Exploring machine learning in chemistry through the classification of spectra: an undergraduate project

Applications of machine learning in chemistry are many and varied, from prediction of structure–property relationships, to modeling of potential energy surfaces for large scale atomistic simulations. We describe a generalized approach for the application of machine learning to the classification of spectra which can be used as the basis for a wide variety of undergraduate projects. While our examples use FTIR and mass spectra, the approach could equally well be used with UV–visible, Raman, NMR, or indeed any other type of spectra. We summarize a number of different unsupervised and supervised machine learning algorithms that can be used to classify spectra into groups, and illustrate their application using data from three different projects carried out by fourth year chemistry undergraduates. The three projects investigated the ability of the various machine learning approaches to correctly classify spectra of a variety of fruits, whiskies, and teas, respectively. In all cases the algorithms were able to differentiate between the various samples used in each study, and the trained machine learning models could then be used to classify unknown samples with a high degree of accuracy (>98% in many cases). Depending on the extent to which students are expected to write their own code to perform the data analysis, the general model adopted in this work can be adapted for a variety of purposes, from short (one to two day) practical exercises and workshops, to much longer independent student projects

The metabolism of anabolic-androgenic steroids in the greyhound

BACKGROUND Effective control of the use of anabolic-androgenic steroids (AASs) in animal sports is essential in order to ensure both animal welfare and integrity. In order to better police their use in Australian and New Zealand greyhound racing, thorough metabolic studies have been carried out on a range of registered human and veterinary AASs available in the region. RESULTS Canine metabolic data are presented for the AASs boldenone, danazol, ethylestrenol, mesterolone, methandriol, nandrolone and norethandrolone. The principal Phase I metabolic processes observed were the reduction of A-ring unsaturations and/or 3-ketones with either 3α,5β- or 3β,5α-stereochemistry, the oxidation of secondary 17β-hydroxyl groups and 16α-hydroxylation. The Phase II β-glucuronylation of sterol metabolites was extensive. CONCLUSION The presented data have enabled the effective analysis of AASs and their metabolites in competition greyhound urine samples.Australian Research Council LP077483

Molecular genetic analysis of the 3p — syndrome

Molecular genetic analysis of five cases of 3p-syndrome (del(3)(qter-p25:)) was performed to investigate the relationship between the molecular pathology and clinical phenotype. Fluorescence in situ hybridization studies and analysis of polymorphic DNA markers from chromosome 3p25-p26 demonstrated that all four informative cases had distal deletions. However, the extent of the deletion was variable: in two patients with the most extensive deletions the deletion breakpoint mapped between RAF1 and D3S1250, in one patient the deletion breakpoint was between D3S1250 and D3S601, and in two patients the deletion commenced telomeric to D3S601 (and telomeric to D3S1317 in one of these). All five patients displayed the classical features of 3p- syndrome (mental retardation, growth retardation, microcephaly, ptosis and micrognathia) demonstrating that loss of sequences centromeric to D3S1317 is not required for expression of the characteristic 3p- syndrome phenotype. The three patients with the most extensive deletions had cardiac septal defects suggesting that a gene involved in normal cardiac development is contained in the interval D3S1250 and D3S18. The PMCA2 gene is contained within this region and deletion of this gene may cause congenital heart defects. At least three patients were deleted for the von Hippel - Lindau (VHL) disease gene although none had yet developed evidence of VHL disease. We conclude that molecular analysis of 3p- syndrome patients enhances the management of affected patients by identifying those at risk for VHL disease, and can be used to elucidate the critical regions for the 3p- syndrome phenotyp

HopScotch - a low-power renewable energy base station network for rural broadband access

The provision of adequate broadband access to communities in sparsely populated rural areas has in the past been severely restricted. In this paper, we present a wireless broadband access test bed running in the Scottish Highlands and Islands which is based on a relay network of low-power base stations. Base stations are powered by a combination of renewable sources creating a low cost and scalable solution suitable for community ownership. The use of the 5~GHz bands allows the network to offer large data rates and the testing of ultra high frequency ``white space'' bands allow expansive coverage whilst reducing the number of base stations or required transmission power. We argue that the reliance on renewable power and the intelligent use of frequency bands makes this approach an economic green radio technology which can address the problem of rural broadband access

Effective action and motion of a cosmic string

We examine the leading order corrections to the Nambu effective action for the motion of a cosmic string, which appear at fourth order in the ratio of the width to radius of curvature of the string. We determine the numerical coefficients of these extrinsic curvature corrections, and derive the equations of motion of the worldsheet. Using these equations, we calculate the corrections to the motion of a collapsing loop, a travelling wave, and a helical breather. From the numerical coefficients we have calculated, we discuss whether the string motion can be labelled as `rigid' or `antirigid,' and hence whether cusp or kink formation might be suppressed or enhanced.Comment: 24 pages revtex, 12 figure

Protein kinase A negatively regulates Ca2+ signalling in Toxoplasma gondii.

The phylum Apicomplexa comprises a group of obligate intracellular parasites that alternate between intracellular replicating stages and actively motile extracellular forms that move through tissue. Parasite cytosolic Ca2+ signalling activates motility, but how this is switched off after invasion is complete to allow for replication to begin is not understood. Here, we show that the cyclic adenosine monophosphate (cAMP)-dependent protein kinase A catalytic subunit 1 (PKAc1) of Toxoplasma is responsible for suppression of Ca2+ signalling upon host cell invasion. We demonstrate that PKAc1 is sequestered to the parasite periphery by dual acylation of PKA regulatory subunit 1 (PKAr1). Upon genetic depletion of PKAc1 we show that newly invaded parasites exit host cells shortly thereafter, in a perforin-like protein 1 (PLP-1)-dependent fashion. Furthermore, we demonstrate that loss of PKAc1 prevents rapid down-regulation of cytosolic [Ca2+] levels shortly after invasion. We also provide evidence that loss of PKAc1 sensitises parasites to cyclic GMP (cGMP)-induced Ca2+ signalling, thus demonstrating a functional link between cAMP and these other signalling modalities. Together, this work provides a new paradigm in understanding how Toxoplasma and related apicomplexan parasites regulate infectivity