Integrating Symbolic Execution with Sensornet Simulation for Efficient Bug Finding

High-coverage testing of sensornet applications is vital for pre-deployment bug cleansing, but has previously been difficult due to the limited set of available tools. We integrate the KleeNet symbolic execution engine with the COOJA network simulator to allow for straight-forward and intuitive high-coverage testing initiated from a simulation environment. A tight coupling of simulation and testing helps detect, narrow down, and fix complex interaction bugs in an early development phase. We demonstrate the seamless transition between COOJA simulation and KleeNet symbolic execution. Our framework enables future research in how high coverage testing tools could be used in cooperation with simulation tools

Šlapimtakio plastika panaudojant burnos gleivinės lopą, esant komplikuotai ilgo segmento šlapimtakio striktūrai: klinikinis atvejis

Background. Recurrent proximal ureteral stricture is a complex rare disease that is difficult to treat. Post-operative scarring, impaired blood supply to the ureter, stricture-related stones, and chronic infection – all factors make the treatment even more complicated. Methods. There are various surgical procedures for ureteral reconstruction, however, most of them are very traumatic and quite often ineffective. Our case reports the first experience of treating a complicated recurrent proximal ureteral stricture with ureteroplasty using a buccal mucosa graft. Results. The patient had a 12-month post-operative follow-up. No stricture recurrence was observed and hydronephrosis decreased. Although the excretory function of the left kidney remained lower, serum creatinine became normal. The most important clinical outcome was the withdrawal of left flank pain. Conclusions. We are lacking high volume clinical trials for appropriate ureteral stricture treatment modality. All available publications in this field compare single cases or low volume studies. While buccal mucosa graft procedures are well established in urethral reconstruction, our case proves that buccal mucosa graft method can be successfully used for ureteroplasty as well, providing good post-operative functional outcomes.Įvadas. Atsikartojanti viršutinio šlapimtakio trečdalio striktūra – tai komplikacija, atsirandanti dėl infekcinių, trauminių ar kitų šlapimtakį žalojančių veiksnių. Ankstesnių operacijų sukelti randai, sutrikusi šlapimtakio kraujotaka, audinių fibrozė lemia šlapimtakio striktūros atsiradimą ir progresavimą. Dėl šlapimtakio striktūros gali susiformuoti hidronefrozė, šlapimo takų akmenys, pacientams nustatomas lėtinis inkstų funkcijos sutrikimas ir lėtinė infekcija, o tai ypač apsunkina gydymą. Šlapimtakio striktūra – reta patologija, todėl mokslinėje literatūroje daugiausia analizuojami pavieniai atvejai, publikuojamos studijos yra nedidelės apimties. Metodai. Žinoma įvairių chirurginių metodų šlapimtakio plastikai atlikti, tačiau daugelis jų pasižymi dideliu traumatiškumu ir dažnai nepakankamu efektyvumu. Straipsnyje pristatoma pirmoji patirtis gydant komplikuotą atsikartojančią proksimalinės dalies šlapimtakio striktūrą, panaudojant burnos gleivinės lopą. Rezultatai. Pacientė operuota dėl 5,5 cm ilgio viršutinio šlapimtakio trečdalio striktūros. Atlikus plastiką, moteris stebėta 12 mėn. Nustatyta, kad po operacijos striktūra neatsinaujino. Hidronefrozė sumažėjo, inksto ekskrecinė funkcija išliko sumažėjusi, bet kreatinino lygis buvo normalus. Svarbiausias klinikinis rezultatas – išnyko juosmens skausmas kairėje pusėje. Išvados. Šlapimtakio striktūra yra sunkiai išgydoma, dažnai recidyvuojanti liga, turinti ilgalaikių pasekmių. Šlapimtakio plastika panaudojant burnos gleivinės lopą yra efektyvi, techniškai paprasta operacija, užtikrinanti gerą pooperacinį funkcinį rezultatą

Template-directed addition of nucleosides to DNA by the BfiI restriction enzyme

Restriction endonucleases catalyse DNA cleavage at specific sites. The BfiI endonuclease cuts DNA to give staggered ends with 1-nt 3′-extensions. We show here that BfiI can also fill in the staggered ends: while cleaving DNA, it can add a 2′-deoxynucleoside to the reaction product to yield directly a blunt-ended DNA. We propose that nucleoside incorporation proceeds through a two-step reaction, in which BfiI first cleaves the DNA to make a covalent enzyme–DNA intermediate and then resolves it by a nucleophilic attack of the 3′-hydroxyl group of the incoming nucleoside, to yield a transesterification product. We demonstrate that base pairing of the incoming nucleoside with the protruding DNA end serves as a template for the incorporation and governs the yield of the elongated product. The efficiency of the template-directed process has been exploited by using BfiI for the site-specific modification of DNA 5′-termini with an amino group using a 5′-amino-5′-deoxythymidine

Overexpression of human virus surface glycoprotein precursors induces cytosolic unfolded protein response in Saccharomyces cerevisiae

<p>Abstract</p> <p>Background</p> <p>The expression of human virus surface proteins, as well as other mammalian glycoproteins, is much more efficient in cells of higher eukaryotes rather than yeasts. The limitations to high-level expression of active viral surface glycoproteins in yeast are not well understood. To identify possible bottlenecks we performed a detailed study on overexpression of recombinant mumps hemagglutinin-neuraminidase (MuHN) and measles hemagglutinin (MeH) in yeast <it>Saccharomyces cerevisiae</it>, combining the analysis of recombinant proteins with a proteomic approach.</p> <p>Results</p> <p>Overexpressed recombinant MuHN and MeH proteins were present in large aggregates, were inactive and totally insoluble under native conditions. Moreover, the majority of recombinant protein was found in immature form of non-glycosylated precursors. Fractionation of yeast lysates revealed that the core of viral surface protein aggregates consists of MuHN or MeH disulfide-linked multimers involving eukaryotic translation elongation factor 1A (eEF1A) and is closely associated with small heat shock proteins (sHsps) that can be removed only under denaturing conditions. Complexes of large Hsps seem to be bound to aggregate core peripherally as they can be easily removed at high salt concentrations. Proteomic analysis revealed that the accumulation of unglycosylated viral protein precursors results in specific cytosolic unfolded protein response (UPR-Cyto) in yeast cells, characterized by different action and regulation of small Hsps versus large chaperones of Hsp70, Hsp90 and Hsp110 families. In contrast to most environmental stresses, in the response to synthesis of recombinant MuHN and MeH, only the large Hsps were upregulated whereas sHsps were not. Interestingly, the amount of eEF1A was also increased during this stress response.</p> <p>Conclusions</p> <p>Inefficient translocation of MuHN and MeH precursors through ER membrane is a bottleneck for high-level expression in yeast. Overexpression of these recombinant proteins induces the UPR's cytosolic counterpart, the UPR-Cyto, which represent a subset of proteins involved in the heat-shock response. The involvement of eEF1A may explain the mechanism by which only large chaperones, but not small Hsps are upregulated during this stress response. Our study highlights important differences between viral surface protein expression in yeast and mammalian cells at the first stage of secretory pathway.</p

Production of recombinant VP1-derived virus-like particles from novel human polyomaviruses in yeast

Background: Eleven new human polyomaviruses (HPyVs) have been identified in the last decade. Serological studies show that these novel HPyVs sub-clinically infect humans at an early age. The routes of infection, entry pathways, and cell tropism of new HPyVs remain unknown. VP1 proteins of polyomaviruses can assembly into virus-like particles (VLPs). As cell culturing systems for HPyV are currently not available, VP1-derived VLPs may be useful tools in basic research and biotechnological applications. Results: Recombinant VP1-derived VLPs from 11 newly identified HPyVs were efficiently expressed in yeast. VP1 proteins derived from Merkel cell polyomavirus (MCPyV), trichodysplasia spinulosa-associated polyomavirus (TSPyV), and New Jersey polyomavirus (NJPyV) self-assembled into homogeneous similarly-sized VLPs. Karolinska Institutet polyomavirus (KIPyV), HPyV7, HPyV9, HPyV10, and St. Louis polyomavirus (STLPyV) VP1 proteins formed VLPs that varied in size with diameters ranging from 20 to 60 nm. Smaller-sized VLPs (25–35 nm in diameter) predominated in preparations from Washington University polyomavirus (WUPyV) and HPyV6. Attempts to express recombinant HPyV12 VP1-derived VLPs in yeast indicate that translation of VP1 might start at the second of two potential translation initiation sites in the VP1-encoding open reading frame (ORF). This translation resulted in a 364-amino acid-long VP1 protein, which efficiently self-assembled into typical PyV VLPs. MCPyV-, KIPyV-, TSPyV-, HPyV9-, HPyV10-, and HPyV12-derived VLPs showed hemagglutination (HA) assay activity in guinea pig erythrocytes, whereas WUPyV-, HPyV6-, HPyV7-, STLPyV- and NJPyV-derived VP1 VLPs did not. Conclusions: The yeast expression system was successfully utilized for high-throughput production of recombinant VP1-derived VLPs from 11 newly identified HPyVs. HPyV12 VP1-derived VLPs were generated from the second of two potential translation initiation sites in the VP1-encoding ORF. Recombinant VLPs produced in yeast originated from different HPyVs demonstrated distinct HA activities and may be useful in virus diagnostics, capsid structure studies, or investigation of entry pathways and cell tropism of HPyVs until cell culture systems for new HPyVs are developed

Pirmoji minimaliai invazinės skrandžio vėžio chirurgijos patirtis Vilniaus universiteto ligoninėje Santaros klinikose ir Nacionaliniame vėžio institute: klinikinių atvejų serija ir literatūros apžvalga

Background. Gastric cancer remains one of the most common cancers in Lithuania and Worldwide. Surgical treatment is the only potentially curative treatment option for it. Historically open gastrectomy was considered as the gold standard approach. Although, the development of minimally invasive surgery and accumulation of the clinical data has led to the adoption of minimally invasive gastrectomy.&nbsp;Clinical cases.&nbsp;We present a series of 8 clinical cases who underwent minimally invasive surgery for early or locally advanced gastric cancer in Vilnius University Hospital Santaros Klinikos and the National Cancer Institute.&nbsp;Discussion.&nbsp;Large scale randomized controlled trials in Asia have proved that laparoscopic surgery is safe and oncologically effective for clinical stage I distal gastric cancer. The increa­sing amount of data supports the safety of minimally invasive gastrectomy for advanced or proximal gastric cancer. Most of the trials performed in Asia confirmed, that laparoscopic gastrectomy has some advantages, including: decreased blood loss, decreased post­operative pain, and morbidity. Recent randomized controlled trials of Western countries proved the safety of laparoscopic gastrectomy and the comparable 1-year long-term outcomes. Although, they failed to show improved recovery after minimally invasive surgery. Currently, there is sufficient evidence to adopt minimally invasive gastrectomy for gastric cancer into routine clinical practice in Lithuania.&nbsp;Conclusions.&nbsp;The first experience of minimally invasive gastric cancer surgery in Vilnius University Hospital Santaros Klinikos and the National Cancer Institute was successful. All gastrectomies were radical, and without major postoperative complications.Įvadas.&nbsp;Skrandžio vėžys išlieka aktuali onkologinė problema Lietuvoje ir pasaulyje. Chirurginis gydymas&nbsp;– galimai vienintelis pasveikti leidžiantis gydymo metodas. Ilgą laiką chirurginio gydymo standartu buvo laikomos atvirosios operacijos. Vis labiau tobulėjant minimaliai invazyviai chirurgijai, susidomėta galimybe šį metodą taikyti skrandžio vėžiui gydyti.&nbsp;Klinikiniai atvejai.&nbsp;Pristatomi 8 klinikiniai atvejai pacientų, kurie dėl ankstyvojo ar pažengusio skrandžio vėžio buvo operuoti minimaliai invaziniu būdu Vilniaus universiteto ligoninėje Santaros klinikose ir Nacionaliniame vėžio institute.&nbsp;Diskusija.&nbsp;Didelių imčių randomizuoti kontroliniai tyrimai, atlikti Azijos šalyse, įrodė, kad laparoskopinė skrandžio vėžio chirurgija yra saugi ir onkologiškai efektyvi, kai operuojamas kliniškai I&nbsp;stadijos distalinės dalies skrandžio vėžys. Daugėja įrodymų apie onkologinį saugumą, atliekant gastrektomiją ar operuojant pažengusį skrandžio vėžį. Dauguma Azijoje atliktų tyrimų nurodo, kad laparoskopinė skrandžio vėžio chirurgija išsiskiria minimaliai invazinei chirurgijai būdingais pranašumais: mažesniu skausmu po operacijos, mažesniu pooperacinių komplikacijų dažniu, mažesniu nukraujavimu operacijos metu. Neseniai pasirodė pirmieji randomizuoti kontroliniai Vakarų populiacijos tyrimai, kuriais įrodyta, jog laparoskopinė skrandžio vėžio chirurgija yra saugi, o vienų metų atokieji gydymo rezultatai yra vienodi. Vis dėlto vakarietiškosios studijos nepagrindžia, kad laparoskopiškai operuoti pacientai greičiau ir sklandžiau sveiksta po operacijos. Šiandien sukaupta pakankamai duomenų, kad minimaliai invazinės skrandžio vėžio chirurgijos programos galėtų būti saugiai taikomos Lietuvoje kaip rutininės klinikinės praktikos dalis.&nbsp;Išvados.&nbsp;Nacionaliniame vėžio institute ir Vilniaus universiteto ligoninės Santaros klinikose pirmosios minimaliai invazinės skrandžio vėžio operacijos atliktos sėkmingai. Operacijos buvo radikalios, didžiųjų pooperacinių komplikacijų nenustatyta