Amplifying control RNA for RT-PCR applications by nucleic acid sequence based amplification (NASBA)

Control RNA for RT-PCR applications was amplified by nucleic acid sequence based amplification (NASBA) using the NucliSens (R) Basic Kit. This method was used to construct positive control RNA for enterovirus, insulin, and G-protein RT-PCR, and for interferon-alpha real-time RT-PCR. The primers were designed to amplify identical RNA from RNA templates, which differs from the usual NASBA procedure, where opposite strand RNA is amplified from the target. This "inverse NASBA" method is easy to use and it does not require any expensive special equipment. The amplification reaction is done using a water bath and detection of amplified product by agarose gel electrophoresis. Generated RNA fragments were 195-714 bases long, of positive polarity and the amount of RNA was sufficient for thousands of RT-PCR reactions depending on the sensitivity of the RT-PCR. (c) 2005 Elsevier B.V. All rights reserved

Anaerobisen mädätysprosessin mallintaminen

Tiivistelmä. Työn tavoite oli tutkia biokaasua tuottavaa anaerobista mädätysprosessia ja sen mallintamista. Lisäksi tavoitteena oli rakentaa prosessia vastaava simulaattori Simulink®-ympäristössä. Työssä selvitettiin anaerobisen mädätysprosessin toimintaa, sen osaprosesseja sekä miten sen toimintaan voidaan vaikuttaa. Anaerobisen mädätysprosessin päävaiheet ovat hydrolyysi, asidogeneesi, asetogeneesi sekä metanogeneesi. Työn kirjallisessa osassa tutkittiin, miten anaerobista mädätysprosessia on mallinnettu aiemmin ja selvitettiin lyhyesti, mitä tasepohjainen dynaaminen mallintaminen on. Työn kokeellisessa osassa rakennettiin prosessia vastaava simulointimalli Simulink®-ohjelmistolla, jonka jälkeen simulaattoria testattiin ja kalibroitiin siten, että se vastaisi aitoa anaerobista mädätysprosessia. Työssä rakennettua simulaattoria on mahdollista käyttää esimerkiksi biokaasun tuotannon tutkimuksissa pohjana uusille aitoja prosesseja vastaaville simulaattoreille. Esimerkkinä simulaattoriin on mahdollista syöttää aidon tuotantoprosessin dataa alkuarvoiksi, ja käyttää simulaattoria prosessikehityksen työkaluna. Lisäksi kehitettyä simulaattoria voidaan käyttää kompleksina esimerkkinä dynaamisen tasepohjaisen mallintamisen opetuksessa

A Novel Tool to Mitigate By-Catch Mortality of Baltic Seals in Coastal Fyke Net Fishery

Developing methods to reduce the incidental catch of non-target species is important, as by-catch mortality poses threats especially to large aquatic predators. We examined the effectiveness of a novel device, a "seal sock", in mitigating the by-catch mortality of seals in coastal fyke net fisheries in the Baltic Sea. The seal sock developed and tested in this study was a cylindrical net attached to the fyke net, allowing the seals access to the surface to breathe while trapped inside fishing gear. The number of dead and live seals caught in fyke nets without a seal sock (years 2008-2010) and with a sock (years 2011-2013) was recorded. The seals caught in fyke nets were mainly juveniles. Of ringed seals (Phoca hispida botnica) both sexes were equally represented, while of grey seals (Halichoerus grypus) the ratio was biased (71%) towards males. All the by-caught seals were dead in the fyke nets without a seal sock, whereas 70% of ringed seals and 11% of grey seals survived when the seal sock was used. The seal sock proved to be effective in reducing the by-catch mortality of ringed seals, but did not perform as well with grey seals.201

System f2lp – computing answer sets of first-order formulas

Abstract. We present an implementation of the general language of stable models proposed by Ferraris, Lee and Lifschitz. Under certain conditions, system f2lp turns a first-order theory under the stable model semantics into an answer set program, so that existing answer set solvers can be used for computing the general language. Quantifiers are first eliminated and then the resulting quantifier-free formulas are turned into rules. Based on the relationship between stable models and circumscription, f2lp can also serve as a reasoning engine for general circumscriptive theories. We illustrate how to use f2lp to compute the circumscriptive event calculus.

Label-Free Concept Bottleneck Models

Concept bottleneck models (CBM) are a popular way of creating more interpretable neural networks by having hidden layer neurons correspond to human-understandable concepts. However, existing CBMs and their variants have two crucial limitations: first, they need to collect labeled data for each of the predefined concepts, which is time consuming and labor intensive; second, the accuracy of a CBM is often significantly lower than that of a standard neural network, especially on more complex datasets. This poor performance creates a barrier for adopting CBMs in practical real world applications. Motivated by these challenges, we propose Label-free CBM which is a novel framework to transform any neural network into an interpretable CBM without labeled concept data, while retaining a high accuracy. Our Label-free CBM has many advantages, it is: scalable - we present the first CBM scaled to ImageNet, efficient - creating a CBM takes only a few hours even for very large datasets, and automated - training it for a new dataset requires minimal human effort. Our code is available at https://github.com/Trustworthy-ML-Lab/Label-free-CBM.Comment: Published at ICLR 202

Kestävä matkailu Ruka-Kuusamon matkailuyrityksissä:kestävyyden käsityksistä toimiin, motivaatioihin ja haasteisiin

Tiivistelmä. Tässä opinnäytetyössä tarkastellaan matkailun kestävyyttä matkailuyritysten näkökulmasta. Tarkoituksena on tutkia kestävän matkailun arvottamista, kestävyyden edistämiseen liittyviä toimia, kestävyyden edistämisen motivaatioita sekä kestävyyden kehittämiseen liittyviä mahdollisia haasteita. Esimerkkitapauksena toimivat Ruka-Kuusamon alueen matkailuyritykset. Tutkielman teoreettinen viitekehys pohjautuu kestävän matkailun ja kestävän kehityksen käsitteisiin sekä näiden toteutumiseen matkailuyrityksissä. Käsitteellisen tarkastelun lisäksi teoriaosuudessa esitellään aiempaa tutkimusta, jota on tehty kestävästä matkailusta matkailuyrityksissä. Tutkimuksen aineisto on kaksiosainen. Ensimmäisenä aineistona toimii kvantitatiivinen kyselyaineisto. Verkkokyselyyn vastasi 34 Ruka-Kuusamon alueella toimivaa matkailuyritystä. Tämän aineiston analysoinnissa hyödynnettiin tilastollisia menetelmiä. Toinen aineisto on kvalitatiivinen ja se koostuu seitsemästä Ruka-Kuusamon alueen matkailuyrityksen haastattelusta. Haastatteluja analysointiin kvalitatiivisin analyysimenetelmin esimerkiksi teemoittelun avulla. Tutkimuksen tulosten perusteella Ruka-Kuusamon matkailuyritykset pitävät kestävän matkailun kaikkia osa-alueita tärkeinä. Tärkeimpinä osa-alueina korostuvat ekologinen ja taloudellinen kestävyys. Myös kestävyyden eteen tehtävät toimet liittyvät yleisimmin näihin kahteen osa-alueeseen. Kestävyyden kehittämisen motivaatiot ovat usein taloudellisia, mutta myös yrittäjän ja yrityksen arvot vaikuttavat halukkuuteen panostaa kestävyyteen. Suurimpina haasteina matkailun kestävyyden kehittämiselle yritykset kokevat toimijoiden asenteet, ajan ja tiedon puutteen sekä sen, miten kaikki alueen toimijat saadaan sitoutettua kestävän matkailun periaatteisiin. Myös muiden toimialojen, etenkin kaivostoiminnan, nähdään aiheuttavan haasteita matkailun kestävyydelle Ruka-Kuusamon alueella. Tulevaisuuden kannalta voisi siten olla tarpeellista löytää jokin taho, joka lähtisi vetämään matkailun kestävyyden kehittämistä koko Ruka-Kuusamon matkailualueella. Kestävää kehitystä voisi olla syytä hallita myös laajemmin alueellisella tasolla eri toimialojen välisten ristiriitojen selvittämiseksi

Analysis of pancreas tissue in a child positive for islet cell antibodies

Conclusions/interpretation These observations suggest that positivity for ICA alone, even when lasting for more than 1 year, is not associated with inflammatory changes in the islets. However, it is most likely that the pancreatic islets were infected by an enterovirus in this child

Counterexample Guided Abstraction Refinement Algorithm for Propositional Circumscription

Circumscription is a representative example of a nonmonotonic reasoning inference technique. Circumscription has often been studied for first order theories, but its propositional version has also been the subject of extensive research, having been shown equivalent to extended closed world assumption (ECWA). Moreover, entailment in propositional circumscription is a well-known example of a decision problem in the second level of the polynomial hierarchy. This paper proposes a new Boolean Satisfiability (SAT)-based algorithm for entailment in propositional circumscription that explores the relationship of propositional circumscription to minimal models. The new algorithm is inspired by ideas commonly used in SAT-based model checking, namely counterexample guided abstraction refinement. In addition, the new algorithm is refined to compute the theory closure for generalized close world assumption (GCWA). Experimental results show that the new algorithm can solve problem instances that other solutions are unable to solve

Recover from a service failure : The differential effects of brand betrayal and brand disappointment on an exclusive brand offering

Brand managers inevitably have to face service failures and respond to them. Undertaking brand recovery is essential as customers might desire to take revenge or spread negative word-of-mouth if they feel betrayed or disappointed by the brand following the service failure. Thus, it is necessary to understand customer responses to brand recovery, which depend on whether they feel betrayed or disappointed (while related, this paper distinguishes these feelings). This research challenges the conventional wisdom by demonstrating that, after presenting customers with an exclusive brand offering during the brand recovery, brand betrayal predicts a positive brand attitude and brand disappointment predicts a negative brand attitude with the service failure. Further, the brand attitude mediates the positive relationship between brand betrayal, positive word-of-mouth, and the likelihood of recommending the brand to others. Thus, the quick recovery that follows an exclusive brand offering positively impacts on the brand relationship among betrayed customers.Peer reviewe

PCR inhibition in stool samples in relation to age of infants

Background: PCR is rapidly replacing traditional methods in diagnostic virus laboratories. PCR inhibitors,which are often present in clinical samples, may lead to false negative test results.Objectives: The aim was to study the presence of PCR inhibitors in stool samples collected from 3- to24-month old children.Study design: Total RNA fraction extracted from stool samples was spiked with a standardized amount ofSemliki Forest Virus RNA and amplified using specific PCR primers. The presence of PCR inhibitors wasdetected by a decrease in amplification rate compared to spiked water samples. Inhibition in differentage groups and dietary origin of PCR inhibitors were analyzed by comparing the samples taken duringexclusive and non-exclusive breastfeeding periods. The inactivation of PCR inhibitors was also assessed.Results: Complete inhibition was seen in 12% (13/108) and partial inhibition in 19% (21/108) of the samples.Inhibition was seen in none of the stool samples (0/31) taken from infants younger than 6 monthscompared to 17% of samples (13/77) taken from6 to 24 months old infants (p more common in younger age group. Addition of bovine serum albumin (BSA) into the reaction mixtureseliminated the effect of inhibitors leading to all samples being positive.Conclusions: PCR inhibitors are frequent in stool samples. They may originate from dietary componentsand can lead to false negative PCR results. The addition of BSA to the cDNA and PCR reactions proved tobe an easy and effective method for eliminating the inhibitory effect of these compounds