Learning Immune-Defectives Graph through Group Tests

This paper deals with an abstraction of a unified problem of drug discovery and pathogen identification. Pathogen identification involves identification of disease-causing biomolecules. Drug discovery involves finding chemical compounds, called lead compounds, that bind to pathogenic proteins and eventually inhibit the function of the protein. In this paper, the lead compounds are abstracted as inhibitors, pathogenic proteins as defectives, and the mixture of "ineffective" chemical compounds and non-pathogenic proteins as normal items. A defective could be immune to the presence of an inhibitor in a test. So, a test containing a defective is positive iff it does not contain its "associated" inhibitor. The goal of this paper is to identify the defectives, inhibitors, and their "associations" with high probability, or in other words, learn the Immune Defectives Graph (IDG) efficiently through group tests. We propose a probabilistic non-adaptive pooling design, a probabilistic two-stage adaptive pooling design and decoding algorithms for learning the IDG. For the two-stage adaptive-pooling design, we show that the sample complexity of the number of tests required to guarantee recovery of the inhibitors, defectives, and their associations with high probability, i.e., the upper bound, exceeds the proposed lower bound by a logarithmic multiplicative factor in the number of items. For the non-adaptive pooling design too, we show that the upper bound exceeds the proposed lower bound by at most a logarithmic multiplicative factor in the number of items.Comment: Double column, 17 pages. Updated with tighter lower bounds and other minor edit

Group testing:an information theory perspective

The group testing problem concerns discovering a small number of defective items within a large population by performing tests on pools of items. A test is positive if the pool contains at least one defective, and negative if it contains no defectives. This is a sparse inference problem with a combinatorial flavour, with applications in medical testing, biology, telecommunications, information technology, data science, and more. In this monograph, we survey recent developments in the group testing problem from an information-theoretic perspective. We cover several related developments: efficient algorithms with practical storage and computation requirements, achievability bounds for optimal decoding methods, and algorithm-independent converse bounds. We assess the theoretical guarantees not only in terms of scaling laws, but also in terms of the constant factors, leading to the notion of the {\em rate} of group testing, indicating the amount of information learned per test. Considering both noiseless and noisy settings, we identify several regimes where existing algorithms are provably optimal or near-optimal, as well as regimes where there remains greater potential for improvement. In addition, we survey results concerning a number of variations on the standard group testing problem, including partial recovery criteria, adaptive algorithms with a limited number of stages, constrained test designs, and sublinear-time algorithms.Comment: Survey paper, 140 pages, 19 figures. To be published in Foundations and Trends in Communications and Information Theor

Pooling Designs for High-Throughput Biological Experiments.

High-throughput experiments provide a fast, automated way to obtain massive amounts of information about biological systems. In several instances, these experiments subject a large number of items (biological samples or entities) individually to identical analysis. The information obtained is often redundant and the measurement systems are error-prone. Pooling designs are multiplexing strategies that test mixtures of items, instead of each item individually, in such a way that every item is tested multiple times. Testing mixtures allows for reduction in measurements, while multiple measurements of each item provide robustness. This thesis achieves three specific advances in applying pooling designs for high-throughput biological experiments. First, a theoretical framework to study pooling designs is described and a specific pooling strategy called the Shifted Transversal Design (STD) is adopted. Its mathematical properties are investigated and found to be useful but some limitations are also identified. Practical constraints encountered in implementing the STD strategy for a high-throughput drug screening application are investigated and novel solutions are provided. Second, the results of a proof-of-concept test of the STD strategy in an actual high-throughput screen are described. Robust decoding strategies are investigated and practical solutions are provided. A novel quantitative decoding procedure is developed to exploit the quantitative nature of data obtained from high-throughput screens. The performances of these decoding strategies are described in the context of the proof-of-concept screen. Third, the quantitative decoding approach is extended to a novel application of pooling designs to gene expression microarray experiments. The results from a small proof-of-concept test of this approach in a microarray experiment are described. Conditions for the successful implementation of this approach are discusses in the context of the experimental results. Overall, this work introduces and consolidates an approach to biological experimentation that is novel and promises to improve the efficiency and robustness of such experiments. Literature from diverse fields is brought together in the service of advancing the pooling approach and making it practical for existing experimental platforms. Two applications of this approach were investigated experimentally and provided several useful lessons for the success of this approach in these and other applications.Ph.D.Chemical Engineering and Scientific ComputingUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/77861/1/raghu_1.pd

Improving clinical outcomes for patients with locally advanced non-small cell lung cancer treated with photon and proton radiotherapy

Objectives To identify mechanisms improving clinical outcomes for patients with unresectable locally advanced non-small-cell lung cancer (LA-NSCLC) treated with photon and proton radiotherapy. Strategies explored include 1. Investigating using routine healthcare datasets to estimate survival outcomes for patients with LA-NSCLC treated with definitive radiotherapy, in order to assess the effectiveness of current strategies; 2. Assessing the physical advantages of protons by conducting a retrospective planning study comparing volumetric modulated arc therapy (VMAT) and pencil beam scanning (PBS) proton plans of superior sulcus tumours (SSTs), a rare subset of LA-NSCLC; 3. Exploring potential biological advantages of protons by examining major cell death pathways following XRT, high and low linear energy transfer (LET) proton irradiation of NSCLC cells. Methods Workflow 1: LA-NSCLC patients receiving definitive radiotherapy were identified. For each, key time points (date of diagnosis, recurrence, death or last clinical encounter) were used to calculate overall survival (OS) and progression free survival (PFS) from manual-data (hospital notes) and compared to estimated OS and PFS from routine-data (electronic databases). Dataset correlations were then tested to establish if routine-data were a reliable proxy measure for manual-data. Workflow 2: Patients with SSTs treated with 4D radiotherapy were identified. Tumour motion was assessed and excluded if >5 mm. Comparative VMAT and PBS plans were generated retrospectively. Robustness analysis was assessed for both plans involving: 1. 5 mm geometric uncertainty scenarios, with an additional 3.5% range uncertainty for proton plans; 2. verification plans at breathing extremes. Comparative dosimetric and robustness analyses were carried out. Workflow 3: Human NSCLC cell lines were irradiated with single doses of 2-15 Gy photon radiotherapy, high- or low-linear energy transfer (LET) protons (12 keV/µm and 1 keV/µm, respectively) and analysed 24-144 hours post-irradiation. DNA damage foci and cell death mechanisms were investigated. Results Workflow 1: In forty-three patients, routine data underestimated PFS by 0.09 months (p=0.86; 95% CI -0.86-1.03) and OS by 1.02 months (p=0.00; 95% CI 0.34-1.69) but there was good correlation with a Pearson correlation coefficient of 0.94 (p=0.00, 95% CI 0.90-0.97) for PFS and 0.97 (p= 0.00, 95% CI 0.95-0.98) for OS. Workflow 2: In ten patients, both modalities achieved similar target coverage with mean clinical target volume D95 of 98.1% + 0.4 (97.5-98.8) and 98.4% + 0.2 (98.1-98.9) for PBS and VMAT plans, respectively. The same four PBS and VMAT plans failed robustness. Proton plans significantly reduced mean lung dose (by 21.9%), lung V5, V10, V20 (by 47.9%, 36.4%, 12.1%, respectively), mean heart dose (by 21.4%) and vertebra dose (by 29.2%) (p<0.05). Workflow 3: XRT predominantly induced mitotic catastrophe, autophagy and senescence. Senescence, established via the p53/p21 pathway, was the major cell death pathway by which protons more effectively reduce clonogenic potential compared to XRT in NSCLC cell lines. High LET protons at a dose of 10 Gy(RBE) resulted in the lowest cell survival. The mechanisms driving the LET- and dose-dependent senescence was unclear but did not appear to be related to differential DNA repair machineries. Conclusions Proton radiotherapy could be pivotal in improving outcomes in select cases of LA-NSCLC. These studies demonstrate that 1. survival-outcomes are reliably estimated by routine data and such a methodology could enable rapid outcomes analysis to keep pace with trial development; 2. robust PBS plans are achievable in carefully selected patients and considerable dose reductions to the lung, heart and thoracic vertebra are possible without compromising target coverage; 3. Identification of LET- and dose-dependent proton-induced cellular senescence may guide radiotherapy optimisation and drug-radiotherapy combinations, maximising tumour cell kill. This work contributes to important preliminary research required to understand the physical and biological strengths and weaknesses prior to trials

Psychological morbidity and facial volume in HIV lipodystrophy: quantification of treatment outcome

INTRODUCTION HIV-associated facial lipoatrophy is a stigmatizing condition associated with significant psychological morbidity. The condition may be treated with soft tissue fillers, although quantification of objective and patient- reported outcomes is lacking. The primary aim of this study was to evaluate change in facial volume and psychological morbidity following treatment for HIV lipodystrophy with autologous fat transfer, Newfill and Bio-alcamid. An additional aim of the study was to compare psychological characteristics between HIV seropositive patients with lipodystrophy (HIV LD) and without lipodystrophy (HIV non -LD) and HIV seronegative men who have sex with men (MSM).METHODS HIV LD patients were treated with autologous fat, Newfill or Bio- alcamid based on a clinical assessment in a prospective, observational study. The Colemnan technique of fat transfer was utilised. Newfill injections were carried out at monthly intervals using 1 vial per cheek. Bio- alcamid was injected subcutaneously under aseptic technique to achieve the desired cheek augmentation. 3 -D images were obtained pre- operatively then at 2, 6 and 12 months post -operatively using the DI3D system. Volume changes in treated areas were measured using DI3D software. The DAS -24 and HADS were used to assess psychological morbidity at similar time intervals. An additional case -control study was conducted to measure psychological morbidity in HIV LD, HIV non -LD and MSM groups utilising the Derriford Appearance Scale (DAS -24) and Hospital Anxiety and Depression Scale (HADS). Data was analyzed using appropriate statistical tests.RESULTS ANOVA tests demonstrated significantly higher DAS -24 scores in the HIV -LD group compared to the HIV non -LD and MSM groups. No difference in HADS -A scores was seen between groups. 48 patients with HIV LD were treated: 16 patients had Bio- alcamid augmentation, 20 patients received Newfill injections and 12 patients underwent fat transfer. The mean injected volume of Bio- alcamid was 25.5cc The Wilcoxin test demonstrated no significant difference in mean volume change relative to zero at 2, 6 and 12 months. The mean injected volume of fat was 20.1cc, which did not differ from the measured volumes at 2 months (1)= 0.15). There was a mean reduction in measured volume of 7.3cc at 6 months and 9cc at 12 months (p <0.001). For Newfill, the mean volume change compared to baseline was 8.7cc at 2months, increasing to 12.6cc at 6 months and 12.3cc at 12 months. ANOVA tests demonstrated no difference in psychological outcomes between groups. There was a significant improvement in DAS -24 scores compared too baseline for all 3 groups throughout follow -up. For Bio- alcamid, a significant improvement in HADS -A and HADS -D scores were seen at 2 months but mean scores increased at 6 and 12 months. In the fat group, some improvement in HADS -A and HADS -D scores were seen at follow -up, although values only reached significance at 6 months. In the Newfill group, small improvements in both HADS -A and HADS -D were demonstrated in the post -treatment scores, although these did not reach significance. No correlation between change in facial volume and psychological measures was demonstrated.CONCLUSIONS The case control study demonstrated that patients with HIV lipodystrophy have greater distress relating to body image and depression compared to HIV-seropositive patients without lipodstrophy and HIV-seronegative MSM control groups. The prospective study of the HIV LD treatment cohort demonstrated a change in 3 -D measured facial volume for all 3 groups. Bio-alcamid produced the greatest, permanent volume change but was associated with the most complications. Newfill was associated with a moderate, delayed volume augmentation but was insufficient for some patients with severe lipoatrophy. Volume enhancement with autologous fat was good immediately post-operatively but variable degrees of fat resorption occurred. Treatment was associated with improved body image perception. However, initial improvements in anxiety and depression symptoms were not maintained in the long term

The Public Service Media and Public Service Internet Manifesto

This book presents the collectively authored Public Service Media and Public Service Internet Manifesto and accompanying materials.The Internet and the media landscape are broken. The dominant commercial Internet platforms endanger democracy. They have created a communications landscape overwhelmed by surveillance, advertising, fake news, hate speech, conspiracy theories, and algorithmic politics. Commercial Internet platforms have harmed citizens, users, everyday life, and society. Democracy and digital democracy require Public Service Media. A democracy-enhancing Internet requires Public Service Media becoming Public Service Internet platforms – an Internet of the public, by the public, and for the public; an Internet that advances instead of threatens democracy and the public sphere. The Public Service Internet is based on Internet platforms operated by a variety of Public Service Media, taking the public service remit into the digital age. The Public Service Internet provides opportunities for public debate, participation, and the advancement of social cohesion. Accompanying the Manifesto are materials that informed its creation: Christian Fuchs’ report of the results of the Public Service Media/Internet Survey, the written version of Graham Murdock’s online talk on public service media today, and a summary of an ecomitee.com discussion of the Manifesto’s foundations

Intrauterine and genetic risk factors for proliferative diabetic retinopathy

Diabetes is a complex progressive metabolic disorder characterized by hyperglycemia and caused by different etiopathogenic factors. Individuals with diabetes have heterogeneous clinical representation and increased risk of micro- and macrovascular complications. Diabetic retinopathy (DR) is the most frequent microvascular complication of diabetes and one of the leading causes of blindness. Currently, existing treatment modalities target a severe sight-threatening form of the disease, proliferative DR (PDR), and are characterized by significant side effects. The prevailing strategy for prevention or slowing down DR progression is glucose-lowering therapy, which is not efficient enough and might be harming to older groups of patients. Risk factors for PDR include duration of diabetes, hypertension, dyslipidemia, genetics and environment, and their interplay. The adverse intrauterine environment, particularly exposure to prenatal famine, was shown to play an important role in predisposition to diverse metabolic disorders in adults such as type 2 diabetes (T2D), hypertension, and cardiovascular diseases (CVD). In this Ph.D. thesis, we aimed to study novel diabetes subgroups based on pathophysiological characteristics of patients, highlighting subgroup(s) with an elevated risk of diabetic complications, particularly PDR. Further, we aimed to investigate the association of intrauterine exposure to famine with the risk of PDR in adult individuals with T2D. Finally, we wanted to study the molecular mechanisms linked to famine-related PDR. In paper 1, we performed a k-means cluster analysis to identify novel subgroups of individuals with new-onset and long-term diabetes, and estimated the risks of diabetic complications using logistic regression. In paper 2, we evaluated effect of intrauterine famine exposure on the risk of PDR in individuals with T2D using logistic regression adjusted for established risk factors such as age, sex, duration of diabetes and HbA1c. In paper 3, we performed candidate gene analysis using generalized estimation equation (GEE) to study the effect of interaction between SNPs and perinatal famine exposure on the risk of PDR. In paper 4, we performed genome-wide association (GWAS) and interaction (GWIS) studies using a linear mixed model (LMM) to investigate molecular underpinnings of famine-related PDR. In paper 1, we identified three subgroups with severe diabetes and two subgroups with mild diabetes. The highest risk of PDR was observed in the severe autoimmune diabetes (SAID) and severe insulin-deficient diabetes (SIDD) subgroups and the lowest in the insulin-resistant obesity-related diabetes 2 (IROD2) subgroup. In paper 2, we demonstrated that individuals with T2D, who were perinatally exposed to famine had an elevated risk of PDR in adult life. In paper 3, we demonstrated a significant association between famine-associated PDR and SNPs which were located in genes with neuronal function. In paper 4, we identified diverse pathways potentially linked to famine-related PDR, among them the most significant were lipid metabolism and inflammation pathways. In conclusion, we suggested that the altered development of neurovascular unit in the retina due to exposure to intrauterine famine may increase susceptibility to PDR later in life. Changes in metabolic adaptations during developmental programming induced by adverse early life events may affect insulin secretion and lipid metabolism, which consequently may increase predisposition to PDR under diabetes environment in adulthood. We suggested that drugs targeting these mechanisms in addition to glucose-lowering treatments may be beneficial for the prevention or slowing down the progression to PDR in the early stages of the disease.Diabetes er en kompleks progressiv metabolsk sykdom som kjennetegnes ved hyperglykemi og er forårsaket av forskjellige etiopatogenetiske faktorer. Personer med diabetes har heterogen klinisk representasjon og økt risiko for mikro- og makrovaskulære komplikasjoner. Diabetisk retinopati (DR) er den hyppigste mikrovaskulære komplikasjonen ved diabetes og en av de viktigste årsakene til blindhet. For tiden er eksisterende behandlingsmetoder rettet mot en alvorlig synstruende form av sykdommen, proliferativ DR (PDR), og medfører betydelige bivirkninger. Den rådende strategien for forebygging eller forsinking av DR-progresjon er glukosesenkende terapi, som ikke er effektiv nok og kan være skadelig for eldre pasienter. Risikofaktorer for PDR inkluderer varighet av diabetes, hypertensjon, dyslipidemi, genetikk og miljø, og deres samspill. Det ugunstige intrauterine miljøet, spesielt eksponering for prenatal hungersnød, ble vist å spille en viktig rolle i predisposisjon for ulike metabolske forstyrrelser hos voksne som type 2 diabetes (T2D), hypertensjon og kardiovaskulære sykdommer (CVD). I denne doktorgradsavhandlingen, har vi hatt som mål å studere nye diabetes-undergrupper basert på patofysiologiske egenskaper hos pasienter, og fremheve undergruppe(r) med økt risiko for diabetiske komplikasjoner, spesielt PDR. Videre hadde vi som mål å undersøke sammenheng mellom intrauterin eksponering for hungersnød og risikoen for utvikling av PDR hos voksne med T2D. Til slutt ønsket vi å studere de molekylære mekanismene knyttet til hungersnød-relatert PDR. I artikkel 1 utførte vi en k-means-klyngeanalyse for å identifisere nye undergrupper av individer med nyoppstått og langvarig diabetes, og estimerte risikoen for diabetiske komplikasjoner ved hjelp av logistisk regresjon. I artikkel 2 evaluerte vi effekten av eksponering for intrauterin hungersnød på risikoen for PDR hos individer med T2D ved bruk av logistisk regresjon justert for etablerte risikofaktorer som alder, kjønn, varighet av diabetes og HbA1c. I artikkel 3 utførte vi kandidatgenanalyse ved å bruke generalisert estimeringsligning (GEE) for å studere effekten av interaksjon mellom SNP-er og perinatal hungersnødeksponering på risikoen for PDR. I artikkel 4 utførte vi genomomfattende assosiasjonsstudier (GWAS) og interaksjonsstudier (GWIS) ved å bruke en lineær blandet modell (LMM) for å undersøke molekylært grunnlag for hungersnødrelatert PDR. I artikkel 1 identifiserte vi tre undergrupper med alvorlig diabetes og to undergrupper med mild diabetes. Den høyeste risikoen for PDR ble observert i undergruppene med alvorlig diabetes type 1 (SAID) og alvorlig diabetes type 2 (SIDD), og den laveste i undergruppen insulinresistent fedme-relatert diabetes 2 (IROD2). I artikkel 2 viste vi at personer med T2D, som ble perinatalt utsatt for hungersnød, hadde en forhøyet risiko for utvikling av PDR i voksenlivet. I artikkel 3 viste vi en signifikant sammenheng mellom hungersnødassosiert PDR og SNP-er som var lokalisert i gener med nevronal funksjon. I artikkel 4 identifiserte vi ulike veier som er potensielt knyttet til hungersnød-relatert PDR, blant dem var de mest betydningsfulle lipidmetabolisme og betennelsesveier. Avslutningsvis foreslo vi at den endrede utviklingen av nevrovaskulær kretsløp i netthinnen på grunn av eksponering for intrauterin hungersnød kan øke følsomheten for PDR senere i livet. Endringer i metabolske tilpasninger under utviklingsprogrammering indusert av uønskede hendelser i tidlig liv kan påvirke insulinsekresjon og lipidmetabolisme, som følgelig kan øke predisposisjon for PDR under diabetesmiljø i voksen alder. Vi foreslo at medikamenter som retter seg mot disse mekanismene i tillegg til glukosesenkende behandlinger kan være gunstig for forebygging eller forsinke progresjon til PDR i de tidlige stadiene av sykdommen.Doktorgradsavhandlin