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.

Security analysis of Australian and E.U. e-passport implementation

This paper makes a formal security analysis of the current Australian e-passport implementation using model checking tools CASPER/CSP/FDR. We highlight security issues in the current implementation and identify new threats when an e-passport system is integrated with an automated processing system like SmartGate. The paper also provides a security analysis of the European Union (EU) proposal for Extended Access Control (EAC) that is intended to provide improved security in protecting biometric information of the e-passport bearer. The current e-passport specification fails to provide a list of adequate security goals that could be used for security evaluation. We fill this gap; we present a collection of security goals for evaluation of e-passport protocols. Our analysis confirms existing security weaknesses that were previously identified and shows that both the Australian e-passport implementation and the EU proposal fail to address many security and privacy aspects that are paramount in implementing a secure border control mechanism. ACM Classification C.2.2 (Communication/Networking and Information Technology – Network Protocols – Model Checking), D.2.4 (Software Engineering – Software/Program Verification – Formal Methods), D.4.6 (Operating Systems – Security and Privacy Protection – Authentication)

Understanding the abnormal brain activity in epilepsy as a potential predictor of the onset of an epileptic seizure

The Brain Research Institute (BRI) uses various types of indirect measurements, including EEG and fMRI, to understand and assess brain activity and function. As well as the recovery of generic information about brain function, research also focuses on the utilisation of such data and understanding to study the initiation, dynamics, spread and suppression of epileptic seizures. To assist with the future focussing of this aspect of their research, the BRI asked the MISG 2010 participants to examine how the available EEG and fMRI data and current knowledge about epilepsy should be analysed and interpreted to yield an enhanced understanding about brain activity occurring before, at commencement of, during, and after a seizure. Though the deliberations of the study group were wide ranging in terms of the related matters considered and discussed, considerable progress was made with the following three aspects. (1) The science behind brain activity investigations depends crucially on the quality of the analysis and interpretation of, as well as the recovery of information from, EEG and fMRI measurements. A number of specific methodologies were discussed and formalised, including independent component analysis, principal component analysis, profile monitoring and change point analysis (hidden Markov modelling, time series analysis, discontinuity identification). (2) Even though EEG measurements accurately and very sensitively record the onset of an epileptic event or seizure, they are, from the perspective of understanding the internal initiation and localisation, of limited utility. They only record neuronal activity in the cortical (surface layer) neurons of the brain, which is a direct reflection of the type of electrical activity they have been designed to record. Because fMRI records, through the monitoring of blood flow activity, the location of localised brain activity within the brain, the possibility of combining fMRI measurements with EEG, as a joint inversion activity, was discussed and examined in detail. (3) A major goal for the BRI is to improve understanding about ``when'' (at what time) an epileptic seizure actually commenced before it is identified on an eeg recording, ``where'' the source of this initiation is located in the brain, and ``what'' is the initiator. Because of the general agreement in the literature that, in one way or another, epileptic events and seizures represent abnormal synchronisations of localised and/or global brain activity the modelling of synchronisations was examined in some detail. References C. M. Michel, G. Thut, S. Morand, A. Khateb, A. J. Pegna, R. Grave de Peralta, S. Gonzalez, M. Seeck and T. Landis, Electric source imaging of human brain functions, Brain Res. 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Binary image steganographic techniques classification based on multi-class steganalysis

In this paper, we propose a new multi-class steganalysis for binary image. The proposed method can identify the type of steganographic technique used by examining on the given binary image. In addition, our proposed method is also capable of differentiating an image with hidden message from the one without hidden message. In order to do that, we will extract some features from the binary image. The feature extraction method used is a combination of the method extended from our previous work and some new methods proposed in this paper. Based on the extracted feature sets, we construct our multi-class steganalysis from the SVM classifier. We also present the empirical works to demonstrate that the proposed method can effectively identify five different types of steganography.

Automated classification of limb fractures from free-text radiology reports using a clinician-informed gazetteer methodology

Background Timely diagnosis and reporting of patient symptoms in hospital emergency departments (ED) is a critical component of health services delivery. However, due to dispersed information resources and a vast amount of manual processing of unstructured information, accurate point-of-care diagnosis is often difficult. Aims The aim of this research is to report initial experimental evaluation of a clinician-informed automated method for the issue of initial misdiagnoses associated with delayed receipt of unstructured radiology reports. Method A method was developed that resembles clinical reasoning for identifying limb abnormalities. The method consists of a gazetteer of keywords related to radiological findings; the method classifies an X-ray report as abnormal if it contains evidence contained in the gazetteer. A set of 99 narrative reports of radiological findings was sourced from a tertiary hospital. Reports were manually assessed by two clinicians and discrepancies were validated by a third expert ED clinician; the final manual classification generated by the expert ED clinician was used as ground truth to empirically evaluate the approach. Results The automated method that attempts to individuate limb abnormalities by searching for keywords expressed by clinicians achieved an F-measure of 0.80 and an accuracy of 0.80. Conclusion While the automated clinician-driven method achieved promising performances, a number of avenues for improvement were identified using advanced natural language processing (NLP) and machine learning techniques.

Classification of cancer-related death certificates using machine learning

Background Cancer monitoring and prevention relies on the critical aspect of timely notification of cancer cases. However, the abstraction and classification of cancer from the free-text of pathology reports and other relevant documents, such as death certificates, exist as complex and time-consuming activities. Aims In this paper, approaches for the automatic detection of notifiable cancer cases as the cause of death from free-text death certificates supplied to Cancer Registries are investigated. Method A number of machine learning classifiers were studied. Features were extracted using natural language techniques and the Medtex toolkit. The numerous features encompassed stemmed words, bi-grams, and concepts from the SNOMED CT medical terminology. The baseline consisted of a keyword spotter using keywords extracted from the long description of ICD-10 cancer related codes. Results Death certificates with notifiable cancer listed as the cause of death can be effectively identified with the methods studied in this paper. A Support Vector Machine (SVM) classifier achieved best performance with an overall F-measure of 0.9866 when evaluated on a set of 5,000 free-text death certificates using the token stem feature set. The SNOMED CT concept plus token stem feature set reached the lowest variance (0.0032) and false negative rate (0.0297) while achieving an F-measure of 0.9864. The SVM classifier accounts for the first 18 of the top 40 evaluated runs, and entails the most robust classifier with a variance of 0.001141, half the variance of the other classifiers. Conclusion The selection of features significantly produced the most influences on the performance of the classifiers, although the type of classifier employed also affects performance. In contrast, the feature weighting schema created a negligible effect on performance. Specifically, it is found that stemmed tokens with or without SNOMED CT concepts create the most effective feature when combined with an SVM classifier.

Epidemiological and molecular features of dengue virus type-1 in New Caledonia, South Pacific, 2001–2013

Background The epidemiology of dengue in the South Pacific has been characterized by transmission of a single dominant serotype for 3–5 years, with subsequent replacement by another serotype. From 2001 to 2008 only DENV-1 was reported in the Pacific. In 2008, DENV-4 emerged and quickly displaced DENV-1 in the Pacific, except in New Caledonia (NC) where DENV-1 and DENV-4 co-circulated in 2008–2009. During 2012–2013, another DENV-1 outbreak occurred in NC, the third DENV-1 outbreak in a decade. Given that dengue is a serotype-specific immunizing infection, the recurrent outbreaks of a single serotype within a 10-year period was unexpected. Findings This study aimed to inform this phenomenon by examining the phylogenetic characteristics of the DENV-1 viruses in NC and other Pacific islands between 2001 and 2013. As a result, we have demonstrated that NC experienced introductions of viruses from both the Pacific (genotype IV) and South-east Asia (genotype I). Moreover, whereas genotype IV and I were co-circulating at the beginning of 2012, we observed that from the second half of 2012, i.e. during the major DENV-1 outbreak, all analyzed viruses were genotype I suggesting that a genotype switch occurred. Conclusions Repeated outbreaks of the same dengue serotype, as observed in NC, is uncommon in the Pacific islands. Why the earlier DENV-1 outbreaks did not induce sufficient herd immunity is unclear, and likely multifactorial, but the robust vector control program may have played a role by limiting transmission and thus maintaining a large susceptible pool in the population. Keywords: Dengue; Phylogeny; Genotype; Epidemics; New Caledonia

Supramolecular selection in molecular and framework co-crystals

An ongoing challenge in chemistry and crystal engineering is the synthesis of functional materials with predictable structures and customisable properties. This may be achieved by crystallising mixtures of different compounds. Co-crystals formed through this method have predictable structures and their properties may be tuned by varying the ratio of the compounds in the crystallising solution. This thesis examines single crystals formed by the co-crystallisation of metal complexes that have similar structures but different physical or chemical properties. A variety of new compounds with interesting properties were prepared, characterised and their significance in the context of crystal engineering was explored.

Part 1 MOO methods for multidisciplinary design using parallel evolutionary algorithms, game theory and hierarchical topology. (Part 1.) Theoretical aspects

Two lecture notes describe recent developments of evolutionary multi objective optimization (MO) techniques in detail and their advantages and drawbacks compared to traditional deterministic optimisers. The role of Game Strategies (GS), such as Pareto, Nash or Stackelberg games as companions or pre-conditioners of Multi objective Optimizers is presented and discussed on simple mathematical functions in Part I , as well as their implementations on simple aeronautical model optimisation problems on the computer using a friendly design framework in Part II. Real life (robust) design applications dealing with UAVs systems or Civil Aircraft and using the EAs and Game Strategies combined material of Part I & Part II are solved and discussed in Part III providing the designer new compromised solutions useful to digital aircraft design and manufacturing. Many details related to Lectures notes Part I, Part II and Part III can be found by the reader in [68].

A Survey of the 2010 Quartz Crystal Microbalance Literature

In 2010 there has again been an increase in the number of papers published involving piezoelectric acoustic sensors, or quartz crystal microbalances (QCM), when compared to the last period reviewed 2006-2009. The average number of QCM publications per annum was 124 in the period 2001-2005, 223 in the period 2006-9, and 273 in 2010. There are trends towards increasing use of QCM in the study of protein adsorption to surfaces (93% increase), homeostasis (67% increase), protein-protein interactions (40% increase), and carbohydrates (43% increase). New commercial systems have been released that are driving the uptake of the technology for characterisation of binding specificities, affinities, kinetics and conformational changes associated with a molecular recognition event. This article highlights theoretical and practical aspects of the principals that underpin acoustic analysis, then reviews exemplary papers in key application areas involving small molecular weight ligands, carbohydrates, proteins, nucleic acids, viruses, bacteria, cells, and membrane interfaces.