Medical free-text to concept mapping as an information retrieval problem

Concept mapping involves determining relevant concepts from a free-text input, where concepts are defined in an external reference ontology. This is an important process that underpins many applications for clinical information reporting, derivation of phenotypic descriptions, and a number of state-of-the-art medical information retrieval methods. Concept mapping can be cast into an information retrieval (IR) problem: free-text mentions are treated as queries and concepts from a reference ontology as the documents to be indexed and retrieved. This paper presents an empirical investigation applying general-purpose IR techniques for concept mapping in the medical domain. A dataset used for evaluating medical information extraction is adapted to measure the effectiveness of the considered IR approaches. Standard IR approaches used here are contrasted with the effectiveness of two established benchmark methods specifically developed for medical concept mapping. The empirical findings show that the IR approaches are comparable with one benchmark method but well below the best benchmark.

Multipurpose nanoporous alumina-carbon nanowall bi-dimensional nano-hybrid platform via catalyzed and catalyst-free plasma CVD

Simple, rapid, plasma-assisted synthesis of large-area arrays of vertically-aligned carbon nanowalls on highly-porous, transparent bare and gold-coated alumina membranes with the two pore sizes is reported. It is demonstrated that the complex patterns of vertically aligned nanowalls can nucleate and form different morphologies in the low-temperature plasmas. The process is stable, and the twofold change in the gas flow (10 and 20 sccm) does not noticeably influence the morphology of the nanowall pattern. Application of a thin (5 nm) gold layer to nanoporous membrane prior to the nanowall growth allows controlling the network morphology.

'Free' surfactant in gastric aspirates and bronchoalveolar lavage in children with and without reflux oesophagitis

Aim: Dipalmitoylphosphatidycholine (DPPC) is the characteristic and main constituent of surfactant. Adsorption of surfactant to epithelial surfaces may be important in the masking of receptors. The aims of the study were to (i) compare the quantity of free DPPC in the airways and gastric aspirates of children with gastroesophageal reflux disease (GORD) to those without and (ii) describe the association between free DPPC levels with airway cellular profile and capsaicin cough sensitivity. Methods: Children aged <14 years were defined as 'coughers' if a history of cough in association with their GORD symptoms was elicited before gastric aspirates and nonbronchoscopic bronchoalveolar lavage (BAL) were obtained during elective flexible upper gastrointestinal endoscopy. GORD was defined as histological presence of reflux oesophagitis. Spirometry and capsaicin cough-sensitivity test was carried out in children aged >6 years before the endoscopy. Results: Median age of the 68 children was 9 years (interquartile range (IQR) 7.2). Median DPPC level in BAL of children with cough (72.7 μg/mL) was similar to noncoughers (88.5). There was also no significant difference in DPPC levels in both BAL and gastric aspirates of children classified according to presence of GORD. There was no correlation between DPPC levels and cellular counts or capsaicin cough-sensitivity outcome measures. Conclusion: We conclude that free DPPC levels in the airways and gastric aspirate is not influenced by presence of cough or GORD defined by histological presence of reflux oesophagitis. Whether quantification of adsorbed surfactant differs in these groups remain unknown. Free DPPC is unlikely to have a role in masking of airway receptors. © 2006 Royal Australasian College of Physicians.

Label-free isolation of a prostate cancer cell among blood cells and the single-cell measurement of drug accumulation using an integrated microfluidic chip

Circulating tumor cells (CTCs) are found in the blood of patients with cancer. Although these cells are rare, they can provide useful information for chemotherapy. However, isolation of these rare cells from blood is technically challenging because they are small in numbers. An integrated microfluidic chip, dubbed as CTC chip, was designed and fabricated for conducting tumor cell isolation. As CTCs usually show multidrug resistance (MDR), the effect of MDR inhibitors on chemotherapeutic drug accumulation in the isolated single tumor cell is measured. As a model of CTC isolation, human prostate tumor cells were mixed with mouse blood cells and the labelfree isolation of the tumor cells was conducted based on cell size difference. The major advantages of the CTC chip are the ability for fast cell isolation, followed by multiple rounds of single-cell measurements, suggesting a potential assay for detecting the drug responses based on the liquid biopsy of cancer patients.

Metal-free graphitic carbon nitride as mechano-catalyst for hydrogen evolution reaction

Graphitic carbon nitride (g-C3N4), as a promising metal-free catalyst for photo-catalytic and electrochemical water splitting, has recently attracted tremendous research interest. However, the underlying catalytic mechanism for the hydrogen evolution reaction (HER) is not fully understood. By using density functional theory calculations, here we have established that the binding free energy of hydrogen atom (ΔGH∗0) on g-C3N4 is very sensitive to mechanical strain, leading to substantial tuning of the HER performance of g-C3N4 at different coverages. The experimentally-observed high HER activity in N-doped graphene supported g-C3N4 (Zheng et al., 2014) is actually attributed to electron-transfer induced strain. A more practical strategy to induce mechanical strain in g-C3N4 is also proposed by doping a bridge carbon atom in g-C3N4 with an isoelectronic silicon atom. The calculated ΔGH∗0 on the Si-doped g-C3N4 is ideal for HER. Our results indicate that g-C3N4 would be an excellent metal-free mechano-catalyst for HER and this finding is expected to guide future experiments to efficiently split water into hydrogen based on the g-C3N4 materials.

Automatic ICD-10 classification of cancers from free-text death certificates

Objective Death certificates provide an invaluable source for cancer mortality statistics; however, this value can only be realised if accurate, quantitative data can be extracted from certificates – an aim hampered by both the volume and variable nature of certificates written in natural language. This paper proposes an automatic classification system for identifying cancer related causes of death from death certificates. Methods Detailed features, including terms, n-grams and SNOMED CT concepts were extracted from a collection of 447,336 death certificates. These features were used to train Support Vector Machine classifiers (one classifier for each cancer type). The classifiers were deployed in a cascaded architecture: the first level identified the presence of cancer (i.e., binary cancer/nocancer) and the second level identified the type of cancer (according to the ICD-10 classification system). A held-out test set was used to evaluate the effectiveness of the classifiers according to precision, recall and F-measure. In addition, detailed feature analysis was performed to reveal the characteristics of a successful cancer classification model. Results The system was highly effective at identifying cancer as the underlying cause of death (F-measure 0.94). The system was also effective at determining the type of cancer for common cancers (F-measure 0.7). Rare cancers, for which there was little training data, were difficult to classify accurately (F-measure 0.12). Factors influencing performance were the amount of training data and certain ambiguous cancers (e.g., those in the stomach region). The feature analysis revealed a combination of features were important for cancer type classification, with SNOMED CT concept and oncology specific morphology features proving the most valuable. Conclusion The system proposed in this study provides automatic identification and characterisation of cancers from large collections of free-text death certificates. This allows organisations such as Cancer Registries to monitor and report on cancer mortality in a timely and accurate manner. In addition, the methods and findings are generally applicable beyond cancer classification and to other sources of medical text besides death certificates.

Porn, censorship, classification and free speech: Global paradoxes in the governance of media content

In this presentation, I reflect upon the global landscape surrounding the governance and classification of media content, at a time of rapid change in media platforms and services for content production and distribution, and contested cultural and social norms. I discuss the tensions and contradictions arising in the relationship between national, regional and global dimensions of media content distribution, as well as the changing relationships between state and non-state actors. These issues will be explored through consideration of issues such as: recent debates over film censorship; the review of the National Classification Scheme conducted by the Australian Law Reform Commission; online controversies such as the future of the Reddit social media site; and videos posted online by the militant group ISIS.

Room temperature gas sensing properties of ultrathin carbon nanotubes by surfactant-free dip coating

Large-scale production of reliable carbon nanotubes (CNTs) based gas sensors involves the development of scalable and reliable processes for the fabrication of films with controlled morphology. Here, we report for the first time on highly scalable, ultrathin CNT films, to be employed as conductometric sensors for NO2 and NH3 detection at room temperature. The sensing films are produced by dip coating using dissolved CNTs in chlorosulfonic acid as a working solution. This surfactant-free approach does not require any post-treatment for the removal of dispersants or any CNTs functionalization, thus promising high quality CNTs for better sensitivity and low production costs. The effect of CNT film thickness and defect density on the gas sensing properties has been investigated. Detection limits of 1 ppm for NO2 and 7 ppm for NH3 have been achieved at room temperature. The experimental results reveal that defect density and film thickness can be controlled to optimize the sensing response. Gas desorption has been accelerated by continuous in-situ UV irradiation.

Catalyst-free plasma enhanced growth of graphene from sustainable sources

Details of a fast and sustainable bottom-up process to grow large area high quality graphene films without the aid of any catalyst are reported in this paper. We used Melaleuca alternifolia, a volatile natural extract from tea tree plant as the precursor. The as-fabricated graphene films yielded a stable contact angle of 135°, indicating their potential application in very high hydrophobic coatings. The electronic devices formed by sandwiching pentacene between graphene and aluminum films demonstrated memristive behavior, and hence, these graphene films could find use in nonvolatile memory devices also.

The validity of the GENEActiv wrist-worn accelerometer for measuring adult sedentary time in free living

OBJECTIVES Based on self-reported measures, sedentary time has been associated with chronic disease and mortality. This study examined the validity of the wrist-worn GENEactiv accelerometer for measuring sedentary time (i.e. sitting and lying) by posture classification, during waking hours in free living adults. DESIGN Fifty-seven participants (age=18-55 years 52% male) were recruited using convenience sampling from a large metropolitan Australian university. METHODS Participants wore a GENEActiv accelerometer on their non-dominant wrist and an activPAL device attached to their right thigh for 24-h (00:00 to 23:59:59). Pearson's Correlation Coefficient was used to examine the convergent validity of the GENEActiv and the activPAL for estimating total sedentary time during waking hours. Agreement was illustrated using Bland and Altman plots, and intra-individual agreement for posture was assessed with the Kappa statistic. RESULTS Estimates of average total sedentary time over 24-h were 623 (SD 103) min/day from the GENEActiv, and 626 (SD 123) min/day from the activPAL, with an Intraclass Correlation Coefficient of 0.80 (95% confidence intervals 0.68-0.88). Bland and Altman plots showed slight underestimation of mean total sedentary time for GENEActiv relative to activPAL (mean difference: -3.44min/day), with moderate limits of agreement (-144 to 137min/day). Mean Kappa for posture was 0.53 (SD 0.12), indicating moderate agreement for this sample at the individual level. CONCLUSIONS The estimation of sedentary time by posture classification of the wrist-worn GENEActiv accelerometer was comparable to the activPAL. The GENEActiv may provide an alternative, easy to wear device based measure for descriptive estimates of sedentary time in population samples

A new type of high-order elements based on the mesh-free interpolations

We propose a new type of high-order elements that incorporates the mesh-free Galerkin formulations into the framework of finite element method. Traditional polynomial interpolation is replaced by mesh-free interpolations in the present high-order elements, and the strain smoothing technique is used for integration of the governing equations based on smoothing cells. The properties of high-order elements, which are influenced by the basis function of mesh-free interpolations and boundary nodes, are discussed through numerical examples. It can be found that the basis function has significant influence on the computational accuracy and upper-lower bounds of energy norm, when the strain smoothing technique retains the softening phenomenon. This new type of high-order elements shows good performance when quadratic basis functions are used in the mesh-free interpolations and present elements prove advantageous in adaptive mesh and nodes refinement schemes. Furthermore, it shows less sensitive to the quality of element because it uses the mesh-free interpolations and obeys the Weakened Weak (W2) formulation as introduced in [3, 5].

FreeS: A fast algorithm to discover frequent free subtrees using a novel canonical form

Web data can often be represented in free tree form; however, free tree mining methods seldom exist. In this paper, a computationally fast algorithm FreeS is presented to discover all frequently occurring free subtrees in a database of labelled free trees. FreeS is designed using an optimal canonical form, BOCF that can uniquely represent free trees even during the presence of isomorphism. To avoid enumeration of false positive candidates, it utilises the enumeration approach based on a tree-structure guided scheme. This paper presents lemmas that introduce conditions to conform the generation of free tree candidates during enumeration. Empirical study using both real and synthetic datasets shows that FreeS is scalable and significantly outperforms (i.e. few orders of magnitude faster than) the state-of-the-art frequent free tree mining algorithms, HybridTreeMiner and FreeTreeMiner.

Free energy calculations of glycosaminoglycan - Protein interactions

Glycosaminoglycans (GAGs) are complex highly charged linear polysaccharides that have a variety of roles in biological processes. We report the first use of molecular dynamics (MD) free energy calculations using the MM/PBSA method to investigate the binding of GAGs to protein molecules, namely the platelet endothelial cell adhesion molecule 1 (PECAM-1) and annexin A2. Calculations of the free energy of the binding of heparin fragments of different sizes reveal the existence of a region of low GAG-binding affinity in domains 5-6 of PECAM-1 and a region of high affinity in domains 2-3, consistent with experimental data and ligand-protein docking studies. A conformational hinge movement between domains 2 and 3 was observed, which allows the binding of heparin fragments of increasing size (pentasaccharides to octasaccharides) with an increasingly higher binding affinity. Similar simulations of the binding of a heparin fragment to annexin A2 reveal the optimization of electrostatic and hydrogen bonding interactions with the protein and protein-bound calcium ions. In general, these free energy calculations reveal that the binding of heparin to protein surfaces is dominated by strong electrostatic interactions for longer fragments, with equally important contributions from van der Waals interactions and vibrational entropy changes, against a large unfavorable desolvation penalty due to the high charge density of these molecules.

Free energy calculations of the interactions of c-Jun-based synthetic peptides with the c-Fos protein

The c-Fos–c-Jun complex forms the activator protein 1 transcription factor, a therapeutic target in the treatment of cancer. Various synthetic peptides have been designed to try to selectively disrupt the interaction between c-Fos and c-Jun at its leucine zipper domain. To evaluate the binding affinity between these synthetic peptides and c-Fos, polarizable and nonpolarizable molecular dynamics (MD) simulations were conducted, and the resulting conformations were analyzed using the molecular mechanics generalized Born surface area (MM/GBSA) method to compute free energies of binding. In contrast to empirical and semiempirical approaches, the estimation of free energies of binding using a combination of MD simulations and the MM/GBSA approach takes into account dynamical properties such as conformational changes, as well as solvation effects and hydrophobic and hydrophilic interactions. The predicted binding affinities of the series of c-Jun-based peptides targeting the c-Fos peptide show good correlation with experimental melting temperatures. This provides the basis for the rational design of peptides based on internal, van der Waals, and electrostatic interactions.