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| 2. |
- Pham, Tuan D
(författare)
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Cancer classification by minimizing fuzzy scattering effect
- 2008
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Konferensbidrag (refereegranskat)abstract
- Proteomic technology has been found promising for classifying complex diseases that leads to early prediction. However, for effective classification, the extraction of good features that can represent the identities of different classes plays the frontal critical factor for any classification problems. In addition, another major problem associated with pattern recognition is how to effectively handle a large feature space. This paper addresses these two frontal issues for mass spectrometry (MS) classification. We apply the theory of linear predictive coding to extract features and fuzzy vector quantization to reduce the large feature space of MS data. The minimization of the fuzzy scattering matrix in the setting of the fuzzy c-means algorithm provides better grouping for feature classification. The proposed methodology was tested using two MS-based cancer datasets and the results are promising.
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| 3. |
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| 4. |
- Dawson, Drew, et al.
(författare)
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Modelling fatigue and the use of fatigue models in work settings
- 2011
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Ingår i: Accident Analysis and Prevention. - : Elsevier BV. - 0001-4575 .- 1879-2057. ; 43:2, s. 549-564
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Tidskriftsartikel (refereegranskat)abstract
- In recent years, theoretical models of the sleep and circadian system developed in laboratory settings have been adapted to predict fatigue and, by inference, performance. This is typically done using the timing of prior sleep and waking or working hours as the primary input and the time course of the predicted variables as the primary output. The aim of these models is to provide employers, unions and regulators with quantitative information on the likely average level of fatigue, or risk, associated with a given pattern of work and sleep with the goal of better managing the risk of fatigue-related errors and accidents/incidents. The first part of this review summarises the variables known to influence workplace fatigue and draws attention to the considerable variability attributable to individual and task variables not included in current models. The second part reviews the current fatigue models described in the scientific and technical literature and classifies them according to whether they predict fatigue directly by using the timing of prior sleep and wake (one-step models) or indirectly by using work schedules to infer an average sleep-wake pattern that is then used to predict fatigue (two-step models). The third part of the review looks at the current use of fatigue models in field settings by organizations and regulators. Given their limitations it is suggested that the current generation of models may be appropriate for use as one element in a fatigue risk management system. The final section of the review looks at the future of these models and recommends a standardised approach for their use as an element of the 'defenses-in-depth' approach to fatigue risk management.
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| 5. |
- Dawson, Deborah, et al.
(författare)
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High-utility conserved avian microsatellite markers enable parentage and population studies across a wide range of species
- 2013
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 14:1, s. 176-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Microsatellites are widely used for many genetic studies. In contrast to single nucleotide polymorphism (SNP) and genotyping-by-sequencing methods, they are readily typed in samples of low DNA quality/concentration (e.g. museum/non-invasive samples), and enable the quick, cheap identification of species, hybrids, clones and ploidy. Microsatellites also have the highest cross-species utility of all types of markers used for genotyping, but, despite this, when isolated from a single species, only a relatively small proportion will be of utility. Marker development of any type requires skill and time. The availability of sufficient "off-the-shelf" markers that are suitable for genotypinga wide range of species would not only save resources but also uniquely enablenew comparisons of diversity among taxa at the same set of loci. No other marker types are capable of enabling this. We therefore developed a set of avianmicrosatellite markers with enhanced cross-species utility. Results: We selected highly-conserved sequences with a high number of repeat units in both of two genetically distant species. Twenty-four primer sets were designed from homologous sequences that possessed at least eight repeat units in both the zebra finch (Taeniopygia guttata) and chicken (Gallus gallus). Each primer sequence was a complete match to zebra finch and, after accounting for degenerate bases, at least 86% similar to chicken. We assessed primer-set utilityby genotyping individuals belonging to eight passerine and four non-passerinespecies. The majority of the new Conserved Avian Microsatellite (CAM) markersamplified in all 12 species tested (on average, 94% in passerines and 95% in non-passerines). This new marker set is of especially high utility in passerines, with amean 68% of loci polymorphic per species, compared with 42% in non-passerinespecies. Conclusions: When combined with previously described conserved loci, this new set of conserved markers will not only reduce the necessity and expense ofmicrosatellite isolation for a wide range of genetic studies, including avianparentage and population analyses, but will also now enable comparisons ofgenetic diversity among different species (and populations) at the same set of loci, with no or reduced bias. Finally, the approach used here can be applied to other taxa in which appropriate genome sequences are available.
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| 6. |
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| 7. |
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| 8. |
- Dawson, Deborah A., et al.
(författare)
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New methods to identify conserved microsatellite loci and develop primer sets of high cross-species utility - as demonstrated for birds
- 2010
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Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 10:3, s. 475-494
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Tidskriftsartikel (refereegranskat)abstract
- We have developed a new approach to create microsatellite primer sets that have high utility across a wide range of species. The success of this method was demonstrated using birds. We selected 35 avian EST microsatellite loci that had a high degree of sequence homology between the zebra finch Taeniopygia guttata and the chicken Gallus gallus and designed primer sets in which the primer bind sites were identical in both species. For 33 conserved primer sets, on average, 100% of loci amplified in each of 17 passerine species and 99% of loci in five non-passerine species. The genotyping of four individuals per species revealed that 24-76% (mean 48%) of loci were polymorphic in the passerines and 18-26% (mean 21%) in the non-passerines. When at least 17 individuals were genotyped per species for four Fringillidae finch species, 71-85% of loci were polymorphic, observed heterozygosity was above 0.50 for most loci and no locus deviated significantly from Hardy-Weinberg proportions. This new set of microsatellite markers is of higher cross-species utility than any set previously designed. The loci described are suitable for a range of applications that require polymorphic avian markers, including paternity and population studies. They will facilitate comparisons of bird genome organization, including genome mapping and studies of recombination, and allow comparisons of genetic variability between species whilst avoiding ascertainment bias. The costs and time to develop new loci can now be avoided for many applications in numerous species. Furthermore, our method can be readily used to develop microsatellite markers of high utility across other taxa.
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| 9. |
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| 10. |
- Hagemann, Martin, et al.
(författare)
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Detection of a phage genome carrying a zonula occludens like toxin gene (zot) in clinical isolates of Stenotrophomonas maltophilia.
- 2006
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Ingår i: Archives of Microbiology. - : Springer Science and Business Media LLC. - 0302-8933 .- 1432-072X. ; 185:6
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Tidskriftsartikel (refereegranskat)abstract
- During a study of the genetic diversity of Stenotrophomonas strains, we found an autonomous replicating DNA molecule in chromosomal DNA preparations of the clinical Stenotrophomonas maltophilia strain c5. The entire sequence of 6,907 bp of the isolated DNA molecule was determined, which was called phiSMA9. Seven ORFs, which code for proteins with considerable similarity to proteins in databases, were identified in the DNA sequence. The largest ORF shows high sequence similarities to the pI protein of the filamentous phage phiLf, which was later shown to be identical to toxin Zot of Vibrio cholerae. Beside the Zot-like protein, six other proteins with similarities to known phage proteins such as a phage replication protein RstA and phage absorption or coat protein are encoded on phiSMA9, which indicate that this circular DNA molecule represents the replicative form of a linear phage genome. A PCR-based screening showed that only five from the totally investigated 47 Stenotrophomonas strains of clinical and environmental origin harbor these genes. Altogether, we describe the first genome of a phage for the nosocomial pathogen Stenotrophomonas, which contains a Zot toxin like gene and might be regarded as the first Stenotrophomonas virulence factor.
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| 11. |
- Perret, E., et al.
(författare)
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Structural, magnetic and electronic properties of pulsed-laser-deposition grown SrFeO3-delta thin films and SrFeO3-delta/La2/3Ca1/3MnO3 multilayers
- 2017
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Ingår i: Journal of Physics. - 0953-8984 .- 1361-648X. ; 29:49
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Tidskriftsartikel (refereegranskat)abstract
- We studied the structural, magnetic and electronic properties of SrFeO3-delta (SFO) thin films and SrFeO3-delta/La2/3Ca1/3MnO3 (LCMO) superlattices that have been grown with pulsed laser deposition (PLD) on La0.3Sr0.7Al0.65Ta0.35O3 (LSAT) substrates. X-ray reflectometry and scanning transmission electron microscopy (STEM) confirm the high structural quality of the films and flat and atomically sharp interfaces of the superlattices. The STEM data also reveal a difference in the interfacial layer stacking with a SrO layer at the LCMO/SFO and a LaO layer at the SFO/LCMO interfaces along the PLD growth direction. The x-ray diffraction (XRD) data suggest that the as grown SFO films and SFO/LCMO superlattices have an oxygen-deficient SrFeO3-delta structure with I4/mmm space group symmetry (delta <= 0.2). Subsequent ozone annealed SFO films are consistent with an almost oxygen stoichiometric structure (delta approximate to 0). The electronic and magnetic properties of these SFO films are similar to the ones of corresponding single crystals. In particular, the as grown SrFeO3-delta films are insulating whereas the ozone annealed films are metallic. The magneto-resistance effects of the as grown SFO films have a similar magnitude as in the single crystals, but extend over a much wider temperature range. Last but not least, for the SFO/LCMO superlattices we observe a rather large exchange bias effect that varies as a function of the cooling field.
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| 12. |
- Burnett, Scott, 1978
(författare)
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White Belongings: Race, Land, and Property in Post-Apartheid South Africa
- 2022
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Bok (övrigt vetenskapligt/konstnärligt)abstract
- White Belongings: Race, Land, and Property in Post-Apartheid South Africa deepens ongoing critical deconstruction of the role of whiteness in maintaining racial order. Scott Burnett , argues that the protection of white entitlement and cultural connection to the land are intimately interwoven, using detailed discourse analysis of campaigns aimed at preventing rhino poaching, stopping fracking in the Karoo, and advocating for the existence of a poverty “crisis,” which reveal how whites hold on to their “belongings” in everyday talk. White Belongings goes beyond the preoccupation with identity in whiteness studies to elaborate how specific subject roles and institutions are motivated and rationalized in hegemonic discursive regimes.
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| 13. |
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| 14. |
- Chapman, Henry N, et al.
(författare)
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Femtosecond time-delay X-ray holography
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 448:7154, s. 676-679
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Tidskriftsartikel (refereegranskat)abstract
- Extremely intense and ultrafast X-ray pulses from free-electron lasers offer unique opportunities to study fundamental aspects of complex transient phenomena in materials. Ultrafast time-resolved methods usually require highly synchronized pulses to initiate a transition and then probe it after a precisely defined time delay. In the X-ray regime, these methods are challenging because they require complex optical systems and diagnostics. Here we propose and apply a simple holographic measurement scheme, inspired by Newton's 'dusty mirror' experiment1, to monitor the X-ray-induced explosion of microscopic objects. The sample is placed near an X-ray mirror; after the pulse traverses the sample, triggering the reaction, it is reflected back onto the sample by the mirror to probe this reaction. The delay is encoded in the resulting diffraction pattern to an accuracy of one femtosecond, and the structural change is holographically recorded with high resolution. We apply the technique to monitor the dynamics of polystyrene spheres in intense free-electron-laser pulses, and observe an explosion occurring well after the initial pulse. Our results support the notion that X-ray flash imaging2, 3 can be used to achieve high resolution, beyond radiation damage limits for biological samples4. With upcoming ultrafast X-ray sources we will be able to explore the three-dimensional dynamics of materials at the timescale of atomic motion.
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| 15. |
- Crevani, Lucia
(författare)
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Studying intersections as production of place(s) : illustrations from outdoors entrepreneuring
- 2013
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Ingår i: the Nordic Academy of Management,NFF, Aug 21-23, 2013, Iceland.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- This paper aims at contributing to the study of intersections by focusing on the simultaneous accomplishment of gender, ethnicity and body ableness. While such enterprise in organization studies often draws on the concept of identity, I propose to bring the concepts of space and place into the discussion. Space is seen as “the sphere of a multiplicity of trajectories”. Hence, space does not exist prior to identities or entities and their relations, space is relationally constituted, space unfolds in interactions and is continuously being made. And space allows for thinking of coexisting heterogeneity, of a plurality of trajectories contemporaneously existing, the simultaneity of stories-so-far. Drawing on human geography, and in particular the work of Doreen Massey, and on a strong process perspective in organization studies, I thus focus on the production of specific places as central to entrepreneuring in the outdoors industry. The idea of place as the local, genuine, “real”, closed, coherent is also challenged by such a take on space. It thus becomes interesting studying how places are produced and reproduced, made coherent (or contested), in connections and disconnections, while doing entrepreneurship – and what kind of configurations of relations are thus achieved, configurations producing and reproducing gender, ethnicity and body ableness.
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| 16. |
- Dawson, D.A., et al.
(författare)
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Towards agreement on ways to measure and report drinking patterns and alcohol-related problems in adult general population surveys
- 2000
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Ingår i: Journal of Substance Abuse. - 0899-3289 .- 1873-6491. ; 12:1-2, s. 1-21
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Tidskriftsartikel (refereegranskat)abstract
- A thematic conference of the Kettil Bruun Society (KBS) for Social and Epidemiological Research on Alcohol was held in Skarpö, near Stockholm, on April 3–7, 2000. The goals of the meeting were to develop consensus sets of questionnaire items for measuring alcohol consumption and social harm, to delineate statistical and practical concerns related to the aggregation of consumption and harm data and to identify summary measures to be used for descriptive purposes and in analyses of the association between alcohol intake and alcohol-related outcomes. The results of the conference discussions are summarized below, with emphasis on both areas where the conference yielded recommendations for measures and methods of aggregation for analysis, and on areas where consensus could not be obtained and/or where additional research is needed.
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| 17. |
- Demšar, Urška, 1972-
(författare)
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Exploring geographical metadata by automatic and visual data mining
- 2004
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Metadata are data about data. They describe characteristicsand content of an original piece of data. Geographical metadatadescribe geospatial data: maps, satellite images and othergeographically referenced material. Such metadata have twocharacteristics, high dimensionality and diversity of attributedata types, which present a problem for traditional data miningalgorithms. Other problems that arise during the exploration ofgeographical metadata are linked to the expertise of the userperforming the analysis. The large amounts of metadata andhundreds of possible attributes limit the exploration for anon-expert user, which results in a potential loss ofinformation that is hidden in metadata. In order to solve some of these problems, this thesispresents an approach for exploration of geographical metadataby a combination of automatic and visual data mining. Visual data mining is a principle that involves the human inthe data exploration by presenting the data in some visualform, allowing the human to get insight into the data and torecognise patterns. The main advantages of visual dataexploration over automatic data mining are that the visualexploration allows a direct interaction with the user, that itis intuitive and does not require complex understanding ofmathematical or statistical algorithms. As a result the userhas a higher confidence in the resulting patterns than if theywere produced by computer only. In the thesis we present the Visual data mining tool (VDMtool), which was developed for exploration of geographicalmetadata for site planning. The tool provides five differentvisualisations: a histogram, a table, a pie chart, a parallelcoordinates visualisation and a clustering visualisation. Thevisualisations are connected using the interactive selectionprinciple called brushing and linking. In the VDM tool the visual data mining concept is integratedwith an automatic data mining method, clustering, which finds ahierarchical structure in the metadata, based on similarity ofmetadata items. In the thesis we present a visualisation of thehierarchical structure in the form of a snowflake graph. Keywords:visualisation, data mining, clustering, treedrawing, geographical metadata.
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| 18. |
- Gerk, Ayla, et al.
(författare)
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Gender Discrimination, Career Aspirations, and Access to Mentorship Among Medical Students in Brazil.
- 2022
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Ingår i: Journal of Surgical Research. - : Elsevier. - 0022-4804 .- 1095-8673. ; 279, s. 702-711
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Tidskriftsartikel (refereegranskat)abstract
- INTRODUCTION: Gender-based discrimination (GBD) creates a hostile environment that can affect medical students. Mentorship has been recognized as a mitigating factor for GBD. We aimed to investigate the impacts of GBD on career selection and well-being of medical students in Brazil and to explore access to mentorship among these students.METHODS: A cross-sectional study was performed using an anonymous survey in Portuguese. The survey was distributed in June 2021 to students enrolled in Brazilian medical schools. It contained 24 questions, including demographics, episodes of GBD experienced by responders and their impact on professional and personal life, and mentorship access.RESULTS: Of 953 respondents, 748 (78%) were cisgender women, 194 (20%) cisgender men, and 11 nonbinary (1%). Sixty-six percent (625/953) of students reported experiencing GBD, with cisgender women and nonbinary being more likely to experience it than cisgender men (P < 0.001). Responders who experiences GBD report moderate to severe impact on career satisfaction (40%, 250/624), safety (68%, 427/624), self-confidence (68%, 426/624), well-being (57%, 357/625), and burnout (62%, 389/625). Cisgender women were more likely to report these effects than men counterparts (P < 0.01). Only 21% of respondents (201/953) had mentors in their medical schools.CONCLUSIONS: Our findings demonstrate that GBD is widespread among Brazilian medical students affecting their personal and professional lives, and most of them do not have access to a mentor. There is an urgent need to increase access to mentors who could mitigate the adverse effects of GBD and help develop a diverse and inclusive medical workforce.
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| 23. |
- Lundberg-Felten, Judith, et al.
(författare)
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Biology, Chemistry and Structure of Tension Wood
- 2013
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Ingår i: Cellular Aspects of Wood Formation. - Berlin, Heidelberg : Springer Berlin Heidelberg. - 9783642364907 ; 20:20, s. 203-224
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Bokkapitel (refereegranskat)
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| 24. |
- Lundberg-Felten, Judith, et al.
(författare)
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Ethylene signaling induces gelatinous layers with typical features of tension wood in hybrid aspen
- 2018
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Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 218:3, s. 999-1014
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Tidskriftsartikel (refereegranskat)abstract
- The phytohormone ethylene impacts secondary stem growth in plants by stimulating cambial activity, xylem development and fiber over vessel formation. We report the effect of ethylene on secondary cell wall formation and the molecular connection between ethylene signaling and wood formation. We applied exogenous ethylene or its precursor 1-aminocyclopropane-1-carboxylic acid (ACC) to wild-type and ethylene-insensitive hybrid aspen trees (Populus tremulaxtremuloides) and studied secondary cell wall anatomy, chemistry and ultrastructure. We furthermore analyzed the transcriptome (RNA Seq) after ACC application to wild-type and ethylene-insensitive trees. We demonstrate that ACC and ethylene induce gelatinous layers (G-layers) and alter the fiber cell wall cellulose microfibril angle. G-layers are tertiary wall layers rich in cellulose, typically found in tension wood of aspen trees. A vast majority of transcripts affected by ACC are downstream of ethylene perception and include a large number of transcription factors (TFs). Motif-analyses reveal potential connections between ethylene TFs (Ethylene Response Factors (ERFs), ETHYLENE INSENSITIVE 3/ETHYLENE INSENSITIVE3-LIKE1 (EIN3/EIL1)) and wood formation. G-layer formation upon ethylene application suggests that the increase in ethylene biosynthesis observed during tension wood formation is important for its formation. Ethylene-regulated TFs of the ERF and EIN3/EIL1 type could transmit the ethylene signal.
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| 25. |
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