Semantics of Exceptions

We describe a trace semantics of exceptions and then derive a weakest precondition semantics. A program that contains exceptions terminates in one of two possible ways (if it terminates at all): either it terminates exceptionally or it terminates normally. We will therefore consider weakest preconditions that are functions of two postconditions. As a preparation we study aribitrary functions of two arguments, and their compositions

ValoMC: a Monte Carlo software and MATLAB toolbox for simulating light transport in biological tissue

A Monte Carlo method for photon transport has gained wide popularity in biomedical optics for studying light behaviour in tissue. Nowadays, typical computation times range from a few minutes to hours. Although various implementations of the Monte Carlo algorithm exist, there is only a limited number of free software available. In addition, these packages may require substantial learning efforts. To address these issues, we present a new Monte Carlo software with a user-friendly interface. The simulation geometry is defined using an unstructured (triangular or tetrahedral) mesh. The program solves the photon fluence in the computation domain and the exitance at the domain boundary. It is capable of simulating complex measurement geometries with spatially varying optical parameter distributions and supports several types of light sources as well as intensity modulated light. Furthermore, attention is given to ease of use and fast problem set up with a MATLAB (The MathWorks Inc., Natick, MA) interface. The simulation code is written in C++ and parallelized using OpenMP. The simulation code has been validated against analytical and numerical solutions of radiative transfer equation and other Monte Carlo software in good agreement. The software is available for download from the homepage https://inverselight.github.io/ValoMC/ and the source code from GitHub https://github.com/InverseLight/ValoMC

Perturbation Monte Carlo Method for Quantitative Photoacoustic Tomography

Quantitative photoacoustic tomography aims at estimating optical parameters from photoacoustic images that are formed utilizing the photoacoustic effect caused by the absorption of an externally introduced light pulse. This optical parameter estimation is an ill-posed inverse problem, and thus it is sensitive to measurement and modeling errors. In this work, we propose a novel way to solve the inverse problem of quantitative photoacoustic tomography based on the perturbation Monte Carlo method. Monte Carlo method for light propagation is a stochastic approach for simulating photon trajectories in a medium with scattering particles. It is widely accepted as an accurate method to simulate light propagation in tissues. Furthermore, it is numerically robust and easy to implement. Perturbation Monte Carlo maintains this robustness and enables forming gradients for the solution of the inverse problem. We validate the method and apply it in the framework of Bayesian inverse problems. The simulations show that the perturbation Monte Carlo method can be used to estimate spatial distributions of both absorption and scattering parameters simultaneously. These estimates are qualitatively good and quantitatively accurate also in parameter scales that are realistic for biological tissues

HLA-B27 aikuisten uveiitissa

Tiivistelmä. Uveiitti on silmän suonikalvoston tulehdus. Suurin osa uveiiteista on anatomisesti anteriorisia. Uveiitti on harvinaisuudestaan huolimatta merkittävä sokeuden ja näkövammautumisen syy. HLA-B27-kudostekijä on osa ihmisen immuunijärjestelmää ja on yksi parhaiten tunnetuista anterioriselle uveiitille altistavista geeneistä. Suomalaisessa väestöässä noin 15% on HLA-B27-positiivisia, kun taas akuuttia anteriorista uveiittia sairastavista vastaava osuus on jopa 80%. Tässä retrospektiivisessä tutkielmassa tutkitaan HLA-B27-kudostekijän vaikutusta anteriorisen uveiitin taudinkuvaan pohjoissuomalaisessa väestössä. Kudostekijän vaikutusta tarkastellaan sairastumisiän, sukupuolen, etiologian ja keston mukaan, vertaamalla tuloksia koko aineiston väestöön. Aineisto koostuu vuonna 2009 Oulun yliopistollisen sairaalan silmätautien yksikössä anteriorisen uveiitin vuoksi käyneistä aikuispotilaista. Alkuperäinen aineisto oli 591 potilasta, joista rajautui tietyin kriteerein 416 potilasta. Tähän tutkielmaan valikoitui 140 potilasta satunnaisesti eli noin kolmasosa aineistosta. Aineiston potilaista 73 oli naisia ja 67 miehiä. Potilaista 61% (85) HLA-B27-kudostekijän tutkimustulos löytyi potilastietojärjestelmästä. Heistä, joilla tulos löytyi, 67% (57) oli HLA-B27-positiivisia ja 33% (28) HLA-B27-negatiivisia. HLA-B27-positiivisia naisia oli 29 ja miehiä 28. Potilaiden iän keskiarvo sairaustuessa ensimmäistä kertaa uveiittiin oli 40,8, vastaava luku HLA-B27-positiivisilla potilailla oli 35,3. Kudostekijäpositiiviset sairastuivat uveiittiin keskimääräistä nuorempina. Idiopaattinen etiologia oli yleisin sekä koko aineistossa (49%) että HLA-B27-positiivisilla (51%). Systeemisairaudet olivat toiseksi yleisin etiologia molemmissa ryhmissä; koko väestössä 35% potilaista uveiitin taustalla oli jokin systeemisairaus ja 42% (24) HLA-B27-positiivisista. Yleisin systeemisairaus HLA-B27-positiivisilla oli selkärankareuma, jota sairasti 14 potilasta. Muita systeemisairauksia oli yksittäisiä. Koko väestössä (66%) ja HLA-B27-positiivisilla (65%) krooninen taudinkuva oli yleisin. Rekurentti eli toistuva akuutti taudinkuva oli hieman yleisempi HLA-B27-positiivisilla (33%) kuin koko aineistossa (23%). Akuutti taudinkuva eli yksittäinen alle 3 kuukautta kestävä uveiittiepisodi oli harvinaisin taudinkuva molemmissa ryhmissä

Automating Deductive Verification for Weak-Memory Programs

Writing correct programs for weak memory models such as the C11 memory model is challenging because of the weak consistency guarantees these models provide. The first program logics for the verification of such programs have recently been proposed, but their usage has been limited thus far to manual proofs. Automating proofs in these logics via first-order solvers is non-trivial, due to reasoning features such as higher-order assertions, modalities and rich permission resources. In this paper, we provide the first implementation of a weak memory program logic using existing deductive verification tools. We tackle three recent program logics: Relaxed Separation Logic and two forms of Fenced Separation Logic, and show how these can be encoded using the Viper verification infrastructure. In doing so, we illustrate several novel encoding techniques which could be employed for other logics. Our work is implemented, and has been evaluated on examples from existing papers as well as the Facebook open-source Folly library.Comment: Extended version of TACAS 2018 publicatio

Distinct neural responses to chord violations: A multiple source analysis study.

The human brain is constantly predicting the auditory environment by representing sequential similarities and extracting temporal regularities. It has been proposed that simple auditory regularities are extracted at lower stations of the auditory cortex and more complex ones at other brain regions, such as the prefrontal cortex. Deviations from auditory regularities elicit a family of early negative electric potentials distributed over the frontal regions of the scalp. In this study, we wished to disentangle the brain processes associated with sequential vs. hierarchical auditory regularities in a musical context by studying the event-related potentials (ERPs), the behavioral responses to violations of these regularities, and the localization of the underlying ERP generators using two different source analysis algorithms. To this aim, participants listened to musical cadences constituted by seven chords, each containing either harmonically congruous chords, harmonically incongruous chords, or harmonically congruous but mistuned chords. EEG was recorded and multiple source analysis was performed. Incongruous chords violating the rules of harmony elicited a bilateral ERAN, whereas mistuned chords within chord sequences elicited a right-lateralized MMN. We found that the dominant cortical sources for the ERAN were localized around Broca's area and its right homolog, whereas the MMN generators were localized around the primary auditory cortex. These findings suggest a predominant role of the auditory cortices in detecting sequential scale regularities and the posterior prefrontal cortex in parsing hierarchical regularities in music

Mechanisms of Stereodirecting Participation and Ester Migration from Near and Far in Glycosylation and Related Reactions

This review is the counterpart of a 2018 Chemical Reviews article (Adero, P. O.; Amarasekara, H.; Wen, P.; Bohe, L.; Crich, D. Chem. Rev. 2018, 118, 8242-8284) that examined the mechanisms of chemical glycosylation in the absence of stereodirecting participation. Attention is now turned to a critical review of the evidence in support of stereodirecting participation in glycosylation reactions by esters from either the vicinal or more remote positions. As participation by esters is often accompanied by ester migration, the mechanism(s) of migration are also reviewed. Esters are central to the entire review, which accordingly opens with an overview of their structure and their influence on the conformations of six-membered rings. Next the structure and relative energetics of dioxacarbeniun ions are covered with emphasis on the influence of ring size. The existing kinetic evidence for participation is then presented followed by an overview of the various intermediates either isolated or characterized spectroscopically. The evidence supporting participation from remote or distal positions is critically examined, and alternative hypotheses for the stereodirecting effect of such esters are presented. The mechanisms of ester migration are first examined from the perspective of glycosylation reactions and then more broadly in the context of partially acylated polyols.Peer reviewe