The opportunity prior: a proof-based prior for criminal cases

One of the greatest challenges to the use of probabilistic reasoning in the assessment of criminal evidence is the ‘problem of the prior’, i.e. the difficulty in establishing an acceptable prior probability of guilt. Even strong supporters of a Bayesian approach have often preferred to ignore priors and focus on the likelihood ratio (LR) of the evidence. But to calculate if the probability of guilt, given the evidence reaches the probability required for conviction (the standard of proof), the LR has to be combined with a prior. In this article, we propose a solution to the ‘problem of the prior’: the defendant shall be treated as a member of the set of ‘possible perpetrators’ defined as the people who had the same or better opportunity as the defendant to commit the crime. For this purpose, we introduce the concept of an ‘extended crime scene’. The number of people who had the same or better opportunity as the defendant is the number of people who were just as close or closer to the crime scene, in time and space. We demonstrate how the opportunity prior is incorporated into a generic Bayesian network model that allows us to integrate other evidence about the case

The Opportunity Prior: A Simple and Practical Solution to the Prior Probability Problem for Legal Cases

One of the greatest impediments to the use of probabilistic reasoning in legal arguments is the difficulty in agreeing on an appropriate prior probability for the ultimate hypothesis, (in criminal cases this is normally “Defendant is guilty of the crime for which he/she is accused”). Even strong supporters of a Bayesian approach prefer to ignore priors and focus instead on considering only the likelihood ratio (LR) of the evidence. But the LR still requires the decision maker (be it a judge or juror during trial, or anybody helping to determine beforehand whether a case should proceed to trial) to consider their own prior; without it the LR has limited value. We show that, in a large class of cases, it is possible to arrive at a realistic prior that is also as consistent as possible with the legal notion of ‘innocent until proven guilty’. The approach can be considered as a formalisation of the ‘island problem’ whereby if it is known the crime took place on an island when n people were present, then each of the people on the island has an equal prior probability 1/n of having carried out the crime. Our prior is based on simple location and time parameters that determine both a) the crime scene/time (within which it is certain the crime took place) and b) the extended crime scene/time which is the ‘smallest’ within which it is certain the suspect was known to have been ‘closest’ in location/time to the crime scene. The method applies to cases where we assume a crime has taken place and that it was committed by one person against one other person (e.g. murder, assault, robbery). The paper considers both the practical and legal implications of the approach. We demonstrate how the opportunity prior probability is naturally incorporated into a generic Bayesian network model that allows us to integrate other evidence about the case

Adipose tissue pathways involved in weight loss of cancer cachexia

White adipose tissue (WAT) constitutes our most expandable tissue and largest endocrine organ secreting hundreds of polypeptides collectively termed adipokines. Changes in WAT mass induce alterations in adipocyte secretion and function, which are linked to disturbed whole-body metabolism. Although the mechanisms controlling this are not clear they are dependent on changes in gene expression, a complex process which is regulated at several levels. Results in recent years have highlighted the role of small non-coding RNA molecules termed microRNAs (miRNAs), which regulate gene expression via post-transcriptional mechanisms. The aim of this thesis was to characterize global gene expression levels and describe novel miRNAs and adipokines controlling the function of human WAT in conditions with pathological increases or decreases in WAT mass. Obesity and cancer cachexia were selected as two models since they are both clinically relevant and characterized by involuntary changes in WAT mass. In Study I, expressional analyses were performed in subcutaneous WAT from cancer patients with or without cachexia and obese versus non-obese subjects. In total, 425 transcripts were found to be regulated in cancer cachexia. Pathway analyses based on this set of genes revealed that processes involving extracellular matrix, actin cytoskeleton and focal adhesion were significantly downregulated, whereas fatty acid metabolism was upregulated comparing cachectic with weight-stable cancer subjects. Furthermore, by overlapping these results with microarray data from an obesity study, many transcripts were found to be reciprocally regulated comparing the two conditions. This suggests that WAT gene expression in cancer cachexia and obesity are regulated by similar, albeit opposing, mechanisms. In Study II, the focus was on the family of fibroblast growth factors (FGFs), members of which have recently been implicated in the development of obesity and insulin resistance. A retrospective analysis of global gene expression data identified several FGFs (FGF1/2/7/9/13/18) to be expressed in WAT. However, only one, FGF1, was actively secreted from WAT and predominantly so from the adipocyte fraction. Moreover, FGF1 release was increased in obese compared to non-obese subjects, but was not normalized by weight loss. Although the clinical significance of these findings is not yet clear, it can be hypothesized that FGF1 may play a role in WAT growth, possibly by promoting fat cell proliferation and/or differentiation. In Study III, we identified adipose miRNAs regulated in obesity. Out of eleven miRNAs regulated by changes in body fat mass, ten controlled the production of the pro-inflammatory chemoattractant chemokine (C-C motif) ligand 2 (CCL2) when overexpressed in fat cells and for two, miR-126 and -193b, signaling circuits were defined. In Study IV, a novel adipokine, semaphorin 3C (SEMA3C), was identified by combining transcriptome and secretome data. Detailed studies focusing on SEMA3C revealed that this factor was secreted from adipocytes and induced the expression of extracellular matrix and matricellular genes in preadipocytes. Furthermore, SEMA3C mRNA levels correlated with interstitial fibrosis and insulin resistance in WAT derived from subjects with a wide range in BMI. In summary, the results presented in this thesis have delineated transcriptional alterations in WAT in two clinically relevant conditions, obesity and cancer cachexia. This has allowed the identification of novel adipokines and microRNAs with potential pathophysiological importance. These findings form the basis for further studies aiming at understanding the central role of WAT in disorders associated with metabolic complications

Genome-wide association study of adipocyte lipolysis in the GENetics of adipocyte lipolysis (GENiAL) cohort.

OBJECTIVES:Lipolysis, hydrolysis of triglycerides to fatty acids in adipocytes, is tightly regulated, poorly understood, and, if perturbed, can lead to metabolic diseases including obesity and type 2 diabetes. The goal of this study was to identify the genetic regulators of lipolysis and elucidate their molecular mechanisms. METHODS:Adipocytes from abdominal subcutaneous adipose tissue biopsies were isolated and were incubated without (spontaneous lipolysis) or with a catecholamine (stimulated lipolysis) to analyze lipolysis. DNA was extracted and genome-wide genotyping and imputation conducted. After quality control, 939 samples with genetic and lipolysis data were available. Genome-wide association studies of spontaneous and stimulated lipolysis were conducted. Subsequent in vitro gene expression analyses were used to identify candidate genes and explore their regulation of adipose tissue biology. RESULTS:One locus on chromosome 19 demonstrated genome-wide significance with spontaneous lipolysis. 60 loci showed suggestive associations with spontaneous or stimulated lipolysis, of which many influenced both traits. In the chromosome 19 locus, only HIF3A was expressed in the adipocytes and displayed genotype-dependent gene expression. HIF3A knockdown in vitro increased lipolysis and the expression of key lipolysis-regulating genes. CONCLUSIONS:In conclusion, we identified a genetic regulator of spontaneous lipolysis and provided evidence of HIF3A as a novel key regulator of lipolysis in subcutaneous adipocytes as the mechanism through which the locus influences adipose tissue biology

Measurements of body fat is associated with markers of inflammation, insulin resistance and lipid levels in both overweight and in lean, healthy subjects

Background & aims: Low-grade inflammation is associated with fat mass in overweight. Whether this association exists in lean persons is unknown. Aims were to investigate associations between anthropometric measures of fat distribution and fat mass (% and kg) assessed by bioelectrical impedance analysis (BIA). Furthermore we wanted to investigate the relationship between fat mass and markers of insulin resistance, inflammation, and lipids in healthy subjects in different BMI categories. Methods: We compared 47 healthy overweight adults (BMI 26e40 kg/m2) and 40 lean (BMI 17e25 kg/ m2) matched for age and sex. Waist and hip circumferences, waist-to-hip ratio, waist-to-height ratio and triceps skinfold were used to evaluate fat distribution. BIA was used to estimate fat mass (% and kg). Markers of insulin resistance, lipids, inflammation and adipokines were measured. Results: Hip circumference was associated (P < 0.01) with BIA-assessed fat mass (%) in both groups (lean: regression coefficient B ¼ 0.4; overweight: B ¼ 0.5). An increase in hip circumference in all tertiles was associated with higher plasma levels of leptin, CRP and C-peptide in both groups. Conclusions: Fat mass may play a role in low-grade inflammation also in subjects within the normal range of BMI. Hip circumference may be a surrogate measure for fat mass in subjects in different BMI categories, and may be useful for identification of people with risk of developing overweight-related chronic disease

Genome-wide analysis of single nucleotide polymorphisms uncovers population structure in Northern Europe

Peer reviewe

Gene Expression Profiling and Chromatin Immunoprecipitation Identify DBN1, SETMAR and HIG2 as Direct Targets of SOX11 in Mantle Cell Lymphoma

The SRY (sex determining region Y)-box 11 (SOX11) gene, located on chromosome 2p25, encodes for a transcription factor that is involved in tissue remodeling during embryogenesis and is crucial for neurogenesis. The role for SOX11 in hematopoiesis has not yet been defined. Two genes under direct control of SOX11 are the class- III β-tubulin gene (TUBB3) in neural cells and the transcription factor TEA domain family member 2 (TEAD2) in neural and mesenchymal progenitor cells. Normal, mature lymphocytes lack SOX11 but express SOX4, another member of the same group of SOX transcription factors. We and others recently identified SOX11 as aberrantly expressed in mantle cell lymphoma (MCL). Since SOX11 is variably expressed in MCL it may not be essential for tumorigenesis, but may carry prognostic information. Currently, no specific functional effects have been linked to SOX11 expression in MCL and it is not known which genes are under influence of SOX11 in lymphoma. In this study we found variable expression of SOX11, SOX4 and SOX12 mRNA in mantle cell lymphoma cell lines. Downregulation of SOX11 expression by siRNA verified that SOX11 controlled the expression of the gene TUBB3 in the MCL cell line Granta 519. Furthermore we identified, by global gene expression analysis, 26 new target genes influenced by siRNA SOX11 downmodulation. Among these genes, DBN1, SETMAR and HIG2 were found to be significantly correlated to SOX11 expression in two cohorts of primary mantle cell lymphomas. Chromatin immunoprecipitation (ChIP) analysis showed that these genes are direct targets of the SOX11 protein. In spite of almost complete downregulation of the SOX11 protein no significant effects on Granta 519 cell proliferation or survival in short term in vitro experiments was found. In summary we have identified a number of genes influenced by SOX11 expression in MCL cell lines and primary MCL. Among these genes, DBN1, SETMAR and HIG2 are direct transcriptional targets of the SOX11 protein

IKK/NF-κB regulates skeletal myogenesis via a signaling switch to inhibit differentiation and promote mitochondrial biogenesis

Nuclear factor κB (NF-κB) is involved in multiple skeletal muscle disorders, but how it functions in differentiation remains elusive given that both anti- and promyogenic activities have been described. In this study, we resolve this by showing that myogenesis is controlled by opposing NF-κB signaling pathways. We find that myogenesis is enhanced in MyoD-expressing fibroblasts deficient in classical pathway components RelA/p65, inhibitor of κB kinase β (IKKβ), or IKKγ. Similar increases occur in myoblasts lacking RelA/p65 or IKKβ, and muscles from RelA/p65 or IKKβ mutant mice also contain higher fiber numbers. Moreover, we show that during differentiation, classical NF-κB signaling decreases, whereas the induction of alternative members IKKα, RelB, and p52 occurs late in myogenesis. Myotube formation does not require alternative signaling, but it is important for myotube maintenance in response to metabolic stress. Furthermore, overexpression or knockdown of IKKα regulates mitochondrial content and function, suggesting that alternative signaling stimulates mitochondrial biogenesis. Together, these data reveal a unique IKK/NF-κB signaling switch that functions to both inhibit differentiation and promote myotube homeostasis

FAS and NF-κB signalling modulate dependence of lung cancers on mutant EGFR

Human lung adenocarcinomas with activating mutations in EGFR (epidermal growth factor receptor) often respond to treatment with EGFR tyrosine kinase inhibitors (TKIs), but the magnitude of tumour regression is variable and transient. This heterogeneity in treatment response could result from genetic modifiers that regulate the degree to which tumour cells are dependent on mutant EGFR. Through a pooled RNA interference screen, we show that knockdown of FAS and several components of the NF-κB pathway specifically enhanced cell death induced by the EGFR TKI erlotinib in EGFR-mutant lung cancer cells. Activation of NF-κB through overexpression of c-FLIP or IKK (also known as CFLAR and IKBKB, respectively), or silencing of IκB (also known as NFKBIA), rescued EGFR-mutant lung cancer cells from EGFR TKI treatment. Genetic or pharmacologic inhibition of NF-κB enhanced erlotinib-induced apoptosis in erlotinib-sensitive and erlotinib-resistant EGFR-mutant lung cancer models. Increased expression of the NF-κB inhibitor IκB predicted for improved response and survival in EGFR-mutant lung cancer patients treated with EGFR TKI. These data identify NF-κB as a potential companion drug target, together with EGFR, in EGFR-mutant lung cancers and provide insight into the mechanisms by which tumour cells escape from oncogene dependence