Enabling technologies for multiplexed biomolecule analysis and cell sorting

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2008.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Includes bibliographical references (p. [109]-122).The quantification and manipulation of biological entities from a physiological sample is extremely important for a broad range of applications in medical diagnostics, therapeutics, and basic science research. From a diagnostics standpoint, the cells, proteins, and nucleic acids that compose our bodies contain an enormous amount of information that can indicate the presence of, progression of, or even susceptibility to a given disease. However, extracting this information is often quite challenging. New tools are constantly being developed to make diagnostic testing more accurate, less invasive, faster, and less expensive. To this end, this thesis describes that advent of technologies to (1) precisely pattern biologically- and magnetically-active beads in hydrogel substrates for cell sorting and pattering, (2) synthesize morphologically and chemically-complex microparticles in a high-throughput fashion, and (3) perform rapid and accurate multiplexed biomolecule quantification using such particles. Bead-Patterned Hydrogels are a class of materials developed in this thesis that consist of microbeads precisely patterned in poly(ethylene glycol) (PEG) matrices. Using microfluidics and projection lithography on a standard microscope, magnetically-active or protein-decorated beads were patterned in close-packed or disperse-bead patterns on glass substrates with high resolution over large areas. Using slight alterations to ... bio-inert PEG matrix, or exposed from the PEG surface. It was shown that bead-patterned hydrogels could be used for the phenotype-specific sorting or patterning of lymphocytes. As was observed in the synthesis of bead-patterned hydrogels, free-radical polymerization is inhibited near microfluidic channel walls due to oxygen diffusion through the porous polydimethoxysilane (PDMS) elastomer composing devices.(cont.) By exploiting this phenomenon using ... an all-PDMS device, C graphy was developed. In stark contrast to traditional methods for anisotropic particle synthesis, this one-phase process provides a simple method to synthesize microparticles with complex morphologies and/or multiple adjacent chemistries in a high-throughput fashion. The processes is broadly applicable to any free-radical reacting monomer. For improved resolution and sharpened interfaces between adjacent chemistries ...by Daniel Colin Pregibon.Ph.D

The distribution of Pearson residuals in generalized linear models

In general, the distribution of residuals cannot be obtained explicitly. We give an asymptotic formula for the density of Pearson residuals in continuous generalized linear models corrected to order $n^{-1}$, where $n$ is the sample size. We define corrected Pearson residuals for these models that, to this order of approximation, have exactly the same distribution of the true Pearson residuals. Applications for important generalized linear models are provided and simulation results for a gamma model illustrate the usefulness of the corrected Pearson residuals

Socioeconomic inequalities in duration of untreated psychosis : evidence from administrative data in England

Background. Duration of untreated psychosis (DUP) is an important measure of access to care as it predicts prognosis and treatment outcomes. Little is known about potential socioeconomic inequalities in DUP. The aim of this study was to investigate inequalities in DUP associated with socioeconomic deprivation in a national cohort in England. Method. We analysed a cohort of 887 patients with a first-episode in psychosis using the administrative Mental Health Services Dataset in England. We used a Generalised Linear Model to account for non-linearity in DUP and looked at inequalities across the whole distribution of DUP using quantile regression. Results. The median DUP was 22 days (mean = 74 days) with considerable variations between and within the 31 hospital providers. We found evidence of significant inequalities regarding the level of socioeconomic deprivation. Patients living in the second, third, and fourth deprived neighbourhood quintiles faced a 36, 24, and 31 day longer DUP than patients from the least deprived neighbourhoods. Inequalities were more prevalent in higher quantiles of the DUP distribution. Unemployment prolonged DUP by 40 days. Having been in contact with mental health care services prior to the psychosis start significantly reduced the DUP by up to 53 days. Conclusions. Socioeconomic deprivation is an important factor in explaining inequalities in DUP. Policies to improve equitable access to care should particularly focus on preventing very long delays in treatment and target unemployed patients as well as people that have not been in contact with any mental health professional in the past

Adaptive business intelligence in healthcare - A platform for optimising surgeries

Adaptive Business Intelligence (ABI) combines predictive with prospective analytics in order to give support to the decision making process. Surgery scheduling in hospital operating rooms is a high complex task due to huge volume of surgeries and the variety of combinations and constraints. This type of activity is critical and is often associated to constant delays and significant rescheduling. The main task of this work is to provide an ABI based platform capable of estimating the time of the surgeries and then optimising the scheduling (minimizing the waste of resources). Combining operational data with analytical tools this platform is able to present complex and competitive information to streamline surgery scheduling. A case study was explored using data from a portuguese hospital. The best achieved relative absolute error attained was 6.22%. The paper also shows that the approach can be used in more general applications.This work has been supported by FCT –Fundação para a Ciência e Tecnologia within the Project Scope: UID/CEC/00319/201

Correlation of high levels of antibodies to multiple pre-erythrocytic Plasmodium falciparum antigens and protection from infection

High levels of antibodies to multiple antigens may be more strongly associated with protection from infection than antibodies to a single antigen. Antibody-associated protection against Plasmodium falciparum infection was assessed in a cohort of 68 adults living in an area of holoendemic malaria in Kenya. Antibodies to the pre-erythrocytic antigens circumsporozoite protein (CSP), liver-stage antigen-1 (LSA-1), thrombospondin-related adhesive protein (TRAP), and blood-stage antigens apical membrane antigen-1 (AMA-1), erythrocyte binding antigen-175 (EBA-175), and merozoite surface protein 1 (MSP-1) were tested. Peptides were used for CSP (NANP repeat) and LSA-1 (central repeat), and recombinant antigens were used for TRAP (aa D(48)-K(394)), AMA-1 (ectodomain, non-glycosylated), EBA-175 (non-glycosylated), and MSP-1 (MSP-1(19)). Weekly microscopy testing for P. falciparum infection was performed over a 12-week period after drug-mediated clearance of P. falciparum parasitemia. Individuals with high levels of IgG antibodies (\u3e 2 arbitrary units) to CSP, LSA-1, and TRAP had a 57% decrease in the risk of infection (95% confidence interval = 20-77%, P = 0.016). This decreased risk remained significant after adjustment for age, prior parasitemia, bed net use, sickle cell trait, and village of residence. In contrast, protection against infection did not correlate with high levels of IgG antibodies to blood-stage antigens or IgM antibodies to pre-erythrocytic or blood-stage antigens. High levels of IgG antibodies to CSP, LSA-1, and TRAP may be useful immune correlates of protection against P. falciparum infection in malaria-endemic populations

Engineering, Characterization and Directional Self-Assembly of Anisotropically Modified Nanocolloids

Along with traditional attributes such as the size, shape, and chemical structure of polymeric micro-objects, control over material distribution, or selective compartmentalization, appears to be increasingly important for maximizing the functionality and efficacy of biomaterials. The fabrication of tri- and tetracompartmental colloids made from biodegradable poly(lactide-co-glycolide) polymers via electrohydrodynamic co-jetting is demonstrated. The presence of three compartments is confirmed via flow cytometry. Additional chemical functionality is introduced via the incorporation of acetylene-functionalized polymers into individual compartments of the particles. Direct visualization of the spatioselective distribution of acetylene groups is demonstrated by confocal Raman microscopy as well as by reaction of the acetylene groups with azide-biotin via ‘click chemistry’. Biotin–streptavidin binding is then utilized for the controlled assembly and orientation of bicompartmental particles onto functionalized, micropatterned substrates prepared via chemical vapor deposition polymerization.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/83480/1/812_ftp.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/83480/2/smll_201001695_sm_suppl.pd

DNA-templated assembly of droplet-derived PEG microtissues

Patterning multiple cell types is a critical step for engineering functional tissues, but few methods provide three-dimensional positioning at the cellular length scale. Here, we present a “bottom-up” approach for fabricating multicellular tissue constructs that utilizes DNA-templated assembly of 3D cell-laden hydrogel microtissues. A flow focusing-generated emulsion of photopolymerizable prepolymer is used to produce 100 μm monodisperse microtissues at a rate of 100 Hz (10[superscript 5] h[superscript −1]). Multiple cell types, including suspension and adherently cultured cells, can be encapsulated into the microtissues with high viability ([similar]97%). We then use a DNA coding scheme to self-assemble microtissues “bottom-up” from a template that is defined using “top-down” techniques. The microtissues are derivatized with single-stranded DNA using a biotin–streptavidin linkage to the polymer network, and are assembled by sequence-specific hybridization onto spotted DNA microarrays. Using orthogonal DNA codes, we achieve multiplexed patterning of multiple microtissue types with high binding efficiency and >90% patterning specificity. Finally, we demonstrate the ability to organize multicomponent constructs composed of epithelial and mesenchymal microtissues while preserving each cell type in a 3D microenvironment. The combination of high throughput microtissue generation with scalable surface-templated assembly offers the potential to dissect mechanisms of cell–cell interaction in three dimensions in healthy and diseased states, as well as provides a framework for templated assembly of larger structures for implantation

Factors associated with care-related Quality of Life of adults with Intellectual Disabilities in England: Implications for Policy and Practice

Over the last three decades, quality of life (QoL) has been advocated as an indicator of social care outcomes for adults with intellectual disabilities. In England, the Adult Social Care Survey (ASCS) is conducted annually by local authorities to contribute to the evidence base of the care-related QoL of people receiving publicly-funded adult social care. This study explores relationships between QoL and non-care related factors to identify relationships that could inform social care policy and practice. Cross-sectional data collected from 13,642 adults who participated in the 2011 and 2012 ASCS were analysed using regression to explore the factors associated with QoL measured using the Adult Social Care Outcomes Toolkit (ASCOT). Self-rated health, rating of the suitability of home design and anxiety/depression were all found to be significantly associated with ASCOT. Other individual and survey completion factors were also found to have weak significant relationships with ASCOT. The models also indicate that there was an increase in overall ASCOT-QoL and in five of the eight ASCOT domains (Personal comfort and cleanliness, Safety, Social participation, Occupation and Dignity) between 2011 and 2012. These findings demonstrate the potential value of QoL data for informing policy for people with intellectual disabilities by identifying key factors associated with QoL, the characteristics of those at risk of lower QoL, and QoL domains that could be targeted for improvement over time. Future research should establish causal relationships and explore the risk-adjustment of scores to account for variation outside of the control of social care support