R1STM: One-class support tensor machine with randomised kernel

Identifying unusual or anomalous patterns in an underlying dataset is an important but challenging task in many applications. The focus of the unsupervised anomaly detection literature has mostly been on vectorised data. However, many applications are more naturally described using higher-order tensor representations. Approaches that vectorise tensorial data can destroy the structural information encoded in the high-dimensional space, and lead to the problem of the curse of dimensionality. In this paper we present the first unsupervised tensorial anomaly detection method, along with a randomised version of our method. Our anomaly detection method, the One-class Support Tensor Machine (1STM), is a generalisation of conventional one-class Support Vector Machines to higher-order spaces. 1STM preserves the multiway structure of tensor data, while achieving significant improvement in accuracy and efficiency over conventional vectorised methods. We then leverage the theory of nonlinear random projections to propose the Randomised 1STM (R1STM). Our empirical analysis on several real and synthetic datasets shows that our R1STM algorithm delivers comparable or better accuracy to a state-of-the-art deep learning method and traditional kernelised approaches for anomaly detection, while being approximately 100 times faster in training and testing.

Structure of Mycobacterium tuberculosis RuvA, a protein involved in recombination

The process of recombinational repair is crucial for maintaining genomic integrity and generating biological diversity. In association with RuvB and RuvC, RuvA plays a central role in processing and resolving Holliday junctions, which are a critical intermediate in homologous recombination. Here, the cloning, purification and structure determination of the RuvA protein from Mycobacterium tuberculosis (MtRuvA) are reported. Analysis of the structure and comparison with other known RuvA proteins reveal an octameric state with conserved subunit-subunit interaction surfaces, indicating the requirement of octamer formation for biological activity. A detailed analysis of plasticity in the RuvA molecules has led to insights into the invariant and variable regions, thus providing a framework for understanding regional flexibility in various aspects of RuvA function.

A 3D in vitro model reflecting the androgen deprivation state in prostate cancer bone metastasis

In castrate-resistant prostate cancer (CRPC), the prevailing organ for metastasis is bone, where the survival of cancer cells is regulated by the permissive metastatic niche offered by the bone marrow. The tumour microenvironment and cellular interactions with the matrix and bone cells enable metastasis and lead to cancer cells becoming androgen resistant. Hence, 3D models that mimic CRPC in terms of an androgen deprivation state (ADS) are needed to identify the mechanisms for CPRC growth in bone and further develop therapeutic strategies.

Experimental studies on a two stage pulse tube cryocooler reaching 2.5K

A two stage Pulse Tube Cryocooler (PTC) is designed and fabricated which reaches a no-load temperature of 2.5K in the second stage and similar to 60 K in the first stage respectively. The system provides a cooling power of similar to 250 mW at 5K in the second stage. Stainless steel meshes (size 200) and lead (Pb) granules are used as the first stage regenerator materials and combination of Pb with Er3Ni / HoCu2 are used as the second stage regenerator materials. The system operates at 1.6 Hz using a 6 kW water cooled helium compressor. Studies conducted by varying the dimensions of Pulse Tubes and regenerators show that the dimensions of the Pulse Tubes are more critical to the performance of the Cryocooler than those of the regenerators. Experimental studies show that the optimum volume ratios of Er3Ni to Pb and HoCu2 to Pb in the second stage regenerator should be 3:2 and 2:3 respectively for the best performance. Further, systems with HoCu2 performed better than those with Er3Ni. The theoretical analysis of the system has been carried out using a simple isothermal model. The experimentally measured cooling powers are in good agreement with the theoretical predictions.

Inferring molecular function: contributions from functional linkages

In the current era of high-throughput sequencing and structure determination, functional annotation has become a bottleneck in biomedical science. Here, we show that automated inference of molecular function using functional linkages among genes increases the accuracy of functional assignments by >= 8% and enriches functional descriptions in >= 34% of top assignments. Furthermore, biochemical literature supports >80% of automated inferences for previously unannotated proteins. These results emphasize the benefit of incorporating functional linkages in protein annotation.

Ultrasonic propagation through aqueous solutions of acetates

Using the pulse method in the range of 2 to 26Mc's the ultrasonic absorption, velocity and the adiabatic compressibility have been studied in eleven aqueous acetate solutions up to a concentration of 1 mole/litre. The substances studied are the acetates of lithium, sodium, potassium, ammonium, magnesium, calcium, strontium, barium, zinc, cadmium and lead. Absorption in mercuric acetate has been studied only at 2 and 6 Mc/s. Two regions of relaxation are noticed, one below 10 Mc/s and the other between 10 and 26 Mc/s. The first relaxation is ascribed to the dissociation reaction of the salt and the second one to the monomerdimer reaction of the acetic acid formed by the hydrolysis of the salt in water.

HARMONY: a server for the assessment of protein structures

Protein structure validation is an important step in computational modeling and structure determination. Stereochemical assessment of protein structures examine internal parameters such as bond lengths and Ramachandran (phi, psi) angles. Gross structure prediction methods such as inverse folding procedure and structure determination especially at low resolution can sometimes give rise to models that are incorrect due to assignment of misfolds or mistracing of electron density maps. Such errors are not reflected as strain in internal parameters. HARMONY is a procedure that examines the compatibility between the sequence and the structure of a protein by assigning scores to individual residues and their amino acid exchange patterns after considering their local environments. Local environments are described by the backbone conformation, solvent accessibility and hydrogen bonding patterns. We are now providing HARMONY through a web server such that users can submit their protein structure files and, if required, the alignment of homologous sequences. Scores are mapped on the structure for subsequent examination that is useful to also recognize regions of possible local errors in protein structures. HARMONY server is located at http://caps.ncbs.res.in/harmony/

Elastic properties of phosphotungstate glasses

Elastic properties of potassium and lead phosphotungstate glasses have been investigated using ultrasonic velocity measurements. The composition dependence of elastic moduli in WO3-K2O-P2O5 glasses suggests that at low alkali oxide concentrations the atomic ring size increases by network modification, which results in the decrease of elastic moduli. In the highly modified regime, due to the presence of coulombic interaction, the rate of decrease of elastic moduli is reduced. In the WO3-PbO-P2O5 glasses the behaviour of elastic moduli suggests that PbO behaves both as a network former and network modifier. The incorporation of PbO into the network is quantitatively determined by the concentration of P2O5 in the system. The results are consistent with the structural model proposed earlier, based on characterization studies.

Iäkkäiden lääkehoitoihin liittyvien riskien kartoittaminen – Arviointityökalun kehittäminen Delfoi-menetelmällä

Tutkimuksen taustalla on väestön ikääntyminen ja iäkkäiden lisääntynyt lääkkeiden käyttö. Ikääntyminen aiheuttaa elimistössä useita muutoksia, jotka voivat muuttaa lääkevastetta ja altistaa potilaan haittavaikutuksille. Iäkkäillä riski joutua sairaalaan lääkkeen haittavaikutuksen vuoksi on arvioitu olevan neljä kertaa suurempi kuin nuoremmilla. Monet lääkkeiden yhteis- ja haittavaikutukset olisivat ehkäistävissä välttämällä iäkkäillä tiettyjä lääkeaineita. Iäkkäiden lääkehoitojen seurantaa ja arviointia varten on kehitetty erilaisia suosituksia sekä Suomessa että kansainvälisesti. Tutkimuksen tavoitteena oli luoda Suomen oloihin soveltuva, hoitajien koulutettuina käytettävissä oleva, avohoidon yli 65-vuotiaiden iäkkäiden lääkitykseen liittyviä riskejä arvioiva työkalu. Työkalun avulla voitaisiin löytää ne potilaat, joiden lääkitykseen liittyy paljon riskejä. Tutkimuksen aineistona olivat laaja kansainvälinen kirjallisuuskatsaus iäkkäiden lääkehoitoihin liittyvistä tekijöistä sekä asiantuntijakommentoinnit, joiden perusteella luotiin alustava arviointityökalu. Alustava arviointityökalu validoitiin kolmikierroksisella Delfoi-menetelmällä. Delfoi-menetelmä on laadullinen konsensusmenetelmä, joka perustuu asiantuntijoiden arvioihin tutkittavasta asiasta. Kaksi ensimmäistä Delfoi-kierrosta mittasivat alustavan arviointityökalun kohtien soveltuvuutta ja kolmas kierros kohtien tärkeyttä arvioitaessa iäkkään lääkityksiin liittyviä riskejä. Tutkimuksen Delfoi-kierroksien vastaajiksi pyydettiin 33 geriatrian asiantuntijaa, joista vastaajiksi lupautui 11 lääkäriä, 3 proviisoria ja 4 sairaanhoitajaa. Delfoi-kierrosten tuloksia analysoitiin sekä kvantitatiivisesti että kvalitatiivisesti. Tutkimuksen tuloksena saatu arviointityökalu käsittää 19 iäkkäiden lääkehoitoa arvioivaa kohtaa. Asiantuntijapaneelin mukaan kaikki arviointityökalun lääkitykseen liittyviä riskejä mittaavat kohdat ovat tärkeitä tai jokseenkin tärkeitä, joten työkalun voidaan olettaa olevan validi mitattaessa lääkitykseen liittyviä riskejä. Jatkotutkimuksissa työkalun käytettävyyttä sekä riskien mittaamiskykyä tulee testata sekä arviointityökalun käyttäjien että potilaiden keskuudessa. Kehitettyä työkalua voidaan jatkossa hyödyntää esimerkiksi koulutustarkoituksissa sen varsinaisen käyttötarkoituksen lisäksi. Työkalun avulla iäkkäiden lääkehoitoa voidaan tulevaisuudessa toteuttaa entistä turvallisemmin ja tarkoituksenmukaisemmin.

Progression of diffuse gliomas - from the first diagnosis to recurrence

Gliomas are the most frequent primary brain tumours. The cardinal features of gliomas are infiltrative growth pattern and progression from low-grade tumours to a more malignant phenotype. These features of gliomas generally prevent their complete surgical excision and cause their inherent tendency to recur after initial treatment and lead to poor long-term prognosis. Increasing knowledge about the molecular biology of gliomas has produced new markers that supplement histopathological diagnostics. Molecular markers are also used to evaluate the prognosis and predict therapeutic response. The purpose of this thesis is to study molecular events involved in the malignant progression of gliomas. Gliomas are highly vascularised tumours. Contrast enhancement in magnetic resonance imaging (MRI) reflects a disrupted blood-brain barrier and is often seen in malignant gliomas. In this thesis, 62 astrocytomas, oligodendrogliomas and oligoastrocytomas were studied by MRI and immunohistochemistry. Contrast enhancement in preoperative MRI was associated with angiogenesis, tumour cell proliferation and histological grade of gliomas. Activation of oncogenes by gene amplification is a common genetic aberration in gliomas. EGFR amplification on chromosome 7p12 occurs in 30-40% of glioblastomas. PDGFRA, KIT and VEGFR2 are receptor tyrosine kinase genes located on chromosome 4q12. Amplification of these genes was studied using in situ hybridisation in the primary and recurrent astrocytomas, oligodendrogliomas and oligoastrocytomas of 87 patients. PDGFRA, KIT or VEGFR2 amplification was found in 22% of primary tumours and 36% of recurrent tumours including low-grade and malignant gliomas. The most frequent aberration was KIT amplification, which occurred in 10% of primary tumours and in 27% of recurrent tumours. The expression of ezrin, cyclooxygenase 2 (COX-2) and HuR was studied immunohistochemically in a series of primary and recurrent gliomas of 113 patients. Ezrin is a cell membrane-cytoskeleton linking-protein involved in the migration of glioma cells. The COX-2 enzyme is implicated in the carcinogenesis of epithelial neoplasms and is overexpressed in gliomas. HuR is an RNA-stabilising protein, which regulates the expression of several proteins including COX-2. Ezrin, COX-2 and HuR were associated with histological grade and the overall survival of glioma patients. However, in multivariate analysis they were not independent prognostic factors. In conclusion, these results suggest that contrast enhancement in MRI can be used as a surrogate marker for the proliferative and angiogenic potential of gliomas. Aberrations of PDGFRA, KIT and VEGFR2 genes, as well as the dysregulated expression of ezrin, COX-2 and HuR proteins, are linked to the progression of gliomas.

The effect of particle size on performance of cathode materials of Li-ion batteries

Beginning with the ‘frog-leg experiment’ by Galvani (1786), followed by the demonstrations of Volta pile by Volta (1792) and lead-acid accumulator by Plante´ (1859), several battery chemistries have been developed and realized commercially. The development of lithium-ion rechargeable battery in the early 1990s is a breakthrough in the science and technology of batteries. Owing to its high energy density and high operating voltage, the Li-ion battery has become the battery of choice for various portable applications such as note-book computers, cellular telephones, camcorders, etc. Huge efforts are underway in succeeding the development of large size batteries for electric vehicle applications. The origin of lithium-ion battery lies in the discovery that Li+-ions can reversibly be intercalated into/de-intercalated from the Van der Walls gap between graphene sheets of carbon materials at a potential close to the Li/Li+ electrode. By employing carbon as the negative electrode material in rechargeable lithium-ion batteries, the problems associated with metallic lithium in rechargeable lithium batteries have been mitigated. Complimentary investigations on intercalation compounds based on transition metals have resulted in establishing LiCoO2 as the promising cathode material. By employing carbon and LiCoO2, respectively, as the negative and positive electrodes in a non-aqueous lithium-salt electrolyte,a Li-ion cell with a voltage value of about 3.5 V has resulted.Subsequent to commercialization of Li-ion batteries, a number of research activities concerning various aspects of the battery components began in several laboratories across the globe. Regarding the positive electrode materials, research priorities have been to develop different kinds of active materials concerning various aspects such as safety, high capacity, low cost, high stability with long cycle-life, environmental compatibility,understanding relationships between crystallographic and electrochemical properties. The present review discusses the published literature on different positive electrode materials of Li-ion batteries, with a focus on the effect of particle size on electrochemical performance.

Thermo-mechanical stability of a cellular assembly of carbon nanotubes in air

Carbon nanotubes (CNT) in bulk form offer outstanding structural and functional properties, and are shown to remain viscoelastic over a wide temperature range (77-1273 K) under inert conditions. We examine the quasi-static and dynamic compressive mechanical response of these cellular CNT materials in ambient air up to a temperature of 773 K. In uniaxial quasi-static compression, several displacement bursts are noted at large strains. These are results of the slippage and zipping of the CNT, and lead to significant mechanical energy absorption. Results of the dynamic mechanical analysis experiments show no degradation in storage modulus and loss coefficient for up to 20 h at 673 K. Hence, these stable cellular CNT structures can be utilized up to a maximum temperature of 673 K in air, which is much higher than the best polymers. (C) 2012 Elsevier Ltd. All rights reserved.

Network approaches to drug discovery

Introduction: Advances in genomics technologies are providing a very large amount of data on genome-wide gene expression profiles, protein molecules and their interactions with other macromolecules and metabolites. Molecular interaction networks provide a useful way to capture this complex data and comprehend it. Networks are beginning to be used in drug discovery, in many steps of the modern discovery pipeline, with large-scale molecular networks being particularly useful for the understanding of the molecular basis of the disease. Areas covered: The authors discuss network approaches used for drug target discovery and lead identification in the drug discovery pipeline. By reconstructing networks of targets, drugs and drug candidates as well as gene expression profiles under normal and disease conditions, the paper illustrates how it is possible to find relationships between different diseases, find biomarkers, explore drug repurposing and study emergence of drug resistance. Furthermore, the authors also look at networks which address particular important aspects such as off-target effects, combination-targets, mechanism of drug action and drug safety. Expert opinion: The network approach represents another paradigm shift in drug discovery science. A network approach provides a fresh perspective of understanding important proteins in the context of their cellular environments, providing a rational basis for deriving useful strategies in drug design. Besides drug target identification and inferring mechanism of action, networks enable us to address new ideas that could prove to be extremely useful for new drug discovery, such as drug repositioning, drug synergy, polypharmacology and personalized medicine.

Can Superflares Occur on Our Sun?

Recent observations of Sun-like stars, similar to our Sun in their surface temperature (5600-6000 K) and slow rotation (rotational period > 10 d), using the Kepler satellite by Maehara et al. (2012, Nature, 485, 478) have revealed the existence of superflares (with energy of 10(33)-10(35) erg). From statistical analyses of these superflares, it was found that superflares with energy of 10(34) erg occur once in 800 yr, and superflares with 10(35) erg occur once in 5000 yr. In this paper, we examine whether superflares with energy of 10(33)-10(35) erg could occur on the present Sun through the use of simple order-of-magnitude estimates based on current ideas related to the mechanisms of the solar dynamo. If magnetic flux is generated by differential rotation at the base of the convection zone, as assumed in typical dynamo models, it is possible that the present Sun would generate a large sunspot with a total magnetic flux of similar to 2 x 10(23) Mx (= G cm(2)) within one solar cycle period, and lead to superflares with an energy of 10(34) erg. To store a total magnetic flux of similar to 10(24) Mx, necessary for generating 10(35) erg superflares, it would take similar to 40 yr. Hot Jupiters have often been argued to be a necessary ingredient for the generation of superflares, but we found that they do not play any essential role in the generation of magnetic flux in the star itself, if we consider only the magnetic interaction between the star and the hot Jupiter. This seems to be consistent with Maehara et al.'s finding of 148 superflare-generating solar-type stars that do not have a hot Jupiter-like companion. Altogether, our simple calculations, combined with Maehara et al.'s analysis of superflares on Sun-like stars, show that there is a possibility that superflares of 10(34) erg would occur once in 800 yr on our present Sun.

Do we see what we should see? Describing non-covalent interactions in protein structures including precision

The power of X-ray crystal structure analysis as a technique is to `see where the atoms are'. The results are extensively used by a wide variety of research communities. However, this `seeing where the atoms are' can give a false sense of security unless the precision of the placement of the atoms has been taken into account. Indeed, the presentation of bond distances and angles to a false precision (i.e. to too many decimal places) is commonplace. This article has three themes. Firstly, a basis for a proper representation of protein crystal structure results is detailed and demonstrated with respect to analyses of Protein Data Bank entries. The basis for establishing the precision of placement of each atom in a protein crystal structure is non-trivial. Secondly, a knowledge base harnessing such a descriptor of precision is presented. It is applied here to the case of salt bridges, i.e. ion pairs, in protein structures; this is the most fundamental place to start with such structure-precision representations since salt bridges are one of the tenets of protein structure stability. Ion pairs also play a central role in protein oligomerization, molecular recognition of ligands and substrates, allosteric regulation, domain motion and alpha-helix capping. A new knowledge base, SBPS (Salt Bridges in Protein Structures), takes these structural precisions into account and is the first of its kind. The third theme of the article is to indicate natural extensions of the need for such a description of precision, such as those involving metalloproteins and the determination of the protonation states of ionizable amino acids. Overall, it is also noted that this work and these examples are also relevant to protein three-dimensional structure molecular graphics software.