An overview to the investigative approach to species testing in wildlife forensic science

The extent of wildlife crime is unknown but it is on the increase and has observable effects with the dramatic decline in many species of flora and fauna. The growing awareness of this area of criminal activity is reflected in the increase in research papers on animal DNA testing, either for the identification of species or for the genetic linkage of a sample to a particular organism. This review focuses on the use of species testing in wildlife crime investigations. Species identification relies primarily on genetic loci within the mitochondrial genome; focusing on the cytochrome b and cytochrome oxidase 1 genes. The use of cytochrome b gained early prominence in species identification through its use in taxonomic and phylogenetic studies, while the gene sequence for cytochrome oxidase was adopted by the Barcode for Life research group. This review compares how these two loci are used in species identification with respect to wildlife crime investigations. As more forensic science laboratories undertake work in the wildlife area, it is important that the quality of work is of the highest standard and that the conclusions reached are based on scientific principles. A key issue in reporting on the identification of a particular species is a knowledge of both the intraspecies variation and the possible overlap of sequence variation from one species to that of a closely related species. Recent data showing this degree of genetic separation in mammalian species will allow greater confidence when preparing a report on an alleged event where the identification of the species is of prime importance. The aim of this review is to illustrate aspects of species testing in wildlife forensic science and to explain how a knowledge of genetic variation at the genus and species level can aid in the reporting of results

Conceptualisation, development and validation of T-QoL© (Teenagers' Quality of Life): a patient-focused measure to assess quality of life of adolescents with skin diseases

Aim To develop and validate a dermatology-specific quality of life (QoL) instrument for adolescents with skin diseases. Methods Qualitative semi-structured interviews were conducted with adolescents with skin disease to gain in-depth understanding of how skin diseases affect their QoL. A prototype instrument based on the themes identified from content analysis of interviews was tested in several stages, using Classical Test Theory (CTT) and Item Response Theory (IRT) models to develop this new tool and conduct its psychometric evaluation. Results Thirty-three QoL issues were identified from semi-structured interviews with 50 adolescents. A questionnaire based on items derived from content analysis of interviews was subjected to Rasch analysis: factor analysis identified three domains, therefore not supporting the validity of T-QoL as a unidimensional measure. Psychometric evaluation of the final 18-item questionnaire was carried out in a cohort of 203 adolescents. Convergent validity was demonstrated by significant correlation with Skindex-Teen and CDLQI or DLQI. The T-QoL showed excellent internal consistency reliability: Cronbach's α=0.89 for total scale score and 0.85, 0.60, and 0.74 respectively for domains 1, 2 and 3. Test-retest reliability was high in stable subjects. T-QoL showed sensitivity to change in two sub-groups of patients who indicated change in their self-assessed disease severity. Conclusion Built on rich qualitative data from patients, the T-QoL is a simple and valid tool to quantify the impact of skin disease on adolescents’ QoL; it could be used as an outcome measure in both clinical practice and clinical research

Sequence selective capture, release and analysis of DNA using a magnetic microbead-assisted toehold-mediated DNA strand displacement reaction

This paper reports on the modification of magnetic beads with oligonucleotide capture probes with a specially designed pendant toehold (overhang) aimed specifically to capture double-stranded PCR products. After capture, the PCR products were selectively released from the magnetic beads by means of a toehold-mediated strand displacement reaction using short artificial oligonucleotide triggers and analysed using capillary electrophoresis. The approach was successfully shown on two genes widely used in human DNA genotyping, namely human c-fms (macrophage colony-stimulating factor) proto-oncogene for the CSF-1 receptor (CSF1PO) and amelogenin

Reconstructing Mammalian Phylogenies: A Detailed Comparison of the Cytochrome b and Cytochrome Oxidase Subunit I Mitochondrial Genes

The phylogeny and taxonomy of mammalian species were originally based upon shared or derived morphological characteristics. However, genetic analyses have more recently played an increasingly important role in confirming existing or establishing often radically different mammalian groupings and phylogenies. The two most commonly used genetic loci in species identification are the cytochrome oxidase I gene (COI) and the cytochrome b gene (cyt b). For the first time this study provides a detailed comparison of the effectiveness of these two loci in reconstructing the phylogeny of mammals at different levels of the taxonomic hierarchy in order to provide a basis for standardizing methodologies in the future. Interspecific and intraspecific variation is assessed and for the first time, to our knowledge, statistical confidence is applied to sequence comparisons. Comparison of the DNA sequences of 217 mammalian species reveals that cyt b more accurately reconstructs their phylogeny and known relationships between species based on other molecular and morphological analyses at Super Order, Order, Family and generic levels. Cyt b correctly assigned 95.85% of mammal species to Super Order, 94.31% to Order and 98.16% to Family compared to 78.34%, 93.36% and 96.93% respectively for COI. Cyt b also gives better resolution when separating species based on sequence data. Using a Kimura 2-parameter p-distance (x100) threshold of 1.5–2.5, cyt b gives a better resolution for separating species with a lower false positive rate and higher positive predictive value than those of COI

Conceptualising computerized adaptive testing for measurement of latent variables associated with physical objects

The notion of that more or less of a physical feature affects in different degrees the users' impression with regard to an underlying attribute of a product has frequently been applied in affective engineering. However, those attributes exist only as a premise that cannot directly be measured and, therefore, inferences based on their assessment are error-prone. To establish and improve measurement of latent attributes it is presented in this paper the concept of a stochastic framework using the Rasch model for a wide range of independent variables referred to as an item bank. Based on an item bank, computerized adaptive testing (CAT) can be developed. A CAT system can converge into a sequence of items bracketing to convey information at a user's particular endorsement level. It is through item banking and CAT that the financial benefits of using the Rasch model in affective engineering can be realised

Land Use Sector Involvement in Mitigation Policies Across Carbon Markets

Different local and international experiences show that the agroforestry sector can be fully included in the global warming mitigation strategies and in the market mechanisms that may have environmental and socioeconomic benefits. At present, however, the primary sector plays only a minor role in mitigation policies within the UNFCCC and under Kyoto’s Protocol, due to problems and difficulties related to emission/absorption accounting models andmonitoring and standardisation systems. If, on one hand, the progress in science has enabled to overcome accountingrelated problems, on the other, there are no adequate mechanisms to encourage and remunerate the primary sector’s efforts. More specifically, if the primary sector is considered as a source of emissions, it should also be recognised that it has beneficial impacts, notably in economic terms, as carbon sink. Therefore, the definition of clear and internationally shared rules might increase the carbon friendly initiatives and help reduce greenhouse gas emissions. This article is focused on the international experiences that have concerned the primary sector and is intended to supply researchers and policymakers with suggestions and recommendations for implementing local market practices related to carbon credits

Search for the Higgs boson in events with missing transverse energy and b quark jets produced in proton-antiproton collisions at s**(1/2)=1.96 TeV

We search for the standard model Higgs boson produced in association with an electroweak vector boson in events with no identified charged leptons, large imbalance in transverse momentum, and two jets where at least one contains a secondary vertex consistent with the decay of b hadrons. We use ~1 fb-1 integrated luminosity of proton-antiproton collisions at s**(1/2)=1.96 TeV recorded by the CDF II experiment at the Tevatron. We find 268 (16) single (double) b-tagged candidate events, where 248 +/- 43 (14.4 +/- 2.7) are expected from standard model background processes. We place 95% confidence level upper limits on the Higgs boson production cross section for several Higgs boson masses ranging from 110 GeV/c2 to 140 GeV/c2. For a mass of 115 GeV/c2 the observed (expected) limit is 20.4 (14.2) times the standard model prediction.Comment: 8 pages, 2 figures, submitted to Phys. Rev. Let

Evidence for t\bar{t}\gamma Production and Measurement of \sigma_t\bar{t}\gamma / \sigma_t\bar{t}

Using data corresponding to 6.0/fb of ppbar collisions at sqrt(s) = 1.96 TeV collected by the CDF II detector, we present a cross section measurement of top-quark pair production with an additional radiated photon. The events are selected by looking for a lepton, a photon, significant transverse momentum imbalance, large total transverse energy, and three or more jets, with at least one identified as containing a b quark. The ttbar+photon sample requires the photon to have 10 GeV or more of transverse energy, and to be in the central region. Using an event selection optimized for the ttbar+photon candidate sample we measure the production cross section of, and the ratio of cross sections of the two samples. Control samples in the dilepton+photon and lepton+photon+\met, channels are constructed to aid in decay product identification and background measurements. We observe 30 ttbar+photon candidate events compared to the standard model expectation of 26.9 +/- 3.4 events. We measure the ttbar+photon cross section to be 0.18+0.08 pb, and the ratio of the cross section of ttbar+photon to ttbar to be 0.024 +/- 0.009. Assuming no ttbar+photon production, we observe a probability of 0.0015 of the background events alone producing 30 events or more, corresponding to 3.0 standard deviations.Comment: 9 pages, 3 figure

A search for resonant production of ttˉt\bar{t} pairs in $4.8\ \rm{fb}^{-1}ofintegratedluminosityof of integrated luminosity of p\bar{p}collisionsat collisions at \sqrt{s}=1.96\ \rm{TeV}$

We search for resonant production of tt pairs in 4.8 fb^{-1} integrated luminosity of ppbar collision data at sqrt{s}=1.96 TeV in the lepton+jets decay channel, where one top quark decays leptonically and the other hadronically. A matrix element reconstruction technique is used; for each event a probability density function (pdf) of the ttbar candidate invariant mass is sampled. These pdfs are used to construct a likelihood function, whereby the cross section for resonant ttbar production is estimated, given a hypothetical resonance mass and width. The data indicate no evidence of resonant production of ttbar pairs. A benchmark model of leptophobic Z \rightarrow ttbar is excluded with m_{Z'} < 900 GeV at 95% confidence level.Comment: accepted for publication in Physical Review D Sep 21, 201

Precision Top-Quark Mass Measurements at CDF

We present a precision measurement of the top-quark mass using the full sample of Tevatron $\sqrt{s}=1.96$ TeV proton-antiproton collisions collected by the CDF II detector, corresponding to an integrated luminosity of 8.7 $fb^{-1}$. Using a sample of $t\bar{t}$ candidate events decaying into the lepton+jets channel, we obtain distributions of the top-quark masses and the invariant mass of two jets from the $W$ boson decays from data. We then compare these distributions to templates derived from signal and background samples to extract the top-quark mass and the energy scale of the calorimeter jets with {\it in situ} calibration. The likelihood fit of the templates from signal and background events to the data yields the single most-precise measurement of the top-quark mass, \mtop = 172.85 \pm$0.71 (stat)$\pm$0.85 (syst) GeV/c^{2}.$Comment: submitted to Phys. Rev. Let