Visualising the Output of the Static Analyser Goblint

Goblint on staatiline andmejooksude analüsaator mitmelõimelistestele C-keelsetele programmidele. Käesoleva töö eesmärk on analüüsida ja tõsta Goblinti kasutatavust. Analüüsi käigus leitakse parandatavad aspektid ja väljundi parema visualiseerimise loogika. Analüüsi põhjal on loodud programm, mis võtab sisendiks esialgse Goblinti väljundi ja lihtsustab seda, tuues välja olulisema ja kaotades vähem olulise. Väljundi lihtsustamiseks leitakse tõekspidamistele vastavad ja nendest hälbivad kohad, kusjuures tõekspidamine on siinkohal komplekt mäluaadressi poole pöördumisest ja selle juures võetud lukust. Tulemused saab järjestada tõekspidamise kindluse järgi. Seeläbi saab esile tuua kõige silmapaistvamad ja kõige kergemini parandatavad vead. Lisaks sellele antakse kogu väljundile kompaktsem kuju, et selle lugemisele kuluks vähem aega. Uus tulemus on esialgsega võrreldes rohkem kui kolmandiku võrra lühem ja annab edasi programmeerijale olulist informatsiooni, mida muidu oleks pidanud käsitsi eraldama.Goblint is a static data race analyzer for multithreaded programs written in C. The goal of this thesis is to improve the usability of Goblint by improving the readability of its output. A strategy for better race warning representation was found and implemented in a separate tool that simplifies Goblint's output. Beliefs are formed based on observed pairings of memory accesses with associated locks. The results are then sorted according to the strength of the belief, prioritizing the most apparent mistakes that violate strong beliefs. The new result is less than a third of the original, and more importantly, beliefs are used to pinpoint the access that is most likely the cause of a potential race. This is a significant improvement over the current Goblint output, which reports all accesses and requires the user to find faulty locations manually

Three-dimensional attenuation model of Sierra Negra Volcano, Galápagos Archipelago

The shallow magma system beneath Sierra Negra was imaged using attenuation tomographic methods. The t∗ spectral decay method for P wave phases was used to highlight regions of high Q-1 p which suggest the presence of magma melt. High-Q-1 p anomalies ranging from 0.005 to 0.04 are concentrated below the caldera from 0.5 to 10.5 km depths. Attenuation is sensitive to temperature and fluid presence; thus, this high attenuation is interpreted as possible zones of magma accumulation. An imaged shallow body is consistent with geodetic studies on caldera deformation that modeled a magma sill or flattopped diapir of unknown thickness at ∼1 km depth below sea level

Opening the AC-Unification Race

This note reports about the implementation of AC-unification algorithms, based on the variable-abstraction method of Stickel and on the constant-abstraction method of Livesey, Siekmann, and Herold. We give a set of 105 benchmark examples and compare execution times for implementations of the two approaches. This documents for other researchers what we consider to be the state-of-the-art performance for elementary AC-unification problems

Synaptotagmins I and II mediate entry of botulinum neurotoxin B into cells

Botulinum neurotoxins (BoNTs) cause botulism by entering neurons and cleaving proteins that mediate neurotransmitter release; disruption of exocytosis results in paralysis and death. The receptors for BoNTs are thought to be composed of both proteins and gangliosides; however, protein components that mediate toxin entry have not been identified. Using gain-of-function and loss-of-function approaches, we report here that the secretory vesicle proteins, synaptotagmins (syts) I and II, mediate the entry of BoNT/B (but not BoNT/A or E) into PC12 cells. Further, we demonstrate that BoNT/B entry into PC12 cells and rat diaphragm motor nerve terminals was activity dependent and can be blocked using fragments of syt II that contain the BoNT/B-binding domain. Finally, we show that syt II fragments, in conjunction with gangliosides, neutralized BoNT/B in intact mice. These findings establish that syts I and II can function as protein receptors for BoNT/B

Widespread Sequence Variations in VAMP1 across Vertebrates Suggest a Potential Selective Pressure from Botulinum Neurotoxins

Botulinum neurotoxins (BoNT/A-G), the most potent toxins known, act by cleaving three SNARE proteins required for synaptic vesicle exocytosis. Previous studies on BoNTs have generally utilized the major SNARE homologues expressed in brain (VAMP2, syntaxin 1, and SNAP-25). However, BoNTs target peripheral motor neurons and cause death by paralyzing respiratory muscles such as the diaphragm. Here we report that VAMP1, but not VAMP2, is the SNARE homologue predominantly expressed in adult rodent diaphragm motor nerve terminals and in differentiated human motor neurons. In contrast to the highly conserved VAMP2, BoNT-resistant variations in VAMP1 are widespread across vertebrates. In particular, we identified a polymorphism at position 48 of VAMP1 in rats, which renders VAMP1 either resistant (I48) or sensitive (M48) to BoNT/D. Taking advantage of this finding, we showed that rat diaphragms with I48 in VAMP1 are insensitive to BoNT/D compared to rat diaphragms with M48 in VAMP1. This unique intra-species comparison establishes VAMP1 as a physiological toxin target in diaphragm motor nerve terminals, and demonstrates that the resistance of VAMP1 to BoNTs can underlie the insensitivity of a species to members of BoNTs. Consistently, human VAMP1 contains I48, which may explain why humans are insensitive to BoNT/D. Finally, we report that residue 48 of VAMP1 varies frequently between M and I across seventeen closely related primate species, suggesting a potential selective pressure from members of BoNTs for resistance in vertebrates

Südamelihase rakkude struktuuri olulisus rakuhingamise regulatsioonis

Viimastel aastatel on järjest selgemaks saanud seos raku energeetilise ainevahetuse ja südamehaiguste vahel, mistõttu on oluline uurida seda mõjutavaid tegureid. Töös uuriti südamelihase rakkude mitokondriaalse hingamise regulatsiooni väga erineva rakustruktuuriga preparaatides: 1) permeabiliseeritud kardiomüotsüütides, kus mitokondrid on regulaarselt organiseeritud; 2) südamelihase fenotüübiga sarnastes kontraheeruvates HL-1 (B HL-1) rakkudes ja 3) HL-1 mittekontraheeruvates (NB HL-1) rakkudes. Nende preparaatide vahel esines suur erinevus mitokondriaalse hingamise regulatsioonis. Selline tulemus näitab raku struktuuri ja funktsiooni vaheliste seoste tähtsust südamelihase rakkudes ning võimaldab paremini mõista protsesse nii terves kui ka patoloogilises südamelihases. Eesti Arst 2008; 87(1):19−2