Empirical assessment of the adoption, use, and effects of pair programming

Developing large software systems requires team work, which in turn calls for lots of communication within the team. However, programming is typically conducted alone by individual software developers. Pair programming, where two persons actively collaborate in the implementation of a single task, is an alternative way of developing software. It has been proposed as a means to increasing software quality, knowledge transfer and learning, among other things. This research studied the adoption, use, and effects of pair programming through a literature study and three empirical studies. The literature study was a systematic mapping study of the previous pair programming research in the industry. The empirical studies consisted of two long industry case studies and an experiment where project teams consisting of experienced students conducted a moderately large software development project. The systematic mapping study analyzed the content of 154 papers. It identified industrially relevant aspects of pair programming and organized them as a pair programming framework containing additional and more detailed aspects of pair programming over the previously published frameworks. The framework grouped all the identified aspects under eighteen factors of pair programming, for which their state of research was analyzed. The analysis showed that of many factors, only a few or no studies had been conducted using rigorous research approaches and data collection methods. The adoption and use of pair programming were analyzed in the two case studies. In the larger, more established organization, there were issues with adoption, related to both infrastructure and organizing of pair programming. A separate pair programming room was a successful solution to the infrastructural issues. However, lack of time for pair programming due to insufficient organizing of its use, remained an issue at the end of the study. The effects of pair programming on software quality and developers' knowledge were positive in all three empirical studies, but the development effort for individual tasks increased. The increase in effort occurred mainly when using pair programming for simple tasks or during the beginning of a project, when the developers were learning pair programming and getting to know one another

Facets of negative affectivity and blood pressure in middle-aged men

Research results suggesting that facets of negative affectivity, i.e. anxiety, anger-hostility, and depression, relate to incident cardiovascular diseases have been steadily increasing. Evidence for depression has been especially extensive. Elevated blood pressure, a major risk factor of cardiovascular diseases, is one probable mediator in this context. The purpose of this study was to clarify the relationship of specific key elements of depressive disposition, i.e. depressive symptoms, hopelessness and vital exhaustion, with health behavior and blood pressure. Study sample was comprised of 710 middle-aged men. Participants completed self-report questionnaires assessing health behavior, depressive symptoms, vital exhaustion and hopelessness. Statistical analyses involved descriptive analyses, correlations and path analysis. Depressive symptoms and vital exhaustion associated with several unfavorable lifestyles such as smoking, alcohol consumption, and inactivity (standardized solution coefficients: 0.10, 0.14, 0.17, accordingly). However, no significant direct associations with blood pressure could be found for depressive symptoms or vital exhaustion. Hopelessness associated only with unhealthy diet (standardized solution coefficient -0.10) Moreover, for hopelessness, results showed a direct but inverse association with systolic blood pressure (standardized solution coefficient -0.08). Results suggest that the previously reported relations of depression and vital exhaustion with blood pressure could be mediated by unfavorable lifestyles. The relation of hopelessness with adverse health behaviors seems to be less significant. Also, the role of hopelessness as a risk factor of elevated blood pressure is not supported by the results of this study

Forest Owners’ Perspectives Concerning Non‑Timber Forest Products, Everyman’s Rights, and Organic Certification of Forests in Eastern Finland

Global trends towards the bioeconomy and multidimensional ecosystem-based approaches are transforming our understanding of forests and expanding access to forest management. The demand for non-timber forest products (NTFPs) is increasing due to the current trends in lifestyle and consumption. Forest owners play a key role in the supply of NTFPs. However, many forest owners are not committed to production or aware of the opportunities for production of their forests. Understanding better the family forest owners’ behaviour and decision making regarding NTFPs is needed to strengthen the role of NTFPs in the Finnish bioeconomy. In this study, forest owners’ perspectives concerning NTFPs, Everyman’s Rights, and organic certification of forests were identified. The survey data were collected by emailing the questionnaire to North Karelian forest owners and analysed by creating forest owner typologies based on their forest ownership motives and perspectives concerning NTFPs. Regarding forest ownership motives, four owner groups of relatively equal size were identified and named as recreationist, conservationists, timber producers, and resigning owners leaving the forest property to the next generation. Regarding their use of NTFPs and interest in producing NTFPs four groups of owners were identified: owners who 1) harvested NTFPs for household use or 2) sale, 3) would allow the harvesting of NTFPs not covered by everyman’s right, and 4) need more information on the joint production of timber and NTFPs not covered by Everyman’s Rights. Most owners were household users. The results can be utilised to promote NTFP production and advocate for the more effective organic certification of forests for different forest owner groups

Human thymic T cell repertoire is imprinted with strong convergence to shared sequences

A highly diverse repertoire of T cell antigen receptors (TCR) is created in the thymus by recombination of gene segments and the insertion or deletion of nucleotides at the junctions. Using next-generation TCR sequencing we define here the features of recombination and selection in the human TCR alpha and TCR beta locus, and show that a strikingly high proportion of the repertoire is shared by unrelated individuals. The thymic TCRa nucleotide repertoire was more diverse than TCR beta, with 4.1 x 10(6) vs. 0.81 x 10(6) unique clonotypes, and contained nonproductive clonotypes at a higher frequency (69.2% vs. 21.2%). The convergence of distinct nucleotide clonotypes to the same amino acid sequences was higher in TCRa than in TCR beta repertoire (1.45 vs. 1.06 nucleotide sequences per amino acid sequence in thymus). The gene segment usage was biased, and generally all individuals favored the same genes in both TCR alpha and TCR beta loci. Despite the high diversity, a large fraction of the repertoire was found in more than one donor. The shared fraction was bigger in TCR alpha than TCR beta repertoire, and more common in in-frame sequences than in nonproductive sequences. Thus, both biases in rearrangement and thymic selection are likely to contribute to the generation of shared repertoire in humans.Peer reviewe

Forest Owners’ Perspectives Concerning Non-Timber Forest Products, Everyman’s Rights, and Organic Certification of Forests in Eastern Finland

Global trends towards the bioeconomy and multidimensional ecosystem-based approaches are transforming our understanding of forests and expanding access to forest management. The demand for non-timber forest products (NTFPs) is increasing due to the current trends in lifestyle and consumption. Forest owners play a key role in the supply of NTFPs. However, many forest owners are not committed to production or aware of the opportunities for production of their forests. Understanding better the family forest owners’ behaviour and decision making regarding NTFPs is needed to strengthen the role of NTFPs in the Finnish bioeconomy. In this study, forest owners’ perspectives concerning NTFPs, Everyman’s Rights, and organic certification of forests were identified. The survey data were collected by emailing the questionnaire to North Karelian forest owners and analysed by creating forest owner typologies based on their forest ownership motives and perspectives concerning NTFPs. Regarding forest ownership motives, four owner groups of relatively equal size were identified and named as recreationist, conservationists, timber producers, and resigning owners leaving the forest property to the next generation. Regarding their use of NTFPs and interest in producing NTFPs four groups of owners were identified: owners who 1) harvested NTFPs for household use or 2) sale, 3) would allow the harvesting of NTFPs not covered by everyman’s right, and 4) need more information on the joint production of timber and NTFPs not covered by Everyman’s Rights. Most owners were household users. The results can be utilised to promote NTFP production and advocate for the more effective organic certification of forests for different forest owner groups

Characterization of human T cell receptor repertoire data in eight thymus samples and four related blood samples

T cell receptor (TCR) is a heterodimer consisting of TCR alpha and TCR beta chains that are generated by somatic recombination of multiple gene segments. Nascent TCR repertoire undergoes thymic selections where non-functional and potentially autoreactive receptors are removed. During the last years, the development of high-throughput sequencing technology has allowed a large scale assessment of TCR repertoire and multiple analysis tools are now also available. In our recent manuscript, Human thymic T cell repertoire is imprinted with strong convergence to shared sequences [1], we show highly overlapping thymic TCR repertoires in unrelated individuals. In the current Data in Brief article, we provide a more detailed characterization of the basic features of these thymic and related peripheral blood TCR repertoires. The thymus samples were collected from eight infants undergoing corrective cardiac surgery, two of whom were monozygous twins [2]. In parallel with the surgery, a small aliquot of peripheral blood was drawn from four of the donors. Genomic DNA was extracted from mechanically released thymocytes and circulating leukocytes. The sequencing of TCR alpha and TCR beta repertoires was performed at ImmunoSEQ platform (Adaptive Biotechnologies). The obtained repertoire data were analysed applying relevant features from immunoSEQ (R) 3.0 Analyzer (Adaptive Biotechnologies) and a freely available VDJTools software package for programming language R [3]. The current data analysis displays the basic features of the sequenced repertoires including observed TCR diversity, various descriptive TCR diversity measures, and V and J gene usage. In addition, multiple methods to calculate repertoire overlap between two individuals are applied. The raw sequence data provide a large database of reference TCRs in healthy individuals at an early developmental stage. The data can be exploited to improve existing computational models on TCR repertoire behaviour as well as in the generation of new models. (C) 2021 The Authors. Published by Elsevier Inc.Peer reviewe

Effect of wood residues on the growth of Ganoderma lucidum

Sawmill industries generate considerable amounts of low value wood residues. Fungal decomposition of lignocellulosic biomass allows the conversion of wood residues into valuable products. The selection of the most suitable fungal strains and media are essential to optimise the bioconversion of wood residues and serves as a basis for mushroom cultivation industries. The aim of this study was to find the best combinations of Ganoderma lucidum strains and substrate media to optimise the cultivation of the fungus. Mycelial growth and culture characteristics of G. lucidum isolated from Betula pubescens and Picea abies in Finland were tested on agar media containing different wood residues. These included Betula sp., Populus tremula, Larix sp., Pinus sylvestris, Alnus incana and P. abies sawdust, which were added to malt extract agar, potato dextrose agar and water agar. The results showed significant differences in the mycelial growth between all interaction levels (agar media, wood species and fungal strain). The addition of malt extract significantly enhanced the growth of the fungus in comparison to potato dextrose or water agar. The wood sawdust most suitable for mycelial growth was Betula sp., followed by P. tremula. Strains originally isolated from P. abies also presented higher mycelial growth in media with hardwood sawdust. These findings demonstrate that Betula sp. and P. tremula sawdust stimulate the growth of G. lucidum. Thus, it is possible to cultivate the fungus on a variety of wood residues from sawmill industries.202

T cell receptor diversity in the human thymus

A diverse T cell receptor (TCR) repertoire is essential for adaptive immune responses and is generated by somatic recombination of TCR alpha and TCR beta gene segments in the thymus. Previous estimates of the total TCR diversity have studied the circulating mature repertoire, identifying 1 to 3 x 10(6) unique TCR beta and 0.5 x 10(6) TCR alpha sequences. Here we provide the first estimate of the total TCR diversity generated in the human thymus, an organ which in principle can be sampled in its entirety. High-throughput sequencing of samples from four pediatric donors detected up to 10.3 x 10(6) unique TCR beta sequences and 3.7 x 10(6) TCR alpha sequences, the highest directly observed diversity so far for either chain. To obtain an estimate of the total diversity we then used three different estimators, preseq and DivE, which measure the saturation of rarefaction curves, and Chao2, which measures the size of the overlap between samples. Our results provide an estimate of a thymic repertoire consisting of 40 to 70 x 10(6) unique TCR beta sequences and 60 to 100 x 10(6) TCR alpha sequences. The thymic repertoire is thus extremely diverse. Moreover, extrapolation of the data and comparison with earlier estimates of peripheral diversity also suggest that the thymic repertoire is transient, with different clones produced at different times. (C) 2016 Elsevier Ltd. All rights reserved.Peer reviewe

Effect of strain, wood substrate and cold treatment on the yield and β-glucan content of Ganoderma lucidum fruiting bodies

Wood residues from forestry industries can be potential raw materials for specialty and edible mushroom production. The aim of this study was to evaluate the suitability of wood residues for the cultivation of Ganoderma lucidum originating from boreal forests. The substrates tested included sawdust and wood chips of Betula spp., Populus tremula, Picea abies, Pinus sylvestris and Larix sp. The suitability of the substrates and the ability of the strains to develop fruiting bodies and produce β-glucan were evaluated. Fruiting body formation was supported by applying two different cold shock treatments to substrate bags. The highest yields were observed with MUS192 strain and Betula spp. and P. tremula wood-based substrates. β-Glucan content in the fruiting bodies was highest with the MUS75 and P. tremula wood-based substrate. Based on these findings, the combination of P. tremula wood residues and the MUS192 strain is proposed to enhance the yieldand β-glucan content of the fruiting bodies. A cold treatment of 5 °C is suggested to induce primordia formation and to increase fruiting probability. This is the first time that strains of G. lucidum originating from boreal forests have been compared and successfully cultivated simulating commercial indoor cultivation.202

Identifying the inheritable component of human thymic T cell repertoire generation in monozygous twins

We have analyzed T cell receptor repertoires in a unique set of thymus samples from a pair of monozygotic twins. While genetics affect the V(D)J rearrangement and generation of junctional sequences, the thymic selections seem largely stochastic and import no detectable inheritable effect at clonal level.Non peer reviewe