Clinician-driven automated classification of limb fractures from free-text radiology reports

The aim of this research is to report initial experimental results and evaluation of a clinician-driven automated method that can address the issue of misdiagnosis from unstructured radiology reports. Timely diagnosis and reporting of patient symptoms in hospital emergency departments (ED) is a critical component of health services delivery. However, due to disperse information resources and vast amounts of manual processing of unstructured information, a point-of-care accurate diagnosis is often difficult. A rule-based method that considers the occurrence of clinician specified keywords related to radiological findings was developed to identify limb abnormalities, such as fractures. A dataset containing 99 narrative reports of radiological findings was sourced from a tertiary hospital. The rule-based method achieved an F-measure of 0.80 and an accuracy of 0.80. While our method achieves promising performance, a number of avenues for improvement were identified using advanced natural language processing (NLP) techniques.

Automatic classification of free-text radiology reports to identify limb fractures using machine learning and the SNOMED CT ontology

Objective To develop and evaluate machine learning techniques that identify limb fractures and other abnormalities (e.g. dislocations) from radiology reports. Materials and Methods 99 free-text reports of limb radiology examinations were acquired from an Australian public hospital. Two clinicians were employed to identify fractures and abnormalities from the reports; a third senior clinician resolved disagreements. These assessors found that, of the 99 reports, 48 referred to fractures or abnormalities of limb structures. Automated methods were then used to extract features from these reports that could be useful for their automatic classification. The Naive Bayes classification algorithm and two implementations of the support vector machine algorithm were formally evaluated using cross-fold validation over the 99 reports. Result Results show that the Naive Bayes classifier accurately identifies fractures and other abnormalities from the radiology reports. These results were achieved when extracting stemmed token bigram and negation features, as well as using these features in combination with SNOMED CT concepts related to abnormalities and disorders. The latter feature has not been used in previous works that attempted classifying free-text radiology reports. Discussion Automated classification methods have proven effective at identifying fractures and other abnormalities from radiology reports (F-Measure up to 92.31%). Key to the success of these techniques are features such as stemmed token bigrams, negations, and SNOMED CT concepts associated with morphologic abnormalities and disorders. Conclusion This investigation shows early promising results and future work will further validate and strengthen the proposed approaches.

BDNF and TNF-α polymorphisms in memory

Here, we investigate the genetic basis of human memory in healthy individuals and the potential role of two polymorphisms, previously implicated in memory function. We have explored aspects of retrospective and prospective memory including semantic, short term, working and long-term memory in conjunction with brain derived neurotrophic factor (BDNF) and tumor necrosis factor-alpha (TNF-alpha). The memory scores for healthy individuals in the population were obtained for each memory type and the population was genotyped via restriction fragment length polymorphism for the BDNF rs6265 (Val66Met) SNP and via pyrosequencing for the TNF-alpha rs113325588 SNP. Using univariate ANOVA, a significant association of the BDNF polymorphism with visual and spatial memory retention and a significant association of the TNF-alpha polymorphism was observed with spatial memory retention. In addition, a significant interactive effect between BDNF and TNF-alpha polymorphisms was observed in spatial memory retention. In practice visual memory involves spatial information and the two memory systems work together, however our data demonstrate that individuals with the Val/Val BDNF genotype have poorer visual memory but higher spatial memory retention, indicating a level of interaction between TNF-alpha and BDNF in spatial memory retention. This is the first study to use genetic analysis to determine the interaction between BDNF and TNF-alpha in relation to memory in normal adults and provides important information regarding the effect of genetic determinants and gene interactions on human memory.

Structures of life : the role of molecular structures in scientists' work

The visual and multidimensional representations like images and graphical structures related to biology provide great insights into understanding the complexities of different organisms. Especially, life scientists use different representations of molecular structures to answer biological questions and to better understand cellular processes. Combining results from two field studies, we explore the role of molecular structures in life scientists’ current work from a humanfactors perspective. Our main conclusion is that different representations of molecular structures, due to their visual nature, are important for supporting collaboration, constructing new knowledge and supporting scientists’ professional activities in general.

Accurate measurement of the molecular thickness of thin organic shells on small inorganic cores using dynamic light scattering

Dynamic light scattering (DLS) has become a primary nanoparticle characterization technique with applications from materials characterization to biological and environmental detection. With the expansion in DLS use from homogeneous spheres to more complicated nanostructures, comes a decrease in accuracy. Much research has been performed to develop different diffusion models that account for the vastly different structures but little attention has been given to the effect on the light scattering properties in relation to DLS. In this work, small (core size < 5 nm) core-shell nanoparticles were used as a case study to measure the capping thickness of a layer of dodecanethiol (DDT) on Au and ZnO nanoparticles by DLS. We find that the DDT shell has very little effect on the scattering properties of the inorganic core and hence can be ignored to a first approximation. However, this results in conventional DLS analysis overestimating the hydrodynamic size in the volume and number weighted distributions. By introducing a simple correction formula that more accurately yields hydrodynamic size distributions a more precise determination of the molecular shell thickness is obtained. With this correction, the measured thickness of the DDT shell was found to be 7.3 ± 0.3 Å, much less than the extended chain length of 16 Å. This organic layer thickness suggests that on small nanoparticles, the DDT monolayer adopts a compact disordered structure rather than an open ordered structure on both ZnO and Au nanoparticle surfaces. These observations are in agreement with published molecular dynamics results.

Spatially-explicit modelling of grassland classes - an improved method of integrating a climate-based classification model with interpolated climate surfaces

Spatially-explicit modelling of grassland classes is important to site-specific planning for improving grassland and environmental management over large areas. In this study, a climate-based grassland classification model, the Comprehensive and Sequential Classification System (CSCS) was integrated with spatially interpolated climate data to classify grassland in Gansu province, China. The study area is characterized by complex topographic features imposed by plateaus, high mountains, basins and deserts. To improve the quality of the interpolated climate data and the quality of the spatial classification over this complex topography, three linear regression methods, namely an analytic method based on multiple regression and residues (AMMRR), a modification of the AMMRR method through adding the effect of slope and aspect to the interpolation analysis (M-AMMRR) and a method which replaces the IDW approach for residue interpolation in M-AMMRR with an ordinary kriging approach (I-AMMRR), for interpolating climate variables were evaluated. The interpolation outcomes from the best interpolation method were then used in the CSCS model to classify the grassland in the study area. Climate variables interpolated included the annual cumulative temperature and annual total precipitation. The results indicated that the AMMRR and M-AMMRR methods generated acceptable climate surfaces but the best model fit and cross validation result were achieved by the I-AMMRR method. Twenty-six grassland classes were classified for the study area. The four grassland vegetation classes that covered more than half of the total study area were "cool temperate-arid temperate zonal semi-desert", "cool temperate-humid forest steppe and deciduous broad-leaved forest", "temperate-extra-arid temperate zonal desert", and "frigid per-humid rain tundra and alpine meadow". The vegetation classification map generated in this study provides spatial information on the locations and extents of the different grassland classes. This information can be used to facilitate government agencies' decision-making in land-use planning and environmental management, and for vegetation and biodiversity conservation. The information can also be used to assist land managers in the estimation of safe carrying capacities which will help to prevent overgrazing and land degradation.

The molecular structure of the vanadate mineral mottramite [PbCu(VO4)(OH)] from Tsumeb, Namibia – a vibrational spectroscopic study

We have studied a mineral sample of mottramite PbCu(VO4)(OH) from Tsumeb, Namibia using a combination of scanning electron microscopy with EDX, Raman and infrared spectroscopy. Chemical analysis shows principally the elements V, Pb and Cu. Ca occurs as partial substitution of Pb as well as P and As in substitution to V. Minor amounts of Si and Cr were also observed. The Raman band of mottramite at 829 cm-1, is assigned to the ν1 symmetric (VO-4) ) stretching mode. The complexity of the spectra is attributed to the chemical composition of the Tsumeb mottramite. The ν3 antisymmetric vibrational mode of mottramite is observed as very low intensity bands at 716 and 747 cm-1. The series of Raman bands at 411, 439, 451 cm-1 and probably also the band at 500 cm-1 are assigned to the (VO-4) ν2 bending mode. The series of Raman bands at 293, 333 and 366 cm-1 are attributed to the (VO-4) ) ν4 bending modes. The ν3, ν3 and ν4 regions are complex for both minerals and this is attributed to symmetry reduction of the vanadate unit from Td to Cs.

Vibrational spectroscopic study of the sulphate mineral glaucocerinite (Zn,Cu)10Al6(SO4)3(OH)32⋅18H2O – a natural layered double hydroxide

We have studied the molecular structure of the mineral glaucocerinite (Zn,Cu)5Al3(SO4)1.5(OH)16�9(H2O) using a combination of Raman and infrared spectroscopy. The mineral is one of the hydrotalcite supergroup of natural layered double hydroxides. The Raman spectrum is characterised by an intense Raman band at 982 cm�1 with a low intensity band at 1083 cm�1. These bands are attributed to the sulphate symmetric and antisymmetric stretching mode. The infrared spectrum is quite broad with a peak at 1020 cm�1. A series of Raman bands at 546, 584, 602, 625 and 651 cm�1 are assigned to the m4 (SO4)2� bending modes. The observation of multiple bands provides evidence for the reduction in symmetry of the sulphate anion from Td to C2v or even lower symmetry. The Raman band at 762 cm�1 is attributed to a hydroxyl deformation mode associated with AlOH units. Vibrational spectroscopy enables aspects of the molecular structure of glaucocerinite to be determined.

A vibrational spectroscopic study of the phosphate mineral churchite (REE)(PO4)⋅2H2O

Vibrational spectroscopy has been used to study the rare earth mineral churchite of formula (REE)(PO4)-⋅2H2O. The mineral contains a range of rare earth metals including yttrium depending on the locality. The Raman spectra of churchite-(REE) are characterized by an intense sharp band at 984 cm-1 assigned to the v1 (PO¾-) symmetric stretching mode. A lower intensity band observed at around 1067 cm-1 is attributed to the v3 (PO¾-) antisymmetric stretching mode. The (PO¾-) bending modes are observed at 497 cm-1 (v2) and 565 cm-1(v4). Raman bands at 649 and 681 cm-1 are assigned to water librational modes. Vibrational spectroscopy enables aspects of the structure of churchite to be ascertained.

The molecular structure of the borate mineral rhodizite (K, Cs)Al4Be4(B, Be)12O28 – A vibrational spectroscopic study

We have studied the borate mineral rhodizite (K, Cs)Al4Be4(B, Be)12O28 using a combination of DEM with EDX and vibrational spectroscopic techniques. The mineral occurs as colorless, gray, yellow to white crystals in the triclinic crystal system. The studied sample is from the Antandrokomby Mine, Sahatany valley, Madagascar. The mineral is prized as a semi-precious jewel. Semi-quantitative chemical composition shows a Al, Ca, borate with minor amounts of K, Mg and Cs. The mineral has a characteristic borate Raman spectrum and bands are assigned to the stretching and bending modes of B, Be and Al. No Raman bands in the OH stretching region were observed.

The molecular structure of the phosphate mineral beraunite Fe2+Fe⅗+(PO4)4(OH)5⋅4H2O– A vibrational spectroscopic study

The mineral beraunite from Boca Rica pegmatite in Minas Gerais with theoretical formula Fe2+Fe5 3+(PO4)4(OH)5⋅4H2O has been studied using a combination of electron microscopy with EDX and vibrational spectroscopic techniques. Raman spectroscopy identifies an intense band at 990 cm-1 and 1011 cm-1. These bands are attributed to the PO4 3- v, symmetric stretching mode. The m3 antisymmetric stretching modes are observed by a large number of Raman bands. The Raman bands at 1034, 1051, 1058, 1069 and 1084 together with the Raman bands at 1098, 1116, 1133, 1155 and 1174 cm-1 are assigned to the m3 antisymmetric stretching vibrations of PO4 3- and the HOPO3 2- units. The observation of these multiple Raman bands in the symmetric and antisymmetric stretching region gives credence to the concept that both phosphate and hydrogen phosphate units exist in the structure of beraunite. The series of Raman bands at 567, 582,601, 644, 661, 673, and 687 cm-1 are assigned to the PO4 3- v2 bending modes. The series of Raman bands at 437, 468, 478, 491, 503 cm-1 are attributed to the PO4 3- and OPO3 2- v4 bending modes. No Raman bands of beraunite which could be attributed to the hydroxyl stretching unit were observed. Infrared bands at 3511 and 3359 cm-1 are ascribed to the OH stretching vibration of the OH units. Very broad bands at 3022 and 3299 cm-1 are attributed to the OH stretching vibrations of water. Vibrational spectroscopy offers insights into the molecular structure of the phosphate mineral beraunite.

Impacts of climatic factors on evolution of molecular diversity and the natural distribution of wild stocks of the giant freshwater prawn (Macrobrachium rosenbergii)

Natural distributions of most freshwater taxa are restricted geographically, a pattern that reflects dispersal limitation. Macrobrachium rosenbergii is unusual because it occurs naturally in rivers from near Pakistan in the west, across India and Bangladesh to the Malay Peninsula, and across the Sunda Shelf and Indonesian archipelago to western Java. Individuals cannot tolerate full marine conditions, so dispersal between river drainage basins must occur at limited geographical scales when ecological or climatic factors are favorable. We examined molecular diversity in wild populations of M. rosenbergii across its complete natural range to document patterns of diversity and to relate them to factors that have driven evolution of diversity in this species. We found 3 clades in the mitochondrial deoxyribonucleic acid (mtDNA) data set that corresponded geographically with eastern, central, and western sets of haplotypes that last shared a common ancestor 1 × 106 y ago. The eastern clade was closest to the common ancestor of all 3 clades and to the common ancestor with its congener, Macrobrachium spinipes, distributed east of Huxley's Line. Macrobrachium rosenbergii could have evolved in the western Indonesian archipelago and spread westward during the early to mid-Pleistocene to India and Sri Lanka. Additional groups identified in the nuclear DNA data set in the central and western clades probably indicate secondary contact via dispersal between regions and modern introductions that have mixed nuclear and mtDNA genes. Pleistocene sea-level fluctuations can explain dispersal across the Indonesian archipelago and parts of mainland southeastern Asia via changing river drainage connections in shallow seas on wide continental shelves. At the western end of the modern distribution where continental shelves are smaller, intermittent freshwater plumes from large rivers probably permitted larval dispersal across inshore areas of lowered salinity.

Molecular dynamics simulation of mechanical behavior of osteopontin-hydroxyapatite interfaces

Bone is characterized with an optimized combination of high stiffness and toughness. The understanding of bone nanomechanics is critical to the development of new artificial biological materials with unique properties. In this work, the mechanical characteristics of the interfaces between osteopontin (OPN, a noncollagenous protein in extrafibrillar protein matrix) and hydroxyapatite (HA, a mineral nanoplatelet in mineralized collagen fibrils) were investigated using molecular dynamics method. We found that the interfacial mechanical behaviour is governed by the electrostatic attraction between acidic amino acid residues in OPN and calcium in HA. Higher energy dissipation is associated with the OPN peptides with a higher number of acidic amino acid residues. When loading in the interface direction, new bonds between some acidic residues and HA surface are formed, resulting in a stick-slip type motion of OPN peptide on the HA surface and high interfacial energy dissipation. The formation of new bonds during loading is considered to be a key mechanism responsible for high fracture resistance observed in bone and other biological materials.

Vibrational spectroscopic characterization of the sulphate mineral leightonite K2Ca2Cu(SO4)4⋅2H2O – Implications for the molecular structure

The mineral leightonite, a rare sulphate mineral of formula K2Ca2Cu(SO4)4.2H2O, has been studied using a combination of electron probe and vibrational spectroscopy. The mineral is characterized by an intense Raman band at 991 cm-1 attributed to the SO2- 4 m1 symmetric stretching mode. A series of Raman bands at 1047, 1120, 1137, 1163 and 1177 cm-1 assigned to the SO2- 4 m3 antisymmetric stretching modes. The observation of multiple bands shows that the symmetry of the sulphate anion is reduced. Multiple Raman and infrared bands in the OH stretching region shows that water in the structure of leightonite is in a range of molecular environments.