional Policy Statements related to the need for multisociety governance of lung cancer screening were developed. High-quality lung cancer screening programs can be developed within the presented framework of nine essential program components outlined by our committees. The statement was developed, reviewed, and formally approved by the leadership of CHEST and the ATS. It was subsequently endorsed by the American Association of Throacic Surgery, American Cancer Society, and the American Society of Preventive Oncology. PMID:25356819

Research and development of a NYNEX switched multi-megabit data service prototype system

NASA Astrophysics Data System (ADS)

Maman, K. H.; Haines, Robert; Chatterjee, Samir

1991-02-01

Switched Multi-megabit Data Service (SMDS) is a proposed high-speed packet-switched service which will support broadband applications such as Local Area Network (LAN) interconnections across a metropolitan area and beyond. This service is designed to take advantage of evolving Metropolitan Area Network (MAN) standards and technology which will provide customers with 45-mbps and 1 . 5-mbps access to high-speed public data communications networks. This paper will briefly discuss SMDS and review its architecture including the Subscriber Network Interface (SNI) and the SMDS Interface Protocol (SIP). It will review the fundamental features of SMDS such as address screening addressing scheme and access classes. Then it will describe the SMDS prototype system developed in-house by NYNEX Science Technology.

PS1-54: Clinical Perspectives on Under- and Overutilization of Cervical Cancer Screening Services

PubMed Central

Coronado, Gloria; Petrik, Amanda; Spofford, Mark; Talbot, Jocelyn; Do, Huyen Hoai; Taylor, Vicky

2013-01-01

Background/Aims The underutilization of cancer screening services is an on-going concern to program planners and policy makers; such underutilization is common among under-insured, ethnic- and language-minority populations and is associated with advanced stage of disease detection, limited treatment options, and diminished survival. At the same time, growing research interest has focused on the over-utilization of cancer screening services. We sought to gather the perceptions of clinic personnel at Latino-serving federally qualified health centers about patients’ utilization of screening services for cervical cancer. Methods We conducted one-on-one interviews among 17 clinic personnel at four Latino-serving federally qualified health center networks in Oregon. Results Estimated proportions of eligible patients who are under-screened ranged from 20% to 60%, with 30% most commonly cited. Under-screening for cervical cancer was thought to occur among low-income, under-insured and undocumented patients. External factors, such as limited funding to pay for screening and access barriers to follow-up testing in patients with positive screens were cited as contributing to under-screening. The most frequently cited proportion of eligible patients who are over-screened was 10%, and ranged from 10% to 50%. Notably, over-screening for cervical cancer was thought to occur among young women (those younger than 21) and women with a recent pregnancy. Inconsistent capture of history of screening in electronic medical records and unclear and changing screening guidelines were thought to contribute to over-screening in some patients. Conclusions The health care providers we interviewed had widely varying perspectives of the under- and over-utilization of screening services for cervical cancer. Our findings may inform future efforts to promote guideline-appropriate cancer screening and coordinated follow-up care.

Identification of Linkages between EDCs in Personal Care Products and Breast Cancer through Data Integration Combined with Gene Network Analysis

PubMed Central

Kim, Jongwoon

2017-01-01

Approximately 1000 chemicals have been reported to possibly have endocrine disrupting effects, some of which are used in consumer products, such as personal care products (PCPs) and cosmetics. We conducted data integration combined with gene network analysis to: (i) identify causal molecular mechanisms between endocrine disrupting chemicals (EDCs) used in PCPs and breast cancer; and (ii) screen candidate EDCs associated with breast cancer. Among EDCs used in PCPs, four EDCs having correlation with breast cancer were selected, and we curated 27 common interacting genes between those EDCs and breast cancer to perform the gene network analysis. Based on the gene network analysis, ESR1, TP53, NCOA1, AKT1, and BCL6 were found to be key genes to demonstrate the molecular mechanisms of EDCs in the development of breast cancer. Using GeneMANIA, we additionally predicted 20 genes which could interact with the 27 common genes. In total, 47 genes combining the common and predicted genes were functionally grouped with the gene ontology and KEGG pathway terms. With those genes, we finally screened candidate EDCs for their potential to increase breast cancer risk. This study highlights that our approach can provide insights to understand mechanisms of breast cancer and identify potential EDCs which are in association with breast cancer. PMID:28973975

A practical approach to screen for authorised and unauthorised genetically modified plants.

PubMed

Waiblinger, Hans-Ulrich; Grohmann, Lutz; Mankertz, Joachim; Engelbert, Dirk; Pietsch, Klaus

2010-03-01

In routine analysis, screening methods based on real-time PCR are most commonly used for the detection of genetically modified (GM) plant material in food and feed. In this paper, it is shown that the combination of five DNA target sequences can be used as a universal screening approach for at least 81 GM plant events authorised or unauthorised for placing on the market and described in publicly available databases. Except for maize event LY038, soybean events DP-305423 and BPS-CV127-9 and cotton event 281-24-236 x 3006-210-23, at least one of the five genetic elements has been inserted in these GM plants and is targeted by this screening approach. For the detection of these sequences, fully validated real-time PCR methods have been selected. A screening table is presented that describes the presence or absence of the target sequences for most of the listed GM plants. These data have been verified either theoretically according to available databases or experimentally using available reference materials. The screening table will be updated regularly by a network of German enforcement laboratories.

CMOS nanoelectrode array for all-electrical intracellular electrophysiological imaging

NASA Astrophysics Data System (ADS)

Abbott, Jeffrey; Ye, Tianyang; Qin, Ling; Jorgolli, Marsela; Gertner, Rona S.; Ham, Donhee; Park, Hongkun

2017-05-01

Developing a new tool capable of high-precision electrophysiological recording of a large network of electrogenic cells has long been an outstanding challenge in neurobiology and cardiology. Here, we combine nanoscale intracellular electrodes with complementary metal-oxide-semiconductor (CMOS) integrated circuits to realize a high-fidelity all-electrical electrophysiological imager for parallel intracellular recording at the network level. Our CMOS nanoelectrode array has 1,024 recording/stimulation 'pixels' equipped with vertical nanoelectrodes, and can simultaneously record intracellular membrane potentials from hundreds of connected in vitro neonatal rat ventricular cardiomyocytes. We demonstrate that this network-level intracellular recording capability can be used to examine the effect of pharmaceuticals on the delicate dynamics of a cardiomyocyte network, thus opening up new opportunities in tissue-based pharmacological screening for cardiac and neuronal diseases as well as fundamental studies of electrogenic cells and their networks.

A screening system for smear-negative pulmonary tuberculosis using artificial neural networks.

PubMed

de O Souza Filho, João B; de Seixas, José Manoel; Galliez, Rafael; de Bragança Pereira, Basilio; de Q Mello, Fernanda C; Dos Santos, Alcione Miranda; Kritski, Afranio Lineu

2016-08-01

Molecular tests show low sensitivity for smear-negative pulmonary tuberculosis (PTB). A screening and risk assessment system for smear-negative PTB using artificial neural networks (ANNs) based on patient signs and symptoms is proposed. The prognostic and risk assessment models exploit a multilayer perceptron (MLP) and inspired adaptive resonance theory (iART) network. Model development considered data from 136 patients with suspected smear-negative PTB in a general hospital. MLP showed higher sensitivity (100%, 95% confidence interval (CI) 78-100%) than the other techniques, such as support vector machine (SVM) linear (86%; 95% CI 60-96%), multivariate logistic regression (MLR) (79%; 95% CI 53-93%), and classification and regression tree (CART) (71%; 95% CI 45-88%). MLR showed a slightly higher specificity (85%; 95% CI 59-96%) than MLP (80%; 95% CI 54-93%), SVM linear (75%, 95% CI 49-90%), and CART (65%; 95% CI 39-84%). In terms of the area under the receiver operating characteristic curve (AUC), the MLP model exhibited a higher value (0.918, 95% CI 0.824-1.000) than the SVM linear (0.796, 95% CI 0.651-0.970) and MLR (0.782, 95% CI 0.663-0.960) models. The significant signs and symptoms identified in risk groups are coherent with clinical practice. In settings with a high prevalence of smear-negative PTB, the system can be useful for screening and also to aid clinical practice in expediting complementary tests for higher risk patients. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Screening for genes and subnetworks associated with pancreatic cancer based on the gene expression profile.

PubMed

Long, Jin; Liu, Zhe; Wu, Xingda; Xu, Yuanhong; Ge, Chunlin

2016-05-01

The present study aimed to screen for potential genes and subnetworks associated with pancreatic cancer (PC) using the gene expression profile. The expression profile GSE 16515 was downloaded from the Gene Expression Omnibus database, which included 36 PC tissue samples and 16 normal samples. Limma package in R language was used to screen differentially expressed genes (DEGs), which were grouped as up‑ and downregulated genes. Then, PFSNet was applied to perform subnetwork analysis for all the DEGs. Moreover, Gene Ontology (GO) and REACTOME pathway enrichment analysis of up‑ and downregulated genes was performed, followed by protein‑protein interaction (PPI) network construction using Search Tool for the Retrieval of Interacting Genes Search Tool for the Retrieval of Interacting Genes. In total, 1,989 DEGs including 1,461 up‑ and 528 downregulated genes were screened out. Subnetworks including pancreatic cancer in PC tissue samples and intercellular adhesion in normal samples were identified, respectively. A total of 8 significant REACTOME pathways for upregulated DEGs, such as hemostasis and cell cycle, mitotic were identified. Moreover, 4 significant REACTOME pathways for downregulated DEGs, including regulation of β‑cell development and transmembrane transport of small molecules were screened out. Additionally, DEGs with high connectivity degrees, such as CCNA2 (cyclin A2) and PBK (PDZ binding kinase), of the module in the protein‑protein interaction network were mainly enriched with cell‑division cycle. CCNA2 and PBK of the module and their relative pathway cell‑division cycle, and two subnetworks (pancreatic cancer and intercellular adhesion subnetworks) may be pivotal for further understanding of the molecular mechanism of PC.

Extragenital gonorrhea and chlamydia testing and infection among men who have sex with men--STD Surveillance Network, United States, 2010-2012.

PubMed

Patton, Monica E; Kidd, Sarah; Llata, Eloisa; Stenger, Mark; Braxton, Jim; Asbel, Lenore; Bernstein, Kyle; Gratzer, Beau; Jespersen, Megan; Kerani, Roxanne; Mettenbrink, Christie; Mohamed, Mukhtar; Pathela, Preeti; Schumacher, Christina; Stirland, Ali; Stover, Jeff; Tabidze, Irina; Kirkcaldy, Robert D; Weinstock, Hillard

2014-06-01

Gonorrhea (GC) and chlamydia (CT) are the most commonly reported notifiable diseases in the United States. The Centers for Disease Control and Prevention recommends that men who have sex with men (MSM) be screened for urogenital GC/CT, rectal GC/CT, and pharyngeal GC. We describe extragenital GC/CT testing and infections among MSM attending sexually transmitted disease (STD) clinics. The STD Surveillance Network collects patient data from 42 STD clinics. We assessed the proportion of MSM attending these clinics during July 2011-June 2012 who were tested and positive for extragenital GC/CT at their most recent visit or in the preceding 12 months and the number of extragenital infections that would have remained undetected with urethral screening alone. Of 21 994 MSM, 83.9% were tested for urogenital GC, 65.9% for pharyngeal GC, 50.4% for rectal GC, 81.4% for urogenital CT, 31.7% for pharyngeal CT, and 45.9% for rectal CT. Of MSM tested, 11.1% tested positive for urogenital GC, 7.9% for pharyngeal GC, 10.2% for rectal GC, 8.4% for urogenital CT, 2.9% for pharyngeal CT, and 14.1% for rectal CT. More than 70% of extragenital GC infections and 85% of extragenital CT infections were associated with negative urethral tests at the same visit and would not have been detected with urethral screening alone. Extragenital GC/CT was common among MSM attending STD clinics, but many MSM were not tested. Most extragenital infections would not have been identified, and likely would have remained untreated, with urethral screening alone. Efforts are needed to facilitate implementation of extragenital GC/CT screening recommendations for MSM.

Extragenital Gonorrhea and Chlamydia Testing and Infection Among Men Who Have Sex With Men—STD Surveillance Network, United States, 2010–2012

PubMed Central

Patton, Monica E.; Kidd, Sarah; Llata, Eloisa; Stenger, Mark; Braxton, Jim; Asbel, Lenore; Bernstein, Kyle; Gratzer, Beau; Jespersen, Megan; Kerani, Roxanne; Mettenbrink, Christie; Mohamed, Mukhtar; Pathela, Preeti; Schumacher, Christina; Stirland, Ali; Stover, Jeff; Tabidze, Irina; Kirkcaldy, Robert D.; Weinstock, Hillard

2015-01-01

Background Gonorrhea (GC) and chlamydia (CT) are the most commonly reported notifiable diseases in the United States. The Centers for Disease Control and Prevention recommends that men who have sex with men (MSM) be screened for urogenital GC/CT, rectal GC/CT, and pharyngeal GC. We describe extragenital GC/CT testing and infections among MSM attending sexually transmitted disease (STD) clinics. Methods The STD Surveillance Network collects patient data from 42 STD clinics. We assessed the proportion of MSM attending these clinics during July 2011–June 2012 who were tested and positive for extragenital GC/CT at their most recent visit or in the preceding 12 months and the number of extragenital infections that would have remained undetected with urethral screening alone. Results Of 21 994 MSM, 83.9% were tested for urogenital GC, 65.9% for pharyngeal GC, 50.4% for rectal GC, 81.4% for urogenital CT, 31.7% for pharyngeal CT, and 45.9% for rectal CT. Of MSM tested, 11.1% tested positive for urogenital GC, 7.9% for pharyngeal GC, 10.2% for rectal GC, 8.4% for urogenital CT, 2.9% for pharyngeal CT, and 14.1% for rectal CT. More than 70% of extragenital GC infections and 85% of extragenital CT infections were associated with negative urethral tests at the same visit and would not have been detected with urethral screening alone. Conclusions Extragenital GC/CT was common among MSM attending STD clinics, but many MSM were not tested. Most extragenital infections would not have been identified, and likely would have remained untreated, with urethral screening alone. Efforts are needed to facilitate implementation of extragenital GC/CT screening recommendations for MSM. PMID:24647015

A Qualitative Study of Doctors of Chiropractic in a Nova Scotian Practice-based Research Network: Barriers and Facilitators to the Screening and Management of Psychosocial Factors for Patients With Low Back Pain.

PubMed

Stilwell, Peter; Hayden, Jill A; Des Rosiers, Piaf; Harman, Katherine; French, Simon D; Curran, Janet A; Hefford, Warren

2018-01-01

This study aimed to assess chiropractors' awareness of clinical practice guidelines for low back pain and to identify barriers and facilitators to the screening and management of psychosocial factors in patients with low back pain. This qualitative study used semi-structured interviews informed by the Theoretical Domains Framework with 10 Nova Scotian chiropractors who were members of a practice-based research network. The participants correctly identified what the guidelines generally recommend and described the value of psychosocial factors; however, none of the participants could name specific clinical practice guidelines for low back pain. We identified 6 themes related to barriers and facilitators for chiropractors screening and managing psychosocial factors. The themes revolved around the participants' desire to fulfill patients' anatomy-focused treatment expectations and a perceived lack of training for managing psychosocial factors. Participants had concerns about going beyond the chiropractic scope of practice, and they perceived a lack of practical psychosocial screening and management resources. Social factors, such as the influence of other health care practitioners, were reported as both barriers and facilitators to screening and managing psychosocial factors. The participants in this study reported that they mostly treated with an anatomical and biomechanical focus and that they did not always address psychosocial factors identified in their patients with low back pain. Although these findings are limited to Nova Scotian chiropractors, the barriers identified appeared to be potentially modifiable and could be considered in other groups. Low-cost interventions, such as continuing education using evidence-informed behavior change techniques, could be considered to address these barriers. Copyright © 2017. Published by Elsevier Inc.

Population-based breast cancer screening in a primary care network

PubMed Central

Atlas, Steven J.; Ashburner, Jeffrey M.; Chang, Yuchiao; Lester, William T.; Barry, Michael J.; Grant, Richard W.

2013-01-01

Objective To assess up to 3-year follow-up of a health information technology system that facilitated population-based breast cancer screening. Study Design Cohort study with 2-year follow-up after completing a 1-year cluster randomized trial. Methods Women 42-69 years old receiving care within a 12-practice primary care network. The trial tested an integrated, non-visit-based population management informatics system that: 1) identified women overdue for mammograms, 2) connected them to primary care providers using a Web-based tool, 3) created automatically-generated outreach letters for patients specified by providers, 4) monitored for subsequent mammography scheduling and completion, and 5) provided practice delegates a list of women remaining unscreened for reminder phone calls. All practices also provided visit-based cancer screening reminders. Eligible women overdue for a mammogram during a one-year study period included those overdue at study start (prevalent cohort) or becoming overdue during follow-up (incident cohort). The main outcome measure was mammography completion rates over three years. Results Among 32,688 eligible women, 9,795 (30%) were overdue for screening including 4,487 in intervention and 5,308 in control practices. Intervention patients were somewhat younger, more likely to be non-Hispanic white, and have health insurance compared to control patients. Among patients in the prevalent cohort (n=6,697), adjusted completion rates were significantly higher among intervention compared to control patients after 3 years (51.7% vs. 45.8%, p=0.002). For patients in the incident cohort (n=3,098), adjusted completion rates after 2 years were 53.8% vs. 48.7%, p=0.052, respectively. Conclusions Population-based informatics systems can enable sustained increases in mammography screening rates beyond that seen with office-based visit reminders. PMID:23286611

Context-based retrieval of functional modules in protein-protein interaction networks.

PubMed

Dobay, Maria Pamela; Stertz, Silke; Delorenzi, Mauro

2017-03-27

Various techniques have been developed for identifying the most probable interactants of a protein under a given biological context. In this article, we dissect the effects of the choice of the protein-protein interaction network (PPI) and the manipulation of PPI settings on the network neighborhood of the influenza A virus (IAV) network, as well as hits in genome-wide small interfering RNA screen results for IAV host factors. We investigate the potential of context filtering, which uses text mining evidence linked to PPI edges, as a complement to the edge confidence scores typically provided in PPIs for filtering, for obtaining more biologically relevant network neighborhoods. Here, we estimate the maximum performance of context filtering to isolate a Kyoto Encyclopedia of Genes and Genomes (KEGG) network Ki from a union of KEGG networks and its network neighborhood. The work gives insights on the use of human PPIs in network neighborhood approaches for functional inference. © The Author 2017. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

The influence of social support relationships on mammography screening in African-American women.

PubMed

Fowler, Barbara Ann

2007-07-01

Evidence indicates that mammography screenings have increased in African-American women who are 50 years of age or older; however, they continue to experience later-stage discovery and poorer survival rates from breast cancer compared to White women. Although research has consistently found that social support relationships affects mammography screening in African-American women, little is known about the preventive health behaviors of individuals in these relationships that may be associated with mammography screening. This study examined that association and found that social support relationships, defined as blood-relatives and extended kinship networks, stressed personal responsibility and accountability for preventive health; therefore, supporting mammography screening. Of perhaps the greatest importance, the relationships emphasized positive strengths of African-American culture and invoked the necessity to confront prior negative experiences in health-care systems. These relationships also negated the fears or fatalistic beliefs about breast cancer that had been perpetuated by myths through informal communication and "deliberate silence" from significant others who had previously discouraged or de-emphasized the importance of mammography screening. Further research is needed to determine if the emphasis on cultural heritage was the only motivator that encouraged personal responsibility for mammography screening.

Teaching strategies to facilitate breast cancer screening by African-American women.

PubMed

Gibson, Lynette M

2008-12-01

The objective of this paper is to report on the recent literature concerning coverage of breast cancer epidemiology, the barriers to breast cancer screening, and the strategies to facilitate screening by African-American women. Based on these findings, the author suggests culturally appropriate techniques to be used to promote breast cancer screening in African-American women. Barriers to breast cancer screening in African-American women include emotional reasons, spiritual/religious reasons, fatalism, logistic concerns, lack of knowledge, and lack of follow-up by health-care professionals. Numerous strategies that have been targeted toward African-American women are reported. These include storytelling, witnessing, and testimonies; providing social support and having social support networks; and conducting multifaceted programs that include culturally specific breast health information. Based on the literature reviewed, the author suggests some examples of creative and culturally appropriate techniques that have been implemented with African-American women and that have resulted in positive feedback. These examples include the use of testimonies, photographs, prose, narratives, poetry, and quotations.

Network Compression as a Quality Measure for Protein Interaction Networks

PubMed Central

Royer, Loic; Reimann, Matthias; Stewart, A. Francis; Schroeder, Michael

2012-01-01

With the advent of large-scale protein interaction studies, there is much debate about data quality. Can different noise levels in the measurements be assessed by analyzing network structure? Because proteomic regulation is inherently co-operative, modular and redundant, it is inherently compressible when represented as a network. Here we propose that network compression can be used to compare false positive and false negative noise levels in protein interaction networks. We validate this hypothesis by first confirming the detrimental effect of false positives and false negatives. Second, we show that gold standard networks are more compressible. Third, we show that compressibility correlates with co-expression, co-localization, and shared function. Fourth, we also observe correlation with better protein tagging methods, physiological expression in contrast to over-expression of tagged proteins, and smart pooling approaches for yeast two-hybrid screens. Overall, this new measure is a proxy for both sensitivity and specificity and gives complementary information to standard measures such as average degree and clustering coefficients. PMID:22719828

3D Convolutional Neural Network for Automatic Detection of Lung Nodules in Chest CT.

PubMed

Hamidian, Sardar; Sahiner, Berkman; Petrick, Nicholas; Pezeshk, Aria

2017-01-01

Deep convolutional neural networks (CNNs) form the backbone of many state-of-the-art computer vision systems for classification and segmentation of 2D images. The same principles and architectures can be extended to three dimensions to obtain 3D CNNs that are suitable for volumetric data such as CT scans. In this work, we train a 3D CNN for automatic detection of pulmonary nodules in chest CT images using volumes of interest extracted from the LIDC dataset. We then convert the 3D CNN which has a fixed field of view to a 3D fully convolutional network (FCN) which can generate the score map for the entire volume efficiently in a single pass. Compared to the sliding window approach for applying a CNN across the entire input volume, the FCN leads to a nearly 800-fold speed-up, and thereby fast generation of output scores for a single case. This screening FCN is used to generate difficult negative examples that are used to train a new discriminant CNN. The overall system consists of the screening FCN for fast generation of candidate regions of interest, followed by the discrimination CNN.

Automated EEG-based screening of depression using deep convolutional neural network.

PubMed

Acharya, U Rajendra; Oh, Shu Lih; Hagiwara, Yuki; Tan, Jen Hong; Adeli, Hojjat; Subha, D P

2018-07-01

In recent years, advanced neurocomputing and machine learning techniques have been used for Electroencephalogram (EEG)-based diagnosis of various neurological disorders. In this paper, a novel computer model is presented for EEG-based screening of depression using a deep neural network machine learning approach, known as Convolutional Neural Network (CNN). The proposed technique does not require a semi-manually-selected set of features to be fed into a classifier for classification. It learns automatically and adaptively from the input EEG signals to differentiate EEGs obtained from depressive and normal subjects. The model was tested using EEGs obtained from 15 normal and 15 depressed patients. The algorithm attained accuracies of 93.5% and 96.0% using EEG signals from the left and right hemisphere, respectively. It was discovered in this research that the EEG signals from the right hemisphere are more distinctive in depression than those from the left hemisphere. This discovery is consistent with recent research and revelation that the depression is associated with a hyperactive right hemisphere. An exciting extension of this research would be diagnosis of different stages and severity of depression and development of a Depression Severity Index (DSI). Copyright © 2018 Elsevier B.V. All rights reserved.

3D convolutional neural network for automatic detection of lung nodules in chest CT

NASA Astrophysics Data System (ADS)

Hamidian, Sardar; Sahiner, Berkman; Petrick, Nicholas; Pezeshk, Aria

2017-03-01

Deep convolutional neural networks (CNNs) form the backbone of many state-of-the-art computer vision systems for classification and segmentation of 2D images. The same principles and architectures can be extended to three dimensions to obtain 3D CNNs that are suitable for volumetric data such as CT scans. In this work, we train a 3D CNN for automatic detection of pulmonary nodules in chest CT images using volumes of interest extracted from the LIDC dataset. We then convert the 3D CNN which has a fixed field of view to a 3D fully convolutional network (FCN) which can generate the score map for the entire volume efficiently in a single pass. Compared to the sliding window approach for applying a CNN across the entire input volume, the FCN leads to a nearly 800-fold speed-up, and thereby fast generation of output scores for a single case. This screening FCN is used to generate difficult negative examples that are used to train a new discriminant CNN. The overall system consists of the screening FCN for fast generation of candidate regions of interest, followed by the discrimination CNN.

Combining Image and Non-Image Data for Automatic Detection of Retina Disease in a Telemedicine Network

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aykac, Deniz; Chaum, Edward; Fox, Karen

A telemedicine network with retina cameras and automated quality control, physiological feature location, and lesion/anomaly detection is a low-cost way of achieving broad-based screening for diabetic retinopathy (DR) and other eye diseases. In the process of a routine eye-screening examination, other non-image data is often available which may be useful in automated diagnosis of disease. In this work, we report on the results of combining this non-image data with image data, using the protocol and processing steps of a prototype system for automated disease diagnosis of retina examinations from a telemedicine network. The system includes quality assessments, automated physiology detection,more » and automated lesion detection to create an archive of known cases. Non-image data such as diabetes onset date and hemoglobin A1c (HgA1c) for each patient examination are included as well, and the system is used to create a content-based image retrieval engine capable of automated diagnosis of disease into 'normal' and 'abnormal' categories. The system achieves a sensitivity and specificity of 91.2% and 71.6% using hold-one-out validation testing.« less

Genetics Home Reference: very long-chain acyl-CoA dehydrogenase deficiency

MedlinePlus

... Very long chain acyl-CoA dehydrogenase deficiency Screening, Technology, and Research in Genetics Virginia Department of Health (PDF) Patient Support and Advocacy Resources (4 links) Children's Mitochondrial Disease Network (UK) FOD (Fatty Oxidation Disorders) ...

Evaluation of the Lewis and Clark travel and tourism information kiosk

DOT National Transportation Integrated Search

2003-12-08

Interactive touch screen kiosks can be a useful access point for people seeking tourism information. The Montana Department of Transportation (MDT) has successfully installed a network of traveler information kiosks under the Greater Yellowstone Regi...

Home Data Banks Turn British On

ERIC Educational Resources Information Center

Science News, 1978

1978-01-01

Describes the operation and numerous capabilities of a British computerized data retrieval system named Prestel. It provides access, through the regular telephone network and a TV screen, to computer-based information supplied by many companies, agencies and commercial outlets. (GA)

Toxico-Cheminformatics: A New Frontier for Predictive Toxicology

EPA Science Inventory

The DSSTox database network and efforts to improve public access to chemical toxicity information resources, coupled with high-throughput screening (HTS) data and efforts to systematize legacy toxicity studies, have the potential to significantly improve predictive capabilities i...

Metadata Standard and Data Exchange Specifications to Describe, Model, and Integrate Complex and Diverse High-Throughput Screening Data from the Library of Integrated Network-based Cellular Signatures (LINCS).

PubMed

Vempati, Uma D; Chung, Caty; Mader, Chris; Koleti, Amar; Datar, Nakul; Vidović, Dušica; Wrobel, David; Erickson, Sean; Muhlich, Jeremy L; Berriz, Gabriel; Benes, Cyril H; Subramanian, Aravind; Pillai, Ajay; Shamu, Caroline E; Schürer, Stephan C

2014-06-01

The National Institutes of Health Library of Integrated Network-based Cellular Signatures (LINCS) program is generating extensive multidimensional data sets, including biochemical, genome-wide transcriptional, and phenotypic cellular response signatures to a variety of small-molecule and genetic perturbations with the goal of creating a sustainable, widely applicable, and readily accessible systems biology knowledge resource. Integration and analysis of diverse LINCS data sets depend on the availability of sufficient metadata to describe the assays and screening results and on their syntactic, structural, and semantic consistency. Here we report metadata specifications for the most important molecular and cellular components and recommend them for adoption beyond the LINCS project. We focus on the minimum required information to model LINCS assays and results based on a number of use cases, and we recommend controlled terminologies and ontologies to annotate assays with syntactic consistency and semantic integrity. We also report specifications for a simple annotation format (SAF) to describe assays and screening results based on our metadata specifications with explicit controlled vocabularies. SAF specifically serves to programmatically access and exchange LINCS data as a prerequisite for a distributed information management infrastructure. We applied the metadata specifications to annotate large numbers of LINCS cell lines, proteins, and small molecules. The resources generated and presented here are freely available. © 2014 Society for Laboratory Automation and Screening.

Taguchi-generalized regression neural network micro-screening for physical and sensory characteristics of bread.

PubMed

Besseris, George J

2018-03-01

Generalized regression neural networks (GRNN) may act as crowdsourcing cognitive agents to screen small, dense and complex datasets. The concurrent screening and optimization of several complex physical and sensory traits of bread is developed using a structured Taguchi-type micro-mining technique. A novel product outlook is offered to industrial operations to cover separate aspects of smart product design, engineering and marketing. Four controlling factors were selected to be modulated directly on a modern production line: 1) the dough weight, 2) the proofing time, 3) the baking time, and 4) the oven zone temperatures. Concentrated experimental recipes were programmed using the Taguchi-type L 9 (3 4 ) OA-sampler to detect potentially non-linear multi-response tendencies. The fused behavior of the master-ranked bread characteristics behavior was smart sampled with GRNN-crowdsourcing and robust analysis. It was found that the combination of the oven zone temperatures to play a highly influential role in all investigated scenarios. Moreover, the oven zone temperatures and the dough weight appeared to be instrumental when attempting to synchronously adjusting all four physical characteristics. The optimal oven-zone temperature setting for concurrent screening-and-optimization was found to be 270-240 °C. The optimized (median) responses for loaf weight, moisture, height, width, color, flavor, crumb structure, softness, and elasticity are: 782 g, 34.8 %, 9.36 cm, 10.41 cm, 6.6, 7.2, 7.6, 7.3, and 7.0, respectively.

Preventive care for low-income women in massachusetts post-health reform.

PubMed

Clark, Cheryl R; Soukup, Jane; Riden, Heather; Tovar, Dora; Orton, Piper; Burdick, Elisabeth; Capistran, Mary Ellen; Morisset, Jennifer; Browne, Elizabeth E; Fitzmaurice, Garrett; Johnson, Paula A

2014-06-01

Before enacting health insurance reform in 2006, Massachusetts provided free breast, cervical cancer, and cardiovascular risk screening for low-income uninsured women through a federally subsidized program called the Women's Health Network (WHN). This article examines whether, as women transitioned to insurance to pay for screening tests after health reform legislation was passed, cancer and cardiovascular disease screening changed among WHN participants between 2004 and 2010. We examined claims data from the Massachusetts health insurance exchange and chart review data to measure utilization of mammography, Pap smear, and blood pressure screening among WHN participants in five community health centers in greater Boston. We conducted a longitudinal analysis, by insurance type, using generalized estimating equations to examine the likelihood of screening at recommended intervals in the postreform period compared to the prereform period. Pre- and postreform, we found a high prevalence of recommended mammography (86% vs. 88%), Pap smear (88% vs. 89%), and blood pressure screening (87% vs. 91%) that was similar or improved for most women postreform. Screening use differed by insurance type. Recommended mammography screening was statistically significantly increased among women with state-subsidized private insurance (odds ratio [OR] 1.58, p<0.05). Women with unsubsidized private insurance or Medicare had decreased Pap smear use postreform. Although screening prevalence was high, 31% of women required state safety-net funds to pay for screening tests. Our results suggest a continued need for safety-net programs to support preventive screening among low-income women after implementation of healthcare reform.

A complex regulatory network coordinating cell cycles during C. elegans development is revealed by a genome-wide RNAi screen.

PubMed

Roy, Sarah H; Tobin, David V; Memar, Nadin; Beltz, Eleanor; Holmen, Jenna; Clayton, Joseph E; Chiu, Daniel J; Young, Laura D; Green, Travis H; Lubin, Isabella; Liu, Yuying; Conradt, Barbara; Saito, R Mako

2014-02-28

The development and homeostasis of multicellular animals requires precise coordination of cell division and differentiation. We performed a genome-wide RNA interference screen in Caenorhabditis elegans to reveal the components of a regulatory network that promotes developmentally programmed cell-cycle quiescence. The 107 identified genes are predicted to constitute regulatory networks that are conserved among higher animals because almost half of the genes are represented by clear human orthologs. Using a series of mutant backgrounds to assess their genetic activities, the RNA interference clones displaying similar properties were clustered to establish potential regulatory relationships within the network. This approach uncovered four distinct genetic pathways controlling cell-cycle entry during intestinal organogenesis. The enhanced phenotypes observed for animals carrying compound mutations attest to the collaboration between distinct mechanisms to ensure strict developmental regulation of cell cycles. Moreover, we characterized ubc-25, a gene encoding an E2 ubiquitin-conjugating enzyme whose human ortholog, UBE2Q2, is deregulated in several cancers. Our genetic analyses suggested that ubc-25 acts in a linear pathway with cul-1/Cul1, in parallel to pathways employing cki-1/p27 and lin-35/pRb to promote cell-cycle quiescence. Further investigation of the potential regulatory mechanism demonstrated that ubc-25 activity negatively regulates CYE-1/cyclin E protein abundance in vivo. Together, our results show that the ubc-25-mediated pathway acts within a complex network that integrates the actions of multiple molecular mechanisms to control cell cycles during development. Copyright © 2014 Roy et al.

Patient Navigation for Comprehensive Cancer Screening in High-Risk Patients Using a Population-Based Health Information Technology System: A Randomized Clinical Trial.

PubMed

Percac-Lima, Sanja; Ashburner, Jeffrey M; Zai, Adrian H; Chang, Yuchiao; Oo, Sarah A; Guimaraes, Erica; Atlas, Steven J

2016-07-01

Patient navigation (PN) to improve cancer screening in low-income and racial/ethnic minority populations usually focuses on navigating for single cancers in community health center settings. We evaluated PN for breast, cervical, and colorectal cancer screening using a population-based information technology (IT) system within a primary care network. Randomized clinical trial conducted from April 2014 to December 2014 in 18 practices in an academic primary care network. All patients eligible and overdue for cancer screening were identified and managed using a population-based IT system. Those at high risk for nonadherence with completing screening were identified using an electronic algorithm (language spoken, number of overdue tests, no-show visit history), and randomized to a PN intervention (n = 792) or usual care (n = 820). Navigators used the IT system to track patients, contact them, and provide intense outreach to help them complete cancer screening. Mean cancer screening test completion rate over 8-month trial for each eligible patient, with all overdue cancer screening tests combined using linear regression models. Secondary outcomes included the proportion of patients completing any and each overdue cancer screening test. Among 1612 patients (673 men and 975 women; median age, 57 years), baseline patient characteristics were similar among randomized groups. Of 792 intervention patients, patient navigators were unable to reach 151 (19%), deferred 246 (38%) (eg, patient declined, competing comorbidity), and navigated 202 (32%). The mean proportion of patients who were up to date with screening among all overdue screening examinations was higher in the intervention vs the control group for all cancers combined (10.2% vs 6.8%; 95% CI [for the difference], 1.5%-5.2%; P < .001), and for breast (14.7% vs 11.0%; 95% CI, 0.2%-7.3%; P = .04), cervical (11.1% vs 5.7%; 95% CI, 0.8%-5.2%; P = .002), and colon (7.6% vs 4.6%; 95% CI, 0.8%-5.2%; P = .01) cancer compared with control. The proportion of overdue patients who completed any cancer screening during follow-up was higher in the intervention group (25.5% vs 17.0%; 95% CI, 4.7%-12.7%; P < .001). The intervention group had more patients completing screening for breast (23.4% vs 16.6%; 95% CI, 1.8%-12.0%; P = .009), cervical (14.4% vs 8.6%; 95% CI, 1.6%-10.5%; P = .007), and colorectal (13.7% vs 7.0%; 95% CI, 3.2%-10.4%; P < .001) cancer. Patient navigation as part of a population-based IT system significantly increased screening rates for breast, cervical, and colorectal cancer in patients at high risk for nonadherence with testing. Integrating patient navigation into population health management activities for low-income and racial/ethnic minority patients might improve equity of cancer care. clinicaltrials.gov Identifier: NCT02553538.

A general protocol for creating high-throughput screening assays for reaction yield and enantiomeric excess applied to hydrobenzoin

PubMed Central

Shabbir, Shagufta H.; Regan, Clinton J.; Anslyn, Eric V.

2009-01-01

A general approach to high-throughput screening of enantiomeric excess (ee) and concentration was developed by using indicator displacement assays (IDAs), and the protocol was then applied to the vicinal diol hydrobenzoin. The method involves the sequential utilization of what we define herein as screening, training, and analysis plates. Several enantioselective boronic acid-based receptors were screened by using 96-well plates, both for their ability to discriminate the enantiomers of hydrobenzoin and to find their optimal pairing with indicators resulting in the largest optical responses. The best receptor/indicator combination was then used to train an artificial neural network to determine concentration and ee. To prove the practicality of the developed protocol, analysis plates were created containing true unknown samples of hydrobenzoin generated by established Sharpless asymmetric dihydroxylation reactions, and the best ligand was correctly identified. PMID:19332790

Molecular recognition and self-assembly special feature: A general protocol for creating high-throughput screening assays for reaction yield and enantiomeric excess applied to hydrobenzoin.

PubMed

Shabbir, Shagufta H; Regan, Clinton J; Anslyn, Eric V

2009-06-30

A general approach to high-throughput screening of enantiomeric excess (ee) and concentration was developed by using indicator displacement assays (IDAs), and the protocol was then applied to the vicinal diol hydrobenzoin. The method involves the sequential utilization of what we define herein as screening, training, and analysis plates. Several enantioselective boronic acid-based receptors were screened by using 96-well plates, both for their ability to discriminate the enantiomers of hydrobenzoin and to find their optimal pairing with indicators resulting in the largest optical responses. The best receptor/indicator combination was then used to train an artificial neural network to determine concentration and ee. To prove the practicality of the developed protocol, analysis plates were created containing true unknown samples of hydrobenzoin generated by established Sharpless asymmetric dihydroxylation reactions, and the best ligand was correctly identified.

Primary prevention of sudden cardiac death of the young athlete: the controversy about the screening electrocardiogram and its innovative artificial intelligence solution.

PubMed

Chang, Anthony C

2012-03-01

The preparticipation screening for athlete participation in sports typically entails a comprehensive medical and family history and a complete physical examination. A 12-lead electrocardiogram (ECG) can increase the likelihood of detecting cardiac diagnoses such as hypertrophic cardiomyopathy, but this diagnostic test as part of the screening process has engendered considerable controversy. The pro position is supported by argument that international screening protocols support its use, positive diagnosis has multiple benefits, history and physical examination are inadequate, primary prevention is essential, and the cost effectiveness is justified. Although the aforementioned myriad of justifications for routine ECG screening of young athletes can be persuasive, several valid contentions oppose supporting such a policy, namely, that the sudden death incidence is very (too) low, the ECG screening will be too costly, the false-positive rate is too high, resources will be allocated away from other diseases, and manpower is insufficient for its execution. Clinicians, including pediatric cardiologists, have an understandable proclivity for avoiding this prodigious national endeavor. The controversy, however, should not be focused on whether an inexpensive, noninvasive test such as an ECG should be mandated but should instead be directed at just how these tests for young athletes can be performed in the clinical imbroglio of these disease states (with variable genetic penetrance and phenotypic expression) with concomitant fiscal accountability and logistical expediency in this era of economic restraint. This monumental endeavor in any city or region requires two crucial elements well known to business scholars: implementation and execution. The eventual solution for the screening ECG dilemma requires a truly innovative and systematic approach that will liberate us from inadequate conventional solutions. Artificial intelligence, specifically the process termed "machine learning" and "neural networking," involves complex algorithms that allow computers to improve the decision-making process based on repeated input of empirical data (e.g., databases and ECGs). These elements all can be improved with a national database, evidence-based medicine, and in the near future, innovation that entails a Kurzweilian artificial intelligence infrastructure with machine learning and neural networking that will construct the ultimate clinical decision-making algorithm.

Study of optical techniques for the Ames unitary wind tunnel: Digital image processing, part 6

NASA Technical Reports Server (NTRS)

Lee, George

1993-01-01

A survey of digital image processing techniques and processing systems for aerodynamic images has been conducted. These images covered many types of flows and were generated by many types of flow diagnostics. These include laser vapor screens, infrared cameras, laser holographic interferometry, Schlieren, and luminescent paints. Some general digital image processing systems, imaging networks, optical sensors, and image computing chips were briefly reviewed. Possible digital imaging network systems for the Ames Unitary Wind Tunnel were explored.

Classroom Design at Binghamton University.

ERIC Educational Resources Information Center

Donahue, Jeffrey B.

2000-01-01

Describes the work of the Classroom Environment Committee at Binghamton University (New York) that created classroom standards for multimedia technology when renovating classrooms. Discusses data display, network connections, screens, laptop computers, lighting, furniture, design considerations, and the need for communication with faculty. (LRW)

Use of roadway attributes in hot spot identification and analysis.

DOT National Transportation Integrated Search

2015-10-01

This research focuses on the addition of roadway attributes in the selection and analysis of hot spots. This : is in conjunction with the framework for highway safety mitigation in Utah with its six primary steps: network : screening, diagnosis...

Two level approach to safety planning incorporating the Highway Safety Manual (HSM) network screening : [summary].

DOT National Transportation Integrated Search

2014-04-01

In this project, University of Central Florida researchers combined two types of safety analysis, microscopic and macroscopic, to overcome their limitations. Microscopic models focus on traffic flows and related parameters. Macroscopic models are bas...

Applying operations research to optimize a novel population management system for cancer screening

PubMed Central

Zai, Adrian H; Kim, Seokjin; Kamis, Arnold; Hung, Ken; Ronquillo, Jeremiah G; Chueh, Henry C; Atlas, Steven J

2014-01-01

Objective To optimize a new visit-independent, population-based cancer screening system (TopCare) by using operations research techniques to simulate changes in patient outreach staffing levels (delegates, navigators), modifications to user workflow within the information technology (IT) system, and changes in cancer screening recommendations. Materials and methods TopCare was modeled as a multiserver, multiphase queueing system. Simulation experiments implemented the queueing network model following a next-event time-advance mechanism, in which systematic adjustments were made to staffing levels, IT workflow settings, and cancer screening frequency in order to assess their impact on overdue screenings per patient. Results TopCare reduced the average number of overdue screenings per patient from 1.17 at inception to 0.86 during simulation to 0.23 at steady state. Increases in the workforce improved the effectiveness of TopCare. In particular, increasing the delegate or navigator staff level by one person improved screening completion rates by 1.3% or 12.2%, respectively. In contrast, changes in the amount of time a patient entry stays on delegate and navigator lists had little impact on overdue screenings. Finally, lengthening the screening interval increased efficiency within TopCare by decreasing overdue screenings at the patient level, resulting in a smaller number of overdue patients needing delegates for screening and a higher fraction of screenings completed by delegates. Conclusions Simulating the impact of changes in staffing, system parameters, and clinical inputs on the effectiveness and efficiency of care can inform the allocation of limited resources in population management. PMID:24043318

ELISA test for anti-neutrophil cytoplasm antibodies detection evaluated by a computer screen photo-assisted technique.

PubMed

Filippini, D; Tejle, K; Lundström, I

2005-08-15

The computer screen photo-assisted technique (CSPT), a method for substance classification based on spectral fingerprinting, which involves just a computer screen and a web camera as measuring platform is used here for the evaluation of a prospective enzyme-linked immunosorbent assay (ELISA). A anti-neutrophil cytoplasm antibodies (ANCA-ELISA) test, typically used for diagnosing patients suffering from chronic inflammatory disorders in the skin, joints, blood vessels and other tissues is comparatively tested with a standard microplate reader and CSPT, yielding equivalent results at a fraction of the instrumental costs. The CSPT approach is discussed as a distributed measuring platform allowing decentralized measurements in routine applications, whereas keeping centralized information management due to its natural network embedded operation.

Points of view: where do we look when we watch TV?

PubMed

Brasel, S Adam; Gips, James

2008-01-01

How is our gaze dispersed across the screen when watching television? An exploratory eyetracker study with a custom-designed show indicated a very strong center-of-screen bias with gaze points following a roughly normal distribution peaked near screen center. Examining the show across time revealed that people were rarely all looking at the same location, and the amount of gaze dispersion within frames was highly variable. Different forms of programming yielded different levels of dispersion: static network 'bumpers' created the tightest visual groupings, and gaze dispersion for frames with show content was less than the dispersion for commercials. Advertising frames with brand logos generated higher dispersion than the non-branded advertisement portions, and repeated advertisements generated higher dispersion than their first-run counterparts.

High variation subarctic topsoil pollutant concentration prediction using neural network residual kriging

NASA Astrophysics Data System (ADS)

Sergeev, A. P.; Tarasov, D. A.; Buevich, A. G.; Subbotina, I. E.; Shichkin, A. V.; Sergeeva, M. V.; Lvova, O. A.

2017-06-01

The work deals with the application of neural networks residual kriging (NNRK) to the spatial prediction of the abnormally distributed soil pollutant (Cr). It is known that combination of geostatistical interpolation approaches (kriging) and neural networks leads to significantly better prediction accuracy and productivity. Generalized regression neural networks and multilayer perceptrons are classes of neural networks widely used for the continuous function mapping. Each network has its own pros and cons; however both demonstrated fast training and good mapping possibilities. In the work, we examined and compared two combined techniques: generalized regression neural network residual kriging (GRNNRK) and multilayer perceptron residual kriging (MLPRK). The case study is based on the real data sets on surface contamination by chromium at a particular location of the subarctic Novy Urengoy, Russia, obtained during the previously conducted screening. The proposed models have been built, implemented and validated using ArcGIS and MATLAB environments. The networks structures have been chosen during a computer simulation based on the minimization of the RMSE. MLRPK showed the best predictive accuracy comparing to the geostatistical approach (kriging) and even to GRNNRK.

Bio-inspired patterned networks (BIPS) for development of wearable/disposable biosensors

NASA Astrophysics Data System (ADS)

McLamore, E. S.; Convertino, M.; Hondred, John; Das, Suprem; Claussen, J. C.; Vanegas, D. C.; Gomes, C.

2016-05-01

Here we demonstrate a novel approach for fabricating point of care (POC) wearable electrochemical biosensors based on 3D patterning of bionanocomposite networks. To create Bio-Inspired Patterned network (BIPS) electrodes, we first generate fractal network in silico models that optimize transport of network fluxes according to an energy function. Network patterns are then inkjet printed onto flexible substrate using conductive graphene ink. We then deposit fractal nanometal structures onto the graphene to create a 3D nanocomposite network. Finally, we biofunctionalize the surface with biorecognition agents using covalent bonding. In this paper, BIPS are used to develop high efficiency, low cost biosensors for measuring glucose as a proof of concept. Our results on the fundamental performance of BIPS sensors show that the biomimetic nanostructures significantly enhance biosensor sensitivity, accuracy, response time, limit of detection, and hysteresis compared to conventional POC non fractal electrodes (serpentine, interdigitated, and screen printed electrodes). BIPs, in particular Apollonian patterned BIPS, represent a new generation of POC biosensors based on nanoscale and microscale fractal networks that significantly improve electrical connectivity, leading to enhanced sensor performance.

"I want to save my life": Conceptions of cervical and breast cancer screening among urban immigrant women of South Asian and Chinese origin.

PubMed

Hulme, Jennifer; Moravac, Catherine; Ahmad, Farah; Cleverly, Shelley; Lofters, Aisha; Ginsburg, Ophira; Dunn, Sheila

2016-10-13

Breast and cervical cancer screening rates remain low among immigrant women and those of low socioeconomic status. The Cancer Awareness: Ready for Education and Screening (CARES) project ran a peer-led multi-lingual educational program between 2012 and 2014 to reach under and never-screened women in Central Toronto, where breast and cervical cancer screening rates remain low. The objective of this qualitative study was to better understand how Chinese and South Asian immigrants - the largest and most under-screened immigrant groups according to national and provincial statistics - conceive of breast and cervical cancer screening. We explored their experiences with screening to date. We explicitly inquired about their perceptions of the health care system, their screening experiences with family physicians and strategies that would support screening in their communities. We conducted 22 individual interviews and two focus groups in Bengali and Mandarin with participants who had attended CARES educational sessions. Transcripts were coded through an iterative constant comparative and interpretative approach. Themes fell into five major, overlapping domains: risk perception and concepts of preventative health and screening; health system engagement and the embedded experience with screening; fear of cancer and procedural pain; self-efficacy, obligation, and willingness to be screened; newcomer barriers and competing priorities. These domains all overlap, and contribute to screening behaviours. Immigrant women experienced a number of barriers to screening related to 'navigating newness', including transportation, language barriers, arrangements for time off work and childcare. Fear of screening and fear of cancer took many forms; painful or traumatic encounters with screening were described. Female gender of the provider was paramount for both groups. Newly screened South Asian women were reassured by their first encounter with screening. Some Chinese women preferred the anonymous screening options available in China. Women generally endorsed a willingness to be screened, and even offered to organize women in their community hubs to access screening. The experience of South Asian and Chinese immigrant women suggests that under and never-screened newcomers may be effectively integrated into screening programs through existing primary care networks, cultural-group specific outreach, and expanding access to convenient community -based screening.

Assessing the Role of Copy Number Variants in Prostate Cancer Risk and Progression Using a Novel Genome-Wide Screening Method

DTIC Science & Technology

2013-10-01

role of copy number variants in prostate cancer risk and progression using a novel genome-wide screening method. 5a. CONTRACT NUMBER 5b. GRANT ...Prostate; Cancer; Risk; Deletion; Prognosismatter Published by Elsevier Inc. .urolonc.2013.06.004 d in part by DOD grant PC081025, by grant arly...Detection Research Network of the National CTRC at UTHSCSA grant P30CA054174. Data omics Core Shared Resource, which is supported CI P30CA054174 (CTRC of

Elasticity in Physically Cross-Linked Amyloid Fibril Networks.

PubMed

Cao, Yiping; Bolisetty, Sreenath; Adamcik, Jozef; Mezzenga, Raffaele

2018-04-13

We provide a constitutive model of semiflexible and rigid amyloid fibril networks by combining the affine thermal model of network elasticity with the Derjaguin-Landau-Vervey-Overbeek (DLVO) theory of electrostatically charged colloids. When compared to rheological experiments on β-lactoglobulin and lysozyme amyloid networks, this approach provides the correct scaling of elasticity versus both concentration (G∼c^{2.2} and G∼c^{2.5} for semiflexible and rigid fibrils, respectively) and ionic strength (G∼I^{4.4} and G∼I^{3.8} for β-lactoglobulin and lysozyme, independent from fibril flexibility). The pivotal role played by the screening salt is to reduce the electrostatic barrier among amyloid fibrils, converting labile physical entanglements into long-lived cross-links. This gives a power-law behavior of G with I having exponents significantly larger than in other semiflexible polymer networks (e.g., actin) and carrying DLVO traits specific to the individual amyloid fibrils.

Elasticity in Physically Cross-Linked Amyloid Fibril Networks

NASA Astrophysics Data System (ADS)

Cao, Yiping; Bolisetty, Sreenath; Adamcik, Jozef; Mezzenga, Raffaele

2018-04-01

We provide a constitutive model of semiflexible and rigid amyloid fibril networks by combining the affine thermal model of network elasticity with the Derjaguin-Landau-Vervey-Overbeek (DLVO) theory of electrostatically charged colloids. When compared to rheological experiments on β -lactoglobulin and lysozyme amyloid networks, this approach provides the correct scaling of elasticity versus both concentration (G ˜c2.2 and G ˜c2.5 for semiflexible and rigid fibrils, respectively) and ionic strength (G ˜I4.4 and G ˜I3.8 for β -lactoglobulin and lysozyme, independent from fibril flexibility). The pivotal role played by the screening salt is to reduce the electrostatic barrier among amyloid fibrils, converting labile physical entanglements into long-lived cross-links. This gives a power-law behavior of G with I having exponents significantly larger than in other semiflexible polymer networks (e.g., actin) and carrying DLVO traits specific to the individual amyloid fibrils.

Visualizing Article Similarities via Sparsified Article Network and Map Projection for Systematic Reviews.

PubMed

Ji, Xiaonan; Machiraju, Raghu; Ritter, Alan; Yen, Po-Yin

2017-01-01

Systematic Reviews (SRs) of biomedical literature summarize evidence from high-quality studies to inform clinical decisions, but are time and labor intensive due to the large number of article collections. Article similarities established from textual features have been shown to assist in the identification of relevant articles, thus facilitating the article screening process efficiently. In this study, we visualized article similarities to extend its utilization in practical settings for SR researchers, aiming to promote human comprehension of article distributions and hidden patterns. To prompt an effective visualization in an interpretable, intuitive, and scalable way, we implemented a graph-based network visualization with three network sparsification approaches and a distance-based map projection via dimensionality reduction. We evaluated and compared three network sparsification approaches and the visualization types (article network vs. article map). We demonstrated the effectiveness in revealing article distribution and exhibiting clustering patterns of relevant articles with practical meanings for SRs.

Detection of pseudosinusoidal epileptic seizure segments in the neonatal EEG by cascading a rule-based algorithm with a neural network.

PubMed

Karayiannis, Nicolaos B; Mukherjee, Amit; Glover, John R; Ktonas, Periklis Y; Frost, James D; Hrachovy, Richard A; Mizrahi, Eli M

2006-04-01

This paper presents an approach to detect epileptic seizure segments in the neonatal electroencephalogram (EEG) by characterizing the spectral features of the EEG waveform using a rule-based algorithm cascaded with a neural network. A rule-based algorithm screens out short segments of pseudosinusoidal EEG patterns as epileptic based on features in the power spectrum. The output of the rule-based algorithm is used to train and compare the performance of conventional feedforward neural networks and quantum neural networks. The results indicate that the trained neural networks, cascaded with the rule-based algorithm, improved the performance of the rule-based algorithm acting by itself. The evaluation of the proposed cascaded scheme for the detection of pseudosinusoidal seizure segments reveals its potential as a building block of the automated seizure detection system under development.

Raising the stakes: assessing the human service response to the advent of a casino.

PubMed

Engel, Rafael J; Rosen, Daniel; Weaver, Addie; Soska, Tracy

2010-12-01

This article reports the findings of one county's human service network's readiness to treat gambling related problems in anticipation of the opening of a new casino. Using a cross-sectional survey design, questionnaires were mailed to executive directors of all mental health, family counseling, drug and alcohol, and faith-based, addiction-related organizations in the county (N = 248); 137 (55.2%) agency directors responded to the questionnaire. The survey requested information about agency demographics, training, screening, treatment, and public awareness/education. Descriptive statistics and bivariate analyses were used to summarize the findings. The analyses revealed a lack of human service response to the impending start of casino gambling. More than three-quarters of respondents had not sent staff for training in screening or treating gambling disorders, did not screen for problem gambling, did not treat problem gambling, and did not refer clients to other agencies for treatment of gambling-related problems. The most common reason offered for not engaging in prevention and treatment activities was that problem gambling is not considered an issue for the agency. There were differences between mental health and/or substance abuse focused agencies and other service providers. Based on the findings of this study, specific strategies to enhance the service delivery network's capacity to address problem gambling are suggested.

Diagnostic Evasion of Highly-Resistant Microorganisms: A Critical Factor in Nosocomial Outbreaks.

PubMed

Zhou, Xuewei; Friedrich, Alexander W; Bathoorn, Erik

2017-01-01

Highly resistant microorganisms (HRMOs) may evade screening strategies used in routine diagnostics. Bacteria that have evolved to evade diagnostic tests may have a selective advantage in the nosocomial environment. Evasion of resistance detection can result from the following mechanisms: low-level expression of resistance genes not resulting in detectable resistance, slow growing variants, mimicry of wild-type-resistance, and resistance mechanisms that are only detected if induced by antibiotic pressure. We reviewed reports on hospital outbreaks in the Netherlands over the past 5 years. Remarkably, many outbreaks including major nation-wide outbreaks were caused by microorganisms able to evade resistance detection by diagnostic screening tests. We describe various examples of diagnostic evasion by several HRMOs and discuss this in a broad and international perspective. The epidemiology of hospital-associated bacteria may strongly be affected by diagnostic screening strategies. This may result in an increasing reservoir of resistance genes in hospital populations that is unnoticed. The resistance elements may horizontally transfer to hosts with systems for high-level expression, resulting in a clinically significant resistance problem. We advise to communicate the identification of HRMOs that evade diagnostics within national and regional networks. Such signaling networks may prevent inter-hospital outbreaks, and allow collaborative development of adapted diagnostic tests.

Mesoscale carbon sequestration site screening and CCS infrastructure analysis.

PubMed

Keating, Gordon N; Middleton, Richard S; Stauffer, Philip H; Viswanathan, Hari S; Letellier, Bruce C; Pasqualini, Donatella; Pawar, Rajesh J; Wolfsberg, Andrew V

2011-01-01

We explore carbon capture and sequestration (CCS) at the meso-scale, a level of study between regional carbon accounting and highly detailed reservoir models for individual sites. We develop an approach to CO(2) sequestration site screening for industries or energy development policies that involves identification of appropriate sequestration basin, analysis of geologic formations, definition of surface sites, design of infrastructure, and analysis of CO(2) transport and storage costs. Our case study involves carbon management for potential oil shale development in the Piceance-Uinta Basin, CO and UT. This study uses new capabilities of the CO(2)-PENS model for site screening, including reservoir capacity, injectivity, and cost calculations for simple reservoirs at multiple sites. We couple this with a model of optimized source-sink-network infrastructure (SimCCS) to design pipeline networks and minimize CCS cost for a given industry or region. The CLEAR(uff) dynamical assessment model calculates the CO(2) source term for various oil production levels. Nine sites in a 13,300 km(2) area have the capacity to store 6.5 GtCO(2), corresponding to shale-oil production of 1.3 Mbbl/day for 50 years (about 1/4 of U.S. crude oil production). Our results highlight the complex, nonlinear relationship between the spatial deployment of CCS infrastructure and the oil-shale production rate.

Differential response to targeted recruitment strategies to fitness promotion research by African-American women of varying body mass index.

PubMed

Yancey, A K; Miles, O L; McCarthy, W J; Sandoval, G; Hill, J; Leslie, J J; Harrison, G G

2001-01-01

To assess patterns of recruitment into a community-based NCI-funded physical activity and dietary lifestyle change program targeting African-American women. Acquisition of a convenience sample to be screened for participation in a randomized, controlled prevention intervention. African-American-owned and -operated health club located in an area of Los Angeles in which African Americans are concentrated. 893 African-American women. RECRUITMENT STRATEGIES: Social networking/word-of-mouth, staff presentations, mass and targeted media, and physician referral. Completion of screening questionnaire indicating a desire to enroll in the study. Screening questionnaire domains included self-reported height and weight, recent participation in organized weight loss programs, ability to walk one mile unassisted, current medication use, smoking status, personal medical history of cancer, sociodemographic variables, and recruitment source. Sociodemographic and anthropometric characteristics distinguished between respondents obtained through different recruitment strategies. In particular, women with a higher body mass index (BMI) were more likely than those with lower BMIs (P = .014) to be recruited through more personalized methods (eg, social networking). Culturally tailored recruitment strategies are critical in securing the participation of members of "hard-to-reach" populations, who are both under-represented in health promotion research and at high risk for chronic diseases.

The relative importance of patient-reported barriers to colorectal cancer screening.

PubMed

Jones, Resa M; Woolf, Steven H; Cunningham, Tina D; Johnson, Robert E; Krist, Alex H; Rothemich, Stephen F; Vernon, Sally W

2010-05-01

Colorectal cancer (CRC) screening rates are suboptimal. The most important barriers identified by patients are poorly understood. A comprehensive assessment of barriers to all recommended modalities is needed. In 2007, a questionnaire was mailed to 6100 patients, aged 50-75 years, from 12 family medicine practices in the Virginia Ambulatory Care Outcomes Research Network. People aged 65-75 years and African Americans were oversampled. Patients were asked to rate 19-21 barriers to each of four recommended tests. In 2008, responses were coded on a 5-point scale; higher scores reflected stronger barrier endorsement. The response rate was 55% (n=3357). Approximately 40% of respondents were aged >/=65 years, 30% were African-American, and 73% were adherent to screening. A clinician's failure to suggest screening and not knowing testing was necessary received the highest mean scores as barriers. Financial concerns and misconceptions were also cited. Barrier scores differed depending on whether respondents were never screened, overdue for screening, or adherent to guidelines. The top five barriers for each modality included test-specific barriers (e.g., handling stool, bowel preparation), which often outranked generic barriers to screening. Not knowing testing was necessary was a top barrier for all tests but colonoscopy. Although physician advice and awareness of the need for screening are important, barriers to screening are not homogenous across tests, and test-specific barriers warrant consideration in designing strategies to improve screening rates. Barrier scores differ by screening status, highlighting the need to address prior screening experience. Evidence that patients are more familiar with colonoscopy than with other modalities suggests an opportunity to improve screening rates by educating patients about alternative tests. 2010 American Journal of Preventive Medicine. Published by Elsevier Inc. All rights reserved.

Burst and Principal Components Analyses of MEA Data Separates Chemicals by Class

EPA Science Inventory

Microelectrode arrays (MEAs) detect drug and chemical induced changes in action potential "spikes" in neuronal networks and can be used to screen chemicals for neurotoxicity. Analytical "fingerprinting," using Principal Components Analysis (PCA) on spike trains recorded from prim...

SWVRHC: On Its Own and Going Strong.

ERIC Educational Resources Information Center

Appalachia, 1985

1985-01-01

Traces Southern West Virginia Regional Health Council's decade of delivering/linking cradle-to-grave health services for 500,000 rural residents. Describes microwave communications radio network; clinics; services in family planning, genetic counseling, prenatal care, maternal/child care, nutrition, heart/respiratory disease screening, renal…

HIGH-CONTENT ANALYSIS OF PRIMARY RAT NEURAL CORTICALCULTURES FOR DEVELOPMENTAL NEUROTOXICITY SCREENING

EPA Science Inventory

Development of the vertebrate nervous system proceeds through a number of critical processes, ultimately concluding with the extension of neurites and establishment of synaptic networks. Early-life exposure to toxicants that perturb these critical developmental processes can po...

Machine Learning-based Virtual Screening and Its Applications to Alzheimer's Drug Discovery: A Review.

PubMed

Carpenter, Kristy A; Huang, Xudong

2018-06-07

Virtual Screening (VS) has emerged as an important tool in the drug development process, as it conducts efficient in silico searches over millions of compounds, ultimately increasing yields of potential drug leads. As a subset of Artificial Intelligence (AI), Machine Learning (ML) is a powerful way of conducting VS for drug leads. ML for VS generally involves assembling a filtered training set of compounds, comprised of known actives and inactives. After training the model, it is validated and, if sufficiently accurate, used on previously unseen databases to screen for novel compounds with desired drug target binding activity. The study aims to review ML-based methods used for VS and applications to Alzheimer's disease (AD) drug discovery. To update the current knowledge on ML for VS, we review thorough backgrounds, explanations, and VS applications of the following ML techniques: Naïve Bayes (NB), k-Nearest Neighbors (kNN), Support Vector Machines (SVM), Random Forests (RF), and Artificial Neural Networks (ANN). All techniques have found success in VS, but the future of VS is likely to lean more heavily toward the use of neural networks - and more specifically, Convolutional Neural Networks (CNN), which are a subset of ANN that utilize convolution. We additionally conceptualize a work flow for conducting ML-based VS for potential therapeutics of for AD, a complex neurodegenerative disease with no known cure and prevention. This both serves as an example of how to apply the concepts introduced earlier in the review and as a potential workflow for future implementation. Different ML techniques are powerful tools for VS, and they have advantages and disadvantages albeit. ML-based VS can be applied to AD drug development. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Collaborating with community-based services to promote evidence-based practice: Process description of a national initiative to improve services for youth with mental health and substance use problems.

PubMed

Henderson, Joanna L; Chaim, Gloria; Brownlie, E B

2017-08-01

Many youth with significant mental health (MH) and/or substance use (SU) difficulties do not receive specialized services. Collaboration between service providers, researchers, and other stakeholders is essential to improve youth service system capacity to provide evidence-based services to meet the complex array of needs of youth. Facilitators and barriers of implementing evidence-based practice have been identified, but few studies provide examples of the processes of collaboration and implementation for youth MH services. This study explicates the design features and implementation processes of a project to improve screening activities in youth services. These processes supported the building of 16 collaborative networks of service providers from diverse youth-serving sectors (e.g., MH, youth justice, child welfare) in urban, rural, suburban, and remote Canadian communities. These cross-sectoral networks implemented an evidence-based practice (screening youth aged 12-24 years for MH and SU problems using the Global Assessment of Individual Needs-Short Screener [GAIN-SS]) across their services. Materials and resources were provided by a centralized research team. Core project components were standardized and adherence to these components was monitored. Over 800 service providers participated in cross-sectoral networks, capacity-building events, joint data analysis, or interpretation and recommendation sessions. Across the 89 participating agencies, service providers for 84% of participating youth implemented the evidence-based practice accurately in accordance with project protocols, with 98% of positive screens reviewed and addressed according to organizational protocols. Service provider feedback is reported. Facilitators, barriers, and implications of promoting implementation of evidence-based practices across sites and sectors are discussed. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Cone penetrometer testing and discrete-depth ground water sampling techniques: A cost-effective method of site characterization in a multiple-aquifer setting

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zemo, D.A.; Pierce, Y.G.; Gallinatti, J.D.

Cone penetrometer testing (CPT), combined with discrete-depth ground water sampling methods, can significantly reduce the time and expense required to characterize large sites that have multiple aquifers. Results from the screening site characterization can then be used to design and install a cost-effective monitoring well network. At a site in northern California, it was necessary to characterize the stratigraphy and the distribution of volatile organic compounds (VOCs). To expedite characterization, a five-week field screening program was implemented that consisted of a shallow ground water survey, CPT soundings and pore-pressure measurements, and discrete-depth ground water sampling. Based on continuous lithologic informationmore » provided by the CPT soundings, four predominantly coarse-grained, water yielding stratigraphic packages were identified. Seventy-nine discrete-depth ground water samples were collected using either shallow ground water survey techniques, the BAT Enviroprobe, or the QED HydroPunch I, depending on subsurface conditions. Using results from these efforts, a 20-well monitoring network was designed and installed to monitor critical points within each stratigraphic package. Good correlation was found for hydraulic head and chemical results between discrete-depth screening data and monitoring well data. Understanding the vertical VOC distribution and concentrations produced substantial time and cost savings by minimizing the number of permanent monitoring wells and reducing the number of costly conductor casings that had to be installed. Additionally, significant long-term cost savings will result from reduced sampling costs, because fewer wells comprise the monitoring network. The authors estimate these savings to be 50% for site characterization costs, 65% for site characterization time, and 60% for long-term monitoring costs.« less

An Analysis of and Recommendations for the Peruvian Blood Collection and Transfusion System

PubMed Central

George, Paul E; Vidal, Julio; Garcia, Patricia J

2016-01-01

Background Peru experienced a crisis in its blood collection and supply system in the mid-2000s, as contaminated blood led to several transfusion-transmitted infections (TTI), occurring in the backdrop of extremely low voluntary donation rates and a national blood supply shortage. Thus, the Peruvian Ministry of Health (MINSA) implemented a national investigation on the safety and quality of the Peruvian blood collection/transfusion network. Methods Every Peruvian blood bank was evaluated by MINSA from 2007–2008. These evaluations consisted of an update of the national registry of blood banks and visits to each blood bank from MINSA oversight teams. Information was collected on the condition of the blood bank personnel, equipment, supplies, and practices. Further, previously-collected blood at each blood bank was randomly selected and screened for TTI-causing pathogens. Results Uncovered in this investigation was a fragmented, under-equipped, and poorly-staffed blood collection and transfusion network, consisting of 241 independent blood banks and resulting in suboptimal allocation of resources. Further, blood with evidence of TTI-causing pathogens (including Hepatitis B, Hepatitis C, and syphilis) and set for transfusion was discovered at three separate blood banks as part of the random screening process. Conclusion Using the successful reorganizations of national blood supply systems in other Latin American countries as examples, Peru would be well-served to form large, high-volume, regional blood collection and transfusion centers, responsible for blood collection and screening for the entire country. The small, separate blood banks would then be transformed into a network of blood transfusion centers, not responsible for blood collection. This reorganization would allow Peru to better utilize its resources, standardize the blood collection and transfusion process, and increase voluntary donation, resulting in a safer, more abundant national blood product. PMID:27761524

An Analysis of and Recommendations for the Peruvian Blood Collection and Transfusion System.

PubMed

George, Paul E; Vidal, Julio; Garcia, Patricia J

2016-05-01

Peru experienced a crisis in its blood collection and supply system in the mid-2000s, as contaminated blood led to several transfusion-transmitted infections (TTI), occurring in the backdrop of extremely low voluntary donation rates and a national blood supply shortage. Thus, the Peruvian Ministry of Health (MINSA) implemented a national investigation on the safety and quality of the Peruvian blood collection/transfusion network. Every Peruvian blood bank was evaluated by MINSA from 2007-2008. These evaluations consisted of an update of the national registry of blood banks and visits to each blood bank from MINSA oversight teams. Information was collected on the condition of the blood bank personnel, equipment, supplies, and practices. Further, previously-collected blood at each blood bank was randomly selected and screened for TTI-causing pathogens. Uncovered in this investigation was a fragmented, under-equipped, and poorly-staffed blood collection and transfusion network, consisting of 241 independent blood banks and resulting in suboptimal allocation of resources. Further, blood with evidence of TTI-causing pathogens (including Hepatitis B, Hepatitis C, and syphilis) and set for transfusion was discovered at three separate blood banks as part of the random screening process. Using the successful reorganizations of national blood supply systems in other Latin American countries as examples, Peru would be well-served to form large, high-volume, regional blood collection and transfusion centers, responsible for blood collection and screening for the entire country. The small, separate blood banks would then be transformed into a network of blood transfusion centers, not responsible for blood collection. This reorganization would allow Peru to better utilize its resources, standardize the blood collection and transfusion process, and increase voluntary donation, resulting in a safer, more abundant national blood product.

Similarity estimation for reference image retrieval in mammograms using convolutional neural network

NASA Astrophysics Data System (ADS)

Muramatsu, Chisako; Higuchi, Shunichi; Morita, Takako; Oiwa, Mikinao; Fujita, Hiroshi

2018-02-01

Periodic breast cancer screening with mammography is considered effective in decreasing breast cancer mortality. For screening programs to be successful, an intelligent image analytic system may support radiologists' efficient image interpretation. In our previous studies, we have investigated image retrieval schemes for diagnostic references of breast lesions on mammograms and ultrasound images. Using a machine learning method, reliable similarity measures that agree with radiologists' similarity were determined and relevant images could be retrieved. However, our previous method includes a feature extraction step, in which hand crafted features were determined based on manual outlines of the masses. Obtaining the manual outlines of masses is not practical in clinical practice and such data would be operator-dependent. In this study, we investigated a similarity estimation scheme using a convolutional neural network (CNN) to skip such procedure and to determine data-driven similarity scores. By using CNN as feature extractor, in which extracted features were employed in determination of similarity measures with a conventional 3-layered neural network, the determined similarity measures were correlated well with the subjective ratings and the precision of retrieving diagnostically relevant images was comparable with that of the conventional method using handcrafted features. By using CNN for determination of similarity measure directly, the result was also comparable. By optimizing the network parameters, results may be further improved. The proposed method has a potential usefulness in determination of similarity measure without precise lesion outlines for retrieval of similar mass images on mammograms.

Intelligent Noninvasive Diagnosis of Aneuploidy: Raw Values and Highly Imbalanced Dataset.

PubMed

Neocleous, Andreas C; Nicolaides, Kypros H; Schizas, Christos N

2017-09-01

The objective of this paper is to introduce a noninvasive diagnosis procedure for aneuploidy and to minimize the social and financial cost of prenatal diagnosis tests that are performed for fetal aneuploidies in an early stage of pregnancy. We propose a method by using artificial neural networks trained with data from singleton pregnancy cases, while undergoing first trimester screening. Three different datasets 1 with a total of 122 362 euploid and 967 aneuploid cases were used in this study. The data for each case contained markers collected from the mother and the fetus. This study, unlike previous studies published by the authors for a similar problem differs in three basic principles: 1) the training of the artificial neural networks is done by using the markers' values in their raw form (unprocessed), 2) a balanced training dataset is created and used by selecting only a representative number of euploids for the training phase, and 3) emphasis is given to the financials and suggest hierarchy and necessity of the available tests. The proposed artificial neural networks models were optimized in the sense of reaching a minimum false positive rate and at the same time securing a 100% detection rate for Trisomy 21. These systems correctly identify other aneuploidies (Trisomies 13&18, Turner, and Triploid syndromes) at a detection rate greater than 80%. In conclusion, we demonstrate that artificial neural network systems can contribute in providing noninvasive, effective early screening for fetal aneuploidies with results that compare favorably to other existing methods.

Reverse logistics network for municipal solid waste management: The inclusion of waste pickers as a Brazilian legal requirement

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ferri, Giovane Lopes, E-mail: giovane.ferri@aluno.ufes.br; Diniz Chaves, Gisele de Lorena, E-mail: gisele.chaves@ufes.br; Ribeiro, Glaydston Mattos, E-mail: glaydston@pet.coppe.ufrj.br

Highlights: • We propose a reverse logistics network for MSW involving waste pickers. • A generic facility location mathematical model was validated in a Brazilian city. • The results enable to predict the capacity for screening and storage centres (SSC). • We minimise the costs for transporting MSW with screening and storage centres. • The use of SSC can be a potential source of revenue and a better use of MSW. - Abstract: This study proposes a reverse logistics network involved in the management of municipal solid waste (MSW) to solve the challenge of economically managing these wastes considering themore » recent legal requirements of the Brazilian Waste Management Policy. The feasibility of the allocation of MSW material recovery facilities (MRF) as intermediate points between the generators of these wastes and the options for reuse and disposal was evaluated, as well as the participation of associations and cooperatives of waste pickers. This network was mathematically modelled and validated through a scenario analysis of the municipality of São Mateus, which makes the location model more complete and applicable in practice. The mathematical model allows the determination of the number of facilities required for the reverse logistics network, their location, capacities, and product flows between these facilities. The fixed costs of installation and operation of the proposed MRF were balanced with the reduction of transport costs, allowing the inclusion of waste pickers to the reverse logistics network. The main contribution of this study lies in the proposition of a reverse logistics network for MSW simultaneously involving legal, environmental, economic and social criteria, which is a very complex goal. This study can guide practices in other countries that have realities similar to those in Brazil of accelerated urbanisation without adequate planning for solid waste management, added to the strong presence of waste pickers that, through the characteristic of social vulnerability, must be included in the system. In addition to the theoretical contribution to the reverse logistics network problem, this study aids in decision-making for public managers who have limited technical and administrative capacities for the management of solid wastes.« less

Identification of GRB2 and GAB1 Coexpression as an Unfavorable Prognostic Factor for Hepatocellular Carcinoma by a Combination of Expression Profile and Network Analysis

PubMed Central

Yang, Mei; Wang, Danhua; Yu, Lingxiang; Guo, Chaonan; Guo, Xiaodong; Lin, Na

2013-01-01

Aim To screen novel markers for hepatocellular carcinoma (HCC) by a combination of expression profile, interaction network analysis and clinical validation. Methods HCC significant molecules which are differentially expressed or had genetic variations in HCC tissues were obtained from five existing HCC related databases (OncoDB.HCC, HCC.net, dbHCCvar, EHCO and Liverome). Then, the protein-protein interaction (PPI) network of these molecules was constructed. Three topological features of the network ('Degree', 'Betweenness', and 'Closeness') and the k-core algorithm were used to screen candidate HCC markers which play crucial roles in tumorigenesis of HCC. Furthermore, the clinical significance of two candidate HCC markers growth factor receptor-bound 2 (GRB2) and GRB2-associated-binding protein 1 (GAB1) was validated. Results In total, 6179 HCC significant genes and 977 HCC significant proteins were collected from existing HCC related databases. After network analysis, 331 candidate HCC markers were identified. Especially, GAB1 has the highest k-coreness suggesting its central localization in HCC related network, and the interaction between GRB2 and GAB1 has the largest edge-betweenness implying it may be biologically important to the function of HCC related network. As the results of clinical validation, the expression levels of both GRB2 and GAB1 proteins were significantly higher in HCC tissues than those in their adjacent nonneoplastic tissues. More importantly, the combined GRB2 and GAB1 protein expression was significantly associated with aggressive tumor progression and poor prognosis in patients with HCC. Conclusion This study provided an integrative analysis by combining expression profile and interaction network analysis to identify a list of biologically significant HCC related markers and pathways. Further experimental validation indicated that the aberrant expression of GRB2 and GAB1 proteins may be strongly related to tumor progression and prognosis in patients with HCC. The overexpression of GRB2 in combination with upregulation of GAB1 may be an unfavorable prognostic factor for HCC. PMID:24391994

Comprehensive outreach, prevention education, and skin cancer screening for Utah ski resorts.

PubMed

Varedi, Amir; Secrest, Aaron M; Harding, Garrett; Maness, Lori; Branson, Donna; Smith, Kristi; Hull, Christopher M

2018-02-15

Outdoor recreation can lead to substantial sun exposure. Employees of outdoor recreation establishments with extended time outdoors have amplified cumulative exposure to ultraviolet (UV) radiation and an increased risk of skin cancer. The "Sun Safe on the Slopes" program was created by Huntsman Cancer Institute at the University of Utah and the Utah Cancer Action Network to address increased UV exposure and skin cancer risk with free skin cancer screenings, outreach, and prevention education to local ski resorts. Herein, we describe the processes and barriers to implementation of a ski resort skin screening and education program and our 5-year report of the experience and screening data. Nine free skin cancer screenings were held at Utah ski resorts between 2011 and 2016, resulting in the presumptive diagnosis of 38 skin cancers (9.6%) in 394 participants. Behavioral data collected from participants indicates suboptimal sun safety practices, including underuse of sunscreen and protective clothing. Ski resort employees who experience sun exposure during peak hours at high altitudes and UV reflection from the snow are at an increased risk of skin cancer. These data indicate a need for emphasis on sun safety education and screening and can serve as a model for future endeavors.

Systematic prediction of gene function in Arabidopsis thaliana using a probabilistic functional gene network

PubMed Central

Hwang, Sohyun; Rhee, Seung Y; Marcotte, Edward M; Lee, Insuk

2012-01-01

AraNet is a functional gene network for the reference plant Arabidopsis and has been constructed in order to identify new genes associated with plant traits. It is highly predictive for diverse biological pathways and can be used to prioritize genes for functional screens. Moreover, AraNet provides a web-based tool with which plant biologists can efficiently discover novel functions of Arabidopsis genes (http://www.functionalnet.org/aranet/). This protocol explains how to conduct network-based prediction of gene functions using AraNet and how to interpret the prediction results. Functional discovery in plant biology is facilitated by combining candidate prioritization by AraNet with focused experimental tests. PMID:21886106

Utilization of screening mammography in New Hampshire: a population-based assessment.

PubMed

Carney, Patricia A; Goodrich, Martha E; Mackenzie, Todd; Weiss, Julia E; Poplack, Steven P; Wells, Wendy S; Titus-Ernstoff, Linda

2005-10-15

The objective of screening mammography is to identify breast carcinoma early, which requires routine screening. Although self-report data indicate that screening utilization is high, the results of this population-based assessment indicated that utilization is lower than reported previously. The authors compared New Hampshire population data from the 2000 Census with clinical encounter data for the corresponding time obtained from the New Hampshire Mammography Network, a mammography registry that captures approximately 90% of the mammograms performed in participating New Hampshire facilities. The results showed that approximately 36% of New Hampshire women either never had a mammogram or had not had a mammogram in > 27 months (irregular screenees), and older women (80 yrs and older) were less likely to be screened (79% unscreened/underscreened) compared with younger women (ages 40-69 yrs; 28-32% unscreened/underscreened). Of the screened women, 44% were adhering to an interval of 14 months, and 21% were adhering within 15 months and 26 months. The remaining 35% of the women had 1 or 2 mammograms and did not return within 27 months. Routine mammography screening may be occurring less often than believed when survey data alone are used. An important, compelling concern is the reason women had one or two mammograms only and then did not return for additional screening. This area deserves additional research. Copyright 2005 American Cancer Society

Wide variation in adoption of screening and infection control interventions for multidrug-resistant organisms: a national study.

PubMed

Pogorzelska, Monika; Stone, Patricia W; Larson, Elaine L

2012-10-01

We performed a survey of National Healthcare Safety Network hospitals in 2008 to describe adoption of screening and infection control policies aimed at multidrug-resistant organisms (MDRO) in intensive care units (ICUs) and identify predictors of their presence, monitoring, and implementation. Four hundred forty-one infection control directors were surveyed using a modified Dillman technique. To explore differences in screening and infection control policies by setting characteristics, bivariate and multivariable logistic regression models were constructed. In total, 250 hospitals participated (57% response rate). Study ICUs (n = 413) routinely screened for methicillin-resistant Staphylococcus aureus (59%); vancomycin-resistant Enterococcus (22%); multidrug-resistant, gram-negative rods (12%); and Clostridium difficile (11%). Directors reported ICU policies to screen all admissions for any MDRO (40%), screen periodically (27%), utilize presumptive isolation/contact precautions pending a screen (31%), and cohort colonized patients (42%). Several independent predictors of the presence and implementation of different interventions including mandatory reporting and teaching status were identified. This study found wide variation in adoption of MDRO screening and infection control interventions, which may reflect differences in published recommendations or their interpretation. Further research is needed to provide additional insight on effective strategies and how best to promote compliance. Copyright © 2012 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Mosby, Inc. All rights reserved.

Chemical-Gene Interactions from ToxCast Bioactivity Data ...

EPA Pesticide Factsheets

Characterizing the effects of chemicals in biological systems is often summarized by chemical-gene interactions, which have sparse coverage in the literature. The ToxCast chemical screening program has produced bioactivity data for nearly 2000 chemicals and over 450 gene targets. To evaluate the information gained from the ToxCast project, a ToxCast bioactivity network was created comprising ToxCast chemical-gene interactions based on assay data and compared to a chemical-gene association network from literature. The literature network was compiled from PubMed articles, excluding ToxCast publications, mapped to genes and chemicals. Genes were identified by curated associations available from NCBI while chemicals were identified by PubChem submissions. The frequencies of chemical-gene associations from the literature network were log-scaled and then compared to the ToxCast bioactivity network. In total, 140 times more chemical-gene associations were present in the ToxCast network in comparison to the literature-derived network highlighting the vast increase in chemical-gene interactions putatively elucidated by the ToxCast research program. There were 165 associations found in the literature network that were reproduced by ToxCast bioactivity data, and 336 associations in the literature network were not reproduced by the ToxCast bioactivity network. The literature network relies on the assumption that chemical-gene associations represent a true chemical-gene inte

The influence of the residency application process on the online social networking behavior of medical students: a single institutional study.

PubMed

Strausburg, Matthew B; Djuricich, Alexander M; Carlos, W Graham; Bosslet, Gabriel T

2013-11-01

To evaluate medical students' behavior regarding online social networks (OSNs) in preparation for the residency matching process. The specific aims were to quantify the use of OSNs by students to determine whether and how these students were changing OSN profiles in preparation for the residency application process, and to determine attitudes toward residency directors using OSNs as a screening method to evaluate potential candidates. An e-mail survey was sent to 618 third- and fourth-year medical students at Indiana University School of Medicine over a three-week period in 2012. Statistical analysis was completed using nonparametric statistical tests. Of the 30.1% (183/608) who responded to the survey, 98.9% (181/183) of students reported using OSNs. More than half, or 60.1% (110/183), reported that they would (or did) alter their OSN profile before residency matching. Respondents' opinions regarding the appropriateness of OSN screening by residency directors were mixed; however, most respondents did not feel that their online OSN profiles should be used in the residency application process. The majority of respondents planned to (or did) alter their OSN profile in preparation for the residency match process. The majority believed that residency directors are screening OSN profiles during the matching process, although most did not believe their OSN profiles should be used in the residency application process. This study implies that the more medical students perceive that residency directors use social media in application screening processes, the more they will alter their online profiles to adapt to protect their professional persona.

Effect of provider and patient reminders, deployment of nurse practitioners, and financial incentives on cervical and breast cancer screening rates.

PubMed

Kaczorowski, Janusz; Hearps, Stephen J C; Lohfeld, Lynne; Goeree, Ron; Donald, Faith; Burgess, Ken; Sebaldt, Rolf J

2013-06-01

To evaluate the effect of the Provider and Patient Reminders in Ontario: Multi-Strategy Prevention Tools (P-PROMPT) reminder and recall system and pay-for-performance incentives on the delivery rates of cervical and breast cancer screening in primary care practices in Ontario, with or without deployment of nurse practitioners (NPs). Before-and-after comparisons of the time-appropriate delivery rates of cervical and breast cancer screening using the automated and NP-augmented strategies of the P-PROMPT reminder and recall system. Southwestern Ontario. A total of 232 physicians from 24 primary care network or family health network groups across 110 different sites eligible for pay-for-performance incentives. The P-PROMPT project combined pay-for-performance incentives with provider and patient reminders and deployment of NPs to enhance the delivery of preventive care services. The mean delivery rates at the practice level of time-appropriate mammograms and Papanicolaou tests completed within the previous 30 months. Before-and-after comparisons of time-appropriate delivery rates (< 30 months) of cancer screening showed the rates of Pap tests and mammograms for eligible women significantly increased over a 1-year period by 6.3% (P < .001) and 5.3% (P < .001), respectively. The NP-augmented strategy achieved comparable rate increases to the automated strategy alone in the delivery rates of both services. The use of provider and patient reminders and pay-for-performance incentives resulted in increases in the uptake of Pap tests and mammograms among eligible primary care patients over a 1-year period in family practices in Ontario.

Moving beyond the Typologies of Managed Care: The Example of Health Plan Predictors of Screening Mammography

PubMed Central

Tye, Sherilyn; Phillips, Kathryn A; Liang, Su-Ying; Haas, Jennifer S

2004-01-01

Objectives To develop a framework of factors to characterize health plans, to identify how plan characteristics were measured in a national survey, and to apply our findings to an analysis of the predictors of screening mammography. Data Source The primary data were from the 1996 Medical Expenditure Panel Survey. Study Design Women ages 40+, with private insurance, and no history of breast cancer were included in the study (N=2,909). We used multivariate logistic regression to estimate mammography utilization in the past two years relative to health plan and demographic factors. Health plan measures included whether there is a defined provider network, whether coverage is restricted to a network, use of gatekeepers, level of cost containment, copayment and deductible amounts, coinsurance rate, and breadth of benefit coverage. Principal Findings We found no significant difference in reported mammography utilization using a dichotomous comparison of individuals enrolled in managed care versus indemnity plans. However, women in health plans with a defined provider network were more likely to report having received a mammogram in the past two years than those without networks (adjusted OR=1.21, 95 percent CI=1.07–1.36), and women in gatekeeper plans were more likely to report receiving mammography than those without gatekeepers (adjusted OR=1.18, 95 percent CI=1.03–1.36). Restricted out-of-network coverage, use of cost containment, enrollee cost sharing, and breadth of benefit coverage did not appear to affect mammography use. Conclusions It is important to examine the effect of individual health plan components on the utilization of health care, rather than use the traditional broader categorizations of managed versus nonmanaged care or simple health plan typologies. PMID:14965083

Use of HCI to screen for developmental neurotoxicity

EPA Science Inventory

The development of the nervous system is a prolonged process. It starts with the generation of neuroepithelial cells during embryogenesis and is not complete until the final stages of synaptic remodeling in the young adult. The outcome is a functionally connected neural network t...

Suicide Prevention in a Treatment Setting.

ERIC Educational Resources Information Center

Litman, Robert E.

1995-01-01

The author anticipates that sophisticated interactive computer programs will be effective in improving screening and case finding of the suicidal and that they will become invaluable in improving training for primary care providers and outpatient mental health workers. Additionally, improved communication networks will help maintain continuity of…

USING DIRECT-PUSH TOOLS TO MAP HYDROSTRATIGRAPHY AND PREDICT MTBE PLUME DIVING

EPA Science Inventory

MTBE plumes have been documented to dive beneath screened intervals of conventional monitoring well networks at a number of LUST sites. This behavior makes these plumes difficult both to detect and remediate. Electrical conductivity logging and pneumatic slug testing performed in...

FNV: light-weight flash-based network and pathway viewer.

PubMed

Dannenfelser, Ruth; Lachmann, Alexander; Szenk, Mariola; Ma'ayan, Avi

2011-04-15

Network diagrams are commonly used to visualize biochemical pathways by displaying the relationships between genes, proteins, mRNAs, microRNAs, metabolites, regulatory DNA elements, diseases, viruses and drugs. While there are several currently available web-based pathway viewers, there is still room for improvement. To this end, we have developed a flash-based network viewer (FNV) for the visualization of small to moderately sized biological networks and pathways. Written in Adobe ActionScript 3.0, the viewer accepts simple Extensible Markup Language (XML) formatted input files to display pathways in vector graphics on any web-page providing flexible layout options, interactivity with the user through tool tips, hyperlinks and the ability to rearrange nodes on the screen. FNV was utilized as a component in several web-based systems, namely Genes2Networks, Lists2Networks, KEA, ChEA and PathwayGenerator. In addition, FVN can be used to embed pathways inside pdf files for the communication of pathways in soft publication materials. FNV is available for use and download along with the supporting documentation and sample networks at http://www.maayanlab.net/FNV. avi.maayan@mssm.edu.

Social networking sites and older users - a systematic review.

PubMed

Nef, Tobias; Ganea, Raluca L; Müri, René M; Mosimann, Urs P

2013-07-01

Social networking sites can be beneficial for senior citizens to promote social participation and to enhance intergenerational communication. Particularly for older adults with impaired mobility, social networking sites can help them to connect with family members and other active social networking users. The aim of this systematic review is to give an overview of existing scientific literature on social networking in older users. Computerized databases were searched and 105 articles were identified and screened using exclusion criteria. After exclusion of 87 articles, 18 articles were included, reviewed, classified, and the key findings were extracted. Common findings are identified and critically discussed and possible future research directions are outlined. The main benefit of using social networking sites for older adults is to enter in an intergenerational communication with younger family members (children and grandchildren) that is appreciated by both sides. Identified barriers are privacy concerns, technical difficulties and the fact that current Web design does not take the needs of older users into account. Under the conditions that these problems are carefully addressed, social networking sites have the potential to support today's and tomorrow's communication between older and younger family members.

The Protein Interaction Network of Bacteriophage Lambda with Its Host, Escherichia coli

PubMed Central

Blasche, Sonja; Wuchty, Stefan; Rajagopala, Seesandra V.

2013-01-01

Although most of the 73 open reading frames (ORFs) in bacteriophage λ have been investigated intensively, the function of many genes in host-phage interactions remains poorly understood. Using yeast two-hybrid screens of all lambda ORFs for interactions with its host Escherichia coli, we determined a raw data set of 631 host-phage interactions resulting in a set of 62 high-confidence interactions after multiple rounds of retesting. These links suggest novel regulatory interactions between the E. coli transcriptional network and lambda proteins. Targeted host proteins and genes required for lambda infection are enriched among highly connected proteins, suggesting that bacteriophages resemble interaction patterns of human viruses. Lambda tail proteins interact with both bacterial fimbrial proteins and E. coli proteins homologous to other phage proteins. Lambda appears to dramatically differ from other phages, such as T7, because of its unusually large number of modified and processed proteins, which reduces the number of host-virus interactions detectable by yeast two-hybrid screens. PMID:24049175

3D Magnetic field modeling of a new superconducting synchronous machine using reluctance network method

NASA Astrophysics Data System (ADS)

Kelouaz, Moussa; Ouazir, Youcef; Hadjout, Larbi; Mezani, Smail; Lubin, Thiery; Berger, Kévin; Lévêque, Jean

2018-05-01

In this paper a new superconducting inductor topology intended for synchronous machine is presented. The studied machine has a standard 3-phase armature and a new kind of 2-poles inductor (claw-pole structure) excited by two coaxial superconducting coils. The air-gap spatial variation of the radial flux density is obtained by inserting a superconducting bulk, which deviates the magnetic field due to the coils. The complex geometry of this inductor usually needs 3D finite elements (FEM) for its analysis. However, to avoid a long computational time inherent to 3D FEM, we propose in this work an alternative modeling, which uses a 3D meshed reluctance network. The results obtained with the developed model are compared to 3D FEM computations as well as to measurements carried out on a laboratory prototype. Finally, a 3D FEM study of the shielding properties of the superconducting screen demonstrates the suitability of using a diamagnetic-like model of the superconducting screen.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shatsky, Maxim; Allen, Simon; Gold, Barbara

Numerous affinity purification – mass-spectrometry (AP-MS) and yeast two hybrid (Y2H) screens have each defined thousands of pairwise protein-protein interactions (PPIs), most between functionally unrelated proteins. The accuracy of these networks, however, is under debate. Here we present an AP-MS survey of the bacterium Desulfovibrio vulgaris together with a critical reanalysis of nine published bacterial Y2H and AP-MS screens. We have identified 459 high confidence PPIs from D. vulgaris and 391 from Escherichia coli. Compared to the nine published interactomes, our two networks are smaller; are much less highly connected; have significantly lower false discovery rates; and are much moremore » enriched in protein pairs that are encoded in the same operon, have similar functions, and are reproducibly detected in other physical interaction assays. Lastly, our work establishes more stringent benchmarks for the properties of protein interactomes and suggests that bona fide PPIs much more frequently involve protein partners that are annotated with similar functions or that can be validated in independent assays than earlier studies suggested.« less

Metabolic Profile of the Cellulolytic Industrial Actinomycete Thermobifida fusca

PubMed Central

Vanee, Niti

2017-01-01

Actinomycetes have a long history of being the source of numerous valuable natural products and medicinals. To expedite product discovery and optimization of biochemical production, high-throughput technologies can now be used to screen the library of compounds present (or produced) at a given time in an organism. This not only facilitates chemical product screening, but also provides a comprehensive methodology to the study cellular metabolic networks to inform cellular engineering. Here, we present some of the first metabolomic data of the industrial cellulolytic actinomycete Thermobifida fusca generated using LC-MS/MS. The underlying objective of conducting global metabolite profiling was to gain better insight on the innate capabilities of T. fusca, with a long-term goal of facilitating T. fusca-based bioprocesses. The T. fusca metabolome was characterized for growth on two cellulose-relevant carbon sources, cellobiose and Avicel. Furthermore, the comprehensive list of measured metabolites was computationally integrated into a metabolic model of T. fusca, to study metabolic shifts in the network flux associated with carbohydrate and amino acid metabolism. PMID:29137138

Collaborative filtering on a family of biological targets.

PubMed

Erhan, Dumitru; L'heureux, Pierre-Jean; Yue, Shi Yi; Bengio, Yoshua

2006-01-01

Building a QSAR model of a new biological target for which few screening data are available is a statistical challenge. However, the new target may be part of a bigger family, for which we have more screening data. Collaborative filtering or, more generally, multi-task learning, is a machine learning approach that improves the generalization performance of an algorithm by using information from related tasks as an inductive bias. We use collaborative filtering techniques for building predictive models that link multiple targets to multiple examples. The more commonalities between the targets, the better the multi-target model that can be built. We show an example of a multi-target neural network that can use family information to produce a predictive model of an undersampled target. We evaluate JRank, a kernel-based method designed for collaborative filtering. We show their performance on compound prioritization for an HTS campaign and the underlying shared representation between targets. JRank outperformed the neural network both in the single- and multi-target models.

Microaneurysm detection using fully convolutional neural networks.

PubMed

Chudzik, Piotr; Majumdar, Somshubra; Calivá, Francesco; Al-Diri, Bashir; Hunter, Andrew

2018-05-01

Diabetic retinopathy is a microvascular complication of diabetes that can lead to sight loss if treated not early enough. Microaneurysms are the earliest clinical signs of diabetic retinopathy. This paper presents an automatic method for detecting microaneurysms in fundus photographies. A novel patch-based fully convolutional neural network with batch normalization layers and Dice loss function is proposed. Compared to other methods that require up to five processing stages, it requires only three. Furthermore, to the best of the authors' knowledge, this is the first paper that shows how to successfully transfer knowledge between datasets in the microaneurysm detection domain. The proposed method was evaluated using three publicly available and widely used datasets: E-Ophtha, DIARETDB1, and ROC. It achieved better results than state-of-the-art methods using the FROC metric. The proposed algorithm accomplished highest sensitivities for low false positive rates, which is particularly important for screening purposes. Performance, simplicity, and robustness of the proposed method demonstrates its suitability for diabetic retinopathy screening applications. Copyright © 2018 Elsevier B.V. All rights reserved.

Box Office Forecasting considering Competitive Environment and Word-of-Mouth in Social Networks: A Case Study of Korean Film Market.

PubMed

Kim, Taegu; Hong, Jungsik; Kang, Pilsung

2017-01-01

Accurate box office forecasting models are developed by considering competition and word-of-mouth (WOM) effects in addition to screening-related information. Nationality, genre, ratings, and distributors of motion pictures running concurrently with the target motion picture are used to describe the competition, whereas the numbers of informative, positive, and negative mentions posted on social network services (SNS) are used to gauge the atmosphere spread by WOM. Among these candidate variables, only significant variables are selected by genetic algorithm (GA), based on which machine learning algorithms are trained to build forecasting models. The forecasts are combined to improve forecasting performance. Experimental results on the Korean film market show that the forecasting accuracy in early screening periods can be significantly improved by considering competition. In addition, WOM has a stronger influence on total box office forecasting. Considering both competition and WOM improves forecasting performance to a larger extent than when only one of them is considered.

A Clonal Genetic Screen for Mutants Causing Defects in Larval Tracheal Morphogenesis in Drosophila

PubMed Central

Baer, Magdalena M.; Bilstein, Andreas; Leptin, Maria

2007-01-01

The initial establishment of the tracheal network in the Drosophila embryo is beginning to be understood in great detail, both in its genetic control cascades and in its cell biological events. By contrast, the vast expansion of the system during larval growth, with its extensive ramification of preexisting tracheal branches, has been analyzed less well. The mutant phenotypes of many genes involved in this process are probably not easy to reveal, as these genes may be required for other functions at earlier developmental stages. We therefore conducted a screen for defects in individual clonal homozygous mutant cells in the tracheal network of heterozygous larvae using the mosaic analysis with a repressible cell marker (MARCM) system to generate marked, recombinant mitotic clones. We describe the identification of a set of mutants with distinct phenotypic effects. In particular we found a range of defects in terminal cells, including failure in lumen formation and reduced or extensive branching. Other mutations affect cell growth, cell shape, and cell migration. PMID:17603107

CGBVS-DNN: Prediction of Compound-protein Interactions Based on Deep Learning.

PubMed

Hamanaka, Masatoshi; Taneishi, Kei; Iwata, Hiroaki; Ye, Jun; Pei, Jianguo; Hou, Jinlong; Okuno, Yasushi

2017-01-01

Computational prediction of compound-protein interactions (CPIs) is of great importance for drug design as the first step in in-silico screening. We previously proposed chemical genomics-based virtual screening (CGBVS), which predicts CPIs by using a support vector machine (SVM). However, the CGBVS has problems when training using more than a million datasets of CPIs since SVMs require an exponential increase in the calculation time and computer memory. To solve this problem, we propose the CGBVS-DNN, in which we use deep neural networks, a kind of deep learning technique, instead of the SVM. Deep learning does not require learning all input data at once because the network can be trained with small mini-batches. Experimental results show that the CGBVS-DNN outperformed the original CGBVS with a quarter million CPIs. Results of cross-validation show that the accuracy of the CGBVS-DNN reaches up to 98.2 % (σ<0.01) with 4 million CPIs. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Genetic and environmental pathways to complex diseases.

PubMed

Gohlke, Julia M; Thomas, Reuben; Zhang, Yonqing; Rosenstein, Michael C; Davis, Allan P; Murphy, Cynthia; Becker, Kevin G; Mattingly, Carolyn J; Portier, Christopher J

2009-05-05

Pathogenesis of complex diseases involves the integration of genetic and environmental factors over time, making it particularly difficult to tease apart relationships between phenotype, genotype, and environmental factors using traditional experimental approaches. Using gene-centered databases, we have developed a network of complex diseases and environmental factors through the identification of key molecular pathways associated with both genetic and environmental contributions. Comparison with known chemical disease relationships and analysis of transcriptional regulation from gene expression datasets for several environmental factors and phenotypes clustered in a metabolic syndrome and neuropsychiatric subnetwork supports our network hypotheses. This analysis identifies natural and synthetic retinoids, antipsychotic medications, Omega 3 fatty acids, and pyrethroid pesticides as potential environmental modulators of metabolic syndrome phenotypes through PPAR and adipocytokine signaling and organophosphate pesticides as potential environmental modulators of neuropsychiatric phenotypes. Identification of key regulatory pathways that integrate genetic and environmental modulators define disease associated targets that will allow for efficient screening of large numbers of environmental factors, screening that could set priorities for further research and guide public health decisions.

Profound Tissue Specificity in Proliferation Control Underlies Cancer Drivers and Aneuploidy Patterns.

PubMed

Sack, Laura Magill; Davoli, Teresa; Li, Mamie Z; Li, Yuyang; Xu, Qikai; Naxerova, Kamila; Wooten, Eric C; Bernardi, Ronald J; Martin, Timothy D; Chen, Ting; Leng, Yumei; Liang, Anthony C; Scorsone, Kathleen A; Westbrook, Thomas F; Wong, Kwok-Kin; Elledge, Stephen J

2018-04-05

Genomics has provided a detailed structural description of the cancer genome. Identifying oncogenic drivers that work primarily through dosage changes is a current challenge. Unrestrained proliferation is a critical hallmark of cancer. We constructed modular, barcoded libraries of human open reading frames (ORFs) and performed screens for proliferation regulators in multiple cell types. Approximately 10% of genes regulate proliferation, with most performing in an unexpectedly highly tissue-specific manner. Proliferation drivers in a given cell type showed specific enrichment in somatic copy number changes (SCNAs) from cognate tumors and helped predict aneuploidy patterns in those tumors, implying that tissue-type-specific genetic network architectures underlie SCNA and driver selection in different cancers. In vivo screening confirmed these results. We report a substantial contribution to the catalog of SCNA-associated cancer drivers, identifying 147 amplified and 107 deleted genes as potential drivers, and derive insights about the genetic network architecture of aneuploidy in tumors. Copyright © 2018 Elsevier Inc. All rights reserved.

Box Office Forecasting considering Competitive Environment and Word-of-Mouth in Social Networks: A Case Study of Korean Film Market

PubMed Central

Kim, Taegu; Hong, Jungsik

2017-01-01

Accurate box office forecasting models are developed by considering competition and word-of-mouth (WOM) effects in addition to screening-related information. Nationality, genre, ratings, and distributors of motion pictures running concurrently with the target motion picture are used to describe the competition, whereas the numbers of informative, positive, and negative mentions posted on social network services (SNS) are used to gauge the atmosphere spread by WOM. Among these candidate variables, only significant variables are selected by genetic algorithm (GA), based on which machine learning algorithms are trained to build forecasting models. The forecasts are combined to improve forecasting performance. Experimental results on the Korean film market show that the forecasting accuracy in early screening periods can be significantly improved by considering competition. In addition, WOM has a stronger influence on total box office forecasting. Considering both competition and WOM improves forecasting performance to a larger extent than when only one of them is considered. PMID:28819355

Web Extensible Display Manager

DOE Office of Scientific and Technical Information (OSTI.GOV)

Slominski, Ryan; Larrieu, Theodore L.

Jefferson Lab's Web Extensible Display Manager (WEDM) allows staff to access EDM control system screens from a web browser in remote offices and from mobile devices. Native browser technologies are leveraged to avoid installing and managing software on remote clients such as browser plugins, tunnel applications, or an EDM environment. Since standard network ports are used firewall exceptions are minimized. To avoid security concerns from remote users modifying a control system, WEDM exposes read-only access and basic web authentication can be used to further restrict access. Updates of monitored EPICS channels are delivered via a Web Socket using a webmore » gateway. The software translates EDM description files (denoted with the edl suffix) to HTML with Scalable Vector Graphics (SVG) following the EDM's edl file vector drawing rules to create faithful screen renderings. The WEDM server parses edl files and creates the HTML equivalent in real-time allowing existing screens to work without modification. Alternatively, the familiar drag and drop EDM screen creation tool can be used to create optimized screens sized specifically for smart phones and then rendered by WEDM.« less

Factors associated with decisions to attend cervical cancer screening among women aged 30-60 years in Chatapadung Contracting Medical Unit, Thailand.

PubMed

Budkaew, Jiratha; Chumworathayi, Bandit

2014-01-01

This study aimed to identify factors associated with women's decisions to attend cervical cancer screening and to explore those linked with intention to attend in the coming year and to continue regular screening. A community based case-control study was conducted among woman 30-60 years of age in catchment area of Chatapadung Contracting Medical Unit (CCMU), networking of Khon Kaen Center Hospital, Thailand. Self-administered questionnaires were used to collect data, and in-depth interviews were then performed to explore in greater detail. There were 195 participants. Only one third (32.3 %) had been screened for cervical cancer within the past 5 years. Some 67.7% reported that they had not been screened because they had no abnormal symptoms, single marital status, and no children. Only 10.6% of those never had screening intent to be screened within the next 12 months. High family income (adjusted OR=2.16, 95%CI=1.13-4.14), good attitude towards a Pap test (OR=1.87, 95%CI=1.09-4.23), and having received a recommendation from health care providers were important factors associated with decisions to attend cervical cancer screening (OR=1.73, 95%CI=1.01-4.63). From in-depth interviews, there were five reasons of their decisions to attend cervical cancer screening including yearly check-up, postpartum check-up, having abnormal symptom, encouragement by health care providers, and request from workplace. High family income, good attitude towards a Pap test, and receiving proper recommendation by health care providers, were important factors associated with decision to have cervical cancer screening among women 30-60 years old. Trying to enhance these factors and reduce barriers regarding screening, may increase the coverage rate for cervical cancer screening in Thailand.

Sensitivity and Specificity of a Five-Minute Cognitive Screening Test in Patients With Heart Failure.

PubMed

Cameron, Janette D; Gallagher, Robyn; Pressler, Susan J; McLennan, Skye N; Ski, Chantal F; Tofler, Geoffrey; Thompson, David R

2016-02-01

Cognitive impairment occurs in up to 80% of patients with heart failure (HF). The National Institute for Neurological Disorders and Stroke (NINDS) and the Canadian Stroke Network (CSN) recommend a 5-minute cognitive screening protocol that has yet to be psychometrically evaluated in HF populations. The aim of this study was to conduct a secondary analysis of the sensitivity and specificity of the NINDS-CSN brief cognitive screening protocol in HF patients. The Montreal Cognitive Assessment (MoCA) was administered to 221 HF patients. The NINDS-CSN screen comprises 3 MoCA items, with lower scores indicating poorer cognitive function. Receiver operator characteristic (ROC) curves were constructed, determining the sensitivity, specificity and appropriate cutoff scores of the NINDS-CSN screen. In an HF population aged 76 ± 12 years, 136 (62%) were characterized with cognitive impairment (MoCA <26). Scores on the NINDS-CSN screen ranged from 3-11. The area under the receiver operating characteristic curve indicated good accuracy in screening for cognitive impairment (0.88; P < .01; 95% CI 0.83-0.92). A cutoff score of ≤9 provided 89% sensitivity and 71% specificity. The NINDS-CSN protocol offers clinicians a feasible telephone method to screen for cognitive impairment in patients with HF. Future studies should include a neuropsychologic battery to more comprehensively examine the diagnostic accuracy of brief cognitive screening protocols. Copyright © 2016 Elsevier Inc. All rights reserved.

Consequences of screening in lung cancer: development and dimensionality of a questionnaire.

PubMed

Brodersen, John; Thorsen, Hanne; Kreiner, Svend

2010-08-01

The objective of this study was to extend the Consequences of Screening (COS) Questionnaire for use in a lung cancer screening by testing for comprehension, content coverage, dimensionality, and reliability. In interviews, the suitability, content coverage, and relevance of the COS were tested on participants in a lung cancer screening program. The results were thematically analyzed to identify the key consequences of abnormal and false-positive screening results. Item Response Theory and Classical Test Theory were used to analyze data. Dimensionality, objectivity, and reliability were established by item analysis, examining the fit between item responses and Rasch models. Eight themes specifically relevant for participants in lung cancer screening results were identified: "self-blame,"focus on symptoms,"stigmatization,"introvert,"harm of smoking,"impulsivity,"empathy," and "regretful of still smoking." Altogether, 26 new items for part I and 16 new items for part II were generated. These themes were confirmed to fit a partial-credit Rasch model measuring different constructs including several of the new items. In conclusion, the reliability and the dimensionality of a condition-specific measure with high content validity for persons having abnormal or false-positive lung cancer screening results have been demonstrated. This new questionnaire called Consequences of Screening in Lung Cancer (COS-LC) covers in two parts the psychosocial experience in lung cancer screening. Part I: "anxiety,"behavior,"dejection,"sleep,"self-blame,"focus on airway symptoms,"stigmatization,"introvert," and "harm of smoking." Part II: "calm/relax,"social network,"existential values,"impulsivity,"empathy," and "regretful of still smoking."

Barriers and Facilitators to Colorectal Cancer Screening in Vietnamese Americans: A Qualitative Analysis

PubMed Central

Kimura, Amanda; Sin, Mo-Kyung; Spigner, Clarence; Tran, Anh; Tu, Shin-Ping

2015-01-01

Background Vietnamese Americans are the fourth largest Asian ethnic group in the United States. Colorectal cancer (CRC) ranks as one of the most common cancers in Vietnamese Americans. However, CRC screening rates remain low among Vietnamese Americans, with 40% of women and 60% of men reporting never having a sigmoidoscopy, colonoscopy, or Fecal Occult Blood Test. Methods We partnered with a Federally Qualified Health Center (FQHC) in Seattle, Washington, to conduct focus groups as part of a process evaluation. Using interpreters, we recruited and conducted three focus groups comprised of 6 women screened for CRC, 6 women not screened for CRC, and 7 men screened for CRC, which made up a total of 19 FQHC patients of Vietnamese descent between 50 and 79 years old. Three team members analyzed transcripts using open coding and axial coding. Major themes were categorized into barriers and facilitators to CRC screening. Results Barriers include lack of health problems, having comorbidities, challenges with medical terminology, and concerns with the colonoscopy. Participants singled out the risk of perforation as a fear they have towards colonoscopy procedures. Facilitators include knowledge about CRC and CRC screening, access to sources of information and social networks, and physician recommendation. Conclusion Our focus groups elicited information that adds to the literature and has not been previously captured through published surveys. Findings from this study can be used to develop more culturally appropriate CRC screening interventions and improve upon existing CRC screening programs for the Vietnamese American population. PMID:24756545

Identification of the Key Genes and Pathways in Esophageal Carcinoma.

PubMed

Su, Peng; Wen, Shiwang; Zhang, Yuefeng; Li, Yong; Xu, Yanzhao; Zhu, Yonggang; Lv, Huilai; Zhang, Fan; Wang, Mingbo; Tian, Ziqiang

2016-01-01

Objective . Esophageal carcinoma (EC) is a frequently common malignancy of gastrointestinal cancer in the world. This study aims to screen key genes and pathways in EC and elucidate the mechanism of it. Methods . 5 microarray datasets of EC were downloaded from Gene Expression Omnibus. Differentially expressed genes (DEGs) were screened by bioinformatics analysis. Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, and protein-protein interaction (PPI) network construction were performed to obtain the biological roles of DEGs in EC. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to verify the expression level of DEGs in EC. Results . A total of 1955 genes were filtered as DEGs in EC. The upregulated genes were significantly enriched in cell cycle and the downregulated genes significantly enriched in Endocytosis. PPI network displayed CDK4 and CCT3 were hub proteins in the network. The expression level of 8 dysregulated DEGs including CDK4, CCT3, THSD4, SIM2, MYBL2, CENPF, CDCA3, and CDKN3 was validated in EC compared to adjacent nontumor tissues and the results were matched with the microarray analysis. Conclusion . The significantly DEGs including CDK4, CCT3, THSD4, and SIM2 may play key roles in tumorigenesis and development of EC involved in cell cycle and Endocytosis.

Identifying novel genes and chemicals related to nasopharyngeal cancer in a heterogeneous network.

PubMed

Li, Zhandong; An, Lifeng; Li, Hao; Wang, ShaoPeng; Zhou, You; Yuan, Fei; Li, Lin

2016-05-05

Nasopharyngeal cancer or nasopharyngeal carcinoma (NPC) is the most common cancer originating in the nasopharynx. The factors that induce nasopharyngeal cancer are still not clear. Additional information about the chemicals or genes related to nasopharyngeal cancer will promote a better understanding of the pathogenesis of this cancer and the factors that induce it. Thus, a computational method NPC-RGCP was proposed in this study to identify the possible relevant chemicals and genes based on the presently known chemicals and genes related to nasopharyngeal cancer. To extensively utilize the functional associations between proteins and chemicals, a heterogeneous network was constructed based on interactions of proteins and chemicals. The NPC-RGCP included two stages: the searching stage and the screening stage. The former stage is for finding new possible genes and chemicals in the heterogeneous network, while the latter stage is for screening and removing false discoveries and selecting the core genes and chemicals. As a result, five putative genes, CXCR3, IRF1, CDK1, GSTP1, and CDH2, and seven putative chemicals, iron, propionic acid, dimethyl sulfoxide, isopropanol, erythrose 4-phosphate, β-D-Fructose 6-phosphate, and flavin adenine dinucleotide, were identified by NPC-RGCP. Extensive analyses provided confirmation that the putative genes and chemicals have significant associations with nasopharyngeal cancer.

Identifying novel genes and chemicals related to nasopharyngeal cancer in a heterogeneous network

PubMed Central

Li, Zhandong; An, Lifeng; Li, Hao; Wang, ShaoPeng; Zhou, You; Yuan, Fei; Li, Lin

2016-01-01

Nasopharyngeal cancer or nasopharyngeal carcinoma (NPC) is the most common cancer originating in the nasopharynx. The factors that induce nasopharyngeal cancer are still not clear. Additional information about the chemicals or genes related to nasopharyngeal cancer will promote a better understanding of the pathogenesis of this cancer and the factors that induce it. Thus, a computational method NPC-RGCP was proposed in this study to identify the possible relevant chemicals and genes based on the presently known chemicals and genes related to nasopharyngeal cancer. To extensively utilize the functional associations between proteins and chemicals, a heterogeneous network was constructed based on interactions of proteins and chemicals. The NPC-RGCP included two stages: the searching stage and the screening stage. The former stage is for finding new possible genes and chemicals in the heterogeneous network, while the latter stage is for screening and removing false discoveries and selecting the core genes and chemicals. As a result, five putative genes, CXCR3, IRF1, CDK1, GSTP1, and CDH2, and seven putative chemicals, iron, propionic acid, dimethyl sulfoxide, isopropanol, erythrose 4-phosphate, β-D-Fructose 6-phosphate, and flavin adenine dinucleotide, were identified by NPC-RGCP. Extensive analyses provided confirmation that the putative genes and chemicals have significant associations with nasopharyngeal cancer. PMID:27149165

Use of Natural Products as Chemical Library for Drug Discovery and Network Pharmacology

PubMed Central

Gu, Jiangyong; Gui, Yuanshen; Chen, Lirong; Yuan, Gu; Lu, Hui-Zhe; Xu, Xiaojie

2013-01-01

Background Natural products have been an important source of lead compounds for drug discovery. How to find and evaluate bioactive natural products is critical to the achievement of drug/lead discovery from natural products. Methodology We collected 19,7201 natural products structures, reported biological activities and virtual screening results. Principal component analysis was employed to explore the chemical space, and we found that there was a large portion of overlap between natural products and FDA-approved drugs in the chemical space, which indicated that natural products had large quantity of potential lead compounds. We also explored the network properties of natural product-target networks and found that polypharmacology was greatly enriched to those compounds with large degree and high betweenness centrality. In order to make up for a lack of experimental data, high throughput virtual screening was employed. All natural products were docked to 332 target proteins of FDA-approved drugs. The most potential natural products for drug discovery and their indications were predicted based on a docking score-weighted prediction model. Conclusions Analysis of molecular descriptors, distribution in chemical space and biological activities of natural products was conducted in this article. Natural products have vast chemical diversity, good drug-like properties and can interact with multiple cellular target proteins. PMID:23638153

Screening of differentially expressed genes between multiple trauma patients with and without sepsis.

PubMed

Ji, S C; Pan, Y T; Lu, Q Y; Sun, Z Y; Liu, Y Z

2014-03-17

The purpose of this study was to identify critical genes associated with septic multiple trauma by comparing peripheral whole blood samples from multiple trauma patients with and without sepsis. A microarray data set was downloaded from the Gene Expression Omnibus (GEO) database. This data set included 70 samples, 36 from multiple trauma patients with sepsis and 34 from multiple trauma patients without sepsis (as a control set). The data were preprocessed, and differentially expressed genes (DEGs) were then screened for using packages of the R language. Functional analysis of DEGs was performed with DAVID. Interaction networks were then established for the most up- and down-regulated genes using HitPredict. Pathway-enrichment analysis was conducted for genes in the networks using WebGestalt. Fifty-eight DEGs were identified. The expression levels of PLAU (down-regulated) and MMP8 (up-regulated) presented the largest fold-changes, and interaction networks were established for these genes. Further analysis revealed that PLAT (plasminogen activator, tissue) and SERPINF2 (serpin peptidase inhibitor, clade F, member 2), which interact with PLAU, play important roles in the pathway of the component and coagulation cascade. We hypothesize that PLAU is a major regulator of the component and coagulation cascade, and down-regulation of PLAU results in dysfunction of the pathway, causing sepsis.

An integrated approach of network-based systems biology, molecular docking, and molecular dynamics approach to unravel the role of existing antiviral molecules against AIDS-associated cancer.

PubMed

Omer, Ankur; Singh, Poonam

2017-05-01

A serious challenge in cancer treatment is to reposition the activity of various already known drug candidates against cancer. There is a need to rewrite and systematically analyze the detailed mechanistic aspect of cellular networks to gain insight into the novel role played by various molecules. Most Human Immunodeficiency Virus infection-associated cancers are caused by oncogenic viruses like Human Papilloma Viruses and Epstein-Bar Virus. As the onset of AIDS-associated cancers marks the severity of AIDS, there might be possible interconnections between the targets and mechanism of both the diseases. We have explored the possibility of certain antiviral compounds to act against major AIDS-associated cancers: Kaposi's Sarcoma, Non-Hodgkin Lymphoma, and Cervical Cancer with the help of systems pharmacology approach that includes screening for targets and molecules through the construction of a series of drug-target and drug-target-diseases network. Two molecules (Calanolide A and Chaetochromin B) and the target "HRAS" were finally screened with the help of molecular docking and molecular dynamics simulation. The results provide novel antiviral molecules against HRAS target to treat AIDS defining cancers and an insight for understanding the pharmacological, therapeutic aspects of similar unexplored molecules against various cancers.

Application of Polynomial Neural Networks to Classification of Acoustic Warfare Signals

DTIC Science & Technology

1993-04-01

on Neural Networks, Vol. II, Jun’e, 1987. [66] Shynk, J.J., "Adaptive IIR filtering," IEEE ASSP Magazine, Vol. 6, No. 2, Apr. 1989. 175 I [67] Specht ...rows This is the size of the yellow capture window which will be displayed on the screen. The best setting for pixel-rows is two greater than exemplar...exemplar size of 4 to be captured by the PNN. The pixel-rows setting is 6, which allows all four rows of I the retina data to fit inside yellow capture

A novel interacting multiple model based network intrusion detection scheme

NASA Astrophysics Data System (ADS)

Xin, Ruichi; Venkatasubramanian, Vijay; Leung, Henry

2006-04-01

In today's information age, information and network security are of primary importance to any organization. Network intrusion is a serious threat to security of computers and data networks. In internet protocol (IP) based network, intrusions originate in different kinds of packets/messages contained in the open system interconnection (OSI) layer 3 or higher layers. Network intrusion detection and prevention systems observe the layer 3 packets (or layer 4 to 7 messages) to screen for intrusions and security threats. Signature based methods use a pre-existing database that document intrusion patterns as perceived in the layer 3 to 7 protocol traffics and match the incoming traffic for potential intrusion attacks. Alternately, network traffic data can be modeled and any huge anomaly from the established traffic pattern can be detected as network intrusion. The latter method, also known as anomaly based detection is gaining popularity for its versatility in learning new patterns and discovering new attacks. It is apparent that for a reliable performance, an accurate model of the network data needs to be established. In this paper, we illustrate using collected data that network traffic is seldom stationary. We propose the use of multiple models to accurately represent the traffic data. The improvement in reliability of the proposed model is verified by measuring the detection and false alarm rates on several datasets.

Policies for implementing network firewalls

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brown, C.D.

1994-05-01

Corporate networks are frequently protected by {open_quotes}firewalls{close_quotes} or gateway systems that control access to/from other networks, e.g., the Internet, in order to reduce the network`s vulnerability to hackers and other unauthorized access. Firewalls typically limit access to particular network nodes and application protocols, and they often perform special authentication and authorization functions. One of the difficult issues associated with network firewalls is determining which applications should be permitted through the firewall. For example, many networks permit the exchange of electronic mail with the outside but do not permit file access to be initiated by outside users, as this might allowmore » outside users to access sensitive data or to surreptitiously modify data or programs (e.g., to intall Trojan Horse software). However, if access through firewalls is severely restricted, legitimate network users may find it difficult or impossible to collaborate with outside users and to share data. Some of the most serious issues regarding firewalls involve setting policies for firewalls with the goal of achieving an acceptable balance between the need for greater functionality and the associated risks. Two common firewall implementation techniques, screening routers and application gateways, are discussed below, followed by some common policies implemented by network firewalls.« less

Avaricious and Envious: Confessions of a Computer-Literate Educator.

ERIC Educational Resources Information Center

Burniske, R. W.

2001-01-01

How did educators become enslaved to networked computers and mesmerized by iridescent screens? The computer encourages endless acquisitions, some motivated by intellectual avarice, others by petty jealousies incited by colleagues raving about the latest "innovation." How much computer literacy is sufficient? What other literacies must…

A renaissance of neural networks in drug discovery.

PubMed

Baskin, Igor I; Winkler, David; Tetko, Igor V

2016-08-01

Neural networks are becoming a very popular method for solving machine learning and artificial intelligence problems. The variety of neural network types and their application to drug discovery requires expert knowledge to choose the most appropriate approach. In this review, the authors discuss traditional and newly emerging neural network approaches to drug discovery. Their focus is on backpropagation neural networks and their variants, self-organizing maps and associated methods, and a relatively new technique, deep learning. The most important technical issues are discussed including overfitting and its prevention through regularization, ensemble and multitask modeling, model interpretation, and estimation of applicability domain. Different aspects of using neural networks in drug discovery are considered: building structure-activity models with respect to various targets; predicting drug selectivity, toxicity profiles, ADMET and physicochemical properties; characteristics of drug-delivery systems and virtual screening. Neural networks continue to grow in importance for drug discovery. Recent developments in deep learning suggests further improvements may be gained in the analysis of large chemical data sets. It's anticipated that neural networks will be more widely used in drug discovery in the future, and applied in non-traditional areas such as drug delivery systems, biologically compatible materials, and regenerative medicine.

Men’s perspectives of prostate cancer screening: A systematic review of qualitative studies

PubMed Central

Wong, Germaine; Craig, Jonathan C.; Hanson, Camilla S.; Ju, Angela; Howard, Kirsten; Usherwood, Tim; Lau, Howard; Tong, Allison

2017-01-01

Background Prostate cancer is the most commonly diagnosed non-skin cancer in men. Screening for prostate cancer is widely accepted; however concerns regarding the harms outweighing the benefits of screening exist. Although patient’s play a pivotal role in the decision making process, men may not be aware of the controversies regarding prostate cancer screening. Therefore we aimed to describe men’s attitudes, beliefs and experiences of prostate cancer screening. Methods Systematic review and thematic synthesis of qualitative studies on men’s perspectives of prostate cancer screening. Electronic databases and reference lists were searched to October 2016. Findings Sixty studies involving 3,029 men aged from 18–89 years, who had been screened for prostate cancer by Prostate Specific Antigen (PSA) or Digital Rectal Examination (DRE) and not screened, across eight countries were included. Five themes were identified: Social prompting (trusting professional opinion, motivation from family and friends, proximity and prominence of cancer); gaining decisional confidence (overcoming fears, survival imperative, peace of mind, mental preparation, prioritising wellbeing); preserving masculinity (bodily invasion, losing sexuality, threatening manhood, medical avoidance); avoiding the unknown and uncertainties (taboo of cancer-related death, lacking tangible cause, physiological and symptomatic obscurity, ambiguity of the procedure, confusing controversies); and prohibitive costs. Conclusions Men are willing to participate in prostate cancer screening to prevent cancer and gain reassurance about their health, particularly when supported or prompted by their social networks or healthcare providers. However, to do so they needed to mentally overcome fears of losing their masculinity and accept the intrusiveness of screening, the ambiguities about the necessity and the potential for substantial costs. Addressing the concerns and priorities of men may facilitate informed decisions about prostate cancer screening and improve patient satisfaction and outcomes. PMID:29182649

Telemedicine and Diabetic Retinopathy: Review of Published Screening Programs

PubMed Central

Tozer, Kevin; Woodward, Maria A.; Newman-Casey, Paula A.

2016-01-01

Background Diabetic Retinopathy (DR) is a leading cause of blindness worldwide even though successful treatments exist. Improving screening and treatment could avoid many cases of vision loss. However, due to an increasing prevalence of diabetes, traditional in-person screening for DR for every diabetic patient is not feasible. Telemedicine is one viable solution to provide high-quality and efficient screening to large number of diabetic patients. Purpose To provide a narrative review of large DR telemedicine screening programs. Methods Articles were identified through a comprehensive search of the English-language literature published between 2000 and 2014. Telemedicine screening programs were included for review if they had published data on at least 150 patients and had available validation studies supporting their model. Screening programs were then categorized according to their American Telemedicine Association Validation Level. Results Seven programs from the US and abroad were identified and included in the review. Three programs were Category 1 programs (Ophdiat, EyePacs, and Digiscope), two were Category 2 programs (Eye Check, NHS Diabetic Eye Screening Program), and two were Category 3 programs (Joslin Vision Network, Alberta Screening Program). No program was identified that claimed category 4 status. Programs ranged from community or city level programs to large nationwide programs including millions of individuals. The programs demonstrated a high level of clinical accuracy in screening for DR. There was no consensus amongst the programs regarding the need for dilation, need for stereoscopic images, or the level of training for approved image graders. Conclusion Telemedicine programs have been clinically validated and successfully implemented across the globe. They can provide a high-level of clinical accuracy for screening for DR while improving patient access in a cost-effective and scalable manner. PMID:27430019

Automated image-based phenotypic analysis in zebrafish embryos

PubMed Central

Vogt, Andreas; Cholewinski, Andrzej; Shen, Xiaoqiang; Nelson, Scott; Lazo, John S.; Tsang, Michael; Hukriede, Neil A.

2009-01-01

Presently, the zebrafish is the only vertebrate model compatible with contemporary paradigms of drug discovery. Zebrafish embryos are amenable to automation necessary for high-throughput chemical screens, and optical transparency makes them potentially suited for image-based screening. However, the lack of tools for automated analysis of complex images presents an obstacle to utilizing the zebrafish as a high-throughput screening model. We have developed an automated system for imaging and analyzing zebrafish embryos in multi-well plates regardless of embryo orientation and without user intervention. Images of fluorescent embryos were acquired on a high-content reader and analyzed using an artificial intelligence-based image analysis method termed Cognition Network Technology (CNT). CNT reliably detected transgenic fluorescent embryos (Tg(fli1:EGFP)y1) arrayed in 96-well plates and quantified intersegmental blood vessel development in embryos treated with small molecule inhibitors of anigiogenesis. The results demonstrate it is feasible to adapt image-based high-content screening methodology to measure complex whole organism phenotypes. PMID:19235725

Using MEDLINE Elemental Similarity to Assist in the Article Screening Process for Systematic Reviews.

PubMed

Ji, Xiaonan; Yen, Po-Yin

2015-08-31

Systematic reviews and their implementation in practice provide high quality evidence for clinical practice but are both time and labor intensive due to the large number of articles. Automatic text classification has proven to be instrumental in identifying relevant articles for systematic reviews. Existing approaches use machine learning model training to generate classification algorithms for the article screening process but have limitations. We applied a network approach to assist in the article screening process for systematic reviews using predetermined article relationships (similarity). The article similarity metric is calculated using the MEDLINE elements title (TI), abstract (AB), medical subject heading (MH), author (AU), and publication type (PT). We used an article network to illustrate the concept of article relationships. Using the concept, each article can be modeled as a node in the network and the relationship between 2 articles is modeled as an edge connecting them. The purpose of our study was to use the article relationship to facilitate an interactive article recommendation process. We used 15 completed systematic reviews produced by the Drug Effectiveness Review Project and demonstrated the use of article networks to assist article recommendation. We evaluated the predictive performance of MEDLINE elements and compared our approach with existing machine learning model training approaches. The performance was measured by work saved over sampling at 95% recall (WSS95) and the F-measure (F1). We also used repeated analysis over variance and Hommel's multiple comparison adjustment to demonstrate statistical evidence. We found that although there is no significant difference across elements (except AU), TI and AB have better predictive capability in general. Collaborative elements bring performance improvement in both F1 and WSS95. With our approach, a simple combination of TI+AB+PT could achieve a WSS95 performance of 37%, which is competitive to traditional machine learning model training approaches (23%-41% WSS95). We demonstrated a new approach to assist in labor intensive systematic reviews. Predictive ability of different elements (both single and composited) was explored. Without using model training approaches, we established a generalizable method that can achieve a competitive performance.

Equity and practice issues in colorectal cancer screening

PubMed Central

Buchman, Sandy; Rozmovits, Linda; Glazier, Richard H.

2016-01-01

Abstract Objective To investigate overall colorectal cancer (CRC) screening rates, patterns in the use of types of CRC screening, and sociodemographic characteristics associated with CRC screening; and to gain insight into physicians’ perceptions about and use of fecal occult blood testing [FOBT] and colonoscopy for patients at average risk of CRC. Design Mixed-methods study using cross-sectional administrative data on patient sociodemographic characteristics and semistructured telephone interviews with physicians. Setting Toronto, Ont. Participants Patients aged 50 to 74 years and physicians in family health teams in the Toronto Central Local Health Integration Network. Main outcome measures Rates of CRC screening by type; sociodemographic characteristics associated with CRC screening; thematic analysis using constant comparative method for semistructured interviews. Main findings Ontario administrative data on CRC screening showed lower overall screening rates among those who were younger, male patients, those who had lower income, and recent immigrants. Colonoscopy rates were especially low among those with lower income and those who were recent immigrants. Semistructured interviews revealed that physician opinions about CRC screening for average-risk patients were divided: one group of physicians accepted the evidence and recommendations for FOBT and the other group of physicians strongly supported colonoscopy for these patients, believing that the FOBT was an inferior screening method. Physicians identified specialist recommendations and patient expectations as factors that influenced their decisions regarding CRC screening type. Conclusion There was considerable variation in CRC screening by sociodemographic characteristics. A key theme that emerged from the interviews was that physicians were divided in their preference for FOBT or colonoscopy; factors that influenced physician preference included the health care system, recommendations by other specialists, and patient characteristics. Providing an informed choice of screening method to patients might result in higher screening rates and fewer disparities. Changes in policy and physician attitudes might be needed in order for this to occur. PMID:27618142

Equity and practice issues in colorectal cancer screening: Mixed-methods study.

PubMed

Buchman, Sandy; Rozmovits, Linda; Glazier, Richard H

2016-04-01

To investigate overall colorectal cancer (CRC) screening rates, patterns in the use of types of CRC screening, and sociodemographic characteristics associated with CRC screening; and to gain insight into physicians' perceptions about and use of fecal occult blood testing [FOBT] and colonoscopy for patients at average risk of CRC. Mixed-methods study using cross-sectional administrative data on patient sociodemographic characteristics and semistructured telephone interviews with physicians. Toronto, Ont. Patients aged 50 to 74 years and physicians in family health teams in the Toronto Central Local Health Integration Network. Rates of CRC screening by type; sociodemographic characteristics associated with CRC screening; thematic analysis using constant comparative method for semistructured interviews. Ontario administrative data on CRC screening showed lower overall screening rates among those who were younger, male patients, those who had lower income, and recent immigrants. Colonoscopy rates were especially low among those with lower income and those who were recent immigrants. Semistructured interviews revealed that physician opinions about CRC screening for average-risk patients were divided: one group of physicians accepted the evidence and recommendations for FOBT and the other group of physicians strongly supported colonoscopy for these patients, believing that the FOBT was an inferior screening method. Physicians identified specialist recommendations and patient expectations as factors that influenced their decisions regarding CRC screening type. There was considerable variation in CRC screening by sociodemographic characteristics. A key theme that emerged from the interviews was that physicians were divided in their preference for FOBT or colonoscopy; factors that influenced physician preference included the health care system, recommendations by other specialists, and patient characteristics. Providing an informed choice of screening method to patients might result in higher screening rates and fewer disparities. Changes in policy and physician attitudes might be needed in order for this to occur. Copyright© the College of Family Physicians of Canada.

Blueprint for antimicrobial hit discovery targeting metabolic networks.

PubMed

Shen, Y; Liu, J; Estiu, G; Isin, B; Ahn, Y-Y; Lee, D-S; Barabási, A-L; Kapatral, V; Wiest, O; Oltvai, Z N

2010-01-19

Advances in genome analysis, network biology, and computational chemistry have the potential to revolutionize drug discovery by combining system-level identification of drug targets with the atomistic modeling of small molecules capable of modulating their activity. To demonstrate the effectiveness of such a discovery pipeline, we deduced common antibiotic targets in Escherichia coli and Staphylococcus aureus by identifying shared tissue-specific or uniformly essential metabolic reactions in their metabolic networks. We then predicted through virtual screening dozens of potential inhibitors for several enzymes of these reactions and showed experimentally that a subset of these inhibited both enzyme activities in vitro and bacterial cell viability. This blueprint is applicable for any sequenced organism with high-quality metabolic reconstruction and suggests a general strategy for strain-specific antiinfective therapy.

Experimental evaluation of the Continuous Risk Profile (CRP) approach to the current Caltrans methodology for high collision concentration location identification

DOT National Transportation Integrated Search

2012-03-31

This report evaluates the performance of Continuous Risk Profile (CRP) compared with the : Sliding Window Method (SWM) and Peak Searching (PS) methods. These three network : screening methods all require the same inputs: traffic collision data and Sa...

Experimental evaluation of the Continuous Risk Profile (CRP) approach to the current Caltrans methodology for high collision concentration location identification.

DOT National Transportation Integrated Search

2012-03-01

This report evaluates the performance of Continuous Risk Profile (CRP) compared with the : Sliding Window Method (SWM) and Peak Searching (PS) methods. These three network : screening methods all require the same inputs: traffic collision data and Sa...

High-resolution genome-wide scan of genes, gene-networks and cellular systems impacting the yeast ionome

USDA-ARS?s Scientific Manuscript database

To balance the demand for uptake of essential elements with their potential toxicity living cells have complex regulatory mechanisms. Here, we describe a genome-wide screen to identify genes that impact the elemental composition (‘ionome’) of yeast Saccharomyces cerevisiae. Using inductively coupled...

Issues in Text Design and Layout for Computer Based Communications.

ERIC Educational Resources Information Center

Andresen, Lee W.

1991-01-01

Discussion of computer-based communications (CBC) focuses on issues involved with screen design and layout for electronic text, based on experiences with electronic messaging, conferencing, and publishing within the Australian Open Learning Information Network (AOLIN). Recommendations for research on design and layout for printed text are also…

Editor's highlight: Evaluation of a Microelectrode Array-based Assay for Neural Network Ontogeny using Training Set Chemicals

EPA Science Inventory

Thousands of compounds in the environment have not been characterized for developmental neurotoxicity (DNT) hazard. To address this issue, methods to screen compounds rapidly for DNT hazard evaluation are necessary and are being developed for key neurodevelopmental processes. In...

Chemical-Gene Interactions from ToxCast Bioactivity Data Expands Universe of Literature Network-Based Associations (SOT)

EPA Science Inventory

Characterizing the effects of chemicals in biological systems is often summarized by chemical-gene interactions, which have sparse coverage in the literature. The ToxCast chemical screening program has produced bioactivity data for nearly 2000 chemicals and over 450 gene targets....

Genetic and Proteomic Interrogation of Lower Confidence Candidate Genes Reveals Signaling Networks in beta-Catenin-Active Cancers | Office of Cancer Genomics

Cancer.gov

Genome-scale expression studies and comprehensive loss-of-function genetic screens have focused almost exclusively on the highest confidence candidate genes. Here, we describe a strategy for characterizing the lower confidence candidates identified by such approaches.

PROPOSED WATER QUALITY SURVEILLANCE NETWORK USING PHYSICAL, CHEMICAL AND BIOLOGICAL EARLY WARNING SYSTEMS (CBEWS)

EPA Science Inventory

The Homeland Protection Act of 2002 specifically calls for the investigation and use of Early Warning Systems (EWS) for water security reasons. The EWS is a screening tool for detecting changes in source water and distribution system water quality. A suite of time-relevant biol...

PROPOSED WATER QUALITY SURVEILLANCE NETWORK USING PHYSICAL, CHEMICAL AND BIOLOGICAL EARLY WARNING SYSTEMS (BEWS)

EPA Science Inventory

The Homeland Protection Act of 2002 specifically calls for the investigation and use of Early Warning Systems (EWS) for water security reasons. The EWS is a screening tool for detecting changes in source water and distribution system water quality. A suite of time-relevant biol...

Methods for identifying high collision concentration locations (HCCL) for potential safety improvements : phase II, Evaluation of alternative methods for identifying HCCL.

DOT National Transportation Integrated Search

2011-01-01

The objective of network screening should ideally be to not only identify sites for safety : investigation but also to prioritize those sites efficiently. Using roadway, intersection, and : collision data from California, this study compared the perf...

Investigating crosstalk between heat tolerance and redox status through suppressor screening of EMS mutagenized Arabidopsis monothioglutaredoxin GRXS17 mutants

USDA-ARS?s Scientific Manuscript database

Global environmental temperature changes threaten innumerable plant species. While various signaling networks regulate plant responses to heat stress (HS), the mechanisms unifying these diverse processes are largely unknown. The thioredoxin (Trx) and glutaredoxin (Grx) systems help control cellular ...

Burst and Principal Components Analyses of MEA Data for 16 Chemicals Describe at Least Three Effects Classes.

EPA Science Inventory

Microelectrode arrays (MEAs) detect drug and chemical induced changes in neuronal network function and have been used for neurotoxicity screening. As a proof-•of-concept, the current study assessed the utility of analytical "fingerprinting" using Principal Components Analysis (P...

Ossification of the posterior longitudinal ligament related genes identification using microarray gene expression profiling and bioinformatics analysis.

PubMed

He, Hailong; Mao, Lingzhou; Xu, Peng; Xi, Yanhai; Xu, Ning; Xue, Mingtao; Yu, Jiangming; Ye, Xiaojian

2014-01-10

Ossification of the posterior longitudinal ligament (OPLL) is a kind of disease with physical barriers and neurological disorders. The objective of this study was to explore the differentially expressed genes (DEGs) in OPLL patient ligament cells and identify the target sites for the prevention and treatment of OPLL in clinic. Gene expression data GSE5464 was downloaded from Gene Expression Omnibus; then DEGs were screened by limma package in R language, and changed functions and pathways of OPLL cells compared to normal cells were identified by DAVID (The Database for Annotation, Visualization and Integrated Discovery); finally, an interaction network of DEGs was constructed by string. A total of 1536 DEGs were screened, with 31 down-regulated and 1505 up-regulated genes. Response to wounding function and Toll-like receptor signaling pathway may involve in the development of OPLL. Genes, such as PDGFB, PRDX2 may involve in OPLL through response to wounding function. Toll-like receptor signaling pathway enriched genes such as TLR1, TLR5, and TLR7 may involve in spine cord injury in OPLL. PIK3R1 was the hub gene in the network of DEGs with the highest degree; INSR was one of the most closely related genes of it. OPLL related genes screened by microarray gene expression profiling and bioinformatics analysis may be helpful for elucidating the mechanism of OPLL. © 2013.

DPubChem: a web tool for QSAR modeling and high-throughput virtual screening.

PubMed

Soufan, Othman; Ba-Alawi, Wail; Magana-Mora, Arturo; Essack, Magbubah; Bajic, Vladimir B

2018-06-14

High-throughput screening (HTS) performs the experimental testing of a large number of chemical compounds aiming to identify those active in the considered assay. Alternatively, faster and cheaper methods of large-scale virtual screening are performed computationally through quantitative structure-activity relationship (QSAR) models. However, the vast amount of available HTS heterogeneous data and the imbalanced ratio of active to inactive compounds in an assay make this a challenging problem. Although different QSAR models have been proposed, they have certain limitations, e.g., high false positive rates, complicated user interface, and limited utilization options. Therefore, we developed DPubChem, a novel web tool for deriving QSAR models that implement the state-of-the-art machine-learning techniques to enhance the precision of the models and enable efficient analyses of experiments from PubChem BioAssay database. DPubChem also has a simple interface that provides various options to users. DPubChem predicted active compounds for 300 datasets with an average geometric mean and F 1 score of 76.68% and 76.53%, respectively. Furthermore, DPubChem builds interaction networks that highlight novel predicted links between chemical compounds and biological assays. Using such a network, DPubChem successfully suggested a novel drug for the Niemann-Pick type C disease. DPubChem is freely available at www.cbrc.kaust.edu.sa/dpubchem .

Cluster randomized trials in comparative effectiveness research: randomizing hospitals to test methods for prevention of healthcare-associated infections.

PubMed

Platt, Richard; Takvorian, Samuel U; Septimus, Edward; Hickok, Jason; Moody, Julia; Perlin, Jonathan; Jernigan, John A; Kleinman, Ken; Huang, Susan S

2010-06-01

The need for evidence about the effectiveness of therapeutics and other medical practices has triggered new interest in methods for comparative effectiveness research. Describe an approach to comparative effectiveness research involving cluster randomized trials in networks of hospitals, health plans, or medical practices with centralized administrative and informatics capabilities. We discuss the example of an ongoing cluster randomized trial to prevent methicillin-resistant Staphylococcus aureus (MRSA) infection in intensive care units (ICUs). The trial randomizes 45 hospitals to: (a) screening cultures of ICU admissions, followed by Contact Precautions if MRSA-positive, (b) screening cultures of ICU admissions followed by decolonization if MRSA-positive, or (c) universal decolonization of ICU admissions without screening. All admissions to adult ICUs. The primary outcome is MRSA-positive clinical cultures occurring >or=2 days following ICU admission. Secondary outcomes include blood and urine infection caused by MRSA (and, separately, all pathogens), as well as the development of resistance to decolonizing agents. Recruitment of hospitals is complete. Data collection will end in Summer 2011. This trial takes advantage of existing personnel, procedures, infrastructure, and information systems in a large integrated hospital network to conduct a low-cost evaluation of prevention strategies under usual practice conditions. This approach is applicable to many comparative effectiveness topics in both inpatient and ambulatory settings.

The COBATEST network: a platform to perform monitoring and evaluation of HIV community-based testing practices in Europe and conduct operational research.

PubMed

Fernàndez-López, L; Reyes-Urueña, J; Agustí, C; Kustec, T; Klavs, I; Casabona, C

2016-01-01

The European project "HIV community-based testing practices in Europe" (HIV-COBATEST) has contributed to the establishment of a network of community-based voluntary counselling and testing services (CBVCTs) that monitors and evaluates HIV testing activity in the communities. The objective of this paper is to describe the data that have been collected during 2014 by the COBATEST network in order to provide an insight into testing activity of CBVCTs in Europe. Members of the CBVCT network share common instruments for data collection and data entry. The network has a common database that allows global data analysis and comparison between different centres. In 2014, 40 CBVCTs of 18 European countries were participating in the network, and, from those, 20 CBVCTs were using the common COBATEST data collection tools. In these 20 CBVCTs, a total of 9266 HIV screening tests were performed on 8554 people, of which 1.58% (135/8554) were reactive and 51.1% (69/135) confirmed positive. Five cases were false positives, and 84.1% (58/69) of the confirmed positive cases were linked to care. Most of the tested individuals were men (70.8%), between 21 and 35 years of age (57.6%) and natives (67.1%). A higher proportion of men who had sex with men (MSM) (38.8%; 3267/8554) were tested compared to heterosexual men (27.7%) and women (23.5%). Rapid blood test was used in 78.5% of the cases and mostly performed in CBVCT offices (88.3%). Among sex workers (SWs), the percentage of reactive screening tests was particularly high (4.0%), especially among male SWs (7.7%) as compared to other risk groups, such as MSM (3.1%). The COBATEST network contributes to the availability of standardized information about the activity and impact of CBVCT centres in Europe. This information and standardized tools can help improve these services and inform decision-makers to better contextualize these interventions within their national HIV-prevention programmes.

Monitoring the Environmental Impact of TiO2 Nanoparticles Using a Plant-Based Sensor Network

PubMed Central

Lenaghan, Scott C.; Li, Yuanyuan; Zhang, Hao; Burris, Jason N.; Stewart, C. Neal; Parker, Lynne E.; Zhang, Mingjun

2016-01-01

The increased manufacturing of nanoparticles for use in cosmetics, foods, and clothing necessitates the need for an effective system to monitor and evaluate the potential environmental impact of these nanoparticles. The goal of this research was to develop a plant-based sensor network for characterizing, monitoring, and understanding the environmental impact of TiO2 nanoparticles. The network consisted of potted Arabidopsis thaliana with a surrounding water supply, which was monitored by cameras attached to a laptop computer running a machine learning algorithm. Using the proposed plant sensor network, we were able to examine the toxicity of TiO2 nanoparticles in two systems: algae and terrestrial plants. Increased terrestrial plant growth was observed upon introduction of the nanoparticles, whereas algal growth decreased significantly. The proposed system can be further automated for high-throughput screening of nanoparticle toxicity in the environment at multiple trophic levels. The proposed plant-based sensor network could be used for more accurate characterization of the environmental impact of nanomaterials. PMID:28458617

Functional wiring of the yeast kinome revealed by global analysis of genetic network motifs

PubMed Central

Sharifpoor, Sara; van Dyk, Dewald; Costanzo, Michael; Baryshnikova, Anastasia; Friesen, Helena; Douglas, Alison C.; Youn, Ji-Young; VanderSluis, Benjamin; Myers, Chad L.; Papp, Balázs; Boone, Charles; Andrews, Brenda J.

2012-01-01

A combinatorial genetic perturbation strategy was applied to interrogate the yeast kinome on a genome-wide scale. We assessed the global effects of gene overexpression or gene deletion to map an integrated genetic interaction network of synthetic dosage lethal (SDL) and loss-of-function genetic interactions (GIs) for 92 kinases, producing a meta-network of 8700 GIs enriched for pathways known to be regulated by cognate kinases. Kinases most sensitive to dosage perturbations had constitutive cell cycle or cell polarity functions under standard growth conditions. Condition-specific screens confirmed that the spectrum of kinase dosage interactions can be expanded substantially in activating conditions. An integrated network composed of systematic SDL, negative and positive loss-of-function GIs, and literature-curated kinase–substrate interactions revealed kinase-dependent regulatory motifs predictive of novel gene-specific phenotypes. Our study provides a valuable resource to unravel novel functional relationships and pathways regulated by kinases and outlines a general strategy for deciphering mutant phenotypes from large-scale GI networks. PMID:22282571

Refining the Patient Navigation Role in a Colorectal Cancer Screening Program: Results From an Intervention Study.

PubMed

Rohan, Elizabeth A; Slotman, Beth; DeGroff, Amy; Morrissey, Kerry Grace; Murillo, Jennifer; Schroy, Paul

2016-11-01

Oncology patient navigators help individuals overcome barriers to increase access to cancer screening, diagnosis, and timely treatment. This study, part of a randomized intervention trial investigating the efficacy of patient navigation in increasing colonoscopy completion, examined navigators' activities to ameliorate barriers to colonoscopy screening in a medically disadvantaged population. This study was conducted from 2012 through 2014 at Boston Medical Center. We analyzed navigator service delivery and survey data collected on 420 participants who were navigated for colonoscopy screening after randomization to this intervention. Key variables under investigation included barriers to colonoscopy, activities navigators undertook to reduce barriers, time navigators spent on each activity and per contact, and patient satisfaction with navigation services. Descriptive analysis assessed how navigators spent their time and examined what aspects of patient navigation were most valued by patients. Navigators spent the most time assessing patient barriers/needs; facilitating appointment scheduling; reminding patients of appointments; educating patients about colorectal cancer, the importance of screening, and the colonoscopy preparation and procedures; and arranging transportation. Navigators spent an average of 44 minutes per patient. Patients valued the navigators, especially for providing emotional/peer support and explaining screening procedures and bowel preparation clearly. Our findings help clarify the role of the navigator in colonoscopy screening within a medically disadvantaged community. These findings may help further refine the navigator role in cancer screening and treatment programs as facilities strive to effectively and efficiently integrate navigation into their services. Copyright © 2016 by the National Comprehensive Cancer Network.

Knowledge and social engagement change in intention to be screened for colorectal cancer.

PubMed

Molina, Yamile; Briant, Katherine J; Sanchez, Janeth I; O'Connell, Mary A; Thompson, Beti

2018-07-01

Innovative technologies have been used to promote colorectal cancer (CRC) screening among the underserved. However, the impact of these innovative technologies on knowledge and social engagement likelihood as they relate to subsequent intention to be screened across different populations has not been fully explored. Using a pre-post-test design with an inflatable walk-through colon, we assessed changes in knowledge and social engagement likelihood across populations and their associations with intention to be screened in two community settings. One was a community setting in Washington State (WA); the other, a college campus in New Mexico (NM). Differential effects on knowledge and social engagement likelihood were examined across demographic groups (race/ethnicity, gender, age, education, insurance status, and geographic region). Finally, we assessed if changes in knowledge and social engagement likelihood were associated with CRC screening intention. NM males had greater gains in CRC knowledge than NM females; in WA, Hispanics, younger, less educated, and uninsured participants had greater gains in knowledge. NM females and younger WA participants were more likely to discuss CRC with their social networks than NM males and older WA participants. In WA, Hispanics and older adults reported greater intention to be screened for CRC. Change in social engagement likelihood, but not knowledge, was associated with intention to be screened. The effectiveness of health promotion technologies on knowledge and social engagement may vary across different demographic characteristics. Further, the importance of social engagement likelihood in interacting with intention to be screened was substantiated.

Childhood ADHD Symptoms: Association with Parental Social Networks and Mental Health Service Use during Adolescence.

PubMed

Bussing, Regina; Meyer, Johanna; Zima, Bonnie T; Mason, Dana M; Gary, Faye A; Garvan, Cynthia Wilson

2015-09-22

This study examines the associations of childhood attention-deficit/hyperactivity disorder (ADHD) risk status with subsequent parental social network characteristics and caregiver strain in adolescence; and examines predictors of adolescent mental health service use. Baseline ADHD screening identified children at high risk (n = 207) and low risk (n = 167) for ADHD. At eight-year follow-up, parents reported their social network characteristics, caregiver strain, adolescents' psychopathology and mental health service utilization, whereas adolescents self-reported their emotional status and ADHD stigma perceptions. Analyses were conducted using ANOVAs and nested logistic regression modeling. Parents of youth with childhood ADHD reported support networks consisting of fewer spouses but more healthcare professionals, and lower levels of support than control parents. Caregiver strain increased with adolescent age and psychopathology. Increased parental network support, youth ADHD symptoms, and caregiver strain, but lower youth stigma perceptions were independently associated with increased service use. Raising children with ADHD appears to significantly impact parental social network experiences. Reduced spousal support and overall lower network support levels may contribute to high caregiver strain commonly reported among parents of ADHD youth. Parental social network experiences influence adolescent ADHD service use. With advances in social networking technology, further research is needed to elucidate ways to enhance caregiver support during ADHD care.

Constrained synaptic connectivity in functional mammalian neuronal networks grown on patterned surfaces.

PubMed

Wyart, Claire; Ybert, Christophe; Bourdieu, Laurent; Herr, Catherine; Prinz, Christelle; Chatenay, Didier

2002-06-30

The use of ordered neuronal networks in vitro is a promising approach to study the development and the activity of small neuronal assemblies. However, in previous attempts, sufficient growth control and physiological maturation of neurons could not be achieved. Here we describe an original protocol in which polylysine patterns confine the adhesion of cellular bodies to prescribed spots and the neuritic growth to thin lines. Hippocampal neurons in these networks are maintained healthy in serum free medium up to 5 weeks in vitro. Electrophysiology and immunochemistry show that neurons exhibit mature excitatory and inhibitory synapses and calcium imaging reveals spontaneous activity of neurons in isolated networks. We demonstrate that neurons in these geometrical networks form functional synapses preferentially to their first neighbors. We have, therefore, established a simple and robust protocol to constrain both the location of neuronal cell bodies and their pattern of connectivity. Moreover, the long term maintenance of the geometry and the physiology of the networks raises the possibility of new applications for systematic screening of pharmacological agents and for electronic to neuron devices.

High-throughput screening for thermoelectric sulphides by using crystal structure features as descriptors

NASA Astrophysics Data System (ADS)

Zhang, Ruizhi; Du, Baoli; Chen, Kan; Reece, Mike; Materials Research Insititute Team

With the increasing computational power and reliable databases, high-throughput screening is playing a more and more important role in the search of new thermoelectric materials. Rather than the well established density functional theory (DFT) calculation based methods, we propose an alternative approach to screen for new TE materials: using crystal structural features as 'descriptors'. We show that a non-distorted transition metal sulphide polyhedral network can be a good descriptor for high power factor according to crystal filed theory. By using Cu/S containing compounds as an example, 1600+ Cu/S containing entries in the Inorganic Crystal Structure Database (ICSD) were screened, and of those 84 phases are identified as promising thermoelectric materials. The screening results are validated by both electronic structure calculations and experimental results from the literature. We also fabricated some new compounds to test our screening results. Another advantage of using crystal structure features as descriptors is that we can easily establish structural relationships between the identified phases. Based on this, two material design approaches are discussed: 1) High-pressure synthesis of metastable phase; 2) In-situ 2-phase composites with coherent interface. This work was supported by a Marie Curie International Incoming Fellowship of the European Community Human Potential Program.

Development of an infection screening system for entry inspection at airport quarantine stations using ear temperature, heart and respiration rates.

PubMed

Sun, Guanghao; Abe, Nobujiro; Sugiyama, Youhei; Nguyen, Quang Vinh; Nozaki, Kohei; Nakayama, Yosuke; Takei, Osamu; Hakozaki, Yukiya; Abe, Shigeto; Matsui, Takemi

2013-01-01

After the outbreak of severe acute respiratory syndrome (SARS) in 2003, many international airport quarantine stations conducted fever-based screening to identify infected passengers using infrared thermography for preventing global pandemics. Due to environmental factors affecting measurement of facial skin temperature with thermography, some previous studies revealed the limits of authenticity in detecting infectious symptoms. In order to implement more strict entry screening in the epidemic seasons of emerging infectious diseases, we developed an infection screening system for airport quarantines using multi-parameter vital signs. This system can automatically detect infected individuals within several tens of seconds by a neural-network-based discriminant function using measured vital signs, i.e., heart rate obtained by a reflective photo sensor, respiration rate determined by a 10-GHz non-contact respiration radar, and the ear temperature monitored by a thermography. In this paper, to reduce the environmental effects on thermography measurement, we adopted the ear temperature as a new screening indicator instead of facial skin. We tested the system on 13 influenza patients and 33 normal subjects. The sensitivity of the infection screening system in detecting influenza were 92.3%, which was higher than the sensitivity reported in our previous paper (88.0%) with average facial skin temperature.

Impact of a Generalizable Reminder System on Colorectal Cancer Screening in Diverse Primary Care Practices

PubMed Central

Nease, Donald E.; Ruffin, Mack T.; Klinkman, Michael S.; Jimbo, Masahito; Braun, Thomas M.; Underwood, Jennifer M.

2015-01-01

Background Computerized reminder systems (CRS) show promise for increasing preventive services such as colorectal cancer (CRC) screening. However, prior research has not evaluated a generalizable CRS across diverse, community primary care practices. We evaluated whether a generalizable CRS, ClinfoTracker, could improve screening rates for CRC in diverse primary care practices. Methods The study was a prospective trial to evaluate ClinfoTracker using historical control data in 12 Great Lakes Research In Practice Network community-based, primary care practices distributed from Southeast to Upper Peninsula Michigan. Our outcome measures were pre- and post-study practice-level CRC screening rates among patients seen during the 9-month study period. Ability to maintain the CRS was measured by days of reminder printing. Field notes were used to examine each practice’s cohesion and technology capabilities. Results All but one practice increased their CRC screening rates, ranging from 3.3% to 16.8% improvement. t tests adjusted for within practice correlation showed improvement in screening rates across all 12 practices, from 41.7% to 50.9%, P = 0.002. Technology capabilities impacted printing days (74% for high technology vs. 45% for low technology practices, P = 0.01), and cohesion demonstrated an impact trend for screening (15.3% rate change for high cohesion vs. 7.9% for low cohesion practices). Conclusions Implementing a generalizable CRS in diverse primary care practices yielded significant improvements in CRC screening rates. Technology capabilities are important in maintaining the system, but practice cohesion may have a greater influence on screening rates. This work has important implications for practices implementing reminder systems. PMID:18725836

A framework to start the debate on neonatal screening policies in the EU: an Expert Opinion Document.

PubMed

Cornel, Martina C; Rigter, Tessel; Weinreich, Stephanie S; Burgard, Peter; Hoffmann, Georg F; Lindner, Martin; Gerard Loeber, J; Rupp, Kathrin; Taruscio, Domenica; Vittozzi, Luciano

2014-01-01

The European Union (EU) Council Recommendation on rare diseases urged the member states to implement national and EU collaborative actions to improve the health care of rare disease patients. Following this recommendation, the European Commission launched a tender on newborn screening (NBS) to report on current practices of laboratory testing, form a network of experts and provide guidance on how to further implement NBS screening in a responsible way, the latter of which was provided in an Expert Opinion document. After consultation of experts from EU member states, (potential) candidate member states and European Free Trade Association countries, in a consensus meeting in June 2011, 70 expert opinions were finalized. They included the need to develop case definitions for all disorders screened for to facilitate assessment and international outcome studies. Decision whether a screening program should be performed can be based on screening criteria updated from the traditional Wilson and Jungner (1968) criteria, relating to disease, treatment, test and cost. The interest of the child should be central in the assessment of pros and cons. A European NBS body should assess evidence on (new) screening candidate disorders. For rare conditions, best level evidence should be used. The health system should ensure treatment to cases diagnosed by screening, controlled and revised by follow-up outcome studies. Screening methodology should aim to avoid unintended findings, such as mild forms and carrier status information, as much as possible. Activities to improve NBS in Europe, such as training and scientific evaluation, could benefit from collaboration at EU level and beyond.

Screening and prevention of neonatal glucose 6-phosphate dehydrogenase deficiency in Guangzhou, China.

PubMed

Jiang, J; Li, B; Cao, W; Jiang, X; Jia, X; Chen, Q; Wu, J

2014-06-09

We aimed to summarize the results of screening protocol and prevention of neonatal glucose 6-phosphate dehydrogenase (G6PD) deficiency during a 22-year-long period to provide a basis of reference for the screening of this disease. About 1,705,569 newborn subjects in Guangzhou City were screened for this deficiency. Specimens were collected according to the conventional method of specimen acquisition for "newborn dried bloodspot screening", preserved, and inspected. The specimens were studied with fluorescent spot test and quantitative fluorescence assay. Diagnosis was performed using the modified NBTG6PD/6PGD ratio method. Bloodspot filter paper specimens were sent to the laboratory within 24 h via EMS Express, and the G6PD test was performed on the same day. The G6PD deficiency-positive rate was 4.2% in the samples screened using the fluorescent spot test, while it was 5% in case of the quantitative fluorescence assay. Neonatal screening for G6PD deficiency for 11,437 cases (6117 boys and 5320 girls) showed positive results in 481 cases. About 420 cases (318 boys and 102 girls) of G6PD deficiency were confirmed with the modified Duchenne NBT ratio method. The total detection rate was 3.7:5.2% for boys and 1.9% for girls. Quantitative fluorescence assay improved the sensitivity and detection rate. Accelerating the speed of sample delivery by using Internet network systems and ensuring online availability of screening results can aid the screening and diagnosis of this deficiency within 1 week of birth.

A prediction model for cognitive performance in health ageing using diffusion tensor imaging with graph theory.

PubMed

Yun, Ruijuan; Lin, Chung-Chih; Wu, Shuicai; Huang, Chu-Chung; Lin, Ching-Po; Chao, Yi-Ping

2013-01-01

In this study, we employed diffusion tensor imaging (DTI) to construct brain structural network and then derive the connection matrices from 96 healthy elderly subjects. The correlation analysis between these topological properties of network based on graph theory and the Cognitive Abilities Screening Instrument (CASI) index were processed to extract the significant network characteristics. These characteristics were then integrated to estimate the models by various machine-learning algorithms to predict user's cognitive performance. From the results, linear regression model and Gaussian processes model showed presented better abilities with lower mean absolute errors of 5.8120 and 6.25 to predict the cognitive performance respectively. Moreover, these extracted topological properties of brain structural network derived from DTI also could be regarded as the bio-signatures for further evaluation of brain degeneration in healthy aged and early diagnosis of mild cognitive impairment (MCI).

Increasing Resilience to Traumatic Stress: Understanding the Protective Role of Well-Being.

PubMed

Tory Toole, J; Rice, Mark A; Cargill, Jordan; Craddock, Travis J A; Nierenberg, Barry; Klimas, Nancy G; Fletcher, Mary Ann; Morris, Mariana; Zysman, Joel; Broderick, Gordon

2018-01-01

The brain maintains homeostasis in part through a network of feedback and feed-forward mechanisms, where neurochemicals and immune markers act as mediators. Using a previously constructed model of biobehavioral feedback, we found that in addition to healthy equilibrium another stable regulatory program supported chronic depression and anxiety. Exploring mechanisms that might underlie the contributions of subjective well-being to improved therapeutic outcomes in depression, we iteratively screened 288 candidate feedback patterns linking well-being to molecular signaling networks for those that maintained the original homeostatic regimes. Simulating stressful trigger events on each candidate network while maintaining high levels of subjective well-being isolated a specific feedback network where well-being was promoted by dopamine and acetylcholine, and itself promoted norepinephrine while inhibiting cortisol expression. This biobehavioral feedback mechanism was especially effective in reproducing well-being's clinically documented ability to promote resilience and protect against onset of depression and anxiety.

TH-A-12A-01: Medical Physicist's Role in Digital Information Security: Threats, Vulnerabilities and Best Practices

DOE Office of Scientific and Technical Information (OSTI.GOV)

McDonald, K; Curran, B

I. Information Security Background (Speaker = Kevin McDonald) Evolution of Medical Devices Living and Working in a Hostile Environment Attack Motivations Attack Vectors Simple Safety Strategies Medical Device Security in the News Medical Devices and Vendors Summary II. Keeping Radiation Oncology IT Systems Secure (Speaker = Bruce Curran) Hardware Security Double-lock Requirements “Foreign” computer systems Portable Device Encryption Patient Data Storage System Requirements Network Configuration Isolating Critical Devices Isolating Clinical Networks Remote Access Considerations Software Applications / Configuration Passwords / Screen Savers Restricted Services / access Software Configuration Restriction Use of DNS to restrict accesse. Patches / Upgrades Awareness Intrusionmore » Prevention Intrusion Detection Threat Risk Analysis Conclusion Learning Objectives: Understanding how Hospital IT Requirements affect Radiation Oncology IT Systems. Illustrating sample practices for hardware, network, and software security. Discussing implementation of good IT security practices in radiation oncology. Understand overall risk and threats scenario in a networked environment.« less

Social networks and health-related quality of life: a population based study among older adults.

PubMed

Gallegos-Carrillo, Katia; Mudgal, Jyoti; Sánchez-García, Sergio; Wagner, Fernando A; Gallo, Joseph J; Salmerón, Jorge; García-Peña, Carmen

2009-01-01

To examine the relationship between components of social networks and health-related quality of life (HRQL) in older adults with and without depressive symptoms. Comparative cross-sectional study with data from the cohort study 'Integral Study of Depression', carried out in Mexico City during 2004. The sample was selected through a multi-stage probability design. HRQL was measured with the SF-36. Geriatric Depression Scale (GDS) and the Short Anxiety Screening Test (SAST) determined depressive symptoms and anxiety. T-test and multiple linear regressions were conducted. Older adults with depressive symptoms had the lowest scores in all HRQL scales. A larger network of close relatives and friends was associated with better HRQL on several scales. Living alone did not significantly affect HRQL level, in either the study or comparison group. A positive association between some components of social networks and good HRQL exists even in older adults with depressive symptoms.

Examining the Distribution, Modularity, and Community Structure in Article Networks for Systematic Reviews.

PubMed

Ji, Xiaonan; Machiraju, Raghu; Ritter, Alan; Yen, Po-Yin

2015-01-01

Systematic reviews (SRs) provide high quality evidence for clinical practice, but the article screening process is time and labor intensive. As SRs aim to identify relevant articles with a specific scope, we propose that a pre-defined article relationship, using similarity metrics, could accelerate this process. In this study, we established the article relationship using MEDLINE element similarities and visualized the article network with the Force Atlas layout. We also analyzed the article networks with graph diameter, closeness centrality, and module classes. The results revealed the distribution of articles and found that included articles tended to aggregate together in some module classes, providing further evidence of the existence of strong relationships among included articles. This approach can be utilized to facilitate the articles selection process through early identification of these dominant module classes. We are optimistic that the use of article network visualization can help better SR work prioritization.

Examining the Distribution, Modularity, and Community Structure in Article Networks for Systematic Reviews

PubMed Central

Ji, Xiaonan; Machiraju, Raghu; Ritter, Alan; Yen, Po-Yin

2015-01-01

Systematic reviews (SRs) provide high quality evidence for clinical practice, but the article screening process is time and labor intensive. As SRs aim to identify relevant articles with a specific scope, we propose that a pre-defined article relationship, using similarity metrics, could accelerate this process. In this study, we established the article relationship using MEDLINE element similarities and visualized the article network with the Force Atlas layout. We also analyzed the article networks with graph diameter, closeness centrality, and module classes. The results revealed the distribution of articles and found that included articles tended to aggregate together in some module classes, providing further evidence of the existence of strong relationships among included articles. This approach can be utilized to facilitate the articles selection process through early identification of these dominant module classes. We are optimistic that the use of article network visualization can help better SR work prioritization. PMID:26958292

The influence of ionic strength on DNA diffusion in gel networks

NASA Astrophysics Data System (ADS)

Fu, Yuanxi; Jee, Ah-Young; Kim, Hyeong-Ju; Granick, Steve

Cations are known to reduce the rigidity of the DNA molecules by screening the negative charge along the sugar phosphate backbone. This was established by optical tweezer pulling experiment of immobilized DNA strands. However, little is known regarding the influence of ions on the motion of DNA molecules as they thread through network meshes. We imaged in real time the Brownian diffusion of fluorescent labeled lambda-DNA in an agarose gel network in the presence of salt with monovalent or multivalent cations. Each movie was analyzed using home-written program to yield a trajectory of center of the mass and the accompanying history of the shape fluctuations. One preliminary finding is that ionic strength has a profound influence on the slope of the trace of mean square displacement (MSD) versus time. The influence of ionic strength on DNA diffusion in gel networks.

Development of a Deep Learning Algorithm for Automatic Diagnosis of Diabetic Retinopathy.

PubMed

Raju, Manoj; Pagidimarri, Venkatesh; Barreto, Ryan; Kadam, Amrit; Kasivajjala, Vamsichandra; Aswath, Arun

2017-01-01

This paper mainly focuses on the deep learning application in classifying the stage of diabetic retinopathy and detecting the laterality of the eye using funduscopic images. Diabetic retinopathy is a chronic, progressive, sight-threatening disease of the retinal blood vessels. Ophthalmologists diagnose diabetic retinopathy through early funduscopic screening. Normally, there is a time delay in reporting and intervention, apart from the financial cost and risk of blindness associated with it. Using a convolutional neural network based approach for automatic diagnosis of diabetic retinopathy, we trained the prediction network on the publicly available Kaggle dataset. Approximately 35,000 images were used to train the network, which observed a sensitivity of 80.28% and a specificity of 92.29% on the validation dataset of ~53,000 images. Using 8,810 images, the network was trained for detecting the laterality of the eye and observed an accuracy of 93.28% on the validation set of 8,816 images.

Prediction of enzymatic pathways by integrative pathway mapping

PubMed Central

Wichelecki, Daniel J; San Francisco, Brian; Zhao, Suwen; Rodionov, Dmitry A; Vetting, Matthew W; Al-Obaidi, Nawar F; Lin, Henry; O'Meara, Matthew J; Scott, David A; Morris, John H; Russel, Daniel; Almo, Steven C; Osterman, Andrei L

2018-01-01

The functions of most proteins are yet to be determined. The function of an enzyme is often defined by its interacting partners, including its substrate and product, and its role in larger metabolic networks. Here, we describe a computational method that predicts the functions of orphan enzymes by organizing them into a linear metabolic pathway. Given candidate enzyme and metabolite pathway members, this aim is achieved by finding those pathways that satisfy structural and network restraints implied by varied input information, including that from virtual screening, chemoinformatics, genomic context analysis, and ligand -binding experiments. We demonstrate this integrative pathway mapping method by predicting the L-gulonate catabolic pathway in Haemophilus influenzae Rd KW20. The prediction was subsequently validated experimentally by enzymology, crystallography, and metabolomics. Integrative pathway mapping by satisfaction of structural and network restraints is extensible to molecular networks in general and thus formally bridges the gap between structural biology and systems biology. PMID:29377793

Lessons from monogenic causes of growth hormone deficiency.

PubMed

Brue, Thierry; Saveanu, Alexandru; Jullien, Nicolas; Fauquier, Teddy; Castinetti, Frédéric; Enjalbert, Alain; Barlier, Anne; Reynaud, Rachel

2017-06-01

Through the multicentric international GENHYPOPIT network, 10 transcription factor genes involved in pituitary development have been screened in more than 1200 patients with constitutional hypopituitarism over the past two decades. The present report summarizes the main lessons learned from this phenotype-based genetic screening: (1) genetically determined hypopituitarism does not necessarily present during childhood; (2) constitutional hypopituitarism may be characterized by a pure endocrine phenotype or by various combinations of endocrine deficits and visceral malformations; (3) syndromic hypopituitarism may also be observed in patients with POU1F1 or PROP1 mutations; (4) in cases of idiopathic hypopituitarism, extensive genetic screening identifies gene alterations in a minority of patients; (5) functional studies are imperfect in determining the involvement of an allelic variant in a specific pituitary phenotype. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Estimating the influenza vaccine effectiveness in elderly on a yearly basis using the Spanish influenza surveillance network--pilot case-control studies using different control groups, 2008-2009 season, Spain.

PubMed

Savulescu, Camelia; Valenciano, Marta; de Mateo, Salvador; Larrauri, Amparo

2010-04-01

We conducted a case-control and screening method studies to estimate influenza vaccine effectiveness (IVE) in the age group >or=65 years, based on the Spanish Influenza Sentinel Surveillance System (SISSS). Cases (influenza laboratory-confirmed) were compared to influenza-negative ILI patients (test-negative) and patients without ILI since the beginning of the season (non-ILI). For the screening method, cases' vaccination coverage was compared to the vaccination coverage of the GPs' catchment population. The results suggested a protective effect of the vaccine against laboratory-confirmed influenza in elderly in 2008-2009. The screening method and the test-negative control designs enable estimating IVE using exclusively SISSS data. (c) 2010 Elsevier Ltd. All rights reserved.

Prevalence of sickle cell disease among Grenadian newborns.

PubMed

Antoine, Magdalene; Lee, Ketty; Donald, Tyhiesia; Belfon, Yonni; Drigo, Ali; Polson, Sharon; Martin, Francis; Mitchell, George; Etienne-Julan, Maryse; Hardy-Dessources, Marie-Dominique

2018-03-01

Objective To establish the birth prevalence of sickle cell disease in Grenada, with a view to assess the requirement for a population-based neonatal screening programme. Methods A two-year pilot neonatal screening programme, involving the Ministry of Health of Grenada, the Sickle Cell Association of Grenada, and the diagnostic laboratory of hemoglobinopathies of the University Hospital of Guadeloupe, was implemented in 2014-2015 under the auspices of the Caribbean Network of Researchers on Sickle Cell Disease and Thalassemia. Results Analysis of 1914 samples processed identified the following abnormal phenotypes: 10 FS, 2 FSC, 183 FAS, 63 FAC. These data indicate β s and β c allele frequencies of 0.054 and 0.018, respectively. Conclusion Neonatal screening conducted in the framework of this Caribbean cooperation can allow rapid detection and earlier management of affected children.

Screening of Critical Genes and MicroRNAs in Blood Samples of Patients with Ruptured Intracranial Aneurysms by Bioinformatic Analysis of Gene Expression Data.

PubMed

Bo, Lijuan; Wei, Bo; Wang, Zhanfeng; Kong, Daliang; Gao, Zheng; Miao, Zhuang

2017-09-20

BACKGROUND This study aimed to identify more potential genes and miRNAs associated with the pathogenesis of intracranial aneurysms (IAs). MATERIAL AND METHODS The dataset of GSE36791 (accession number) was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were screened for in the blood samples from patients with ruptured IAs and controls, followed by functional and pathway enrichment analyses. In addition, gene co-expression network was constructed and significant modules were extracted from the network by WGCNA R package. Screening for miRNAs that could regulate DEGs in the modules was performed and an analysis of regulatory relationships was conducted. RESULTS A total of 304 DEGs (167 up-regulated and 137 down-regulated genes) were screened for in blood samples from patients with ruptured IAs compared with those from controls. Functional enrichment analysis showed that the up-regulated genes were mainly associated with immune response and the down-regulated DEGs were mainly concerned with the structure of ribosome and translation. Besides, six functional modules were significantly identified, including four modules enriched by up-regulated genes and two modules enriched by down-regulated genes. Thereinto, the blue, yellow, and turquoise modules of up-regulated genes were all linked with immune response. Additionally, 16 miRNAs were predicted to regulate DEGs in the three modules associated with immune response, such as hsa-miR-1304, hsa-miR-33b, hsa-miR-125b, and hsa-miR-125a-5p. CONCLUSIONS Several genes and miRNAs (such as miR-1304, miR-33b, IRS2 and KCNJ2) may take part in the pathogenesis of IAs.

Reduced Expiratory Flow Rate among Heavy Smokers Increases Lung Cancer Risk. Results from the National Lung Screening Trial-American College of Radiology Imaging Network Cohort.

PubMed

Hopkins, Raewyn J; Duan, Fenghai; Chiles, Caroline; Greco, Erin M; Gamble, Greg D; Aberle, Denise; Young, Robert P

2017-03-01

Although epidemiological studies consistently show that chronic obstructive pulmonary disease is associated with an increased risk of lung cancer, debate exists as to whether there is a linear relationship between the severity of airflow limitation and lung cancer risk. We examined this in a large, prospective study of older heavy smokers from the American College of Radiology Imaging Network subcohort of the National Lung Screening Trial (ACRIN). Airflow limitation was defined by prebronchodilator spirometry subgrouped according to Global Initiative for Chronic Obstructive Lung Disease (GOLD) grades 1-4. In the National Lung Screening Trial-ACRIN cohort of 18,473 screening participants, 6,436 had airflow limitation (35%) and 12,037 (65%) had no airflow limitation. From these groups, 758 lung cancer cases were prospectively identified. Participants with airflow limitation were stratified according to GOLD groups 1 (n = 1,607), 2 (n = 3,528), 3 (n = 1,083), and 4 (n = 211). Lung cancer incidence at study end (mean follow-up, 6.4 yr) was compared between the GOLD groups and those with no airflow limitation (referent group). Compared with those with no airflow limitation, where lung cancer incidence was 3.78/1,000 person years, incidence rates increased in a simple linear relationship: GOLD 1 (6.27/1,000 person yr); GOLD 2 (7.86/1,000 person yr); GOLD 3 (10.71/1,000 person yr); and GOLD 4 (13.25/1,000 person yr). All relationships were significant versus the reference group at a P value of 0.0001 or less. In a large prospective study of high-risk cigarette smokers, we report a strong linear relationship between increasing severity of airflow limitation and risk of lung cancer.

Standardised pre-competitive screening of athletes in some European and African countries: the SMILE study.

PubMed

Assanelli, Deodato; Deodato, Assanelli; Ermolao, Andrea; Andrea, Ermolao; Carre, François; François, Carré; Deligiannis, Asterios; Asterios, Deligiannis; Mellwig, Klaus; Mellwig, Klaus; Klaus, Mellwig; Tahmi, Mohamed; Mohamed, Tahmi; Cesana, Bruno Mario; Mario, Cesana Bruno; Levaggi, Rosella; Rosella, Levaggi; Aliverti, Paola; Paola, Aliverti; Sharma, Sanjay; Sanjay, Sharma

2014-06-01

Most of the available data on the cardiovascular screening of athletes come from Italy, with fewer records being available outside of Italy and for non-Caucasian populations. The goals of the SMILE project (Sport Medicine Intervention to save Lives through ECG) are to evaluate the usefulness of 12-lead ECGs for the detection of cardiac diseases in athletes from three European countries and one African country and to estimate how many second-level examinations are needed subsequent to the initial screening in order to classify athletes with abnormal characteristics. A digital network consisting of Sport Centres and second and third opinion centres was set up in Greece, Germany, France and Algeria. Standard digital data input was carried out through the application of 12-lead ECGs, Bethesda questionnaires and physical examinations. Two hundred ninety-three of the 6,634 consecutive athletes required further evaluation, mostly (88.4 %) as a consequence of abnormal ECGs. After careful evaluation, 237 were determined to be healthy or apparently healthy, while 56 athletes were found to have cardiac disorders and were thus disqualified from active participation in sports. There was a large difference in the prevalence of diseases detected in Europe as compared with Algeria (0.23 and 4.01 %, respectively). Our data confirmed the noteworthy value of 12-lead resting ECGs as compared with other first-level evaluations, especially in athletes with asymptomatic cardiac diseases. Its value seems to have been even higher in Algeria than in the European countries. The establishment of a digital network of Sport Centres for second/third opinions in conjunction with the use of standard digital data input seems to be a valuable means for increasing the effectiveness of screening.

Do HMO market level factors lead to racial/ethnic disparities in colorectal cancer screening? A comparison between high-risk Asian and Pacific Islander Americans and high-risk whites.

PubMed

Ponce, Ninez A; Huh, Soonim; Bastani, Roshan

2005-11-01

Few studies have explored health care market structure and colorectal cancer (CRC) screening test use, and little is known whether market factors contribute to racial/ethnic screening disparities. We investigated whether HMO market level factors, controlling for individual covariates, differentially impact Asian American and Pacific Islander (AAPI) subjects' access to CRC screening compared with white subjects. We used random intercept hierarchical models to predict CRC test use. Individual-level survey data was linked to market data by metropolitan statistical areas from InterStudy. Insured first-degree relatives, ages 40-80, of a random sample of colorectal cancer cases identified from the California Cancer Registry: 515 white subjects and 396 AAPI subjects residing in 36 metropolitan statistical areas (MSAs). Dependent variables were receipt of (1) annual fecal occult blood test only; (2) sigmoidoscopy in the past 5 years; (3) colonoscopy in the past 10 years; and (4) any of these tests over the recommended time interval. Market characteristics were HMO penetration, HMO competition, and proportion of staff/group/network HMOs. Market characteristics were as important as individual-level characteristics for AAPI but not for white subjects. Among AAPI subjects, a 10% increase in the percent of group/staff/network model HMO was associated with a reduction in colonoscopy use (28.9% to 20.5%) and in receipt of any of the CRC tests (53.2% to 45.4%). The prevailing organizational structure of a health care market confers a penalty on access to CRC test use among high-risk AAPI subjects but not among high-risk white subjects. Identifying the differential effect of market structure on race/ethnicity can potentially reduce the cancer burden among disadvantaged racial groups.

Understanding network concepts in modules

PubMed Central

2007-01-01

Background Network concepts are increasingly used in biology and genetics. For example, the clustering coefficient has been used to understand network architecture; the connectivity (also known as degree) has been used to screen for cancer targets; and the topological overlap matrix has been used to define modules and to annotate genes. Dozens of potentially useful network concepts are known from graph theory. Results Here we study network concepts in special types of networks, which we refer to as approximately factorizable networks. In these networks, the pairwise connection strength (adjacency) between 2 network nodes can be factored into node specific contributions, named node 'conformity'. The node conformity turns out to be highly related to the connectivity. To provide a formalism for relating network concepts to each other, we define three types of network concepts: fundamental-, conformity-based-, and approximate conformity-based concepts. Fundamental concepts include the standard definitions of connectivity, density, centralization, heterogeneity, clustering coefficient, and topological overlap. The approximate conformity-based analogs of fundamental network concepts have several theoretical advantages. First, they allow one to derive simple relationships between seemingly disparate networks concepts. For example, we derive simple relationships between the clustering coefficient, the heterogeneity, the density, the centralization, and the topological overlap. The second advantage of approximate conformity-based network concepts is that they allow one to show that fundamental network concepts can be approximated by simple functions of the connectivity in module networks. Conclusion Using protein-protein interaction, gene co-expression, and simulated data, we show that a) many networks comprised of module nodes are approximately factorizable and b) in these types of networks, simple relationships exist between seemingly disparate network concepts. Our results are implemented in freely available R software code, which can be downloaded from the following webpage: http://www.genetics.ucla.edu/labs/horvath/ModuleConformity/ModuleNetworks PMID:17547772

Smoking cessation results in a clinical lung cancer screening program.

PubMed

Borondy Kitts, Andrea K; McKee, Andrea B; Regis, Shawn M; Wald, Christoph; Flacke, Sebastian; McKee, Brady J

2016-07-01

Lung cancer screening may provide a "teachable moment" for promoting smoking cessation. This study assessed smoking cessation and relapse rates among individuals undergoing follow-up low-dose chest computed tomography (CT) in a clinical CT lung screening program and assessed the influence of initial screening results on smoking behavior. Self-reported smoking status for individuals enrolled in a clinical CT lung screening program undergoing a follow-up CT lung screening exam between 1st February, 2014 and 31st March, 2015 was retrospectively reviewed and compared to self-reported smoking status using a standardized questionnaire at program entry. Point prevalence smoking cessation and relapse rates were calculated across the entire population and compared with exam results. All individuals undergoing screening fulfilled the National Comprehensive Cancer Network Clinical Practice Guidelines in Oncology: Lung Cancer Screening v1.2012(®) high-risk criteria and had an order for CT lung screening. A total of 1,483 individuals underwent a follow-up CT lung screening exam during the study interval. Smoking status at time of follow-up exam was available for 1,461/1,483 (98.5%). A total of 46% (678/1,461) were active smokers at program entry. The overall point prevalence smoking cessation and relapse rates were 20.8% and 9.3%, respectively. Prior positive screening exam results were not predictive of smoking cessation (OR 1.092; 95% CI, 0.715-1.693) but were predictive of reduced relapse among former smokers who had stopped smoking for 2 years or less (OR 0.330; 95% CI, 0.143-0.710). Duration of program enrollment was predictive of smoking cessation (OR 0.647; 95% CI, 0.477-0.877). Smoking cessation and relapse rates in a clinical CT lung screening program rates are more favorable than those observed in the general population. Duration of participation in the screening program correlated with increased smoking cessation rates. A positive exam result correlated with reduced relapse rates among smokers recently quit smoking.

Controversies about cervical cancer screening: A qualitative study of Roma women's (non)participation in cervical cancer screening in Romania.

PubMed

Andreassen, Trude; Weiderpass, Elisabete; Nicula, Florian; Suteu, Ofelia; Itu, Andreea; Bumbu, Minodora; Tincu, Aida; Ursin, Giske; Moen, Kåre

2017-06-01

Romania has Europe's highest incidence and mortality of cervical cancer. While a free national cervical cancer-screening programme has been in operation since 2012, participation in the programme is low, particularly in minority populations. The aim of this study was to explore Roma women's (non)participation in the programme from women's own perspectives and those of healthcare providers and policy makers. We carried out fieldwork for a period of 125 days in 2015/16 involving 144 study participants in Cluj and Bucharest counties. Fieldwork entailed participant observation, qualitative interviewing and focus group discussions. A striking finding was that screening providers and Roma women had highly different takes on the national screening programme. We identified four fundamental questions about which there was considerable disagreement between them: whether a free national screening programme existed in the first place, whether Roma women were meant to be included in the programme if it did, whether Roma women wanted to take part in screening, and to what degree screening participation would really benefit women's health. On the background of insights from actor-network theory, the article discusses to what degree the programme could be said to speak to the interest of its intended Roma public, and considers the controversies in light of the literature on patient centred care and user involvement in health care. The paper contributes to the understanding of the health and health-related circumstances of the largest minority in Europe. It also problematizes the use of the concept of "barriers" in research into participation in cancer screening, and exemplifies how user involvement can potentially help transform and improve screening programmes. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Predicting clinical outcome of neuroblastoma patients using an integrative network-based approach.

PubMed

Tranchevent, Léon-Charles; Nazarov, Petr V; Kaoma, Tony; Schmartz, Georges P; Muller, Arnaud; Kim, Sang-Yoon; Rajapakse, Jagath C; Azuaje, Francisco

2018-06-07

One of the main current challenges in computational biology is to make sense of the huge amounts of multidimensional experimental data that are being produced. For instance, large cohorts of patients are often screened using different high-throughput technologies, effectively producing multiple patient-specific molecular profiles for hundreds or thousands of patients. We propose and implement a network-based method that integrates such patient omics data into Patient Similarity Networks. Topological features derived from these networks were then used to predict relevant clinical features. As part of the 2017 CAMDA challenge, we have successfully applied this strategy to a neuroblastoma dataset, consisting of genomic and transcriptomic data. In particular, we observe that models built on our network-based approach perform at least as well as state of the art models. We furthermore explore the effectiveness of various topological features and observe, for instance, that redundant centrality metrics can be combined to build more powerful models. We demonstrate that the networks inferred from omics data contain clinically relevant information and that patient clinical outcomes can be predicted using only network topological data. This article was reviewed by Yang-Yu Liu, Tomislav Smuc and Isabel Nepomuceno.

SIR model on a dynamical network and the endemic state of an infectious disease

NASA Astrophysics Data System (ADS)

Dottori, M.; Fabricius, G.

2015-09-01

In this work we performed a numerical study of an epidemic model that mimics the endemic state of whooping cough in the pre-vaccine era. We considered a stochastic SIR model on dynamical networks that involve local and global contacts among individuals and analysed the influence of the network properties on the characterization of the quasi-stationary state. We computed probability density functions (PDF) for infected fraction of individuals and found that they are well fitted by gamma functions, excepted the tails of the distributions that are q-exponentials. We also computed the fluctuation power spectra of infective time series for different networks. We found that network effects can be partially absorbed by rescaling the rate of infective contacts of the model. An explicit relation between the effective transmission rate of the disease and the correlation of susceptible individuals with their infective nearest neighbours was obtained. This relation quantifies the known screening of infective individuals observed in these networks. We finally discuss the goodness and limitations of the SIR model with homogeneous mixing and parameters taken from epidemiological data to describe the dynamic behaviour observed in the networks studied.

Ebola 2014: Setting up a port health screening programme at an international train station.

PubMed

Cleary, Vivien; Wynne-Evans, Edward; Freed, James; Fleet, Katie; Thorn, Simone; Turbitt, Deborah

2017-12-01

An outbreak of Ebola virus disease (EVD) began in Guinea in December 2013 and was declared a Public Health Emergency of International Concern by the World Health Organization in August 2014. In October, the UK government tasked Public Health England (PHE) to set up EVD screening at key ports. The key aim of port-of-entry screening was to identify passengers coming from areas with high risk of EVD, and give them advice to raise their awareness of symptoms and what actions to take. Direct flights from Sierra Leone, Guinea or Liberia had all been cancelled, so intelligence on passenger numbers and routes was used to identify the most commonly used routes from the affected countries into the UK. One of these was St Pancras International train station. Screening had never previously been implemented at a UK train station so had to be set up from scratch. Key to the success of this was excellent multi-agency working between PHE, the UK Border Force, Eurostar, Network Rail and the Cabinet Office. This paper gives an overview of the activation of EVD screening at St Pancras International and the subsequent decommissioning.

Development and application of a DNA microarray-based yeast two-hybrid system

PubMed Central

Suter, Bernhard; Fontaine, Jean-Fred; Yildirimman, Reha; Raskó, Tamás; Schaefer, Martin H.; Rasche, Axel; Porras, Pablo; Vázquez-Álvarez, Blanca M.; Russ, Jenny; Rau, Kirstin; Foulle, Raphaele; Zenkner, Martina; Saar, Kathrin; Herwig, Ralf; Andrade-Navarro, Miguel A.; Wanker, Erich E.

2013-01-01

The yeast two-hybrid (Y2H) system is the most widely applied methodology for systematic protein–protein interaction (PPI) screening and the generation of comprehensive interaction networks. We developed a novel Y2H interaction screening procedure using DNA microarrays for high-throughput quantitative PPI detection. Applying a global pooling and selection scheme to a large collection of human open reading frames, proof-of-principle Y2H interaction screens were performed for the human neurodegenerative disease proteins huntingtin and ataxin-1. Using systematic controls for unspecific Y2H results and quantitative benchmarking, we identified and scored a large number of known and novel partner proteins for both huntingtin and ataxin-1. Moreover, we show that this parallelized screening procedure and the global inspection of Y2H interaction data are uniquely suited to define specific PPI patterns and their alteration by disease-causing mutations in huntingtin and ataxin-1. This approach takes advantage of the specificity and flexibility of DNA microarrays and of the existence of solid-related statistical methods for the analysis of DNA microarray data, and allows a quantitative approach toward interaction screens in human and in model organisms. PMID:23275563

Large-scale screening of transcription factor–promoter interactions in spruce reveals a transcriptional network involved in vascular development

PubMed Central

Lachance, Denis; Giguère, Isabelle; Séguin, Armand

2014-01-01

This research aimed to investigate the role of diverse transcription factors (TFs) and to delineate gene regulatory networks directly in conifers at a relatively high-throughput level. The approach integrated sequence analyses, transcript profiling, and development of a conifer-specific activation assay. Transcript accumulation profiles of 102 TFs and potential target genes were clustered to identify groups of coordinately expressed genes. Several different patterns of transcript accumulation were observed by profiling in nine different organs and tissues: 27 genes were preferential to secondary xylem both in stems and roots, and other genes were preferential to phelloderm and periderm or were more ubiquitous. A robust system has been established as a screening approach to define which TFs have the ability to regulate a given promoter in planta. Trans-activation or repression effects were observed in 30% of TF–candidate gene promoter combinations. As a proof of concept, phylogenetic analysis and expression and trans-activation data were used to demonstrate that two spruce NAC-domain proteins most likely play key roles in secondary vascular growth as observed in other plant species. This study tested many TFs from diverse families in a conifer tree species, which broadens the knowledge of promoter–TF interactions in wood development and enables comparisons of gene regulatory networks found in angiosperms and gymnosperms. PMID:24713992

Elementary screening of lymph node metastatic-related genes in gastric cancer based on the co-expression network of messenger RNA, microRNA and long non-coding RNA.

PubMed

Song, Zhonghua; Zhao, Wenhua; Cao, Danfeng; Zhang, Jinqing; Chen, Shouhua

2018-01-01

Gastric cancer (GC) is the fifth most common cancer and the third leading cause of cancer-related deaths worldwide. The high mortality might be attributed to delay in detection and is closely related to lymph node metastasis. Therefore, it is of great importance to explore the mechanism of lymph node metastasis and find strategies to block GC metastasis. Messenger RNA (mRNA), microRNA (miRNA) and long non-coding RNA (lncRNA) expression data and clinical data were downloaded from The Cancer Genome Atlas (TCGA) database. A total of 908 differentially expressed factors with variance >0.5 including 542 genes, 42 miRNA, and 324 lncRNA were screened using significant analysis microarray algorithm, and interaction networks were constructed using these differentially expressed factors. Furthermore, we conducted functional modules analysis in the network, and found that yellow and turquoise modules could separate samples efficiently. The groups classified in the yellow and turquoise modules had a significant difference in survival time, which was verified in another independent GC mRNA dataset (GSE62254). The results suggested that differentially expressed factors in the yellow and turquoise modules may participate in lymph node metastasis of GC and could be applied as potential biomarkers or therapeutic targets for GC.

Drug synergy screen and network modeling in dedifferentiated liposarcoma identifies CDK4 and IGF1R as synergistic drug targets.

PubMed

Miller, Martin L; Molinelli, Evan J; Nair, Jayasree S; Sheikh, Tahir; Samy, Rita; Jing, Xiaohong; He, Qin; Korkut, Anil; Crago, Aimee M; Singer, Samuel; Schwartz, Gary K; Sander, Chris

2013-09-24

Dedifferentiated liposarcoma (DDLS) is a rare but aggressive cancer with high recurrence and low response rates to targeted therapies. Increasing treatment efficacy may require combinations of targeted agents that counteract the effects of multiple abnormalities. To identify a possible multicomponent therapy, we performed a combinatorial drug screen in a DDLS-derived cell line and identified cyclin-dependent kinase 4 (CDK4) and insulin-like growth factor 1 receptor (IGF1R) as synergistic drug targets. We measured the phosphorylation of multiple proteins and cell viability in response to systematic drug combinations and derived computational models of the signaling network. These models predict that the observed synergy in reducing cell viability with CDK4 and IGF1R inhibitors depends on the activity of the AKT pathway. Experiments confirmed that combined inhibition of CDK4 and IGF1R cooperatively suppresses the activation of proteins within the AKT pathway. Consistent with these findings, synergistic reductions in cell viability were also found when combining CDK4 inhibition with inhibition of either AKT or epidermal growth factor receptor (EGFR), another receptor similar to IGF1R that activates AKT. Thus, network models derived from context-specific proteomic measurements of systematically perturbed cancer cells may reveal cancer-specific signaling mechanisms and aid in the design of effective combination therapies.

Drug Synergy Screen and Network Modeling in Dedifferentiated Liposarcoma Identifies CDK4 and IGF1R as Synergistic Drug Targets

PubMed Central

Miller, Martin L.; Molinelli, Evan J.; Nair, Jayasree S.; Sheikh, Tahir; Samy, Rita; Jing, Xiaohong; He, Qin; Korkut, Anil; Crago, Aimee M.; Singer, Samuel; Schwartz, Gary K.; Sander, Chris

2014-01-01

Dedifferentiated liposarcoma (DDLS) is a rare but aggressive cancer with high recurrence and low response rates to targeted therapies. Increasing treatment efficacy may require combinations of targeted agents that counteract the effects of multiple abnormalities. To identify a possible multicomponent therapy, we performed a combinatorial drug screen in a DDLS-derived cell line and identified cyclin-dependent kinase 4 (CDK4) and insulin-like growth factor 1 receptor (IGF1R) as synergistic drug targets. We measured the phosphorylation of multiple proteins and cell viability in response to systematic drug combinations and derived computational models of the signaling network. These models predict that the observed synergy in reducing cell viability with CDK4 and IGF1R inhibitors depend on activity of the AKT pathway. Experiments confirmed that combined inhibition of CDK4 and IGF1R cooperatively suppresses the activation of proteins within the AKT pathway. Consistent with these findings, synergistic reductions in cell viability were also found when combining CDK4 inhibition with inhibition of either AKT or epidermal growth factor receptor (EGFR), another receptor similar to IGF1R that activates AKT. Thus, network models derived from context-specific proteomic measurements of systematically perturbed cancer cells may reveal cancer-specific signaling mechanisms and aid in the design of effective combination therapies. PMID:24065146

Proteomic Screening and Lasso Regression Reveal Differential Signaling in Insulin and Insulin-like Growth Factor I (IGF1) Pathways *

PubMed Central

Erdem, Cemal; Nagle, Alison M.; Casa, Angelo J.; Litzenburger, Beate C.; Wang, Yu-fen; Taylor, D. Lansing; Lee, Adrian V.; Lezon, Timothy R.

2016-01-01

Insulin and insulin-like growth factor I (IGF1) influence cancer risk and progression through poorly understood mechanisms. To better understand the roles of insulin and IGF1 signaling in breast cancer, we combined proteomic screening with computational network inference to uncover differences in IGF1 and insulin induced signaling. Using reverse phase protein array, we measured the levels of 134 proteins in 21 breast cancer cell lines stimulated with IGF1 or insulin for up to 48 h. We then constructed directed protein expression networks using three separate methods: (i) lasso regression, (ii) conventional matrix inversion, and (iii) entropy maximization. These networks, named here as the time translation models, were analyzed and the inferred interactions were ranked by differential magnitude to identify pathway differences. The two top candidates, chosen for experimental validation, were shown to regulate IGF1/insulin induced phosphorylation events. First, acetyl-CoA carboxylase (ACC) knock-down was shown to increase the level of mitogen-activated protein kinase (MAPK) phosphorylation. Second, stable knock-down of E-Cadherin increased the phospho-Akt protein levels. Both of the knock-down perturbations incurred phosphorylation responses stronger in IGF1 stimulated cells compared with insulin. Overall, the time-translation modeling coupled to wet-lab experiments has proven to be powerful in inferring differential interactions downstream of IGF1 and insulin signaling, in vitro. PMID:27364358

Elementary screening of lymph node metastatic-related genes in gastric cancer based on the co-expression network of messenger RNA, microRNA and long non-coding RNA

PubMed Central

Song, Zhonghua; Zhao, Wenhua; Cao, Danfeng; Zhang, Jinqing; Chen, Shouhua

2018-01-01

Gastric cancer (GC) is the fifth most common cancer and the third leading cause of cancer-related deaths worldwide. The high mortality might be attributed to delay in detection and is closely related to lymph node metastasis. Therefore, it is of great importance to explore the mechanism of lymph node metastasis and find strategies to block GC metastasis. Messenger RNA (mRNA), microRNA (miRNA) and long non-coding RNA (lncRNA) expression data and clinical data were downloaded from The Cancer Genome Atlas (TCGA) database. A total of 908 differentially expressed factors with variance >0.5 including 542 genes, 42 miRNA, and 324 lncRNA were screened using significant analysis microarray algorithm, and interaction networks were constructed using these differentially expressed factors. Furthermore, we conducted functional modules analysis in the network, and found that yellow and turquoise modules could separate samples efficiently. The groups classified in the yellow and turquoise modules had a significant difference in survival time, which was verified in another independent GC mRNA dataset (GSE62254). The results suggested that differentially expressed factors in the yellow and turquoise modules may participate in lymph node metastasis of GC and could be applied as potential biomarkers or therapeutic targets for GC. PMID:29489999

Network characteristics of people who inject drugs within a new HIV epidemic following austerity in Athens, Greece

PubMed Central

Tsang, Michelle A.; Schneider, John A.; Sypsa, Vana; Schumm, Phil; Nikolopoulos, Georgios K.; Paraskevis, Dimitrios; Friedman, Samuel R.; Malliori, Meni; Hatzakis, Angelos

2015-01-01

Background Greece experienced an unprecedented increase in HIV cases among drug injectors in 2011 following economic crisis. Network level factors are increasingly understood to drive HIV transmission in emerging epidemics. Methods We examined the relationship between networks, risk behaviors and HIV serostatus among 1,404 people who inject drugs in Athens, Greece. We generated networks using the chain-referral structure within a large HIV screening program. Network proportions, the proportion of a respondent’s network with a given characteristic, were calculated. Multiple logistic regression were used to assess the relationship between network proportions and individual HIV seroprevalance, injection frequency and unprotected sex. Results 1030 networks were generated. Respondent HIV seroprevalence was associated with greater proportions of network members who were HIV infected (i.e. those with ≥50% of network members HIV-positive vs. those with no network members HIV-positive) [AOR, 3.11; 95% CI, 2.10 to 4.62], divided drugs [AOR, 1.60; 95% CI, 1.10 to 2.35] or injected frequently [AOR, 1.50; 95% CI, 1.02 to 2.21]. Homelessness was the only sociodemographic characteristic associated with a risk outcome measure – high-frequency injecting [AOR, 1.41; 95% CI, 1.03 to 1.93]. These associations were weaker for more distal second and third degree networks and not present when examined within random networks. Conclusion Networks are an independently important contributor to the HIV outbreak in Athens Greece. Network associations were strongest for the immediate network, with residual associations for distal networks. Homelessness was associated with high frequency injecting. Prevention programs should consider including network-level interventions to prevent future emerging epidemics. PMID:26115439

Identification, sequencing and expression of an integral membrane protein of the trans-Golgi network (TGN38).

PubMed Central

Luzio, J P; Brake, B; Banting, G; Howell, K E; Braghetta, P; Stanley, K K

1990-01-01

Organelle-specific integral membrane proteins were identified by a novel strategy which gives rise to monospecific antibodies to these proteins as well as to the cDNA clones encoding them. A cDNA expression library was screened with a polyclonal antiserum raised against Triton X-114-extracted organelle proteins and clones were then grouped using antibodies affinity-purified on individual fusion proteins. The identification, molecular cloning and sequencing are described of a type 1 membrane protein (TGN38) which is located specifically in the trans-Golgi network. Images Fig. 1. Fig. 3. PMID:2204342

Latino recruitment to cancer prevention/screening trials in the Southwest: setting a research agenda.

PubMed

Larkey, Linda K; Ogden, Sheryl L; Tenorio, Sally; Ewell, Teresa

2008-02-01

Examples of cancer prevention and screening trials in the Southwest are reviewed as a platform for highlighting gaps in research on Latino recruitment. Three trials are described, using "message/source/channel" categories as a framework. Each trial engaged community members to facilitate recruitment and developed tailored strategies to meet challenges emerging after recruitment began. Although we affirm that culturally relevant messages, community member referral networks, and adjustment to community realities seem important to Latino recruitment, current anecdotal and research findings do not allow evidence-based recommendations to be made. We suggest a research agenda to further illuminate critical factors for successful Latino recruitment.

NCCN Guidelines as a Model of Extended Criteria for Lung Cancer Screening.

PubMed

McKee, Brady J; Regis, Shawn; Borondy-Kitts, Andrea K; Hashim, Jeffrey A; French, Robert J; Wald, Christoph; McKee, Andrea B

2018-04-01

Background: This review assessed the performance of patients in NCCN high-risk group 2 in a clinical CT lung screening (CTLS) program. Methods: We retrospectively reviewed screening results for all patients from our institution undergoing clinical CTLS from January 2012 through December 2016, with follow-up through June 2017. To qualify for screening, patients had to meet the NCCN Guidelines high-risk criteria for CTLS, have a physician order for screening, be asymptomatic, be lung cancer-free for 5 years, and have no known metastatic disease. We compared demographics and screening performance of NCCN high-risk groups 1 and 2 across >4 rounds of screening. Screening metrics assessed included rates of positive and suspicious examinations, significant incidental and infectious/inflammatory findings, false negatives, and cancer detection. We also compared cancer stage and histology detected in each NCCN high-risk group. Results: A total of 2,927 individuals underwent baseline screening, of which 698 (24%) were in NCCN group 2. On average, group 2 patients were younger (60.6 vs 63.1 years), smoked less (38.8 vs 50.8 pack-years), had quit longer (18.1 vs 6.3 years), and were more often former smokers (61.4% vs 44.2%). Positive and suspicious examination rates, false negatives, and rates of infectious/inflammatory findings were equivalent in groups 1 and 2 across all rounds of screening. An increased rate of cancer detection was observed in group 2 during the second annual (T2) screening round (2.7% vs 0.5%; P =.005), with no difference in the other screening rounds: baseline (T0; 2% vs 2.3%; P =.61), first annual (T1; 1.2% vs 1.7%; P =.41), and third annual and beyond (≥T3; 1.2% vs 1.1%; P =1.00). Conclusions: CTLS appears to be equally effective in both NCCN high-risk groups. Copyright © 2018 by the National Comprehensive Cancer Network.

Consolidating newborn screening efforts in the Asia Pacific region : Networking and shared education.

PubMed

Padilla, Carmencita David; Therrell, Bradford L

2012-01-01

Many of the countries in the Asia Pacific Region, particularly those with depressed and developing economies, are just initiating newborn screening programs for selected metabolic and other congenital disorders. The cultural, geographic, language, and economic differences that exist throughout the region add to the challenges of developing sustainable newborn screening systems. There are currently more developing programs than developed programs within the region. Newborn screening activities in the Asia Pacific Region are particularly important since births there account for approximately half of the world's births. To date, there have been two workshops to facilitate formation of the Asia Pacific Newborn Screening Collaboratives. The 1st Workshop on Consolidating Newborn Screening Efforts in the Asia Pacific Region occurred in Cebu, Philippines, on March 30-April 1, 2008, as a satellite meeting to the 7th Asia Pacific Conference on Human Genetics. The second workshop was held on June 4-5, 2010, in Manila, Philippines. Workshop participants included key policy-makers, service providers, researchers, and consumer advocates from 11 countries with 50% or less newborn screening coverage. Expert lectures included experiences in the United States and the Netherlands, international quality assurance activities and ongoing and potential research activities. Additional meeting support was provided by the U.S. National Institutes of Health, the Centers for Disease Control and Prevention, the U.S. National Newborn Screening and Genetics Resource Center, the International Society for Neonatal Screening, and the March of Dimes. As part of both meeting activities, participants shared individual experiences in program implementation with formal updates of screening information for each country. This report reviews the activities and country reports from two Workshops on Consolidating Newborn Screening Efforts in the Asia Pacific Region with emphasis on the second workshop. It also updates the literature on screening activities and implementation/expansion challenges in the participating countries.

Breast cancer screening in the Czech Republic: time trends in performance indicators during the first seven years of the organised programme

PubMed Central

2011-01-01

Background The Czech Breast Cancer Screening Programme (CBCSP) was initiated in September 2002 by establishing a network of accredited centres. The aim of this article is to describe progress in the programme quality over time after the inception of the organised programme. Methods The CBCSP is monitored using an information system consisting of three principal components: 1) the national cancer registry, 2) a screening registry collecting data on all screening examinations, further assessments and final diagnoses at accredited programme centres, and 3) administrative databases of healthcare payers. Key performance indicators from the European Guidelines have been adopted for continuous monitoring. Results Breast cancer incidence in the Czech Republic has steadily been increasing, however with a growing proportion of less advanced stages. The mortality rate has recently stabilised. The screening registry includes 2,083,285 records on screening episodes between 2002 and 2008. In 2007-2008, 51% of eligible women aged 45-69 were screened. In 2008, the detection rates were 6.1 and 3.7 per 1,000 women in initial and subsequent screening respectively. Corresponding recall rates are 3.9% and 2.2%, however, it is necessary to pay attention to further assessment performed during the screening visits. Benign to malignant open biopsy ratio was 0.1. Of invasive cases detected in screening, 35.6% was less than 10 mm in diameter. Values of early performance indicators, as measured by both crude and standardized estimates, are generally improving and fulfil desirable targets set by European Guidelines. Conclusions Mammography screening in the Czech Republic underwent successful transformation from opportunistic prevention to an organised programme. Values of early indicators confirm continuous improvement in different aspects of process quality. Further stimulation of participation through invitation system is necessary to exploit the full potential of screening mammography at the population level. PMID:21554747

Delineating the Construct Network of the Personnel Reaction Blank: Associations with Externalizing Tendencies and Normal Personality

ERIC Educational Resources Information Center

Blonigen, Daniel M.; Patrick, Christopher J.; Gasperi, Marianna; Steffen, Benjamin; Ones, Deniz S.; Arvey, Richard D.; de Oliveira Baumgartl, Viviane; do Nascimento, Elizabeth

2011-01-01

Integrity testing has long been utilized in personnel selection to screen for tendencies toward counterproductive workplace behaviors. The construct of externalizing from the psychopathology literature represents a coherent spectrum marked by disinhibitory traits and behaviors. The present study drew on a sample of male and female undergraduates…

Screening for contaminants of emerging concern in Northern Colorado Plateau Network waters: 2015 surface-water data

USGS Publications Warehouse

Weissinger, R; Battaglin, William A.; Bradley, Paul M.

2016-01-01

Patterns of detections at other sampling locations will be explored in future reports. This is an interim report. Limited sampling will continue in 2016 at selected sites in coordination with the USGS. A final report is expected upon completion of the USGS project in 2017.

Application of the ToxMiner Database: Network Analysis Linking the ToxCast Chemicals to Known Disease-Gene Associations

EPA Science Inventory

The US EPA ToxCast program is using in vitro HTS (High-Throughput Screening) methods to profile and model bioactivity of environmental chemicals. The main goals of the ToxCast program are to generate predictive signatures of toxicity, and ultimately provide rapid and cost-effecti...

In vitro screening of silver nanoparticles and ionic silver using neural networks yields differential effects on spontaneous activity and pharmacological responses.

EPA Science Inventory

Silver nanoparticles (AgNPs) are used in a wide range of consumer and medical products because of their antimicrobial and antifungal properties. Numerous studies have demonstrated that silver can translocate to distal organs following exposure to AgNPs. Therefore, it is essential...

Sparse Measurement Systems: Applications, Analysis, Algorithms and Design

ERIC Educational Resources Information Center

Narayanaswamy, Balakrishnan

2011-01-01

This thesis deals with "large-scale" detection problems that arise in many real world applications such as sensor networks, mapping with mobile robots and group testing for biological screening and drug discovery. These are problems where the values of a large number of inputs need to be inferred from noisy observations and where the…

Search Path Evaluation Incorporating Object Placement Structure

DTIC Science & Technology

2007-12-20

the probability of the set complement of this event: Pr(Ed) = 1 - kP PC (83) (k,t)I iIG Equation (83) provides the probability that if there is an...Networks," to appear in IEEE Transactions on Aerospace and Electronic Systems. 3. B. G. Koopman, Search and Screening: General Principles and Historical

FloorPlan. Courseware Evaluation for Vocational and Technical Education.

ERIC Educational Resources Information Center

Rosenfeld, Vila M.; And Others

This courseware evaluation rates the "FloorPlan" program developed by the Learning Seed. (The program--not included in this document--allows room design and arrangement to be performed on the computer screen.) The courseware was rated by a team of home economists participating in a network for the dissemination of courseware reviews.…

A Biologically Informed Framework for the Analysis of the PPAR Signaling Pathway using a Bayesian Network

EPA Science Inventory

The US EPA’s ToxCastTM program seeks to combine advances in high-throughput screening technology with methodologies from statistics and computer science to develop high-throughput decision support tools for assessing chemical hazard and risk. To develop new methods of analysis of...

Words on the Screen: Broadening Analyses of Interactions among Fanfiction Writers and Reviewers

ERIC Educational Resources Information Center

Magnifico, Alecia Marie; Curwood, Jen Scott; Lammers, Jayne C.

2015-01-01

Young fanfiction writers use the Internet to build networks of reading, writing and editing--literacy practices that are highly valued in schools, universities and workplaces. While prior research shows that online spaces frame multiple kinds of participation as legitimate, much of this work focuses on the extensive contributions of exceptional…

ToxCast Assay Network (TCAN) Viewer: A Visualization Tool for High-throughput Assay Chemical Data (SOT)

EPA Science Inventory

USEPA’s ToxCast program has generated high-throughput bioactivity screening (HTS) data on thousands of chemicals. The ToxCast program has described and annotated the HTS assay battery with respect to assay design and target information (e.g., gene target). Recent stakeholder and ...

Strategies for Media Literacy: Audiovisual Skills and the Citizenship in Andalusia

ERIC Educational Resources Information Center

Aguaded-Gómez, Ignacio; Pérez-Rodríguez, M. Amor

2012-01-01

Media consumption is an undeniable fact in present-day society. The hours that members of all social segments spend in front of a screen take up a large part of their leisure time worldwide. Audiovisual communication becomes especially important within the context of today's digital society (society-network), where information and communication…

Biologically driven neural platform invoking parallel electrophoretic separation and urinary metabolite screening.

PubMed

Page, Tessa; Nguyen, Huong Thi Huynh; Hilts, Lindsey; Ramos, Lorena; Hanrahan, Grady

2012-06-01

This work reveals a computational framework for parallel electrophoretic separation of complex biological macromolecules and model urinary metabolites. More specifically, the implementation of a particle swarm optimization (PSO) algorithm on a neural network platform for multiparameter optimization of multiplexed 24-capillary electrophoresis technology with UV detection is highlighted. Two experimental systems were examined: (1) separation of purified rabbit metallothioneins and (2) separation of model toluene urinary metabolites and selected organic acids. Results proved superior to the use of neural networks employing standard back propagation when examining training error, fitting response, and predictive abilities. Simulation runs were obtained as a result of metaheuristic examination of the global search space with experimental responses in good agreement with predicted values. Full separation of selected analytes was realized after employing optimal model conditions. This framework provides guidance for the application of metaheuristic computational tools to aid in future studies involving parallel chemical separation and screening. Adaptable pseudo-code is provided to enable users of varied software packages and modeling framework to implement the PSO algorithm for their desired use.

An Allele of Sequoia Dominantly Enhances a Trio Mutant Phenotype to Influence Drosophila Larval Behavior

PubMed Central

Liebl, Eric C.

2013-01-01

The transition of Drosophila third instar larvae from feeding, photo-phobic foragers to non-feeding, photo-neutral wanderers is a classic behavioral switch that precedes pupariation. The neuronal network responsible for this behavior has recently begun to be defined. Previous genetic analyses have identified signaling components for food and light sensory inputs and neuropeptide hormonal outputs as being critical for the forager to wanderer transition. Trio is a Rho-Guanine Nucleotide Exchange Factor integrated into a variety of signaling networks including those governing axon pathfinding in early development. Sequoia is a pan-neuronally expressed zinc-finger transcription factor that governs dendrite and axon outgrowth. Using pre-pupal lethality as an endpoint, we have screened for dominant second-site enhancers of a weakly lethal trio mutant background. In these screens, an allele of sequoia has been identified. While these mutants have no obvious disruption of embryonic central nervous system architecture and survive to third instar larvae similar to controls, they retain forager behavior and thus fail to pupariate at high frequency. PMID:24376789

An allele of sequoia dominantly enhances a trio mutant phenotype to influence Drosophila larval behavior.

PubMed

Dean, Kathryn E; Fields, April; Geer, Marcus J; King, Eric C; Lynch, Brian T; Manohar, Rohan R; McCall, Julianne R; Palozola, Katherine C; Zhang, Yan; Liebl, Eric C

2013-01-01

The transition of Drosophila third instar larvae from feeding, photo-phobic foragers to non-feeding, photo-neutral wanderers is a classic behavioral switch that precedes pupariation. The neuronal network responsible for this behavior has recently begun to be defined. Previous genetic analyses have identified signaling components for food and light sensory inputs and neuropeptide hormonal outputs as being critical for the forager to wanderer transition. Trio is a Rho-Guanine Nucleotide Exchange Factor integrated into a variety of signaling networks including those governing axon pathfinding in early development. Sequoia is a pan-neuronally expressed zinc-finger transcription factor that governs dendrite and axon outgrowth. Using pre-pupal lethality as an endpoint, we have screened for dominant second-site enhancers of a weakly lethal trio mutant background. In these screens, an allele of sequoia has been identified. While these mutants have no obvious disruption of embryonic central nervous system architecture and survive to third instar larvae similar to controls, they retain forager behavior and thus fail to pupariate at high frequency.

Integrated analysis of miRNA and mRNA expression data identifies multiple miRNAs regulatory networks for the tumorigenesis of colorectal cancer.

PubMed

Xu, Peng; Wang, Junhua; Sun, Bo; Xiao, Zhongdang

2018-06-15

Investigating the potential biological function of differential changed genes through integrating multiple omics data including miRNA and mRNA expression profiles, is always hot topic. However, how to evaluate the repression effect on target genes integrating miRNA and mRNA expression profiles are not fully solved. In this study, we provide an analyzing method by integrating both miRNAs and mRNAs expression data simultaneously. Difference analysis was adopted based on the repression score, then significantly repressed mRNAs were screened out by DEGseq. Pathway analysis for the significantly repressed mRNAs shows that multiple pathways such as MAPK signaling pathway, TGF-beta signaling pathway and so on, may correlated to the colorectal cancer(CRC). Focusing on the MAPK signaling pathway, a miRNA-mRNA network that centering the cell fate genes was constructed. Finally, the miRNA-mRNAs that potentially important in the CRC carcinogenesis were screened out and scored by impact index. Copyright © 2018 Elsevier B.V. All rights reserved.

Bacterial interactomes: Interacting protein partners share similar function and are validated in independent assays more frequently than previously reported.

DOE PAGES

Shatsky, Maxim; Allen, Simon; Gold, Barbara; ...

2016-05-01

Numerous affinity purification – mass-spectrometry (AP-MS) and yeast two hybrid (Y2H) screens have each defined thousands of pairwise protein-protein interactions (PPIs), most between functionally unrelated proteins. The accuracy of these networks, however, is under debate. Here we present an AP-MS survey of the bacterium Desulfovibrio vulgaris together with a critical reanalysis of nine published bacterial Y2H and AP-MS screens. We have identified 459 high confidence PPIs from D. vulgaris and 391 from Escherichia coli. Compared to the nine published interactomes, our two networks are smaller; are much less highly connected; have significantly lower false discovery rates; and are much moremore » enriched in protein pairs that are encoded in the same operon, have similar functions, and are reproducibly detected in other physical interaction assays. Lastly, our work establishes more stringent benchmarks for the properties of protein interactomes and suggests that bona fide PPIs much more frequently involve protein partners that are annotated with similar functions or that can be validated in independent assays than earlier studies suggested.« less

Mass detection in digital breast tomosynthesis data using convolutional neural networks and multiple instance learning.

PubMed

Yousefi, Mina; Krzyżak, Adam; Suen, Ching Y

2018-05-01

Digital breast tomosynthesis (DBT) was developed in the field of breast cancer screening as a new tomographic technique to minimize the limitations of conventional digital mammography breast screening methods. A computer-aided detection (CAD) framework for mass detection in DBT has been developed and is described in this paper. The proposed framework operates on a set of two-dimensional (2D) slices. With plane-to-plane analysis on corresponding 2D slices from each DBT, it automatically learns complex patterns of 2D slices through a deep convolutional neural network (DCNN). It then applies multiple instance learning (MIL) with a randomized trees approach to classify DBT images based on extracted information from 2D slices. This CAD framework was developed and evaluated using 5040 2D image slices derived from 87 DBT volumes. The empirical results demonstrate that this proposed CAD framework achieves much better performance than CAD systems that use hand-crafted features and deep cardinality-restricted Bolzmann machines to detect masses in DBTs. Copyright © 2018 Elsevier Ltd. All rights reserved.

Sonification of network traffic flow for monitoring and situational awareness

PubMed Central

2018-01-01

Maintaining situational awareness of what is happening within a computer network is challenging, not only because the behaviour happens within machines, but also because data traffic speeds and volumes are beyond human ability to process. Visualisation techniques are widely used to present information about network traffic dynamics. Although they provide operators with an overall view and specific information about particular traffic or attacks on the network, they often still fail to represent the events in an understandable way. Also, because they require visual attention they are not well suited to continuous monitoring scenarios in which network administrators must carry out other tasks. Here we present SoNSTAR (Sonification of Networks for SiTuational AwaReness), a real-time sonification system for monitoring computer networks to support network administrators’ situational awareness. SoNSTAR provides an auditory representation of all the TCP/IP traffic within a network based on the different traffic flows between between network hosts. A user study showed that SoNSTAR raises situational awareness levels by enabling operators to understand network behaviour and with the benefit of lower workload demands (as measured by the NASA TLX method) than visual techniques. SoNSTAR identifies network traffic features by inspecting the status flags of TCP/IP packet headers. Combinations of these features define particular traffic events which are mapped to recorded sounds to generate a soundscape that represents the real-time status of the network traffic environment. The sequence, timing, and loudness of the different sounds allow the network to be monitored and anomalous behaviour to be detected without the need to continuously watch a monitor screen. PMID:29672543

Sonification of network traffic flow for monitoring and situational awareness.

PubMed

Debashi, Mohamed; Vickers, Paul

2018-01-01

Maintaining situational awareness of what is happening within a computer network is challenging, not only because the behaviour happens within machines, but also because data traffic speeds and volumes are beyond human ability to process. Visualisation techniques are widely used to present information about network traffic dynamics. Although they provide operators with an overall view and specific information about particular traffic or attacks on the network, they often still fail to represent the events in an understandable way. Also, because they require visual attention they are not well suited to continuous monitoring scenarios in which network administrators must carry out other tasks. Here we present SoNSTAR (Sonification of Networks for SiTuational AwaReness), a real-time sonification system for monitoring computer networks to support network administrators' situational awareness. SoNSTAR provides an auditory representation of all the TCP/IP traffic within a network based on the different traffic flows between between network hosts. A user study showed that SoNSTAR raises situational awareness levels by enabling operators to understand network behaviour and with the benefit of lower workload demands (as measured by the NASA TLX method) than visual techniques. SoNSTAR identifies network traffic features by inspecting the status flags of TCP/IP packet headers. Combinations of these features define particular traffic events which are mapped to recorded sounds to generate a soundscape that represents the real-time status of the network traffic environment. The sequence, timing, and loudness of the different sounds allow the network to be monitored and anomalous behaviour to be detected without the need to continuously watch a monitor screen.

The association between social network relationships and depressive symptoms among older Americans: what matters most?

PubMed

Litwin, Howard

2011-08-01

Although social network relationships are linked to mental health in late life, it is still unclear whether it is the structure of social networks or their perceived quality that matters. The current study regressed a dichotomous 8-item version of the Center for Epidemiological Studies Depression Scale (CESD-8) score on measures of social network relationships among Americans, aged 65-85 years, from the first wave of the National Social Life, Health and Aging Project. The network indicators included a structural variable - social network type - and a series of relationship quality indicators: perceived positive and negative ties with family, friends and spouse/ partner. Multivariate logistic regression analyses controlled for age, gender, education, income, race/ethnicity, religious affiliation, functional health and physical health. The perceived social network quality variables were unrelated to the presence of a high level of depressive symptoms, but social network type maintained an association with this mental health outcome even after controlling for confounders. Respondents embedded in resourceful social network types in terms of social capital--"diverse," "friend" and "congregant" networks--reported less presence of depressive symptoms, to varying degrees. The results show that the structure of the network seems to matter more than the perceived quality of the ties as an indicator of depressive symptoms. Moreover, the composite network type variable stands out in capturing the differences in mental state. The construct of network type should be incorporated in mental health screening among older people who reside in the community. One's social network type can be an important initial indicator that one is at risk.

Blueprint for antimicrobial hit discovery targeting metabolic networks

PubMed Central

Shen, Y.; Liu, J.; Estiu, G.; Isin, B.; Ahn, Y-Y.; Lee, D-S.; Barabási, A-L.; Kapatral, V.; Wiest, O.; Oltvai, Z. N.

2010-01-01

Advances in genome analysis, network biology, and computational chemistry have the potential to revolutionize drug discovery by combining system-level identification of drug targets with the atomistic modeling of small molecules capable of modulating their activity. To demonstrate the effectiveness of such a discovery pipeline, we deduced common antibiotic targets in Escherichia coli and Staphylococcus aureus by identifying shared tissue-specific or uniformly essential metabolic reactions in their metabolic networks. We then predicted through virtual screening dozens of potential inhibitors for several enzymes of these reactions and showed experimentally that a subset of these inhibited both enzyme activities in vitro and bacterial cell viability. This blueprint is applicable for any sequenced organism with high-quality metabolic reconstruction and suggests a general strategy for strain-specific antiinfective therapy. PMID:20080587

Retina Image Analysis and Ocular Telehealth: The Oak Ridge National Laboratory-Hamilton Eye Institute Case Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Karnowski, Thomas Paul; Giancardo, Luca; Li, Yaquin

2013-01-01

Automated retina image analysis has reached a high level of maturity in recent years, and thus the question of how validation is performed in these systems is beginning to grow in importance. One application of retina image analysis is in telemedicine, where an automated system could enable the automated detection of diabetic retinopathy and other eye diseases as a low-cost method for broad-based screening. In this work we discuss our experiences in developing a telemedical network for retina image analysis, including our progression from a manual diagnosis network to a more fully automated one. We pay special attention to howmore » validations of our algorithm steps are performed, both using data from the telemedicine network and other public databases.« less

A Multi-Center Diabetes Eye Screening Study in Community Settings: Study Design and Methodology.

PubMed

Murchison, Ann P; Friedman, David S; Gower, Emily W; Haller, Julia A; Lam, Byron L; Lee, David J; McGwin, Gerald; Owsley, Cynthia; Saaddine, Jinan; Insight Study Group

2016-01-01

Diabetes is the leading cause of new cases of blindness among adults aged 20-74 years within the United States. The Innovative Network for Sight Research group (INSIGHT) designed the Diabetic Eye Screening Study (DESS) to examine the feasibility and short-term effectiveness of non-mydriatic diabetic retinopathy (DR) screening for adults with diabetes in community-based settings. Study enrollment began in December 2011 at four sites: an internal medicine clinic at a county hospital in Birmingham, Alabama; a Federally-qualified community healthcare center in Miami-Dade County, Florida; a university-affiliated outpatient pharmacy in Philadelphia, Pennsylvania; and a medical home in Winston-Salem, North Carolina. People 18 years or older with previously diagnosed diabetes were offered free DR screening using non-mydriatic retinal photography that was preceded by a brief questionnaire addressing demographic information and previous eye care use. Visual acuity was also measured for each eye. Images were evaluated at a telemedicine reading center by trained evaluators using the National Health System DR grading classification. Participants and their physicians were sent screening report results and telephoned for a follow-up survey 3 months post-screening to determine whether participants had sought follow-up comprehensive eye care and their experiences with the screening process. Target enrollment at each site was a minimum of 500 persons. Three of the four sites met this enrollment goal. The INSIGHT/DESS is intended to establish the feasibility and short-term effectiveness of DR screening using non-mydriatic retinal photography in persons with diabetes who seek services in community-based clinic and pharmacy settings.

A Genome-Wide RNAi Screen for Modifiers of the Circadian Clock in Human Cells

PubMed Central

Zhang, Eric E.; Liu, Andrew C.; Hirota, Tsuyoshi; Miraglia, Loren J.; Welch, Genevieve; Pongsawakul, Pagkapol Y.; Liu, Xianzhong; Atwood, Ann; Huss, Jon W.; Janes, Jeff; Su, Andrew I.; Hogenesch, John B.; Kay, Steve A.

2009-01-01

Summary Two decades of research identified more than a dozen clock genes and defined a biochemical feedback mechanism of circadian oscillator function. To identify additional clock genes and modifiers, we conducted a genome-wide siRNA screen in a human cellular clock model. Knockdown of nearly a thousand genes reduced rhythm amplitude. Potent effects on period length or increased amplitude were less frequent; we found hundreds of these and confirmed them in secondary screens. Characterization of a subset of these genes demonstrated a dosage-dependent effect on oscillator function. Protein interaction network analysis showed that dozens of gene products directly or indirectly associate with known clock components. Pathway analysis revealed these genes are overrepresented for components of insulin and hedgehog signaling, the cell cycle, and the folate metabolism. Coupled with data showing many of these pathways are clock-regulated, we conclude the clock is interconnected with many aspects of cellular function. PMID:19765810

A Forward Genetic Approach in Chlamydomonas reinhardtii as a Strategy for Exploring Starch Catabolism

PubMed Central

Duchêne, Thierry; Cogez, Virginie; Cousin, Charlotte; Peltier, Gilles; Ball, Steven G.; Dauvillée, David

2013-01-01

A screen was recently developed to study the mobilization of starch in the unicellular green alga Chlamydomonas reinhardtii. This screen relies on starch synthesis accumulation during nitrogen starvation followed by the supply of nitrogen and the switch to darkness. Hence multiple regulatory networks including those of nutrient starvation, cell cycle control and light to dark transitions are likely to impact the recovery of mutant candidates. In this paper we monitor the specificity of this mutant screen by characterizing the nature of the genes disrupted in the selected mutants. We show that one third of the mutants consisted of strains mutated in genes previously reported to be of paramount importance in starch catabolism such as those encoding β-amylases, the maltose export protein, and branching enzyme I. The other mutants were defective for previously uncharacterized functions some of which are likely to define novel proteins affecting starch mobilization in green algae. PMID:24019981

Amphibian (Xenopus sp.) iodothyronine deiodinase ...

EPA Pesticide Factsheets

The U.S. EPA-MED amphibian thyroid group is currently screening chemicals for inhibition of human iodothyronine deiodinase activity as components of the thyroid system important in human development. Amphibians are a bellwether taxonomic group to gauge toxicity of chemicals in the environment. Amphibian thyroid function is not only important in development but also metamorphosis. Xenopus sp. have been used extensively as model organisms and are well characterized genetically. We propose to screen a list of chemicals (selected from the human DIO screening results) to test for inhibition of Xenopus deiodinases. Large quantities of the enzymes will be produced using an adenovirus system. Our preliminary results show that there may be catalytic differences between human and Xenopus deiodinases. The Twin Ports Early Career Scientists is a new group formed within the Duluth-Superior scientific community. This presentation will provide a basic introduction to my research and our mission at EPA, and help to establish networking and collaboration relationships across disciplines and institutions.

Genome-wide bisulfite sensitivity profiling of yeast suggests bisulfite inhibits transcription.

PubMed

Segovia, Romulo; Mathew, Veena; Tam, Annie S; Stirling, Peter C

2017-09-01

Bisulfite, in the form of sodium bisulfite or metabisulfite, is used commercially as a food preservative. Bisulfite is used in the laboratory as a single-stranded DNA mutagen in epigenomic analyses of DNA methylation. Recently it has also been used on whole yeast cells to induce mutations in exposed single-stranded regions in vivo. To understand the effects of bisulfite on live cells we conducted a genome-wide screen for bisulfite sensitive mutants in yeast. Screening the deletion mutant array, and collections of essential gene mutants we define a genetic network of bisulfite sensitive mutants. Validation of screen hits revealed hyper-sensitivity of transcription and RNA processing mutants, rather than DNA repair pathways and follow-up analyses support a role in perturbation of RNA transactions. We propose a model in which bisulfite-modified nucleotides may interfere with transcription or RNA metabolism when used in vivo. Copyright © 2017 Elsevier B.V. All rights reserved.

High-throughput matrix screening identifies synergistic and antagonistic antimalarial drug combinations

PubMed Central

Mott, Bryan T.; Eastman, Richard T.; Guha, Rajarshi; Sherlach, Katy S.; Siriwardana, Amila; Shinn, Paul; McKnight, Crystal; Michael, Sam; Lacerda-Queiroz, Norinne; Patel, Paresma R.; Khine, Pwint; Sun, Hongmao; Kasbekar, Monica; Aghdam, Nima; Fontaine, Shaun D.; Liu, Dongbo; Mierzwa, Tim; Mathews-Griner, Lesley A.; Ferrer, Marc; Renslo, Adam R.; Inglese, James; Yuan, Jing; Roepe, Paul D.; Su, Xin-zhuan; Thomas, Craig J.

2015-01-01

Drug resistance in Plasmodium parasites is a constant threat. Novel therapeutics, especially new drug combinations, must be identified at a faster rate. In response to the urgent need for new antimalarial drug combinations we screened a large collection of approved and investigational drugs, tested 13,910 drug pairs, and identified many promising antimalarial drug combinations. The activity of known antimalarial drug regimens was confirmed and a myriad of new classes of positively interacting drug pairings were discovered. Network and clustering analyses reinforced established mechanistic relationships for known drug combinations and identified several novel mechanistic hypotheses. From eleven screens comprising >4,600 combinations per parasite strain (including duplicates) we further investigated interactions between approved antimalarials, calcium homeostasis modulators, and inhibitors of phosphatidylinositide 3-kinases (PI3K) and the mammalian target of rapamycin (mTOR). These studies highlight important targets and pathways and provide promising leads for clinically actionable antimalarial therapy. PMID:26403635

Computer-Aided Screening of Conjugated Polymers for Organic Solar Cell: Classification by Random Forest.

PubMed

Nagasawa, Shinji; Al-Naamani, Eman; Saeki, Akinori

2018-05-17

Owing to the diverse chemical structures, organic photovoltaic (OPV) applications with a bulk heterojunction framework have greatly evolved over the last two decades, which has produced numerous organic semiconductors exhibiting improved power conversion efficiencies (PCEs). Despite the recent fast progress in materials informatics and data science, data-driven molecular design of OPV materials remains challenging. We report a screening of conjugated molecules for polymer-fullerene OPV applications by supervised learning methods (artificial neural network (ANN) and random forest (RF)). Approximately 1000 experimental parameters including PCE, molecular weight, and electronic properties are manually collected from the literature and subjected to machine learning with digitized chemical structures. Contrary to the low correlation coefficient in ANN, RF yields an acceptable accuracy, which is twice that of random classification. We demonstrate the application of RF screening for the design, synthesis, and characterization of a conjugated polymer, which facilitates a rapid development of optoelectronic materials.

PAPNET-assisted primary screening of conventional cervical smears.

PubMed

Cenci, M; Nagar, C; Vecchione, A

2000-01-01

The PAPNET System is the only device with a neural-network-based-artificial intelligence to detect and show the images of abnormal cells on the monitor to be evaluated in an interactive way. We effectively used the PAPNET in rescreening of conventional cervical smears and we detected its advantages and its disadvantages. In this paper, we report our results from PAPNET-assisted primary screening performed on 20,154 conventional smears. The smears were classified as Negative or as Review. The Negative cases were rapidly rescreened mainly near the coverslip edges, which are the slide areas not analyzed by automated devices because of focusing problems. The Review cases were fully reanalyzed by the optic microscope. In summary, 140 positive smears were detected: 57 cases showed changes due to HPV, 63 LSIL, 15 HSIL, and 5 carcinomas. Therefore, the PAPNET System was confirmed as useful in primary screening of conventional cervical samples as well as rescreening.

Rapid Countermeasure Discovery against Francisella tularensis Based on a Metabolic Network Reconstruction

PubMed Central

Chaudhury, Sidhartha; Abdulhameed, Mohamed Diwan M.; Singh, Narender; Tawa, Gregory J.; D’haeseleer, Patrik M.; Zemla, Adam T.; Navid, Ali; Zhou, Carol E.; Franklin, Matthew C.; Cheung, Jonah; Rudolph, Michael J.; Love, James; Graf, John F.; Rozak, David A.; Dankmeyer, Jennifer L.; Amemiya, Kei; Daefler, Simon; Wallqvist, Anders

2013-01-01

In the future, we may be faced with the need to provide treatment for an emergent biological threat against which existing vaccines and drugs have limited efficacy or availability. To prepare for this eventuality, our objective was to use a metabolic network-based approach to rapidly identify potential drug targets and prospectively screen and validate novel small-molecule antimicrobials. Our target organism was the fully virulent Francisella tularensis subspecies tularensis Schu S4 strain, a highly infectious intracellular pathogen that is the causative agent of tularemia and is classified as a category A biological agent by the Centers for Disease Control and Prevention. We proceeded with a staggered computational and experimental workflow that used a strain-specific metabolic network model, homology modeling and X-ray crystallography of protein targets, and ligand- and structure-based drug design. Selected compounds were subsequently filtered based on physiological-based pharmacokinetic modeling, and we selected a final set of 40 compounds for experimental validation of antimicrobial activity. We began screening these compounds in whole bacterial cell-based assays in biosafety level 3 facilities in the 20th week of the study and completed the screens within 12 weeks. Six compounds showed significant growth inhibition of F. tularensis, and we determined their respective minimum inhibitory concentrations and mammalian cell cytotoxicities. The most promising compound had a low molecular weight, was non-toxic, and abolished bacterial growth at 13 µM, with putative activity against pantetheine-phosphate adenylyltransferase, an enzyme involved in the biosynthesis of coenzyme A, encoded by gene coaD. The novel antimicrobial compounds identified in this study serve as starting points for lead optimization, animal testing, and drug development against tularemia. Our integrated in silico/in vitro approach had an overall 15% success rate in terms of active versus tested compounds over an elapsed time period of 32 weeks, from pathogen strain identification to selection and validation of novel antimicrobial compounds. PMID:23704901

Addressing Low Colorectal Cancer Screening in African Americans: Using Focus Groups to Inform the Development of Effective Interventions.

PubMed

May, Folasade P; Whitman, Cynthia B; Varlyguina, Ksenia; Bromley, Erica G; Spiegel, Brennan M R

2016-09-01

African Americans have the highest burden of colorectal cancer (CRC) in the United States of America (USA) yet lower CRC screening rates than whites. Although poor screening has prompted efforts to increase screening uptake, there is a persistent need to develop public health interventions in partnership with the African American community. The aim of this study was to conduct focus groups with African Americans to determine preferences for the content and mode of dissemination of culturally tailored CRC screening interventions. In June 2013, 45-75-year-old African Americans were recruited through online advertisements and from an urban Veterans Affairs system to create four focus groups. A semi-structured interview script employing open-ended elicitation was used, and transcripts were analyzed using ATLAS.ti software to code and group data into a concept network. A total of 38 participants (mean age = 54) were enrolled, and 59 ATLAS.ti codes were generated. Commonly reported barriers to screening included perceived invasiveness of colonoscopy, fear of pain, and financial concerns. Facilitators included poor diet/health and desire to prevent CRC. Common sources of health information included media and medical providers. CRC screening information was commonly obtained from medical personnel or media. Participants suggested dissemination of CRC screening education through commercials, billboards, influential African American public figures, Internet, and radio. Participants suggested future interventions include culturally specific information, including details about increased risk, accessing care, and dispelling of myths. Public health interventions to improve CRC screening among African Americans should employ media outlets, emphasize increased risk among African Americans, and address race-specific barriers. Specific recommendations are presented for developing future interventions.

International variation in management of screen-detected ductal carcinoma in situ of the breast

PubMed Central

Ponti, Antonio; Lynge, Elsebeth; James, Ted; Májek, Ondřej; von Euler-Chelpin, My; Anttila, Ahti; Fitzpatrick, Patricia; Mano, Maria Piera; Kawai, Masaaki; Scharpantgen, Astrid; Fracheboud, Jacques; Hofvind, Solveig; Vidal, Carmen; Ascunce, Nieves; Salas, Dolores; Bulliard, Jean-Luc; Segnan, Nereo; Kerlikowske, Karla; Taplin, Stephen

2014-01-01

Background Ductal carcinoma in situ (DCIS) incidence has grown with the implementation of screening and its detection varies across International Cancer Screening Network (ICSN) countries. The aim of this survey is to describe the management of screen-detected DCIS in ICSN countries and to evaluate the potential for treatment related morbidity. Methods We sought screen-detected DCIS data from the ICSN countries identified during 2004–2008. We adopted standardised data collection forms and analysis and explored DCIS diagnosis and treatment processes ranging from pre-operative diagnosis to type of surgery and radiotherapy. Results Twelve countries contributed data from a total of 15 screening programmes, all from Europe except the United States of America and Japan. Among women aged 50–69 years, 7,176,050 screening tests and 5324 screen-detected DCIS were reported. From 21% to 93% of DCIS had a pre-operative diagnosis (PO); 67–90% of DCIS received breast conservation surgery (BCS), and in 41–100% of the cases this was followed by radiotherapy; 6.4–59% received sentinel lymph node biopsy (SLNB) only and 0.8–49% axillary dissection (ALND) with 0.6% (range by programmes 0–8.1%) being node positive. Among BCS patients 35% received SLNB only and 4.8% received ALND. Starting in 2006, PO and SLNB use increased while ALND remained stable. SLNB and ALND were associated with larger size and higher grade DCIS lesions. Conclusions Variation in DCIS management among screened women is wide and includes lymph node surgery beyond what is currently recommended. This indicates the presence of varying levels of overtreatment and the potential for its reduction. PMID:25149183

Comparison of clinical and survival characteristics between prostate cancer patients of PSA-based screening and clinical diagnosis in China.

PubMed

Xu, Libo; Wang, Jinguo; Guo, Baofeng; Zhang, Haixia; Wang, Kaichen; Wang, Ding; Dai, Chang; Zhang, Ling; Zhao, Xuejian

2018-01-02

Prostate-specific antigen (PSA)-based mass screening remains the most controversial topic in prostate cancer. PSA-based mass screening has not been widely used in China yet. The aim of our study was to evaluate the effect of the PSA-based screening in China. The cohort consisted of 1,012 prostate cancer patients. Data were retrospectively collected and clinical characteristics of the cohorts were investigated. Survival was analyzed for prostatic carcinoma of both PSA screened and clinically diagnosed patients according to clinical characteristics and the National Comprehensive Cancer Network (NCCN) risk classification. Cox Proportional Hazards Model analysis was done for risk predictor identification. The median age was 71 years old. Five-year overall and prostate-cancer-specific survival in prostatic adenocarcinoma patients were 77.52% and 79.65%; 10-year survivals were 62.57% and 68.60%, respectively. Survival was significantly poorer in patients with metastases and non-curative management. T staging and Gleason score by NCCN classification effectively stratified prostatic adenocarcinoma patients into different risk groups. T staging was a significant predictor of survival by COX Proportional Hazard Model. PSA screened patients had a significantly higher percentage diagnosed in early stage. PSA screened prostatic adenocarcinoma patients had a better prognosis in both overall and prostate cancer-specific survivals. This Chinese cohort had a lower overall and prostate cancer survival rate than it is reported in western countries. The incidence of early-stage prostate cancer found in PSA-based mass screening was high and there were significant differences in both overall and prostate cancer-specific survival between the PSA-screened and clinically diagnosed patients.

Comparison of clinical and survival characteristics between prostate cancer patients of PSA-based screening and clinical diagnosis in China

PubMed Central

Xu, Libo; Wang, Jinguo; Guo, Baofeng; Zhang, Haixia; Wang, Kaichen; Wang, Ding; Dai, Chang; Zhang, Ling; Zhao, Xuejian

2018-01-01

Prostate-specific antigen (PSA)-based mass screening remains the most controversial topic in prostate cancer. PSA-based mass screening has not been widely used in China yet. The aim of our study was to evaluate the effect of the PSA-based screening in China. The cohort consisted of 1,012 prostate cancer patients. Data were retrospectively collected and clinical characteristics of the cohorts were investigated. Survival was analyzed for prostatic carcinoma of both PSA screened and clinically diagnosed patients according to clinical characteristics and the National Comprehensive Cancer Network (NCCN) risk classification. Cox Proportional Hazards Model analysis was done for risk predictor identification. The median age was 71 years old. Five-year overall and prostate-cancer-specific survival in prostatic adenocarcinoma patients were 77.52% and 79.65%; 10-year survivals were 62.57% and 68.60%, respectively. Survival was significantly poorer in patients with metastases and non-curative management. T staging and Gleason score by NCCN classification effectively stratified prostatic adenocarcinoma patients into different risk groups. T staging was a significant predictor of survival by COX Proportional Hazard Model. PSA screened patients had a significantly higher percentage diagnosed in early stage. PSA screened prostatic adenocarcinoma patients had a better prognosis in both overall and prostate cancer-specific survivals. This Chinese cohort had a lower overall and prostate cancer survival rate than it is reported in western countries. The incidence of early-stage prostate cancer found in PSA-based mass screening was high and there were significant differences in both overall and prostate cancer-specific survival between the PSA-screened and clinically diagnosed patients. PMID:29416625

Dynamics of Intersubject Brain Networks during Anxious Anticipation

PubMed Central

Najafi, Mahshid; Kinnison, Joshua; Pessoa, Luiz

2017-01-01

How do large-scale brain networks reorganize during the waxing and waning of anxious anticipation? Here, threat was dynamically modulated during human functional MRI as two circles slowly meandered on the screen; if they touched, an unpleasant shock was delivered. We employed intersubject correlation analysis, which allowed the investigation of network-level functional connectivity across brains, and sought to determine how network connectivity changed during periods of approach (circles moving closer) and periods of retreat (circles moving apart). Analysis of positive connection weights revealed that dynamic threat altered connectivity within and between the salience, executive, and task-negative networks. For example, dynamic functional connectivity increased within the salience network during approach and decreased during retreat. The opposite pattern was found for the functional connectivity between the salience and task-negative networks: decreases during approach and increases during approach. Functional connections between subcortical regions and the salience network also changed dynamically during approach and retreat periods. Subcortical regions exhibiting such changes included the putative periaqueductal gray, putative habenula, and putative bed nucleus of the stria terminalis. Additional analysis of negative functional connections revealed dynamic changes, too. For example, negative weights within the salience network decreased during approach and increased during retreat, opposite what was found for positive weights. Together, our findings unraveled dynamic features of functional connectivity of large-scale networks and subcortical regions across participants while threat levels varied continuously, and demonstrate the potential of characterizing emotional processing at the level of dynamic networks. PMID:29209184

Dengue-2 structural proteins associate with human proteins to produce a coagulation and innate immune response biased interactome.

PubMed

Folly, Brenda B; Weffort-Santos, Almeriane M; Fathman, C G; Soares, Luis R B

2011-01-31

Dengue virus infection is a public health threat to hundreds of millions of individuals in the tropical regions of the globe. Although Dengue infection usually manifests itself in its mildest, though often debilitating clinical form, dengue fever, life-threatening complications commonly arise in the form of hemorrhagic shock and encephalitis. The etiological basis for the virus-induced pathology in general, and the different clinical manifestations in particular, are not well understood. We reasoned that a detailed knowledge of the global biological processes affected by virus entry into a cell might help shed new light on this long-standing problem. A bacterial two-hybrid screen using DENV2 structural proteins as bait was performed, and the results were used to feed a manually curated, global dengue-human protein interaction network. Gene ontology and pathway enrichment, along with network topology and microarray meta-analysis, were used to generate hypothesis regarding dengue disease biology. Combining bioinformatic tools with two-hybrid technology, we screened human cDNA libraries to catalogue proteins physically interacting with the DENV2 virus structural proteins, Env, cap and PrM. We identified 31 interacting human proteins representing distinct biological processes that are closely related to the major clinical diagnostic feature of dengue infection: haemostatic imbalance. In addition, we found dengue-binding human proteins involved with additional key aspects, previously described as fundamental for virus entry into cells and the innate immune response to infection. Construction of a DENV2-human global protein interaction network revealed interesting biological properties suggested by simple network topology analysis. Our experimental strategy revealed that dengue structural proteins interact with human protein targets involved in the maintenance of blood coagulation and innate anti-viral response processes, and predicts that the interaction of dengue proteins with a proposed human protein interaction network produces a modified biological outcome that may be behind the hallmark pathologies of dengue infection.

Mathematical Model of a Telomerase Transcriptional Regulatory Network Developed by Cell-Based Screening: Analysis of Inhibitor Effects and Telomerase Expression Mechanisms

PubMed Central

Bilsland, Alan E.; Stevenson, Katrina; Liu, Yu; Hoare, Stacey; Cairney, Claire J.; Roffey, Jon; Keith, W. Nicol

2014-01-01

Cancer cells depend on transcription of telomerase reverse transcriptase (TERT). Many transcription factors affect TERT, though regulation occurs in context of a broader network. Network effects on telomerase regulation have not been investigated, though deeper understanding of TERT transcription requires a systems view. However, control over individual interactions in complex networks is not easily achievable. Mathematical modelling provides an attractive approach for analysis of complex systems and some models may prove useful in systems pharmacology approaches to drug discovery. In this report, we used transfection screening to test interactions among 14 TERT regulatory transcription factors and their respective promoters in ovarian cancer cells. The results were used to generate a network model of TERT transcription and to implement a dynamic Boolean model whose steady states were analysed. Modelled effects of signal transduction inhibitors successfully predicted TERT repression by Src-family inhibitor SU6656 and lack of repression by ERK inhibitor FR180204, results confirmed by RT-QPCR analysis of endogenous TERT expression in treated cells. Modelled effects of GSK3 inhibitor 6-bromoindirubin-3′-oxime (BIO) predicted unstable TERT repression dependent on noise and expression of JUN, corresponding with observations from a previous study. MYC expression is critical in TERT activation in the model, consistent with its well known function in endogenous TERT regulation. Loss of MYC caused complete TERT suppression in our model, substantially rescued only by co-suppression of AR. Interestingly expression was easily rescued under modelled Ets-factor gain of function, as occurs in TERT promoter mutation. RNAi targeting AR, JUN, MXD1, SP3, or TP53, showed that AR suppression does rescue endogenous TERT expression following MYC knockdown in these cells and SP3 or TP53 siRNA also cause partial recovery. The model therefore successfully predicted several aspects of TERT regulation including previously unknown mechanisms. An extrapolation suggests that a dominant stimulatory system may programme TERT for transcriptional stability. PMID:24550717

Graph Theory-Based Technique for Isolating Corrupted Boundary Conditions in Continental-Scale River Network Hydrodynamic Simulation

NASA Astrophysics Data System (ADS)

Yu, C. W.; Hodges, B. R.; Liu, F.

2017-12-01

Development of continental-scale river network models creates challenges where the massive amount of boundary condition data encounters the sensitivity of a dynamic nu- merical model. The topographic data sets used to define the river channel characteristics may include either corrupt data or complex configurations that cause instabilities in a numerical solution of the Saint-Venant equations. For local-scale river models (e.g. HEC- RAS), modelers typically rely on past experience to make ad hoc boundary condition adjustments that ensure a stable solution - the proof of the adjustment is merely the sta- bility of the solution. To date, there do not exist any formal methodologies or automated procedures for a priori detecting/fixing boundary conditions that cause instabilities in a dynamic model. Formal methodologies for data screening and adjustment are a critical need for simulations with a large number of river reaches that draw their boundary con- dition data from a wide variety of sources. At the continental scale, we simply cannot assume that we will have access to river-channel cross-section data that has been ade- quately analyzed and processed. Herein, we argue that problematic boundary condition data for unsteady dynamic modeling can be identified through numerical modeling with the steady-state Saint-Venant equations. The fragility of numerical stability increases with the complexity of branching in river network system and instabilities (even in an unsteady solution) are typically triggered by the nonlinear advection term in Saint-Venant equations. It follows that the behavior of the simpler steady-state equations (which retain the nonlin- ear term) can be used to screen the boundary condition data for problematic regions. In this research, we propose a graph-theory based method to isolate the location of corrupted boundary condition data in a continental-scale river network and demonstrate its utility with a network of O(10^4) elements. Acknowledgement: This research is supported by the National Science Foundation un- der grant number CCF-1331610.

Machine Learning–Based Differential Network Analysis: A Study of Stress-Responsive Transcriptomes in Arabidopsis[W

PubMed Central

Ma, Chuang; Xin, Mingming; Feldmann, Kenneth A.; Wang, Xiangfeng

2014-01-01

Machine learning (ML) is an intelligent data mining technique that builds a prediction model based on the learning of prior knowledge to recognize patterns in large-scale data sets. We present an ML-based methodology for transcriptome analysis via comparison of gene coexpression networks, implemented as an R package called machine learning–based differential network analysis (mlDNA) and apply this method to reanalyze a set of abiotic stress expression data in Arabidopsis thaliana. The mlDNA first used a ML-based filtering process to remove nonexpressed, constitutively expressed, or non-stress-responsive “noninformative” genes prior to network construction, through learning the patterns of 32 expression characteristics of known stress-related genes. The retained “informative” genes were subsequently analyzed by ML-based network comparison to predict candidate stress-related genes showing expression and network differences between control and stress networks, based on 33 network topological characteristics. Comparative evaluation of the network-centric and gene-centric analytic methods showed that mlDNA substantially outperformed traditional statistical testing–based differential expression analysis at identifying stress-related genes, with markedly improved prediction accuracy. To experimentally validate the mlDNA predictions, we selected 89 candidates out of the 1784 predicted salt stress–related genes with available SALK T-DNA mutagenesis lines for phenotypic screening and identified two previously unreported genes, mutants of which showed salt-sensitive phenotypes. PMID:24520154

Automatic classification of DMSA scans using an artificial neural network

NASA Astrophysics Data System (ADS)

Wright, J. W.; Duguid, R.; Mckiddie, F.; Staff, R. T.

2014-04-01

DMSA imaging is carried out in nuclear medicine to assess the level of functional renal tissue in patients. This study investigated the use of an artificial neural network to perform diagnostic classification of these scans. Using the radiological report as the gold standard, the network was trained to classify DMSA scans as positive or negative for defects using a representative sample of 257 previously reported images. The trained network was then independently tested using a further 193 scans and achieved a binary classification accuracy of 95.9%. The performance of the network was compared with three qualified expert observers who were asked to grade each scan in the 193 image testing set on a six point defect scale, from ‘definitely normal’ to ‘definitely abnormal’. A receiver operating characteristic analysis comparison between a consensus operator, generated from the scores of the three expert observers, and the network revealed a statistically significant increase (α < 0.05) in performance between the network and operators. A further result from this work was that when suitably optimized, a negative predictive value of 100% for renal defects was achieved by the network, while still managing to identify 93% of the negative cases in the dataset. These results are encouraging for application of such a network as a screening tool or quality assurance assistant in clinical practice.

The Role of Retinal Imaging and Portable Screening Devices in Tele-ophthalmology Applications for Diabetic Retinopathy Management.

PubMed

DeBuc, Delia Cabrera

2016-12-01

In the years since its introduction, retinal imaging has transformed our capability to visualize the posterior pole of the eye. Increasing practical advances in mobile technology, regular monitoring, and population screening for diabetic retinopathy management offer the opportunity for further development of cost-effective applications through remote assessment of the diabetic eye using portable retinal cameras, smart-phone-based devices and telemedicine networks. Numerous retinal imaging methods and mobile technologies in tele-ophthalmology applications have been reported for diabetic retinopathy screening and management. They provide several advantages of automation, sensitivity, specificity, portability, and miniaturization for the development of point-of-care diagnostics for eye complications in diabetes. The aim of this paper is to review the role of retinal imaging and mobile technologies in tele-ophthalmology applications for diabetic retinopathy screening and management. At large, although improvements in current technology and telemedicine services are still needed, telemedicine has demonstrated to be a worthy tool to support health caregivers in the effective management and prevention of diabetes and its complications.

Screening the molecular targets of ovarian cancer based on bioinformatics analysis.

PubMed

Du, Lei; Qian, Xiaolei; Dai, Chenyang; Wang, Lihua; Huang, Ding; Wang, Shuying; Shen, Xiaowei

2015-01-01

Ovarian cancer (OC) is the most lethal gynecologic malignancy. This study aims to explore the molecular mechanisms of OC and identify potential molecular targets for OC treatment. Microarray gene expression data (GSE14407) including 12 normal ovarian surface epithelia samples and 12 OC epithelia samples were downloaded from Gene Expression Omnibus database. Differentially expressed genes (DEGs) between 2 kinds of ovarian tissue were identified by using limma package in R language (|log2 fold change| gt;1 and false discovery rate [FDR] lt;0.05). Protein-protein interactions (PPIs) and known OC-related genes were screened from COXPRESdb and GenBank database, respectively. Furthermore, PPI network of top 10 upregulated DEGs and top 10 downregulated DEGs was constructed and visualized through Cytoscape software. Finally, for the genes involved in PPI network, functional enrichment analysis was performed by using DAVID (FDR lt;0.05). In total, 1136 DEGs were identified, including 544 downregulated and 592 upregulated DEGs. Then, PPI network was constructed, and DEGs CDKN2A, MUC1, OGN, ZIC1, SOX17, and TFAP2A interacted with known OC-related genes CDK4, EGFR/JUN, SRC, CLI1, CTNNB1, and TP53, respectively. Moreover, functions about oxygen transport and embryonic development were enriched by the genes involved in the network of downregulated DEGs. We propose that 4 DEGs (OGN, ZIC1, SOX17, and TFAP2A) and 2 functions (oxygen transport and embryonic development) might play a role in the development of OC. These 4 DEGs and known OC-related genes might serve as therapeutic targets for OC. Further studies are required to validate these predictions.

Systematically Studying Kinase Inhibitor Induced Signaling Network Signatures by Integrating Both Therapeutic and Side Effects

PubMed Central

Shao, Hongwei; Peng, Tao; Ji, Zhiwei; Su, Jing; Zhou, Xiaobo

2013-01-01

Substantial effort in recent years has been devoted to analyzing data based large-scale biological networks, which provide valuable insight into the topologies of complex biological networks but are rarely context specific and cannot be used to predict the responses of cell signaling proteins to specific ligands or compounds. In this work, we proposed a novel strategy to investigate kinase inhibitor induced pathway signatures by integrating multiplex data in Library of Integrated Network-based Cellular Signatures (LINCS), e.g. KINOMEscan data and cell proliferation/mitosis imaging data. Using this strategy, we first established a PC9 cell line specific pathway model to investigate the pathway signatures in PC9 cell line when perturbed by a small molecule kinase inhibitor GW843682. This specific pathway revealed the role of PI3K/AKT in modulating the cell proliferation process and the absence of two anti-proliferation links, which indicated a potential mechanism of abnormal expansion in PC9 cell number. Incorporating the pathway model for side effects on primary human hepatocytes, it was used to screen 27 kinase inhibitors in LINCS database and PF02341066, known as Crizotinib, was finally suggested with an optimal concentration 4.6 uM to suppress PC9 cancer cell expansion while avoiding severe damage to primary human hepatocytes. Drug combination analysis revealed that the synergistic effect region can be predicted straightforwardly based on a threshold which is an inherent property of each kinase inhibitor. Furthermore, this integration strategy can be easily extended to other specific cell lines to be a powerful tool for drug screen before clinical trials. PMID:24339888