Concentrations and d13C compositions of n-alkanes, n-alcohols, n-alkanoic acids in a 34-month time series of suspended sediments from the outflow of the Congo River

The concentrations, distributions, and stable carbon isotopes (d13C) of plant waxes carried by fluvial suspended sediments contain valuable information about terrestrial ecosystem characteristics. To properly interpret past changes recorded in sedimentary archives it is crucial to understand the sources and variability of exported plant waxes in modern systems on seasonal to inter-annual timescales. To determine such variability, we present concentrations and d13C compositions of three compound classes (n-alkanes, n-alcohols, n-alkanoic acids) in a 34-month time series of suspended sediments from the outflow of the Congo River. We show that exported plant-dominated n-alkanes (C25-C35) represent a mixture of C3 and C4 end members, each with distinct molecular distributions, as evidenced by an 8.1 ± 0.7 per mil (±1Sigma standard deviation) spread in d13C values across chain-lengths, and weak correlations between individual homologue concentrations (r = 0.52-0.94). In contrast, plant-dominated n-alcohols (C26-C36) and n-alkanoic acids (C26-C36) exhibit stronger positive correlations (r = 0.70-0.99) between homologue concentrations and depleted d13C values (individual homologues average <= -31.3 per mil and -30.8 per mil, respectively), with lower d13C variability across chain-lengths (2.6 ± 0.6 per mil and 2.0 ± 1.1 per mil, respectively). All individual plant-wax lipids show little temporal d13C variability throughout the time-series (1 Sigma <= 0.9 per mil), indicating that their stable carbon isotopes are not a sensitive tracer for temporal changes in plant-wax source in the Congo basin on seasonal to inter-annual timescales. Carbon-normalized concentrations and relative abundances of n-alcohols (19-58% of total plant-wax lipids) and n-alkanoic acids (26-76%) respond rapidly to seasonal changes in runoff, indicating that they are mostly derived from a recently entrained local source. In contrast, a lack of correlation with discharge and low, stable relative abundances (5-16%) indicate that n-alkanes better represent a catchment-integrated signal with minimal response to discharge seasonality. Comparison to published data on other large watersheds indicates that this phenomenon is not limited to the Congo River, and that analysis of multiple plant-wax lipid classes and chain lengths can be used to better resolve local vs. distal ecosystem structure in river catchments.

Development of calix[4]arene-functionalized microcantilever array sensing system for the rapid, sensitive and simultaneous detection of metal ions in aqueous solutions

The work described in this thesis was conducted with the aim of: 1) investigating the binding capabilities of calix[4]arene-functionalized microcantilevers towards specific metal ions and 2) developing a new16-microcantilever array sensing system for the rapid, and simultaneous detection of metal ions in fresh water. Part I of this thesis reports on the use of three new bimodal calix[4]arenes (methoxy, ethoxy and crown) as potential host/guest sensing layers for detecting selected ions in dilute aqueous solutions using single microcantilever experimental system. In this work it was shown that modifying the upper rim of the calix[4]arenes with a thioacetate end group allow calix[4]arenes to self-assemble on Au(111) forming complete highly ordered monolayers. It was also found that incubating the microcantilevers coated with 5 nm of Inconel and 40 nm of Au for 1 h in a 1.0 M solution of calix[4]arene produced the highest sensitivity. Methoxy-functionalized microcantilevers showed a definite preference for Ca²⁺ ions over other cationic guests and were able to detect trace concentration as low as 10⁻¹² M in aqueous solutions. Microcantilevers modified with ethoxy calix[4]arene displayed their highest sensitivity towards Sr²⁺ and to a lesser extent Ca²⁺ ions. Crown calix[4]arene-modified microcantilevers were however found to bind selectively towards Cs⁺ ions. In addition, the counter anion was also found to contribute to the deflection. For example methoxy calix[4]arene-modified microcantilever was found to be more sensitive to CaCl₂ over other water-soluble calcium salts such as Ca(NO₃)₂ , CaBr₂ and CaI₂. These findings suggest that the response of calix[4]arene-modified microcantilevers should be attributed to the target ionic species as a whole instead of only considering the specific cation and/or anion. Part II presents the development of a 16-microcantilever sensor setup. The implementation of this system involved the creation of data analysis software that incorporates data from the motorized actuator and a two-axis photosensitive detector to obtain the deflection signal originating from each individual microcantilever in the array. The system was shown to be capable of simultaneous measurements of multiple microcantilevers with different coatings. A functionalization unit was also developed that allows four microcantilevers in the array to be coated with an individual sensing layer one at the time. Because of the variability of the spring constants of different cantilevers within the array, results presented were quoted in units of surface stress unit in order to compare values between the microcantilevers in the array.

Building autonomous sensitive artificial listeners (Extended abstract)

This paper describes a substantial effort to build a real-time interactive multimodal dialogue system with a focus on emotional and non-verbal interaction capabilities. The work is motivated by the aim to provide technology with competences in perceiving and producing the emotional and non-verbal behaviours required to sustain a conversational dialogue. We present the Sensitive Artificial Listener (SAL) scenario as a setting which seems particularly suited for the study of emotional and non-verbal behaviour, since it requires only very limited verbal understanding on the part of the machine. This scenario allows us to concentrate on non-verbal capabilities without having to address at the same time the challenges of spoken language understanding, task modeling etc. We first summarise three prototype versions of the SAL scenario, in which the behaviour of the Sensitive Artificial Listener characters was determined by a human operator. These prototypes served the purpose of verifying the effectiveness of the SAL scenario and allowed us to collect data required for building system components for analysing and synthesising the respective behaviours. We then describe the fully autonomous integrated real-time system we created, which combines incremental analysis of user behaviour, dialogue management, and synthesis of speaker and listener behaviour of a SAL character displayed as a virtual agent. We discuss principles that should underlie the evaluation of SAL-type systems. Since the system is designed for modularity and reuse, and since it is publicly available, the SAL system has potential as a joint research tool in the affective computing research community.

Free-stretch-blow Investigation of Poly(ethylene terephthalate) over a Large Process Window

This paper highlights for the first time a full comprehension of the deformation procedure during the injection stretch blow moulding (ISBM) process of poly(ethylene terephthalate) (PET) containers, namely thin-walled rigid bottles. The processes required to form PET bottles are complicated and extensive; any development in understanding the nature of material deformation can potentially improve the bottle optimisation process. Removing the bottle mould and performing free-stretch-blow (FSB) experiments revealed insight into the bottle forming characteristics at various preform temperatures and blowing rates. Process outputs cavity pressure and stretch-rod force were recorded using at instrumented stretch-rod and preform surface strain mapping was determined using a combination of a unique patterning procedure and high speed stereoscopic digital image correlation. The unprecedented experimental analysis reveals that the deformation behaviour varies considerably with contrasting process input parameters. Investigation into the effect on deformation mode, strain rate and final bottle shape provide a basis for full understanding of the process optimisation and therefore how the process inputs may aid development of the preferred optimised container.

ARB: Phase II window of opportunity study of short-term preoperative treatment with enzalutamide in ER-positive and triple-negative breast cancer

The androgen receptor (AR) is expressed in 60-80% of breast cancers (BC) across all molecular phenotypes, with a higher incidence in oestrogen receptor positive (ER+) BC compared to ER negative tumours. In ER+ disease, AR-expression has been linked to endocrine resistance which might be reversed with combined treatment targeting ER and AR. In triple negative BCs (TNBC), preclinical and clinical investigations have described a subset of patients that express the AR and are sensitive to androgen blockade, providing a novel therapeutic target. Enzalutamide, a potent 2nd generation anti-androgen, has demonstrated substantial preclinical and clinical anti-tumour activity in AR+ breast cancer. Short-term preoperative window of opportunity studies are a validated strategy for novel treatments to provide proof-of-concept and define the most appropriate patient population by directly assessing treatment effects in tumour tissue before and after treatment. The ARB study aims to assess the anti-tumour effects of enzalutamide in early ER+ breast cancer and TNBC, to identify the optimal target population for further studies and to directly explore the biologic effects of enzalutamide on BC and stromal cells. Methods: ARB is an international, investigator sponsored WOO phase II study in women with newly diagnosed primary ER+ BC or AR+ TNBC of ≥ 1cm. The study has two cohorts. In the ER+ cohort, postmenopausal patients will be randomised 2:1 to receive either enzalutamide (160mg OD) plus exemestane (50mg OD) or exemestane (25mg OD). In the TNBC cohort, AR+ will receive single agent treatment with enzalutamide (160mg OD). Study treatment is planned for 15–29 days, followed by surgery or neo-adjuvant therapy. Tissue and blood samples are collected before treatment and on the last day of study treatment. The primary endpoint is inhibition of tumour-cell proliferation, as measured by change in Ki67 expression, determined centrally by 2 investigators. Secondary endpoints include induction of apoptosis (Caspase3), circulating hormone levels and safety. ARB aims to recruit ≈235 patients from ≈40 sites in the UK, Germany, Spain and USA. The study is open to recruitment.

Application of self-quenched JH consensus primers for real-time quantitative PCR of IGH gene to minimal residual disease evaluation in multiple myeloma.

Monitoring multiple myeloma patients for relapse requires sensitive methods to measure minimal residual disease and to establish a more precise prognosis. The present study aimed to standardize a real-time quantitative polymerase chain reaction (PCR) test for the IgH gene with a JH consensus self-quenched fluorescence reverse primer and a VDJH or DJH allele-specific sense primer (self-quenched PCR). This method was compared with allele-specific real-time quantitative PCR test for the IgH gene using a TaqMan probe and a JH consensus primer (TaqMan PCR). We studied nine multiple myeloma patients from the Spanish group treated with the MM2000 therapeutic protocol. Self-quenched PCR demonstrated sensitivity of >or=10(-4) or 16 genomes in most cases, efficiency was 1.71 to 2.14, and intra-assay and interassay reproducibilities were 1.18 and 0.75%, respectively. Sensitivity, efficiency, and residual disease detection were similar with both PCR methods. TaqMan PCR failed in one case because of a mutation in the JH primer binding site, and self-quenched PCR worked well in this case. In conclusion, self-quenched PCR is a sensitive and reproducible method for quantifying residual disease in multiple myeloma patients; it yields similar results to TaqMan PCR and may be more effective than the latter when somatic mutations are present in the JH intronic primer binding site.

Minimal residual disease monitoring in multiple myeloma: a comparison between allelic-specific oligonucleotide real-time quantitative polymerase chain reaction and flow cytometry.

BACKGROUND AND OBJECTIVES: Minimal residual disease (MRD) studies are useful in multiple myeloma (MM). However, the definition of the best technique and clinical utility are still unresolved issues. The aim of this study was to analyze and compare the clinical utility of MRD studies in MM with two different techniques: allelic-specific oligonucleotide real-time quantitative PCR (ASO-RQ-PCR), and flow cytometry (FCM). DESIGN AND METHODS: Bone marrow samples from 32 MM patients who had achieved complete response after transplantation were evaluated by ASO-RQ-PCR, using TaqMan technology, and multiparametric FCM. RESULTS: ASO-RQ-PCR was only applicable in 75% of patients for a variety of technical reasons, while FCM was applicable in up to 90%. Therefore, simultaneous PCR/FCM analysis was possible in only 24 patients. The number of residual tumor cells identified by both techniques was very similar (mean=0.29%, range=0.001-1.61%, correlation coefficient=0.861). However, RQ-PCR was able to detect residual myelomatous cells in 17 patients while FCM only did so in 11; thus, 6 cases were FCM negative but PCR positive, all of them displaying a very low number of clonal cells (median=0.014%, range=0.001-0.11). Using an MRD threshold of 0.01% (10(-4)) two risk groups with significantly different progression-free survival could be identified by either PCR (34 vs. 15m, p=0.04) or FCM (27 vs. 10m, p=0.05). INTERPRETATION AND CONCLUSIONS: Although MRD evaluation by ASO-RQ-PCR is slightly more sensitive and specific than FCM, it is applicable in a lower proportion of MM patients and is more time-consuming, while both techniques provide similar prognostic information.

Identifying the Impact of Incomplete Datasets on Process Cycle Time Prediction in an Aerospace Assembly Line

Supply Chain Simulation (SCS) is applied to acquire information to support outsourcing decisions but obtaining enough detail in key parameters can often be a barrier to making well informed decisions.
One aspect of SCS that has been relatively unexplored is the impact of inaccurate data around delays within the SC. The impact of the magnitude and variability of process cycle time on typical performance indicators in a SC context is studied.
System cycle time, WIP levels and throughput are more sensitive to the magnitude of deterministic deviations in process cycle time than variable deviations. Manufacturing costs are not very sensitive to these deviations.
Future opportunities include investigating the impact of process failure or product defects, including logistics and transportation between SC members and using alternative costing methodologies.

Fast and sensitive aflatoxin B1 and total aflatoxins ELISAs for analysis of peanuts, maize and feed ingredients

Aflatoxins are a group of carcinogenic compounds produced by Aspergillus fungi that can grow on different agricultural crops. Both acute and chronic exposure to these mycotoxins can cause serious illness. Due to the high occurrence of aflatoxins in crops worldwide fast and cost-effective analytical methods are required for the identification of contaminated agricultural commodities before they are processed into final products and placed on the market. In order to provide new tools for aflatoxin screening two prototype fast ELISA methods: one for the detection of aflatoxin B₁ and the other for total aflatoxins were developed. Seven monoclonal antibodies with unique high sensitivity and at the same time good cross-reactivity profiles were produced. The monoclonal antibodies were characterized and two antibodies showing IC₅₀ of 0.037 ng/mL and 0.031 ng/mL for aflatoxin B₁ were applied in simple and fast direct competitive ELISA tests. The methods were validated for peanut matrix as this crop is one of the most affected by aflatoxin contamination. The detection capabilities of aflatoxin B₁ and total aflatoxins ELISAs were 0.4 μg/kg and 0.3 μg/kg for aflatoxin B₁, respectively, which are one of the lowest reported values. Total aflatoxins ELISA was also validated for the detection of aflatoxins B₂, G₁ and G₂. The application of the developed tests was demonstrated by screening 32 peanut samples collected from the UK retailers. Total aflatoxins ELISA was further applied to analyse naturally contaminated maize porridge and distiller's dried grain with solubles samples and the results were correlated with these obtained by UHPLC-MS/MS method.

Development and application of sensitive genome-wide platforms to study the genetic and epigenetic (DNA methylation) makeup of gametes and early bovine embryos

Pour ce projet, nous avons développé une plateforme pour l’analyse pangénomique de la méthylation de l’ADN chez le bovin qui est compatible avec des échantillons de petites tailles. Cet outil est utilisé pour étudier les caractéristiques génétiques et épigénétiques (méthylation de l’ADN) des gamètes soumis aux procédures de procréation médicalement assisitée et des embryons précoces. Dans un premier temps, une plateforme d’analyse de biopuces spécifiques pour l’étude de la méthylation de l’ADN chez l’espèce bovine a été développée. Cette plateforme a ensuite été optimisée pour produire des analyses pangénomiques de méthylation de l’ADN fiables et reproductibles à partir d’échantillons de très petites tailles telle que les embryons précoces (≥ 10 ng d’ADN a été utilisé, ce qui correspond à 10 blastocystes en expansion). En outre, cet outil a permis d’évaluer de façon simultanée la méthylation de l’ADN et le transcriptome dans le même échantillon, fournissant ainsi une image complète des profils génétiques et épigénétiques (méthylation de l’ADN). Comme preuve de concept, les profils comparatifs de méthylation de l’ADN spermatique et de blastocystes bovins ont été analysés au niveau de l’ensemble du génome. Dans un deuxième temps, grâce à cette plateforme, les profils globaux de méthylation de l’ADN de taureaux jumeaux monozygotes (MZ) ont été analysés. Malgré qu’ils sont génétiquement identiques, les taureaux jumeaux MZ ont des descendants avec des performances différentes. Par conséquent, l’hypothèse que le profil de méthylation de l’ADN spermatique de taureaux jumeaux MZ est différent a été émise. Dans notre étude, des différences significatives entre les jumeaux MZ au niveau des caractéristiques de la semence ainsi que de la méthylation de l’ADN ont été trouvées, chacune pouvant contribuer à l’obtention de performances divergentes incongrues des filles engendrées par ces jumeaux MZ. Dans la troisième partie de ce projet, la même plateforme a été utilisée pour découvrir les impacts d’une supplémentation à forte concentration en donneur de méthyle universel sur les embryons précoces bovins. La supplémentation avec de grandes quantités d’acide folique (AF) a été largement utilisée et recommandée chez les femmes enceintes pour sa capacité bien établie à prévenir les malformations du tube neural chez les enfants. Cependant, plus récemment, plusieurs études ont rapporté des effets indésirables de l’AF utilisé à des concentrations élevées, non seulement sur le développement de l’embryon, mais aussi chez les adultes. Au niveau cellulaire, l’AF entre dans le métabolisme monocarboné, la seule voie de production de S-adénosyl méthionine (SAM), un donneur universel de groupements méthyles pour une grande variété de biomolécules, y compris l’ADN. Par conséquent, pour résoudre cette controverse, une forte dose de SAM a été utilisée pour traiter des embryons produits in vitro chez le bovin. Ceci a non seulement permis d’influencer le phénotype des embryons précoces, mais aussi d’avoir un impact sur le transcriptome et le méthylome de l’ADN. En somme, le projet en cours a permis le développement d’une plateforme d’analyse de la méthylation de l’ADN à l’échelle du génome entier chez le bovin à coût raisonnable et facile à utiliser qui est compatible avec les embryons précoces. De plus, puisque c’est l’une des premières études de ce genre en biologie de la reproduction bovine, ce projet avait trois objectifs qui a donné plusieurs nouveaux résultats, incluant les profils comparatifs de méthylation de l’ADN au niveau : i) blastocystes versus spermatozoïdes ; ii) semence de taureaux jumeaux MZ et iii) embryons précoces traités à de fortes doses de SAM versus des embryons précoces non traités.

What is Crossing the Virtual Window? Collaboration in Virtual Team Teaching

Virtual Team Teaching (VTT) is a form of collaborative teaching and learning at the college level that involves two teachers with their respective classes working together in real time from two distant classrooms. This paper looks at collaboration that occurs during VTT practice in order to examine factors that support and inhibit collaboration. It is aimed at teachers, administrators, technical support, and pedagogical advisors concerned with collaborative practices at the college level. What kind of affordances does Virtual Team Teaching provide for teachers and students in terms of collaboration? 1) How do teachers collaborate to build the activities and content for a VTT session? 2) What are some of the outcomes of this collaboration between these teachers? 3) How do students collaborate across the two classrooms? 4) What are some outcomes of this collaboration between students? And 5) Does the teachers’ collaborative effort impact the students’ collaboration, and vice versa?

Development of a real time Image analysis system for traffic monitoring applications.

Image processing offers unparalleled potential for traffic monitoring and control. For many years engineers have attempted to perfect the art of automatic data abstraction from sequences of video images. This paper outlines a research project undertaken at Napier University by the authors in the field of image processing for automatic traffic analysis. A software based system implementing TRIP algorithms to count cars and measure vehicle speed has been developed by members of the Transport Engineering Research Unit (TERU) at the University. The TRIP algorithm has been ported and evaluated on an IBM PC platform with a view to hardware implementation of the pre-processing routines required for vehicle detection. Results show that a software based traffic counting system is realisable for single window processing. Due to the high volume of data required to be processed for full frames or multiple lanes, system operations in real time are limited. Therefore specific hardware is required to be designed. The paper outlines a hardware design for implementation of inter-frame and background differencing, background updating and shadow removal techniques. Preliminary results showing the processing time and counting accuracy for the routines implemented in software are presented and a real time hardware pre-processing architecture is described.

Real-Time PCR Assays for the Detection of Puccinia psidii

Puccinia psidii (Myrtle rust) is an emerging pathogen that has a wide host range in the Myrtaceae family; it continues to show an increase in geographic range and is considered to be a significant threat to Myrtaceae plants worldwide. In this study, we describe the development and validation of three novel real-time polymerase reaction (qPCR) assays using ribosomal DNA and β-tubulin gene sequences to detect P. psidii. All qPCR assays were able to detect P. psidii DNA extracted from urediniospores and from infected plants, including asymptomatic leaf tissues. Depending on the gene target, qPCR was able to detect down to 0.011 pg of P. psidii DNA. The most optimum qPCR assay was shown to be highly specific, repeatable, and reproducible following testing using different qPCR reagents and real-time PCR platforms in different laboratories. In addition, a duplex qPCR assay was developed to allow coamplification of the cytochrome oxidase gene from host plants for use as an internal PCR control. The most optimum qPCR assay proved to be faster and more sensitive than the previously published nested PCR assay and will be particularly useful for high-throughput testing and to detect P. psidii at the early stages of infection, before the development of sporulating rust pustules.

High Quality Acoustic Time History Measurements of Rotor Harmonic Noise in Confined Spaces

A methodology has been developed and presented to enable the use of small to medium scale acoustic hover facilities for the quantitative measurement of rotor impulsive noise. The methodology was applied to the University of Maryland Acoustic Chamber resulting in accurate measurements of High Speed Impulsive (HSI) noise for rotors running at tip Mach numbers between 0.65 and 0.85 – with accuracy increasing as the tip Mach number was increased. Several factors contributed to the success of this methodology including: • High Speed Impulsive (HSI) noise is characterized by very distinct pulses radiated from the rotor. The pulses radiate high frequency energy – but the energy is contained in short duration time pulses. • The first reflections from these pulses can be tracked (using ray theory) and, through adjustment of the microphone position and suitably applied acoustic treatment at the reflected surface, reduced to small levels. A computer code was developed that automates this process. The code also tracks first bounce reflection timing, making it possible to position the first bounce reflections outside of a measurement window. • Using a rotor with a small number of blades (preferably one) reduces the number of interfering first bounce reflections and generally improves the measured signal fidelity. The methodology will help the gathering of quantitative hovering rotor noise data in less than optimal acoustic facilities and thus enable basic rotorcraft research and rotor blade acoustic design.

Variação temporal das assembleias de drosofilídeos (Diptera, Drosophilidae) na reserva ecológica do IBGE

Dissertação (mestrado)—Universidade de Brasília, Instituto de Ciências Biológicas, Programa de Pós-Graduação em Ecologia, 2016.