Åbo Akademi University

RNA-sequencing (RNA-seq) has a wide variety of applications, but no single analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data analysis, including experimental design, quality control, read alignment, quantification of gene and transcript levels, visualization, differential gene expression, alternative splicing, functional analysis, gene fusion detection and eQTL mapping. We highlight the challenges associated with each step. We discuss the analysis of small RNAs and the integration of RNA-seq with other functional genomics techniques. Finally, we discuss the outlook for novel technologies that are changing the state of the art in transcriptomics.

Bullying was investigated as a group process, a social phenomenon taking place in a school setting among 573 Finnish sixth-grade children (286 girls, 287 boys) aged 12–13 years. Different Participant Roles taken by individual children in the bullying process were examined and related to a) self-estimated behavior in bullying situations, b) social acceptance and social rejection, and c) belongingness to one of the five sociometric status groups (popular, rejected, neglected, controversial, and average). The Participant Roles assigned to the subject were Victim, Bully, Reinforcer of the bully, Assistant of the bully, Defender of the victim, and Outsider. There were significant sex differences in the distribution of Participant Roles. Boys were more frequently in the roles of Bully, Reinforcer and Assistant, while the most frequent roles of the girls were those of Defender and Outsider. The subjects were moderately well aware of their Participant Roles, although they underestimated their participation in active bullying behavior and emphasized that they acted as Defenders and Outsiders. The sociometric status of the children was found to be connected to their Participant Roles. © 1996 Wiley-Liss, Inc.

The widespread popularity of density functional theory has given rise to an extensive range of dedicated codes for predicting molecular and crystalline properties. However, each code implements the formalism in a different way, raising questions about the reproducibility of such predictions. We report the results of a community-wide effort that compared 15 solid-state codes, using 40 different potentials or basis set types, to assess the quality of the Perdew-Burke-Ernzerhof equations of state for 71 elemental crystals. We conclude that predictions from recent codes and pseudopotentials agree very well, with pairwise differences that are comparable to those between different high-precision experiments. Older methods, however, have less precise agreement. Our benchmark provides a framework for users and developers to document the precision of new applications and methodological improvements.

Gender differences in regard to aggressive behaviour were investigated in a series of studies of schoolchildren of different age cohorts: 8-year-olds (N = 85), 11-year-olds (N = 167), and 15-year-olds (N = 127). Different types of aggressive behaviour were measured with peer nomination techniques, supported by self-ratings. The social structure of the peer groups were also studied. The results of the 11-year-old cohort were previously presented by Lagerspetz et al. [1988; Aggressive Behavior 14:403–414], but they are compared here with the other age groups. The principal finding was that girls of the two older cohorts overall make greater use of indirect means of aggression, whereas boys tend to employ direct means. Previously, the main difference between the genders has been thought to be that boys use physical aggressive strategies, while girls prefer verbal ones. Our studies suggest that the differentiation between direct and indirect strategies of aggression presents a more exact picture. Indirect aggressive strategies were not yet fully developed among the 8-year-old girls, but they were already prominent among the 11-year-old girls. Aggressive behaviour was assessed overall by the children themselves to be the highest in this age group.

We first reported that polyvinylpyrrolidone-protected graphene was dispersed well in water and had good electrochemical reduction toward O(2) and H(2)O(2). With glucose oxidase (GOD) as an enzyme model, we constructed a novel polyvinylpyrrolidone-protected graphene/polyethylenimine-functionalized ionic liquid/GOD electrochemical biosensor, which achieved the direct electron transfer of GOD, maintained its bioactivity and showed potential application for the fabrication of novel glucose biosensors with linear glucose response up to 14 mM.

Paper is ubiquitous in everyday life and a truly low-cost substrate. The use of paper substrates could be extended even further, if electronic applications would be applied next to or below the printed graphics. However, applying electronics on paper is challenging. The paper surface is not only very rough compared to plastics, but is also porous. While this is detrimental for most electronic devices manufactured directly onto paper substrates, there are also approaches that are compatible with the rough and absorptive paper surface. In this review, recent advances and possibilities of these approaches are evaluated and the limitations of paper electronics are discussed.

TrackMate is an automated tracking software used to analyze bioimages and is distributed as a Fiji plugin. Here, we introduce a new version of TrackMate. TrackMate 7 is built to address the broad spectrum of modern challenges researchers face by integrating state-of-the-art segmentation algorithms into tracking pipelines. We illustrate qualitatively and quantitatively that these new capabilities function effectively across a wide range of bio-imaging experiments. TrackMate 7 combines the benefits of machine and deep learning-based image segmentation with accurate object tracking to enable improved 2D and 3D tracking of diverse objects in biological research.

RNA sequencing (RNA-seq) is a genomic approach for the detection and quantitative analysis of messenger RNA molecules in a biological sample and is useful for studying cellular responses. RNA-seq has fueled much discovery and innovation in medicine over recent years. For practical reasons, the technique is usually conducted on samples comprising thousands to millions of cells. However, this has hindered direct assessment of the fundamental unit of biology-the cell. Since the first single-cell RNA-sequencing (scRNA-seq) study was published in 2009, many more have been conducted, mostly by specialist laboratories with unique skills in wet-lab single-cell genomics, bioinformatics, and computation. However, with the increasing commercial availability of scRNA-seq platforms, and the rapid ongoing maturation of bioinformatics approaches, a point has been reached where any biomedical researcher or clinician can use scRNA-seq to make exciting discoveries. In this review, we present a practical guide to help researchers design their first scRNA-seq studies, including introductory information on experimental hardware, protocol choice, quality control, data analysis and biological interpretation.

There are two parts in this book. The first part is devoted mainly to the proper ties of linear diffusions in general and Brownian motion in particular. The second part consists of tables of distribut

This paper attempts to renew interest in a line of research that largely has been ignored for two decades but which is critical to the study of entrepreneurial cognitions, intentions, and their conversion into entrepreneurial behaviors. That area is entrepreneurial motivation. This is not a comprehensive review of all areas of motivation research but rather a challenge a reinvigorate research efforts on an important aspect of the entrepreneurial process that has been examined only at the margins so far. It is an attempt to show how one very important topic, “entrepreneurial motivation,” still needs more study if we are to address the question of “have we learned anything at all about entrepreneurs?”

ABSTRACT The heat shock response, characterized by increased expression of heat shock proteins (Hsps) is induced by exposure of cells and tissues to extreme conditions that cause acute or chronic stress. Hsps function as molecular chaperones in regulating cellular homeostasis and promoting survival. If the stress is too severe, a signal that leads to programmed cell death, apoptosis, is activated, thereby providing a finely tuned balance between survival and death. In addition to extracellular stimuli, several nonstressful conditions induce Hsps during normal cellular growth and development. The enhanced heat shock gene expression in response to various stimuli is regulated by heat shock transcription factors (HSFs). After the discovery of the family of HSFs (i.e., murine and human HSF1, 2, and 4 and a unique avian HSF3), the functional relevance of distinct HSFs is now emerging. HSF1, an HSF prototype, and HSF3 are responsible for heat‐induced Hsp expression, whereas HSF2 is refractory to classical stressors. HSF4 is expressed in a tissue‐specific manner;similar to HSF1 and HSF2, alternatively spliced isoforms add further complexity to its regulation. Recently developed powerful genetic models have provided evidence for both cooperative and specific functions of HSFs that expand beyond the heat shock response. Certain specialized functions of HSFs may even include regulation of novel target genes in response to distinct stimuli.—Pirkkala, L., Nykanen, P, Sistonen, L. Roles of the heat shock transcription factors in regulation of the heat shock response and beyond.—Pirkkala, L., Nykäen, P, Sistonen, L. Roles of the heat shock transcription factors in regulation of the heat shock response and beyond. FASEB J . 15, 1118–1131 (2001)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPotentiometric Ion SensorsJohan Bobacka, Ari Ivaska, and Andrzej LewenstamView Author Information Åbo Akademi University, Process Chemistry Centre, c/o Laboratory of Analytical Chemistry, Biskopsgatan 8, FI-20500 Turku-Åbo, Finland; Faculty of Material Science and Ceramics, AGH-University of Science and Technology, Al. Mickiewicza 30, PL-30059 Cracow, Poland; and Åbo Akademi University, Process Chemistry Centre, c/o Center for Process Analytical Chemistry and Sensor Technology (ProSens), Biskopsgatan 8, FI-20500 Turku-Åbo, Finland Cite this: Chem. Rev. 2008, 108, 2, 329–351Publication Date (Web):January 12, 2008Publication History Received25 April 2007Published online12 January 2008Published inissue 1 February 2008https://pubs.acs.org/doi/10.1021/cr068100whttps://doi.org/10.1021/cr068100wresearch-articleACS PublicationsCopyright © 2008 American Chemical SocietyRequest reuse permissionsArticle Views10742Altmetric-Citations797LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Electrodes,Ions,Membranes,Plastics,Polymers Get e-Alerts

In inflammation, bacterial products and proinflammatory cytokines induce the formation of large amounts of nitric oxide (NO) by inducible nitric oxide synthase (iNOS), and compounds that inhibit NO production have anti-inflammatory effects. In the present study, we systematically investigated the effects of 36 naturally occurring flavonoids and related compounds on NO production in macrophages exposed to an inflammatory stimulus (lipopolysaccharide, LPS), and evaluated the mechanisms of action of the effective compounds. Flavone, the isoflavones daidzein and genistein, the flavonols isorhamnetin, kaempferol and quercetin, the flavanone naringenin, and the anthocyanin pelargonidin inhibited iNOS protein and mRNA expression and also NO production in a dose-dependent manner. All eight active compounds inhibited the activation of nuclear factor-kappaB (NF-kappaB), which is a significant transcription factor for iNOS. Genistein, kaempferol, quercetin, and daidzein also inhibited the activation of the signal transducer and activator of transcription 1 (STAT-1), another important transcription factor for iNOS. The present study characterises the effects and mechanisms of naturally occurring phenolic compounds on iNOS expression and NO production in activated macrophages. The results partially explain the pharmacological efficacy of flavonoids as anti-inflammatory compounds.

In this article, we argue that a major reason the United States failed to ratify the Kyoto Protocol to ameliorate global warming is the opposition of the American conservative movement, a key segment of the antienvironmental countermovement. We examine how the conservative movement mobilized between 1990 and 1997 to construct the “non-problematicity ” of global warming. After we describe how conservative think tanks mobilized to challenge the global warming claims of mainstream climate science, we examine how these countermovement organizations aligned themselves with prominent American climate change skeptics known for their staunch criticism of mainstream climate research and their af�liations with the fossil fuels industry. We then examine how the efforts of these conservative think tanks were enhanced by the shift in the political opportunity structure created by the 1994 Republican takeover of Congress. This study demonstrates how a powerful countermovement effectively challenged the environmental community’s de�nition of global warming as a social problem and blocked the passage of any signi�cant climate change policy. Since the early 1980s a robust international consensus about the reality and seriousness of climate change has emerged, as evidenced by several comprehensive reports from the

We know from animal studies that a stimulating and enriched environment can enhance recovery after stroke, but little is known about the effects of an enriched sound environment on recovery from neural damage in humans. In humans, music listening activates a wide-spread bilateral network of brain regions related to attention, semantic processing, memory, motor functions, and emotional processing. Music exposure also enhances emotional and cognitive functioning in healthy subjects and in various clinical patient groups. The potential role of music in neurological rehabilitation, however, has not been systematically investigated. This single-blind, randomized, and controlled trial was designed to determine whether everyday music listening can facilitate the recovery of cognitive functions and mood after stroke. In the acute recovery phase, 60 patients with a left or right hemisphere middle cerebral artery (MCA) stroke were randomly assigned to a music group, a language group, or a control group. During the following two months, the music and language groups listened daily to self-selected music or audio books, respectively, while the control group received no listening material. In addition, all patients received standard medical care and rehabilitation. All patients underwent an extensive neuropsychological assessment, which included a wide range of cognitive tests as well as mood and quality of life questionnaires, one week (baseline), 3 months, and 6 months after the stroke. Fifty-four patients completed the study. Results showed that recovery in the domains of verbal memory and focused attention improved significantly more in the music group than in the language and control groups. The music group also experienced less depressed and confused mood than the control group. These findings demonstrate for the first time that music listening during the early post-stroke stage can enhance cognitive recovery and prevent negative mood. The neural mechanisms potentially underlying these effects are discussed.

Gender differences regarding aggressive behaviour were investigated in 167 school children, 11 to 12 years of age, through peer-rating techniques supported by self-ratings and interviews. The social structure of the peer groups also was studied. The principal finding was that girls made greater use of indirect means of aggression, whereas the boys tended to employ direct means. Gender differences in verbal aggression were less pronounced. The social structure of peer groups was found to be tighter among girls, making it easier for them to exploit relationships and harm their victims by indirect manipulative aggression. Because indirect aggression has rarely been satisfactorily studied with tests of aggression, this finding may help to explain 1) the generally lower correlation found between peer-rated and self-rated aggression in girls than among boys (indirect means not being so readily recognized by the subject as a kind of aggression) and 2) the low stability of aggressiveness in girls often found in developmental studies.

BACKGROUND: During the most recent decade many Bayesian statistical models and software for answering questions related to the genetic structure underlying population samples have appeared in the scientific literature. Most of these methods utilize molecular markers for the inferences, while some are also capable of handling DNA sequence data. In a number of earlier works, we have introduced an array of statistical methods for population genetic inference that are implemented in the software BAPS. However, the complexity of biological problems related to genetic structure analysis keeps increasing such that in many cases the current methods may provide either inappropriate or insufficient solutions. RESULTS: We discuss the necessity of enhancing the statistical approaches to face the challenges posed by the ever-increasing amounts of molecular data generated by scientists over a wide range of research areas and introduce an array of new statistical tools implemented in the most recent version of BAPS. With these methods it is possible, e.g., to fit genetic mixture models using user-specified numbers of clusters and to estimate levels of admixture under a genetic linkage model. Also, alleles representing a different ancestry compared to the average observed genomic positions can be tracked for the sampled individuals, and a priori specified hypotheses about genetic population structure can be directly compared using Bayes' theorem. In general, we have improved further the computational characteristics of the algorithms behind the methods implemented in BAPS facilitating the analyses of large and complex datasets. In particular, analysis of a single dataset can now be spread over multiple computers using a script interface to the software. CONCLUSION: The Bayesian modelling methods introduced in this article represent an array of enhanced tools for learning the genetic structure of populations. Their implementations in the BAPS software are designed to meet the increasing need for analyzing large-scale population genetics data. The software is freely downloadable for Windows, Linux and Mac OS X systems at http://web.abo.fi/fak/mnf//mate/jc/software/baps.html.

We introduce the concept of directed loops in stochastic series expansion and path-integral quantum Monte Carlo methods. Using the detailed balance rules for directed loops, we show that it is possible to smoothly connect generally applicable simulation schemes (in which it is necessary to include backtracking processes in the loop construction) to more restricted loop algorithms that can be constructed only for a limited range of Hamiltonians (where backtracking can be avoided). The "algorithmic discontinuities" between general and special points (or regions) in parameter space can hence be eliminated. As a specific example, we consider the anisotropic S=1/2 Heisenberg antiferromagnet in an external magnetic field. We show that directed-loop simulations are very efficient for the full range of magnetic fields (zero to the saturation point) and anisotropies. In particular, for weak fields and anisotropies, the autocorrelations are significantly reduced relative to those of previous approaches. The back-tracking probability vanishes continuously as the isotropic Heisenberg point is approached. For the XY model, we show that back tracking can be avoided for all fields extending up to the saturation field. The method is hence particularly efficient in this case. We use directed-loop simulations to study the magnetization process in the two-dimensional Heisenberg model at very low temperatures. For LxL lattices with L up to 64, we utilize the step structure in the magnetization curve to extract gaps between different spin sectors. Finite-size scaling of the gaps gives an accurate estimate of the transverse susceptibility in the thermodynamic limit: chi( perpendicular )=0.0659+/-0.0002.

Subsumed under the umbrella of User Experience (UX), practitioners and academics of Human–Computer Interaction look for ways to broaden their understanding of what constitutes "pleasurable experiences" with technology. The present study considered the fulfilment of universal psychological needs, such as competence, relatedness, popularity, stimulation, meaning, security, or autonomy, to be the major source of positive experience with interactive technologies. To explore this, we collected over 500 positive experiences with interactive products (e.g., mobile phones, computers). As expected, we found a clear relationship between need fulfilment and positive affect, with stimulation, relatedness, competence and popularity being especially salient needs. Experiences could be further categorized by the primary need they fulfil, with apparent qualitative differences among some of the categories in terms of the emotions involved. Need fulfilment was clearly linked to hedonic quality perceptions, but not as strongly to pragmatic quality (i.e., perceived usability), which supports the notion of hedonic quality as "motivator" and pragmatic quality as "hygiene factor." Whether hedonic quality ratings reflected need fulfilment depended on the belief that the product was responsible for the experience (i.e., attribution).

Abstract Although many companies investigate sustainability management and publish sustainability reports, their main focus in this endeavour remains unclear. Often, it seems that sustainability issues are pursued more coincidentally than with a clear strategy. On one hand, research is done for the identification and determination of distinct aspects concerning economic, ecological and social dimensions of sustainability. Guidelines to develop a sustainability report are popular examples of this. On the other hand, scientific effort is recognizable regarding the establishment of specific sustainability strategies, e.g. strategies that focus on internal/external orientation of sustainability commitment. Strategies should be designed to work to improve performance in terms of the issues identified, but in many cases the link between aspects and sustainability strategies is missing in practice. This paper aims to narrow this gap by developing specific aspect profiles for sustainability strategies. Relating to the characteristics of various sustainability strategies, key sustainability issues are determined, which have to be implemented in order to reach defined sustainability goals efficiently. The paper helps companies that already commit to sustainability to verify whether they are consistent in the implementation of a distinct sustainability strategy. Copyright © 2010 John Wiley & Sons, Ltd and ERP Environment.