Using natural language processing techniques to inform research on nanotechnology

Literature in the field of nanotechnology is exponentially increasing with more and more engineered nanomaterials being created, characterized, and tested for performance and safety. With the deluge of published data, there is a need for natural language processing approaches to semi-automate the cataloguing of engineered nanomaterials and their associated physico-chemical properties, performance, exposure scenarios, and biological effects. In this paper, we review the different informatics methods that have been applied to patent mining, nanomaterial/device characterization, nanomedicine, and environmental risk assessment. Nine natural language processing (NLP)-based tools were identified: NanoPort, NanoMapper, TechPerceptor, a Text Mining Framework, a Nanodevice Analyzer, a Clinical Trial Document Classifier, Nanotoxicity Searcher, NanoSifter, and NEIMiner. We conclude with recommendations for sharing NLP-related tools through online repositories to broaden participation in nanoinformatics

Thyroid research: stepping forward.

It is eight years since Thyroid Research was launched with an aim to enhance opportunities for scientists and clinicians, working in the rapidly advancing field of thyroidology, to publish their research (Thyroid Res 1(1):1, 2008). Right from the outset, Thyroid Research aspired to become a prominent journal in thyroidology with high quality publications. Over the years, the journal has not only survived in the increasingly competitive field of open-access academic journal publication, it has also been making a steady progress towards achieving this ambitious goal. Now, Thyroid Research is ready to step forward to begin a new chapter in its publication.This article is freely available via Open Access. Click on the 'Additional Link' above to access the full-text from the publisher's site.Published

The Influence of Start Position, Initial Step Type, and Usage of a Focal Point on Sprinting Performance

International Journal of Exercise Science 6(4) : 320-327, 2013. For many athletes, sprinting acceleration is vital to sport performance. The purpose of this study was to observe the influences of starting position, type of initial step taken, and a focal point on sprinting velocity, stride length, and acceleration over a 9.1 m distance. Two trials of four conditions were video recorded in which subjects had no focal point (n = 10) or a lateral focal point (n = 9). The four conditions were: forwards (control), backwards, 90° left (90°L), and 90° right (90°R). Lower velocities (p \u3e 0.05) were observed with focal point usage from the 90°R and 90°L starting positions. Four initial steps were observed during the forwards, 90°L, and 90°R conditions: backwards step, anterior tilt with forward step, pivot-crossover step, and lateral side step. The use of a backwards step resulted in an increased velocity (+0.80 m·s-1, p \u3c 0.01) for the 90° turn trials and increased acceleration (+ 0.37 m·s-2,p \u3c 0.01). Our results indicate that looking at a target can cause a decline in sprint velocity and acceleration over a short distance. Moreover, utilizing a backwards step to initiate a 90° turn may generate more power and force, increasing their velocity for short sprints. We recommend training athletes with a target or focal points to help combat the reduced speed and initiate movement with initial backwards step

Exchanges in a Virtual Environment for Diabetes Self-Management Education and Support: Social Network Analysis.

BACKGROUND: Diabetes remains a major health problem in the United States, affecting an estimated 10.5% of the population. Diabetes self-management interventions improve diabetes knowledge, self-management behaviors, and clinical outcomes. Widespread internet connectivity facilitates the use of eHealth interventions, which positively impacts knowledge, social support, and clinical and behavioral outcomes. In particular, diabetes interventions based on virtual environments have the potential to improve diabetes self-efficacy and support, while being highly feasible and usable. However, little is known about the patterns of social interactions and support taking place within type 2 diabetes-specific virtual communities. OBJECTIVE: The objective of this study was to examine social support exchanges from a type 2 diabetes self-management education and support intervention that was delivered via a virtual environment. METHODS: Data comprised virtual environment-mediated synchronous interactions among participants and between participants and providers from an intervention for type 2 diabetes self-management education and support. Network data derived from such social interactions were used to create networks to analyze patterns of social support exchange with the lens of social network analysis. Additionally, network correlations were used to explore associations between social support networks. RESULTS: The findings revealed structural differences between support networks, as well as key network characteristics of supportive interactions facilitated by the intervention. Emotional and appraisal support networks are the larger, most centralized, and most active networks, suggesting that virtual communities can be good sources for these types of support. In addition, appraisal and instrumental support networks are more connected, suggesting that members of virtual communities are more likely to engage in larger group interactions where these types of support can be exchanged. Lastly, network correlations suggest that participants who exchange emotional support are likely to exchange appraisal or instrumental support, and participants who exchange appraisal support are likely to exchange instrumental support. CONCLUSIONS: Social interaction patterns from disease-specific virtual environments can be studied using a social network analysis approach to better understand the exchange of social support. Network data can provide valuable insights into the design of novel and effective eHealth interventions given the unique opportunity virtual environments have facilitating realistic environments that are effective and sustainable, where social interactions can be leveraged to achieve diverse health goals

Nanocuration workflows: Establishing best practices for identifying, inputting, and sharing data to inform decisions on nanomaterials

There is a critical opportunity in the field of nanoscience to compare and integrate information across diverse fields of study through informatics (i.e., nanoinformatics). This paper is one in a series of articles on the data curation process in nanoinformatics (nanocuration). Other articles in this series discuss key aspects of nanocuration (temporal metadata, data completeness, database integration), while the focus of this article is on the nanocuration workflow, or the process of identifying, inputting, and reviewing nanomaterial data in a data repository. In particular, the article discusses: 1) the rationale and importance of a defined workflow in nanocuration, 2) the influence of organizational goals or purpose on the workflow, 3) established workflow practices in other fields, 4) current workflow practices in nanocuration, 5) key challenges for workflows in emerging fields like nanomaterials, 6) examples to make these challenges more tangible, and 7) recommendations to address the identified challenges. Throughout the article, there is an emphasis on illustrating key concepts and current practices in the field. Data on current practices in the field are from a group of stakeholders active in nanocuration. In general, the development of workflows for nanocuration is nascent, with few individuals formally trained in data curation or utilizing available nanocuration resources (e.g., ISA-TAB-Nano). Additional emphasis on the potential benefits of cultivating nanomaterial data via nanocuration processes (e.g., capability to analyze data from across research groups) and providing nanocuration resources (e.g., training) will likely prove crucial for the wider application of nanocuration workflows in the scientific community

T cells enhance gold nanoparticle delivery to tumors in vivo

Gold nanoparticle-mediated photothermal therapy (PTT) has shown great potential for the treatment of cancer in mouse studies and is now being evaluated in clinical trials. For this therapy, gold nanoparticles (AuNPs) are injected intravenously and are allowed to accumulate within the tumor via the enhanced permeability and retention (EPR) effect. The tumor is then irradiated with a near infrared laser, whose energy is absorbed by the AuNPs and translated into heat. While reliance on the EPR effect for tumor targeting has proven adequate for vascularized tumors in small animal models, the efficiency and specificity of tumor delivery in vivo, particularly in tumors with poor blood supply, has proven challenging. In this study, we examine whether human T cells can be used as cellular delivery vehicles for AuNP transport into tumors. We first demonstrate that T cells can be efficiently loaded with 45 nm gold colloid nanoparticles without affecting viability or function (e.g. migration and cytokine production). Using a human tumor xenograft mouse model, we next demonstrate that AuNP-loaded T cells retain their capacity to migrate to tumor sites in vivo. In addition, the efficiency of AuNP delivery to tumors in vivo is increased by more than four-fold compared to injection of free PEGylated AuNPs and the use of the T cell delivery system also dramatically alters the overall nanoparticle biodistribution. Thus, the use of T cell chaperones for AuNP delivery could enhance the efficacy of nanoparticle-based therapies and imaging applications by increasing AuNP tumor accumulation

Size-controlled synthesis of monodispersed gold nanoparticles via carbon monoxide gas reduction

An in depth analysis of gold nanoparticle (AuNP) synthesis and size tuning, utilizing carbon monoxide (CO) gas as a reducing agent, is presented for the first time. The sizes of the AuNPs are tunable from ~4 to 100 nm by altering the concentration of HAuCl4 and inlet CO gas-injection flow rate. It is also found that speciation of aqueous HAuCl4, prior to reduction, influences the size, morphology, and properties of AuNPs when reduced with CO gas. Ensemble extinction spectra and TEM images provide clear evidence that CO reduction offers a high level of monodispersity with standard deviations as low as 3%. Upon synthesis, no excess reducing agent remains in solution eliminating the need for purification. The time necessary to synthesize AuNPs, using CO, is less than 2 min

Evaluation of the cobas Cdiff Test for Detection of Toxigenic Clostridium difficile in Stool Samples

Nucleic acid amplification tests (NAATs) are reliable tools for the detection of toxigenic Clostridium difficile from unformed (liquid or soft) stool samples. The objective of this study was to evaluate performance of the cobas Cdiff test on the cobas 4800 system using prospectively collected stool specimens from patients suspected of having C. difficile infection (CDI). The performance of the cobas Cdiff test was compared to the results of combined direct and broth-enriched toxigenic culture methods in a large, multicenter clinical trial. Additional discrepancy analysis was performed by using the Xpert C. difficile Epi test. Sample storage was evaluated by using contrived and fresh samples before and after storage at -20°C. Testing was performed on samples from 683 subjects (306 males and 377 females); 113 (16.5%) of 683 subjects were positive for toxigenic C. difficile by direct toxigenic culture, and 141 of 682 subjects were positive by using the combined direct and enriched toxigenic culture method (reference method), for a prevalence rate of 20.7%. The sensitivity and specificity of the cobas Cdiff test compared to the combined direct and enriched culture method were 92.9% (131/141; 95% confidence interval [CI], 87.4% to 96.1%) and 98.7% (534/541; 95% CI, 97.4% to 99.4%), respectively. Discrepancy analysis using results for retested samples from a second NAAT (Xpert C. difficile/Epi test; Cepheid, Sunnyvale, CA) found no false-negative and 4 false-positive cobas Cdiff test results. There was no difference in positive and negative results in comparisons of fresh and stored samples. These results support the use of the cobas Cdiff test as a robust aid in the diagnosis of CDI