Improved clonality assessment in germinal centre/post-germinal centre non-Hodgkin's lymphomas with high rates of somatic hypermutation.

BACKGROUND: PCR detects clonal rearrangements of the Ig gene in lymphoproliferative disorders. False negativity occurs in germinal centre/post-germinal centre lymphomas (GC/PGCLs) as they display a high rate of somatic hypermutation (SHM), which causes primer mismatching when detecting Ig rearrangements by PCR. AIMS: To investigate the degree of SHM in a group of GC/PGCLs and assess the rate of false negativity when using BIOMED-2 PCR when compared with previously published strategies. METHODS: DNA was isolated from snap-frozen tissue from 49 patients with GC/PGCL (23 diffuse large B cell lymphomas (DLBCLs), 26 follicular lymphomas (FLs)) and PCR-amplified for complete (VDJH), incomplete (DJH) and Ig kappa/lambda rearrangements using the BIOMED-2 protocols, and compared with previously published methods using consensus primers. Germinal centre phenotype was defined by immunohistochemistry based on CD10, Bcl-6 and MUM-1. RESULTS: Clonality detection by amplifying Ig rearrangements using BIOMED-2 family-specific primers was considerably higher than that found using consensus primers (74% DLBCL and 96% FL vs 69% DLBCL and 73% FL). Addition of BIOMED-2 DJH rearrangements increased detection of clonality by 22% in DLBCL. SHM was present in VDJH rearrangements from all patients with DLBCL (median (range) 5.7% (2.5-13.5)) and FL (median (range) 5.3% (2.3-11.9)) with a clonal rearrangement. CONCLUSIONS: Use of BIOMED-2 primers has significantly reduced the false negative rate associated with GC/PGCL when compared with consensus primers, and the inclusion of DJH rearrangements represents a potential complementary target for clonality assessment, as SHM is thought not to occur in these types of rearrangements.

Heteroduplex analysis of VDJ amplified segments from rearranged IgH genes for clonality assessments in B-cell non-Hodgkin's lymphoma. A comparison between different strategies.

BACKGROUND AND OBJECTIVE: The main difficulty of PCR-based clonality studies for B-cell lymphoproliferative disorders (B-LPD) is discrimination between monoclonal and polyclonal PCR products, especially when there is a high background of polyclonal B cells in the tumor sample. Actually, PCR-based methods for clonality assessment require additional analysis of the PCR products in order to discern between monoclonal and polyclonal samples. Heteroduplex analysis represents an attractive approach since it is easy to perform and avoids the use of radioactive substrates or expensive equipment. DESIGN AND METHODS: We studied the sensitivity and specificity of heteroduplex PCR analysis for monoclonal detection in samples from 90 B-cell non Hodgkin's lymphoma (B-NHL) patients and in 28 individuals without neoplastic B-cell disorders (negative controls). Furthermore, in 42 B-NHL and in the same 28 negative controls, we compared heteroduplex analysis vs the classical PCR technique. We also compared ethidium bromide (EtBr) vs. silver nitrate (AgNO(3)) staining as well as agarose vs. polyacrylamide gel electrophoresis (PAGE). RESULTS: Using two pair consensus primers sited at VH (FR3 and FR2) and at JH, 91% of B-NHL samples displayed monoclonal products after heteroduplex PCR analysis using PAGE and AgNO(3) staining. Moreover, no polyclonal sample showed a monoclonal PCR product. By contrast, false positive results were obtained when using agarose (5/28) and PAGE without heteroduplex analysis: 2/28 and 8/28 with EtBr and AgNO(3) staining, respectively. In addition, false negative results only appeared with EtBr staining: 13/42 in agarose, 4/42 in PAGE without heteroduplex analysis and 7/42 in PAGE after heteroduplex analysis. INTERPRETATION AND CONCLUSIONS: We conclude that AgNO(3) stained PAGE after heteroduplex analysis is the most suitable strategy for detecting monoclonal rearrangements in B-NHL samples because it does not produce false-positive results and the risk of false-negative results is very low.

A Loop-mediated Isothermal Amplification Method for Rapid Direct Detection and Differentiation of Non-pathogenic and Verocytotoxigenic Escherichia coli in Beef and Bovine Faeces

The aim of this study was to develop a multiplex loop-mediated isothermal amplification (LAMP) method capable of detecting Escherichia coli generally and verocytotoxigenic E. coli (VTEC) specifically in beef and bovine faeces. The LAMP assay developed was highly specific (100%) and able to distinguish between E. coli and VTEC based on the amplification of the phoA, and stx1 and/or stx2 genes, respectively. In the absence of an enrichment step, the limit of detection 50% (LOD50) of the LAMP assay was determined to be 2.83, 3.17 and 2.83-3.17 log CFU/g for E. coli with phoA, stx1 and stx2 genes, respectively, when artificially inoculated minced beef and bovine faeces were tested. The LAMP calibration curves generated with pure cultures, and spiked beef and faeces, suggested that the assay had good quantification capability. Validation of the assay, performed using retail beef and bovine faeces samples, demonstrated good correlation between counts obtained by the LAMP assay and by a conventional culture method, but suggested the possibility of false negative LAMP results for 12.5-14.7% of samples tested. The multiplex LAMP assay developed potentially represents a rapid alternative to culture for monitoring E.coli levels in beef or faeces and it would provide additional information on the presence of VTEC. However, some further optimisation is needed to improve detection sensitivity.

Thomson scattering on non-thermal atmospheric pressure plasma jets

To characterize non-thermal atmospheric pressure plasmas experimentally, a large variety of methods and techniques is available, each having its own specific possibilities and limitations. A rewarding method to investigate these plasma sources is laser Thomson scattering. However, that is challenging. Non-thermal atmospheric pressure plasmas (gas temperatures close to room temperature and electron temperatures of a few eV) have usually small dimensions (below 1 mm) and a low degree of ionization (below 10^-4). Here an overview is presented of how Thomson scattering can be applied to such plasmas and used to measure directly spatially and temporally resolved the electron density and energy distribution. A general description of the scattering of photons and the guidelines for an experimental setup of this active diagnostic are provided. Special attention is given to the design concepts required to achieve the maximum signal photon flux with a minimum of unwanted signals. Recent results from the literature are also presented and discussed.

Non-invasive diagnosis of pediatric tuberculosis

Thesis (Master's)--University of Washington, 2016-08

Understanding of genetic test results for osteogenesis imperfecta by attorneys and child welfare workers in non-accidental injury cases

Thesis (Ph.D.)--University of Washington, 2016-08

Point de vue des toxicomanes sur les sources de motivation qui sont à la base de leurs changements de comportements

La problématique de cette recherche trouve son existence dans le fait que la motivation du toxicomane est un secteur d'activités humaines qui pose des problèmes importants tant sur le plan social et individuel qu'au point de vue de l'intervention thérapeutique. Ces derniers se manifestent à travers des ennuis sociaux comme celui de la conduite automobile avec facultés affaiblies, de l'absentéisme et des accidents au travail et parfois de la consommation et du commerce de drogues illicites. Le problème existe aussi au plan individuel: abandons et échecs scolaires, séparations et divorces, maladies physiques et troubles émotionnels. Au niveau thérapeutique, le taux de succès dépasse rarement les 35%, l'abandon au cours du processus de réadaptation est fréquent et le niveau de récidives ou de rechutes est élevé. À travers les différentes approches utilisées pour mesurer le degré de motivation à changer de comportements de la part du toxicomane (motivation et psychanalyse, motivation et behaviorisme, motivation et cognitivisme), l'auteure de cette recherche suggère que la motivation du toxicomane soit examinée sous une nouvelle perspective. Elle propose de demander individuellement l'opinion de toxicomanes non pas simplement à ne plus consommer mais à tout ce qui touche à l'ensemble de leur vie courante. Cette étude présente ainsi la perception de toxicomanes sur les sources de motivations qui sont sous-jacentes à certaines modifications de comportements. Au terme de la lecture de ce mémoire, le lecteur ou la lectrice connaîtra l'opinion de toxicomanes sur les motifs prioritaires qui génèrent le démarrage, la mise en mouvement, la motivation nécessaire à une modification de comportements. La méthode utilisée dans cette recherche s'inspire des travaux réalisés par Erick Klinger, professeur de psychologie à l'université du Minnesota, aux États-Unis. L'auteure a traduit, adapté et préexpérimenté le questionnaire sur les structures de motivations tiré de l'étude de Klinger et Cox, Motivational Structure Questionnaire. (Klinger, E., & Cox, W.M., 1986). Ce questionnaire présente vingt-sept activités de la vie courante qui peuvent présenter suffisamment d'intérêt pour mettre une personne en mouvement. Une question a été posée à quatre-vingt toxicomanes de la région de Sherbrooke qui ont fait une demande d'aide pour leur réadaptation. La question posée était: "Qu'est qui vous motive à changer de comportements?" Il s'avère que les toxicomanes interrogés accordent une grande importance à plus de douze motifs (motivations) autres que l'alcool, les drogues et les médicaments lorsqu'ils désirent changer. Pour l'auteure, ces résultats sont surprenants. L'idée de départ étant qu'il existe possiblement diverses raisons qui conduisent un ou une toxicomane vers une ressource d'aide mais pas autant que ce que l'étude en dénombre […].

Sources of antibiotic resistance in the environment

The discovery of antibiotics was a major breakthrough in medicine. However, short after their introduction in clinical practice resistant bacteria were detected. Nowadays, antibiotic resistance constitutes a serious public health problem. In hospital settings, with high resistance levels, reducing drastically the therapeutic options. Carbapenems are last-resort antibiotics used in Portugal, only in hospitals, to treat serious infections. Bacterial resistance towards this class of antibiotics has increased during last years. In Gram-negative bacteria the production of carbapenemases is a common resistance mechanism. OXA-48 is a carbapenemase of Ambler class D and represents a major concern for human health. It is frequently detected in clinical isolates of Enterobacteriaceae. There are few studies suggesting that genes encoding for OXA-48 variants originated from genes present in the chromosome of members of genus Shewanella, and have disseminated to Enterobacteriaceae members, associated with mobile genetic elements. The aim of this study was to characterize strains from different sources of Shewanella to confirm its role as OXA-48 progenitor. For this, the phylogenetic affiliation of 33 strains of Shewanella was performed by 16SrDNA and gyrB sequencing. The most common species were S. hafniensis and S. xiamenensis, but also S. aestuarii, S. baltica, S. indica, S. haliotis, S. putrefaciens, S. algidipiscicola, S. irciniae, S. algae and S. fodinae were identified. blaOXA-48-like genes were detected in 21 isolates: S. hafniensis (8/8), S. xiamenensis (5/5), S. baltica (4/4), S. algae (1/1), S. fodinae (1/1), S. putrefaciens (1/2) and S. algidipiscicola (1/2). Sequence analysis revealed that genes encoded enzymes identical to OXA-48, OXA-181 and OXA-204 but also new variants differing from OXA-48 from 2 to 81 aminoacids. Genetic context analysis revealed the C15 gene upstream and lysR gene downstream, identical to what has been identified so far flanking blaOXA-48-like genes in Shewanella spp. The assessment of antibiotic susceptibility was performed for all isolates using the disk diffusion method. In general, it was observed a great sensitivity for all antibiotics except to amoxicillin and aztreonam. Multidrug resistance was detected in only 1 isolate. Other resistance genes and the presence of integrons were not identified. Plasmids were detected in 30.3% isolates (10/ 33). These results reinforce the role of Shewanella spp. as origin of blaOXA-48-like genes.

Social Cognition, Negative Symptoms and Psychosocial Functioning in Schizophrenia.

Although functional recovery could be advocated as an achievable treatment goal, many effective interventions for the treatment of psychotic symptoms, such as antipsychotic drugs, may not improve functioning. The last two decades of cognitive and clinical research on schizophrenia were a turning point for the firm acknowledgment of how relevant social cognitive deficits and negative symptoms could be in predicting psychosocial functioning. The relevance of social cognition dysfunction in schizophrenia patients’ daily living is now unabated. In fact, social cognition deficits could be the most significant predictor of functionality in patients with schizophrenia, non-redundantly with neurocognition. Emerging evidence suggests that negative symptoms appear to play an indirect role, mediating the relationship between neurocognition and social cognition with functional outcomes. Further explorations of this mediating role of negative symptoms have revealed that motivational deficits appear to be particularly important in explaining the relationship between both neurocognitive and social cognitive dysfunction and functional outcomes in schizophrenia. In this paper we will address the relative contribution of two key constructs—social cognitive deficits and negative symptoms, namely how intertwined they could be in daily life functioning of patients with schizophrenia.

Characterization of Non-linear Polymer Properties to Predict Process Induced Warpage and Residual Stress of Electronic Packages

Nonlinear thermo-mechanical properties of advanced polymers are crucial to accurate prediction of the process induced warpage and residual stress of electronics packages. The Fiber Bragg grating (FBG) sensor based method is advanced and implemented to determine temperature and time dependent nonlinear properties. The FBG sensor is embedded in the center of the cylindrical specimen, which deforms together with the specimen. The strains of the specimen at different loading conditions are monitored by the FBG sensor. Two main sources of the warpage are considered: curing induced warpage and coefficient of thermal expansion (CTE) mismatch induced warpage. The effective chemical shrinkage and the equilibrium modulus are needed for the curing induced warpage prediction. Considering various polymeric materials used in microelectronic packages, unique curing setups and procedures are developed for elastomers (extremely low modulus, medium viscosity, room temperature curing), underfill materials (medium modulus, low viscosity, high temperature curing), and epoxy molding compound (EMC: high modulus, high viscosity, high temperature pressure curing), most notably, (1) zero-constraint mold for elastomers; (2) a two-stage curing procedure for underfill materials and (3) an air-cylinder based novel setup for EMC. For the CTE mismatch induced warpage, the temperature dependent CTE and the comprehensive viscoelastic properties are measured. The cured cylindrical specimen with a FBG sensor embedded in the center is further used for viscoelastic property measurements. A uni-axial compressive loading is applied to the specimen to measure the time dependent Young’s modulus. The test is repeated from room temperature to the reflow temperature to capture the time-temperature dependent Young’s modulus. A separate high pressure system is developed for the bulk modulus measurement. The time temperature dependent bulk modulus is measured at the same temperatures as the Young’s modulus. The master curve of the Young’s modulus and bulk modulus of the EMC is created and a single set of the shift factors is determined from the time temperature superposition. The supplementary experiments are conducted to verify the validity of the assumptions associated with the linear viscoelasticity. The measured time-temperature dependent properties are further verified by a shadow moiré and Twyman/Green test.

Non-Celiac Gluten Sensitivity and Autoimmunity. A Case Report

Introduction, objective: To present a case report in which the finding of non-coeliac gluten sensitivity was decisive for the treatment of a complex autoimmune disease. Materials and methods: A 43-year-old woman with polyarthritis, psoriatic features, anti-SSA/Ro and anti-cyclic citrullinated peptide antibodies, with refractory course, was evaluated for gluten sensitivity despite negative serology for coeliac disease. Results: The patient carried the HLA DQ2 haplotype and duodenal biopsy showed lymphocytic enteritis. A gluten-free diet resolved the clinical picture and permitted tapering of immunosuppressive therapy. Conclusion: Non-coeliac gluten sensitivity can be associated with autoimmunity despite the absence of the specific autoantibodies of coeliac disease.

Design and development of distributed feedback transistor lasers

The transistor laser is a unique three-port device that operates simultaneously as a transistor and a laser. With quantum wells incorporated in the base regions of heterojunction bipolar transistors, the transistor laser possesses advantageous characteristics of fast base spontaneous carrier lifetime, high differential optical gain, and electrical-optical characteristics for direct “read-out” of its optical properties. These devices have demonstrated many useful features such as high-speed optical transmission without the limitations of resonance, non-linear mixing, frequency multiplication, negative resistance, and photon-assisted switching. To date, all of these devices operate as multi-mode lasers without any type of wavelength selection or stabilizing mechanisms. Stable single-mode distributed feedback diode laser sources are important in many applications including spectroscopy, as pump sources for amplifiers and solid-state lasers, for use in coherent communication systems, and now as TLs potentially for integrated optoelectronics. The subject of this work is to expand the future applications of the transistor laser by demonstrating the theoretical background, process development and device design necessary to achieve singlelongitudinal- mode operation in a three-port transistor laser. A third-order distributed feedback surface grating is fabricated in the top emitter AlGaAs confining layers using soft photocurable nanoimprint lithography. The device produces continuous wave laser operation with a peak wavelength of 959.75 nm and threshold current of 13 mA operating at -70 °C. For devices with cleaved ends a side-mode suppression ratio greater than 25 dB has been achieved.

Non-comital women of twelfth-century England: a charter based analysis

This thesis sets out to explore the place and agency of non-comital women in twelfth-century Anglo-Norman England. Until now, broad generalisations have been applied to all aristocratic women based on a long established scholarship on royal and comital women. Non-comital women have been overlooked, mainly because of an assumed lack of suitable sources from this time period. The first aim of this thesis is to demonstrate that there is a sufficient corpus of charters for a study of this social group of women. It is based on a database created from 5545 charters, of which 3046 were issued by non-comital women and men, taken from three case study counties, Oxfordshire, Suffolk and Yorkshire, and is also supported by other government records. This thesis demonstrates that non-comital women had significant social and economic agency in their own person. By means of a detailed analysis of charters and their clauses this thesis argues that scholarship on non-comital women must rethink the framework applied to the study of non-comital women to address the lifecycle as one of continuities and as active agents in a wider public society. Non-comital women’s agency and identity was not only based on land or in widowhood, which has been the one period in their life cycles where scholars have recognised some level of autonomy, and women had agency in all stages of their life cycle. Women’s agency and identity were drawn from and part of a wider framework that included their families, their kin, and broader local political, religious, and social networks. Natal families continued to be important sources of agency and identity to women long after they had married. Part A of the thesis applies modern charter diplomatic analysis methods to the corpus of charters to bring out and explore women’s presence therein. Part B contextualises these findings and explores women’s agency in their families, landholding, the gift-economy, and the wider religious and social networks of which they were a part.

Nickel isotope fractionation during laterite Ni ore smelting and refining: implications for tracing the sources of Ni in smelter-affected soils

Nickel isotope ratios were measured in ores, fly ash, slags and FeNi samples from two metallurgical plants located in the Goiás State, Brazil (Barro Alto, Niquelândia). This allowed investigating the mass-dependent fractionation of Ni isotopes during the Ni-laterite ore smelting and refining. Feeding material exhibits a large range of δ60Ni values (from 0.02 ± 0.10 ‰ to 0.20 ± 0.05 ‰, n=7), explained by the diversity of Ni-bearing phases, and the average of δ60Nifeeding materials was found equal to 0.08 ± 0.08‰ (2SD, n=7). Both δ60Ni values of fly ash (δ60Ni = 0.07 ± 0.07‰, n=10) and final FeNi produced (0.05 ± 0.02 ‰, n=2) were not significantly different from the feeding materials ones. These values are consistent with the very high production yield of the factories. However, smelting slags present the heaviest δ60Ni values of all the smelter samples, with δ60Ni ranging from 0.11 ± 0.05 ‰ to 0.27 ± 0.05 ‰ (n=8). Soils were also collected near and far from the Niquelândia metallurgical plant, to evaluate the potential of Ni isotopes for tracing the natural vs anthropogenic Ni in soils. The Ni isotopic composition of the non-impacted topsoils developed on ultramafic rocks ranges from -0.26 ± 0.09 ‰ to -0.04 ± 0.05 ‰ (n=20). On the contrary, the Ni isotopic composition of the non-ultramafic topsoils, collected close to the plant, exhibit a large variation of δ60Ni, ranging from -0.19 ± 0.13 ‰ up to 0.10 ± 0.05 ‰ (n=4). This slight but significant enrichment in heavy isotopes highlight the potential impact of smelting activity in the surrounding area, as well as the potential of Ni isotopes for discerning anthropogenic samples (heavier δ60Ni values) from natural ones (lighter δ60Ni values). However, given the global range of published δ60Ni values (from -1.03 to 2.5 ‰) and more particularly those associated to natural weathering of ultramafic rocks (from -0.61 to 0.32‰), the use of Ni isotopes for tracing environmental contamination from smelters will remain challenging.

Formation of seep carbonates along the makran convergent margin, northern Arabian sea and a molecular and isotopic approach to constrain the carbon isotopic composition of parent methane

Authigenic carbonate deposits have been sampled with the remotely operated vehicle ‘MARUM-QUEST 4000 m’ from five methane seeps between 731 and 1823 m water depth along the convergent Makran continental margin, offshore Pakistan (northern Arabian Sea). Two seeps on the upper slope are located within the oxygen minimum zone (OMZ; ca. 100 to 1100 m water depth), the other sites are situated in oxygenated water below the OMZ (below 1100 m water depth). The carbonate deposits vary with regard to their spatial extent, sedimentary fabrics, and associated seep fauna: Within the OMZ, carbonates are spatially restricted and associated with microbial mats, whereas in the oxygenated zone below the OMZ extensive carbonate crusts are exposed on the seafloor with abundant metazoans (bathymodiolin mussels, tube worms, galatheid crabs). Aragonite and Mg-calcite are the dominant carbonate minerals, forming common early diagenetic microcrystalline cement and clotted to radial-fibrous cement. The δ18Ocarbonate values range from 1.3 to 4.2‰ V-PDB, indicating carbonate precipitation at ambient bottom-water temperature in shallow sediment depth. Extremely low δ13Ccarbonate values (as low − 54.6‰ V-PDB) point to anaerobic oxidation of methane (AOM) as trigger for carbonate precipitation, with biogenic methane as dominant carbon source. Prevalence of biogenic methane in the seepage gas is corroborated by δ13Cmethane values ranging from − 70.3 to − 66.7‰ V-PDB, and also by back-calculations considering δ13Cmethane values of carbonate and incorporated lipid biomarkers. These calculations (Δδ13Cmethane–carbonate, Δδ13CANME–methane, Δδ13CMOX–methane) prove to be useful to assess the carbon stable isotope composition of seeping methane if this has not been determined in the first place; such an approach represents a useful tool to reconstruct fluid composition of ancient seeps. AOM is also revealed by lipid biomarkers of anaerobic methane oxidizing archaea such as crocetane, pentamethylicosane (PMI), and sn2-hydroxyarchaeol strongly depleted in 13C (δ13C values as low as − 127‰ V-PDB). Biomarkers of sulphate-reducing bacteria are also abundant, showing slightly less negative δ13C values, but still significantly 13C-depleted (average values as low as − 101‰). Other bacterial biomarkers, such as bacteriohopanepolyols (BHPs), hopanols, and hopanoic acids are detected in most carbonates, but are particularly common in seep carbonates from the non-OMZ sites. The BHP patterns of these carbonates and their low δ13C values resemble patterns of aerobic methanotrophic bacteria. In the shallower OMZ sites, BHPs revealed much lower contents and varying compositions, most likely reflecting other sources than aerobic methanotrophic bacteria. 230Th/U carbonate ages indicate that AOM-induced carbonate precipitation at the deeper non-OMZ seeps occurred mainly during the late Pleistocene-Holocene transition, i.e. between 19 and 15 ka before present, when the global sea level was lower than today.