Performance Tuning Non-Uniform Sampling for Sensitivity Enhancement of Signal-Limited Biological NMR

Non-uniform sampling (NUS) has been established as a route to obtaining true sensitivity enhancements when recording indirect dimensions of decaying signals in the same total experimental time as traditional uniform incrementation of the indirect evolution period. Theory and experiments have shown that NUS can yield up to two-fold improvements in the intrinsic signal-to-noise ratio (SNR) of each dimension, while even conservative protocols can yield 20-40 % improvements in the intrinsic SNR of NMR data. Applications of biological NMR that can benefit from these improvements are emerging, and in this work we develop some practical aspects of applying NUS nD-NMR to studies that approach the traditional detection limit of nD-NMR spectroscopy. Conditions for obtaining high NUS sensitivity enhancements are considered here in the context of enabling H-1,N-15-HSQC experiments on natural abundance protein samples and H-1,C-13-HMBC experiments on a challenging natural product. Through systematic studies we arrive at more precise guidelines to contrast sensitivity enhancements with reduced line shape constraints, and report an alternative sampling density based on a quarter-wave sinusoidal distribution that returns the highest fidelity we have seen to date in line shapes obtained by maximum entropy processing of non-uniformly sampled data.

Hepatic gene expression involved in glucose and lipid metabolism in transition cows: effects of fat mobilization during early lactation in relation to milk performance and metabolic changes.

Insufficient feed intake during early lactation results in elevated body fat mobilization to meet energy demands for milk production. Hepatic energy metabolism is involved by increasing endogenous glucose production and hepatic glucose output for milk synthesis and by adaptation of postcalving fuel oxidation. Given that cows differ in their degree of fat mobilization around parturition, indicated by variable total liver fat concentration (LFC), the study investigated the influence of peripartum fat mobilization on hepatic gene expression involved in gluconeogenesis, fatty acid oxidation, ketogenesis, and cholesterol synthesis, as well as transcriptional factors referring to energy metabolism. German Holstein cows were grouped according to mean total LFC on d 1, 14, and 28 after parturition as low [<200mg of total fat/g of dry matter (DM); n=10], medium (200-300 mg of total fat/g of DM; n=10), and high (>300 mg of total fat/g of DM; n=7), indicating fat mobilization during early lactation. Cows were fed total mixed rations ad libitum and held under equal conditions. Liver biopsies were taken at d 56 and 15 before and d 1, 14, 28, and 49 after parturition to measure mRNA abundances of pyruvate carboxylase (PC); phosphoenolpyruvate carboxykinase; glucose-6-phosphatase; propionyl-coenzyme A (CoA) carboxylase α; carnitine palmitoyl-transferase 1A (CPT1A); acyl-CoA synthetase, long chain 1 (ASCL1); acyl-CoA dehydrogenase, very long chain; 3-hydroxy-3-methylglutaryl-CoA synthase 1 and 2; sterol regulatory element-binding factor 1; and peroxisome proliferator-activated factor α. Total LFC postpartum differed greatly among cows, and the mRNA abundance of most enzymes and transcription factors changed with time during the experimental period. Abundance of PC mRNA increased at parturition to a greater extent in high- and medium-LFC groups than in the low-LFC group. Significant LFC × time interactions for ACSL1 and CPT1A during the experimental period indicated variable gene expression depending on LFC after parturition. Correlations between hepatic gene expression and performance data and plasma concentrations of metabolites and hormones showed time-specific relations during the transition period. Elevated body fat mobilization during early lactation affected gene expression involved in gluconeogenesis to a greater extent than gene expression involved in lipid metabolism, indicating the dependence of hepatic glucose metabolism on hepatic lipid status and fat mobilization during early lactation.

Performance of gene-expression profiling test score variability to predict future clinical events in heart transplant recipients.

BACKGROUND A single non-invasive gene expression profiling (GEP) test (AlloMap®) is often used to discriminate if a heart transplant recipient is at a low risk of acute cellular rejection at time of testing. In a randomized trial, use of the test (a GEP score from 0-40) has been shown to be non-inferior to a routine endomyocardial biopsy for surveillance after heart transplantation in selected low-risk patients with respect to clinical outcomes. Recently, it was suggested that the within-patient variability of consecutive GEP scores may be used to independently predict future clinical events; however, future studies were recommended. Here we performed an analysis of an independent patient population to determine the prognostic utility of within-patient variability of GEP scores in predicting future clinical events. METHODS We defined the GEP score variability as the standard deviation of four GEP scores collected ≥315 days post-transplantation. Of the 737 patients from the Cardiac Allograft Rejection Gene Expression Observational (CARGO) II trial, 36 were assigned to the composite event group (death, re-transplantation or graft failure ≥315 days post-transplantation and within 3 years of the final GEP test) and 55 were assigned to the control group (non-event patients). In this case-controlled study, the performance of GEP score variability to predict future events was evaluated by the area under the receiver operator characteristics curve (AUC ROC). The negative predictive values (NPV) and positive predictive values (PPV) including 95 % confidence intervals (CI) of GEP score variability were calculated. RESULTS The estimated prevalence of events was 17 %. Events occurred at a median of 391 (inter-quartile range 376) days after the final GEP test. The GEP variability AUC ROC for the prediction of a composite event was 0.72 (95 % CI 0.6-0.8). The NPV for GEP score variability of 0.6 was 97 % (95 % CI 91.4-100.0); the PPV for GEP score variability of 1.5 was 35.4 % (95 % CI 13.5-75.8). CONCLUSION In heart transplant recipients, a GEP score variability may be used to predict the probability that a composite event will occur within 3 years after the last GEP score. TRIAL REGISTRATION Clinicaltrials.gov identifier NCT00761787.

A study to determine the association between medical decision-making and the performance of an institutional ethics committee

This study developed proxy measures to test the independent effects of medical specialty, institutional ethics committee (IEC) and the interaction between the two, upon a proxy for the dependent variable of the medical decision to withhold/withdraw care for the dying--the resuscitation index (R-index). Five clinical vignettes were constructed and validated to convey the realism and contextual factors implicit in the decision to withhold/withdraw care. A scale was developed to determine the range of contact by an IEC in terms of physician knowledge and use of IEC policy.^ This study was composed of a sample of 215 physicians in a teaching hospital in the Southwest where proxy measures were tested for two competing influences, medical specialty and IEC, which alternately oppose and support the decision to withhold/withdraw care for the dying. A sub-sample of surgeons supported the hypothesis that an IEC is influential in opposing the medical training imperative to prolong life.^ Those surgeons with a low IEC score were 326 percent more likely to continue care than were surgeons with a high IEC score when compared to all other specialties. IEC alone was also found to significantly predict the decision to withhold/withdraw care. Interaction of IEC with the specialty of surgery was found to be the best predictor for a decision to withhold/withdraw care for the dying. ^

Enhancement of the Electrochemical Performance of SWCNT dispersed in a Silica Sol-gel Matrix by Reactive Insertion of a Conducting Polymer

The electroassisted encapsulation of Single-Walled Carbon Nanotubes was performed into silica matrices (SWCNT@SiO2). This material was used as the host for the potentiostatic growth of polyaniline (PANI) to yield a hybrid nanocomposite electrode, which was then characterized by both electrochemical and imaging techniques. The electrochemical properties of the SWCNT@SiO2-PANI composite material were tested against inorganic (Fe3+/Fe2+) and organic (dopamine) redox probes. It was observed that the electron transfer constants for the electrochemical reactions increased significantly when a dispersion of either SWCNT or PANI was carried out inside of the SiO2 matrix. However, the best results were obtained when polyaniline was grown through the pores of the SWCNT@SiO2 material. The enhanced reversibility of the redox reactions was ascribed to the synergy between the two electrocatalytic components (SWCNTs and PANI) of the composite material.

A pragmatic approach for engineering porous mannitol and mechanistic evaluation of particle performance

The importance of mannitol has increased recently as an emerging diluent for orodispersible dosage forms. The study aims to prepare spray dried mannitol retaining high porosity and mechanical strength for the development of orally disintegrating tablets (ODTs). Aqueous feed of d-mannitol (10% w/v) comprising ammonium bicarbonate, NH4HCO3 (5% w/v) as pore former was spray dried at inlet temperature of 110-170°C. Compacts were prepared at 151MPa and characterized for porosity, hardness and disintegration time. Particle morphology and drying mechanisms were studied using thermal (HSM, DSC and TGA) and polymorphic (XRD) methods. Tablet porosity increased from 0.20±0.002 for pure mannitol to 0.53±0.03 using fabricated porous mannitol. Disintegration time dropped by 50-77% from 135±5.29s for pure mannitol to 75.33±2.52-31.67±1.53s for mannitol 110-170°C. Hardness increased by 150% at 110°C (258.67±28.89N) and 30% at 150°C (152.70±10.58N) compared to pure mannitol tablets (104.17±1.70N). Increasing inlet temperature resulted in reducing tablet hardness due to generation of 'micro-sponge'-like particles exhibiting significant elastic recovery. Impact of mannitol polymorphism on plasticity/elasticity cannot be ruled out as a mixture of α and β polymorphs formed upon spray drying.

Le cognitive enhancement en milieu universitaire : entre souffrance psychique individuelle, culture de performance et insécurités sociales

Ce projet de mémoire s’intéresse à la mise en relation du cognitive enhancement observé dans les universités occidentales contemporaines et de la société dans laquelle il s’insère. Nous avons voulu détacher la perspective du phénomène des analyses principalement orientées vers les programmes de sciences de la santé et de droit, ainsi que de l’approche quantitative, clinique, athéorique et somme toute moralisatrice qui lui est usuellement accordée afin d’explorer la nature des pratiques d’usages de psychotropes des étudiants universitaires en sciences humaines et sociales en vue d’augmenter leurs performances cognitives, d’approfondir la compréhension des raisonnements sous-jacents à ces pratiques, puis de resituer ces derniers dans leur contexte élargi. Nous avons interrogé treize étudiants de divers programmes de sciences humaines et sociales consommant, ou ayant déjà consommé, des psychotropes en vue de rehausser leurs performances cognitives en contexte académique. Les résultats suggèrent un écart dans la nature de leurs pratiques d’usage par rapport aux domaines d’études habituellement préconisés en ce sens qu’une grande variété de substances sont considérées comme supports cognitifs ; ensuite, que le recours aux psychotropes dans une visée de performance cognitive s’éloigne des logiques de la nécessité médicale et de la toxicomanie. En premier lieu, le cognitive enhancement est associé par plusieurs à une souffrance psychique liée à une perte de repères existentiels et les étudiants y ont recours dans une optique de compréhension de soi et de quête de repères dans un monde qu’ils ressentent comme instable. En second lieu, la consommation de psychotropes s’apparente davantage à un désir de satisfaire aux conditions incertaines et menaçantes des demandes externes de performance telles qu’ils les appréhendent qu’à un souci de soigner quelque condition médicale de la cognition. Nous pensons que le rapport au psychotrope qu’entretiennent les étudiants universitaires en sciences humaines et sociales s’insère en toute cohérence dans les discours et injonctions contemporaines de performance, en ce sens que leur souffrance psychique individuelle expose les limites de ce que la société attend d’eux.

Enhancement of a novel gene therapy approach for Sandhoff disease through complimentary drug therapy

GM2 gangliosidoses is a family of severe, neurodegenerative disorders resulting from a deficiency in the β-hexosaminidase A (Hex A) enzyme. This disorder is typically caused by a mutation to either the HEXA gene, causing Tay Sachs disease, or a mutation to the HEXB gene, causing Sandhoff disease. The HEXA and HEXB genes are required to produce the α and β subunits of the Hex A enzyme respectively. Using a Sandhoff disease (SD) mouse model (Hexb-/-) we tested the potential of a low dose of systemically delivered single stranded adeno-associated virus 9 (ssAAV9) expressing human HEXB and human HEXA cDNA under the control of a single promoter through the use of a bicistronic vector design with a P2A linker to correct the neurological phenotype. Neonatal mice were injected with either this ssAAV9-HexB-P2A-HexA vector (HexB-HexA) or a vehicle solution via the superficial temporal vein. HexB-HexA treatment alone conferred an increase in survival of 56% compared to vehicle-injected controls and biochemical analysis of the brain tissue and serum revealed an increase in HexA activity and a decrease in brain GM2 ganglioside buildup. Additionally, treatments with the non-steroidal anti-inflammatory drug indomethacin (Indo), the histone deactylase inhibitor ITF2357 (ITF) and the pharmacological chaperone pyrimethamine (Pyr) were tested. The anti-inflammatory treatments of Indo and ITF conferred an increase in survival of 12% and 8% respectively while causing no alteration in the HexA activity or GM2 ganglioside buildup. Pyr had no observable effect on disease progression. Lastly HexB-HexA treatment was tested in conjunction with Indo, ITF and Pyr individually. Additive increases in survival and behavioural testing results were observed with Indo and ITF treatments while no additional benefit to HexA activity or GM2 ganglioside levels in the brain tissue was observed. This indicates the two treatments slowed the progression of the disease through a different mechanism than the reduction of the GM2 ganglioside substrate. Pyr treatment was shown to have no effect when combined with HexB-HexA treatment. This study demonstrates the potential amelioration of SD with a novel AAV9 gene therapy approach as well as helped to identify the additive potential of anti-inflammatory treatments in gene therapy of GM2 gangliosidoses.

Immune function, gene expression, blood indices and performance in transition dairy cows affected by diet and inflammation

The transition period is associated with the peak incidence of production problems, metabolic disorders and infectious diseases in dairy cows (Drackley, 1999). During this time the cow’s immune system seems to be weakened; it is apparent that metabolic challenges associated with the onset of lactation are factors capable of affecting immune function. However, the reasons for this state are not entirely clear (Goff, 2006). The negative energy balance associated with parturition leads to extensive mobilization of fatty acids stored in adipose tissue, thus, causing marked elevations in blood non-esterified fatty acids (NEFA) and B-hydroxybutyrate (BHBA) concentrations (Drackley et al., 2001). Prepartal level of dietary energy can potentially affect adipose tissue deposition and, thus, the amount of NEFA released into blood and available for metabolism in liver (Drackley et al., 2005). The current feeding practices for pregnant non-lactating cows has been called into question because increasing amounts of moderate-to-high energy diets (i.e. those more similar to lactation diets in the content of energy) during the last 3 wk postpartum have largely failed to overcome peripartal health problems, excessive body condition loss after calving, or declining fertility (Beever, 2006). Current prepartal feeding practices can lead to elevated intakes of energy, which can increase fat deposition in the viscera and upon parturition lead to compromised liver metabolism (Beever, 2006, Drackley et al., 2005). Our general hypothesis was that overfeeding dietary energy during the dry period, accompanied by the metabolic challenges associated with the onset of lactation would render the cow’s immune function less responsive early postpartum. The chapters in this dissertation evaluated neutrophil function, metabolic and inflammation indices and gene expression affected by the plane of dietary energy prepartum and an early post-partum inflammatory challenge in dairy cows. The diet effect in this experiment was transcendental during the transition period and potentially during the entire lactation. Changes in energy balance were observed and provided a good model to study the challenges associated with the onset of lactation. Overall the LPS model provided a consistent response representing an inflammation incident; however the changes in metabolic indices were sudden and hard to detect in most of the cases during the days following the challenge. In general overfeeding dietary energy during the dry period resulted in a less responsive immune function during the early postpartum. In other words, controlling the dietary energy prepartum has more benefits for the dairy cow during transition.

Le cognitive enhancement en milieu universitaire : entre souffrance psychique individuelle, culture de performance et insécurités sociales

Ce projet de mémoire s’intéresse à la mise en relation du cognitive enhancement observé dans les universités occidentales contemporaines et de la société dans laquelle il s’insère. Nous avons voulu détacher la perspective du phénomène des analyses principalement orientées vers les programmes de sciences de la santé et de droit, ainsi que de l’approche quantitative, clinique, athéorique et somme toute moralisatrice qui lui est usuellement accordée afin d’explorer la nature des pratiques d’usages de psychotropes des étudiants universitaires en sciences humaines et sociales en vue d’augmenter leurs performances cognitives, d’approfondir la compréhension des raisonnements sous-jacents à ces pratiques, puis de resituer ces derniers dans leur contexte élargi. Nous avons interrogé treize étudiants de divers programmes de sciences humaines et sociales consommant, ou ayant déjà consommé, des psychotropes en vue de rehausser leurs performances cognitives en contexte académique. Les résultats suggèrent un écart dans la nature de leurs pratiques d’usage par rapport aux domaines d’études habituellement préconisés en ce sens qu’une grande variété de substances sont considérées comme supports cognitifs ; ensuite, que le recours aux psychotropes dans une visée de performance cognitive s’éloigne des logiques de la nécessité médicale et de la toxicomanie. En premier lieu, le cognitive enhancement est associé par plusieurs à une souffrance psychique liée à une perte de repères existentiels et les étudiants y ont recours dans une optique de compréhension de soi et de quête de repères dans un monde qu’ils ressentent comme instable. En second lieu, la consommation de psychotropes s’apparente davantage à un désir de satisfaire aux conditions incertaines et menaçantes des demandes externes de performance telles qu’ils les appréhendent qu’à un souci de soigner quelque condition médicale de la cognition. Nous pensons que le rapport au psychotrope qu’entretiennent les étudiants universitaires en sciences humaines et sociales s’insère en toute cohérence dans les discours et injonctions contemporaines de performance, en ce sens que leur souffrance psychique individuelle expose les limites de ce que la société attend d’eux.

The RGBarrier assay: the parallel study of gene regulatory element performance at defined chromosomal locations

Vertebrate genomes are organised into a variety of nuclear environments and chromatin states that have profound effects on the regulation of gene transcription. This variation presents a major challenge to the expression of transgenes for experimental research, genetic therapies and the production of biopharmaceuticals. The majority of transgenes succumb to transcriptional silencing by their chromosomal environment when they are randomly integrated into the genome, a phenomenon known as chromosomal position effect (CPE). It is not always feasible to target transgene integration to transcriptionally permissive “safe harbour” loci that favour transgene expression, so there remains an unmet need to identify gene regulatory elements that can be added to transgenes which protect them against CPE. Dominant regulatory elements (DREs) with chromatin barrier (or boundary) activity have been shown to protect transgenes from CPE. The HS4 element from the chicken beta-globin locus and the A2UCOE element from a human housekeeping gene locus have been shown to function as DRE barriers in a wide variety of cell types and species. Despite rapid advances in the profiling of transcription factor binding, chromatin states and chromosomal looping interactions, progress towards functionally validating the many candidate barrier elements in vertebrates has been very slow. This is largely due to the lack of a tractable and efficient assay for chromatin barrier activity. In this study, I have developed the RGBarrier assay system to test the chromatin barrier activity of candidate DREs at pre-defined isogenic loci in human cells. The RGBarrier assay consists in a Flp-based RMCE reaction for the integration of an expression construct, carrying candidate DREs, in a pre-characterised chromosomal location. The RGBarrier system involves the tracking of red, green and blue fluorescent proteins by flow cytometry to monitor on-target versus off-target integration and transgene expression. The analysis of the reporter (GFP) expression for several weeks gives a measure of the protective ability of each candidate elements from chromosomal silencing. This assay can be scaled up to test tens of new putative barrier elements in the same chromosomal context in parallel. The defined chromosomal contexts of the RGBarrier assays will allow for detailed mechanistic studies of chromosomal silencing and DRE barrier element action. Understanding these mechanisms will be of paramount importance for the design of specific solutions for overcoming chromosomal silencing in specific transgenic applications.

Role of nitrogen doping on the performance of carbon nanotube catalysts: a catalytic wet peroxide oxidation application

Four magnetic carbon nanotube samples (CNTs: undoped, completely N-doped and two selectively N-doped) have been synthesized by chemical vapor deposition. The materials were tested in the catalytic wet peroxide oxidation (CWPO) of highly concentrated 4 nitrophenol solutions (4-NP, 5 g L-1). Relatively mild operating conditions were considered (atmospheric pressure, T = 50 ºC, pH = 3), using a catalyst load of 2.5 g L-1 and the stoichiometric amount of H2O2 needed for the complete mineralization of 4-NP. N doping was identified to influence considerably the CWPO performance of the materials. In particular, undoped CNTs, with a moderate hydrophobicity, favor the controllable and efficient decomposition of H2O2 into highly reactive hydroxyl radicals (HO•), thus showing high catalytic activity for 4-NP degradation. On the other hand, the completely N-doped catalyst, fully hydrophilic, favors a quick decomposition of H2O2 into non-reactive O2 and H2O species. The selectively N-doped amphiphilic catalysts, i.e. hybrid structures containing undoped sections followed by N-doped ones, provided intermediate results, namely: a higher N content favored H2O2 decomposition towards non-reactive H2O and O2 species, whilst a lower N content resulted in the formation of HO•, increasing 4-NP mineralization. Catalyst stability and reusability were also investigated by consecutive CWPO runs.