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SummaryWe presenthidecan, an R package for generating visualisations that summarise the results of one or more genome-wide association studies and differential expression analyses, as well as manually curated candidate genes, e.g. extracted from the literature.Availability and ImplementationThe hidecan package is implemented in R and is publicly available on the CRAN repository (https://CRAN.R-project.org/package=hidecan) and on GitHub (https://github.com/PlantandFoodResearch/hidecan). A description of the package, as well as a detailed tutorial are available athttps://plantandfoodresearch.github.io/hidecan/.Contactolivia.angelin-bonnet@plantandfood.co.nz.Supplementary informationSupplementary data are available.

Much is known about the role of vocabulary in reading and the instructional procedures that improve vocabulary. Relatively less is known about feasible approaches to implement vocabulary interventi...

Vocabulary skills are important for overall reading competence, but vocabulary assessment approaches that inform instructional decision-making and are sensitive to improvement are limited. This article describes a process for developing vocabulary measures designed to facilitate data-driven decision-making for kindergarten and first-grade students who are at risk in vocabulary. A pilot study suggested the measures could be administered and scored with fidelity, and also produced promising data for indices of reliability, criterion-related validity, and sensitivity to growth, particularly for a rating-based scoring metric. Implications and considerations for developing instructionally relevant vocabulary measures are discussed.

There was a highly publicised cluster of at least ten suicides in South Wales, United Kingdom, in 2007–2008. We carried out a qualitative descriptive study using cross-case thematic analysis to investigate the experiences and narratives of eight individuals who lived in the area where the cluster occurred and who survived an episode of near-fatal self-harm at the time of the cluster. Interviews were conducted from 01.01.2015 to 31.12.2015. All interviewees denied that the other deaths in the area had affected their own suicidal behaviour. However, in other sections of the interviews they spoke about the cluster contributing to difficulties they were experiencing at the time, including damage to social relationships, feelings of loss and being out of control. When asked about support, the interviewees emphasized the importance of counselling, which they would have found helpful but in most cases did not receive, even in the case of close contacts of individuals who had died. The findings suggest that effective prevention messaging must be subtle, since those affected may not be explicitly aware of or acknowledge the imitative aspects of their behaviour. This could be related to stigma attached to suicidal behaviour in a cluster context. Lessons for prevention include changing the message from asking if people ‘have been affected by’ the suicide deaths to emphasising the preventability of suicide, and directly reaching out to individuals rather than relying on people to come forward.

The social categories “Hutu” and “Tutsi” have long been central to Rwandan politics, though never more so than during the 1994 genocide, when they formed the ultimate divide: kill (Hutu) or be killed (Tutsi). Since then, the Rwandan government has sought to eliminate these categories and replace them with a new, national identity category of “Rwandan.” This chapter draws on theories of state symbolic power and legibility to analyze how top-down projects of remaking Rwandans are being received from below. Specifically, we examine ordinary Rwandans’ responses to gacaca, a community justice practice central to the state’s National Unity and Reconciliation Program, and find Rwandans resent efforts to “unmake race” in favor of “nation” because the state’s account of genocide in gacaca does not allow them to sincerely express their experiences; it activates traumatic pasts for what they feel is superficial national reconciliation; and it detracts from their material needs. These findings highlight the importance of distinguishing between compliance and conviction in research on state efforts to transform civilian subjectivities. They also suggest directions for further research. Namely, future research on state symbolic power should attend to how individual experiences with violence mediate topdown efforts at remaking civilian subjectivities, to how different forms of governance shape civilian resistance to state categorization and classification projects, and to what kinds of interests are likely to motivate people to alter their self-perceptions. We conclude by arguing for more work on state race and nation-making from the perspectives of its targets.

In June 2012, Rwanda's community-based gacaca (ga-cha-cha) courts closed after processing almost two million cases for crimes of genocide. The courts are at the heart of government efforts to achieve national unity and reconciliation following the violence of the 1994 genocide. In just 100 days, ethnic Hutu militias orchestrated the deaths of their ethnic Tutsi kin and kith. The sheer size and scale of the violence of the 1994 genocide makes post-genocide justice a complicated affair, as the ...

Commercially grown kiwifruit (genus Actinidia) are generally of two sub-species which have a base haploid genome of 29 chromosomes. The yellow-fleshed Actinidia chinensis var. chinensis, is either diploid (2n = 2x = 58) or tetraploid (2n = 4x = 116) and the green-fleshed cultivar A. chinensis var. deliciosa “Hayward,” is hexaploid (2n = 6x = 174). Advances in breeding green kiwifruit could be greatly sped up by the use of molecular resources for more efficient and faster selection, for example using marker-assisted selection (MAS). The key genetic marker that has been implemented for MAS in hexaploid kiwifruit is for gender testing. The limited marker-trait association has been reported for other polyploid kiwifruit for fruit and production traits. We have constructed a high-density linkage map for hexaploid green kiwifruit using genotyping-by-sequence (GBS). The linkage map obtained consists of 3686 and 3940 markers organized in 183 and 176 linkage groups for the female and male parents, respectively. Both parental linkage maps are co-linear with the A. chinensis “Red5” reference genome of kiwifruit. The linkage map was then used for quantitative trait locus (QTL) mapping, and successfully identified QTLs for king flower number, fruit number and weight, dry matter accumulation, and storage firmness. These are the first QTLs to be reported and discovered for complex traits in hexaploid kiwifruit.

BACKGROUND: The benefits of clinical pharmacy services are established within hospital practice but staff numbers required for service delivery are not well described and staffing levels vary. The need for a consistent, objective method of determining staffing levels was recognised at a UK University Hospital and a Clinical Pharmacy Workforce Calculator (CPWC) was developed. OBJECTIVE: To develop the Activity Standard (AS) for pharmaceutical care and establish the reliability of the CPWC across acute hospital settings in UK. SETTING: Acute hospital in-patient clinical pharmacy services on medical and surgical wards METHOD: Using the World Health Organisation's Workload Indicators of Staffing Need (WISN) methodology, a two-round Delphi study was undertaken. This developed the Activity Standard for pharmaceutical care and identified the staff-time unavailable for clinical work. Consenting panel members then tested the CPWC, calculating the staff required for three scenarios to determine whether it could be reliably used by different operators. RESULTS: Thirty-six participants consented to participate. Data was returned from 22 (61%) of whom 20 (56%) supplied analysable data. Consensus was achieved on the tasks required for pharmaceutical care delivery, the mean time each takes, how frequently they should be completed and the time unavailable for clinical work for each grade of staff. The CPWC calculates staffing requirements using this data. Eleven participants (55%) tested the CPWC and analysis of responses demonstrated that 30 of 33 (91%) calculations were accurately completed. DISCUSSION: This study defined the WISN Activity Standard for UK pharmaceutical care delivery to hospital inpatients and showed content validity for the CPWC in acute medical and surgical hospital settings. Different operators used the CPWC reliably and applied it to local sites. CONCLUSION: The CPWC offers hospital pharmacy managers a useful tool to negotiate adequate staffing to deliver pharmaceutical care. Its development methodology could be applied widely in pharmacy practice.

Background Genomic methods for identifying causative variants for trait loci applicable to a wide range of germplasm are required for plant biologists and breeders to understand the genetic control of trait variation. Results We implemented Cas9-targeted sequencing for fine-mapping in apple, a method combining CRISPR-Cas9 targeted cleavage of a region of interest, followed by enrichment and long-read sequencing using the Oxford Nanopore Technology (ONT). We demonstrated the capability of this methodology to specifically cleave and enrich a plant genomic locus spanning 8 kb. The repeated mini-satellite motif located upstream of the Malus × domestica (apple) MYB10 transcription factor gene, causing red fruit colouration when present in a heterozygous state, was our exemplar to demonstrate the efficiency of this method: it contains a genomic region with a long structural variant normally ignored by short-read sequencing technologies Cleavage specificity of the guide RNAs was demonstrated using polymerase chain reaction products, before using them to specify cleavage of high molecular weight apple DNA. An enriched library was subsequently prepared and sequenced using an ONT MinION flow cell (R.9.4.1). Of the 7,056 ONT reads base-called using both Albacore2 (v2.3.4) and Guppy (v3.2.4), with a median length of 9.78 and 9.89 kb, respectively, 85.35 and 91.38%, aligned to the reference apple genome. Of the aligned reads, 2.98 and 3.04% were on-target with read depths of 180 × and 196 × for Albacore2 and Guppy, respectively, and only five genomic loci were off-target with read depth greater than 25 × , which demonstrated the efficiency of the enrichment method and specificity of the CRISPR-Cas9 cleavage. Conclusions We demonstrated that this method can isolate and resolve single-nucleotide and structural variants at the haplotype level in plant genomic regions. The combination of CRISPR-Cas9 target enrichment and ONT sequencing provides a more efficient technology for fine-mapping loci than genome-walking approaches.

Polyploidy is a key driver of significant evolutionary changes in plant species. The genus Actinidia (kiwifruit) exhibits multiple ploidy levels, which contribute to novel fruit traits, high yields and resistance to the canker-causing dieback disease incited by Pseudomonas syringae pv. actinidiae (Psa) biovar 3. However, the genetic mechanism for resistance to Psa observed in polyploid kiwifruit is not yet known. In this study we performed detailed genetic analysis of a tetraploid Actinidia chinensis var. chinensis population derived from a cross between a female parent that exhibits weak tolerance to Psa and a highly Psa-resistant male parent. We used the capture-sequencing approach across the whole kiwifruit genome and generated the first ultra-dense maps in a tetraploid kiwifruit population. We located quantitative trait loci (QTLs) for Psa resistance on these maps. Our approach to QTL mapping is based on the use of identity-by-descent trait mapping, which allowed us to relate the contribution of specific alleles from their respective homologues in the male and female parent, to the control of Psa resistance in the progeny. We identified genes in the diploid reference genome whose function is suggested to be involved in plant defense, which underly the QTLs, including receptor-like kinases. Our study is the first to cast light on the genetics of a polyploid kiwifruit and suggest a plausible mechanism for Psa resistance in this species.

Rather than addressing the trauma inflicted by genocidal violence, the ruling party has used a program of national ethnic unity and reconciliation to reinforce its political authority.

To increase our understanding of the role gender plays in spousal loss, this qualitative study analyzes bereavement narratives of 33 recent widowers, aged 45–89 years, all of whom accessed the National Widowers’ Organization website. In particular, we look at how these widowers’ lives changed, the impact of changing gender norms, and coping strategies. To illuminate the temporal process evident in these narratives, we utilize Silverman’s nonlinear characteristics of bereavement and the anthropological concept of liminality. In contrast to studies of widowers in earlier decades, our analysis reveals questioning and rejection of stereotypical masculine gender norms, a wide variety of creative responses to spousal loss, and the need for individualized support.

Tubers are vegetative reproduction organs formed from underground extensions of the plant stem. Potato tubers are harvested and stored for months. Storage under cold temperatures of 2–4 °C is advantageous for supressing sprouting and diseases. However, development of reducing sugars can occur with cold storage through a process called cold-induced sweetening (CIS). CIS is undesirable as it leads to darkened color with fry processing. The purpose of the current study was to find differences in biological responses in eight cultivars with variation in CIS resistance. Transcriptome sequencing was done on tubers before and after cold storage and three approaches were taken for gene expression analysis: 1. Gene expression correlated with end-point glucose after cold storage, 2. Gene expression correlated with increased glucose after cold storage (after-before), and 3. Differential gene expression before and after cold storage. Cultivars with high CIS resistance (low glucose after cold) were found to increase expression of an invertase inhibitor gene and genes involved in DNA replication and repair after cold storage. The cultivars with low CIS resistance (high glucose after cold) showed increased expression of genes involved in abiotic stress response, gene expression, protein turnover and the mitochondria. There was a small number of genes with similar expression patterns for all cultivars including genes involved in cell wall strengthening and phospholipases. It is proposed that the pattern of gene expression is related to chilling-induced DNA damage repair and cold acclimation and that genetic variation in these processes are related to CIS.

Summary We present sismonr, an R package for an integral generation and simulation of in silico biological systems. The package generates gene regulatory networks, which include protein-coding and non-coding genes along with different transcriptional and post-transcriptional regulations. The effect of genetic mutations on the system behaviour is accounted for via the simulation of genetically different in silico individuals. The ploidy of the system is not restricted to the usual haploid or diploid situations but can be defined by the user to higher ploidies. A choice of stochastic simulation algorithms allows us to simulate the expression profiles of the genes in the in silico system. We illustrate the use of sismonr by simulating the anthocyanin biosynthesis regulation pathway for three genetically distinct in silico plants. Availability and implementation The sismonr package is implemented in R and Julia and is publicly available on the CRAN repository (https://CRAN.R-project.org/package=sismonr). A detailed tutorial is available from GitHub at https://oliviaab.github.io/sismonr/. Supplementary information Supplementary data are available at Bioinformatics online.

During analysis of kiwifruit derived from hybrids between the high AsA species Actinidia eriantha and A. chinensis var chinensis, we observed bimodal segregation of fruit AsA concentration suggesting major gene segregation. To test this hypothesis we performed whole-genome sequencing on pools of high and low AsA fruit from tetraploid A. chinensis var. deliciosa x A. eriantha backcross families. Pool-GWAS revealed a single QTL spanning more than 5 Mbp on chromosome 26, which we denote as qAsA26.1. A co-dominant PCR marker was used to validate this association in four diploid (A. chinensis x A. eriantha) x A. chinensis backcross families, showing that the eriantha allele at this locus increases fruit AsA levels by 250 mg/100 g fresh weight. Inspection of genome composition and recombination in other A. chinensis genetic maps confirmed that the qAsA26.1 region bears hallmarks of suppressed recombination. The molecular fingerprint of this locus was examined in leaves of backcross validation families by RNASEQ. This confirmed strong allelic expression bias across this region as well as differential expression of transcripts on other chromosomes. This evidence suggests that the region harboring qAsA26.1 constitutes a supergene, which may condition multiple pleiotropic effects on metabolism.

There is a growing niche market for coloured-skin potatoes, and breeders are developing new cultivars that not only exhibit coloured tuber skin but are also improved for agronomic and nutritional traits. Molecular markers provide a mechanism to increase the efficiency of such breeding programmes through marker-assisted selection (MAS) of both parents and elite seedlings in breeding populations. In our study, we used next-generation sequencing and high-resolution DNA melting (HRM) to develop single nucleotide polymorphism (SNP)-based markers from candidate genes associated with tuber skin colour in tetraploid potato, including small amplicon assays and dosage-sensitive unlabelled probes. We present SNP-based HRM markers for Stan2 and Stan3 (D locus), dfr (R locus) and f3′5′h (P locus) as predictors of tuber skin colour in potato, employing a genetic resource of 19 parental accessions for marker development and then demonstrating their application in three segregating populations. To our knowledge, this is not only the first report of HRM unlabelled probe and short amplicon assays at the D locus, but also the first report of the implementation of MAS for tuber skin colour, using a combination of markers at the D, R and P loci. Our estimation of allele dosage for these genes highlights the usefulness of this methodology for parental selection targeting oligogenic traits.

This is the summary of Qualitative Transparency Deliberations Final Report on Research Ethics and Human Subjects: A Reflexive Openness Approach, Working Group number I.2.

The foremost ethical obligation and therefore the first duty of scholars is the ethical treatment of people affected by our research, particularly its human subjects. Our working group's report discusses the implications of the primacy of the ethical treatment of human participants – our term for "human subjects" – for empirical research in political science. Although research ethics encompasses a broader range of issues (including honesty, integrity, competence, and the respectful treatment of students and colleagues, among others), we focus on the primacy of human participants both because the human costs of violating this obligation are likely much higher than, for example, plagiarism, and because this principle may conflict with evolving norms of transparency in the social sciences. We acknowledge that "transparency" frequently has benefits, but nonetheless focus on the tensions between it and the primary obligation to human subjects and other ethical obligations in a wide range of research contexts, including settings of violence and repression. To support our ethical positions, we advance a broad and distinct approach of "reflexive openness" that incorporates sustained reflection on the ethics of research practices, what ethnographers term "reflexivity." This approach has three important elements. First, it promotes ongoing reflexivity by the author vis-a-vis her research participants. Second, it encourages all scholars to provide a reasoned ethical justification of their research practices, especially when seeking to publish their analysis. Finally, the ethical expectations guiding reflexive openness are universal, and thus the approach is inclusive of researchers regardless of subfield, methodology, topic, and empirical context.

In recent years, a variety of efforts have been made in political science to enable, encourage, or require scholars to be more open and explicit about the bases of their empirical claims and, in turn, make those claims more readily evaluable by others. While qualitative scholars have long taken an interest in making their research open, reflexive, and systematic, the recent push for overarching transparency norms and requirements has provoked serious concern within qualitative research communities and raised fundamental questions about the meaning, value, costs, and intellectual relevance of transparency for qualitative inquiry. This essay is the introduction to a symposium that crystallizes the central findings of a three-year deliberative process – the Qualitative Transparency Deliberations (QTD) – involving hundreds of political scientists in a broad discussion of these issues. The symposium’s centerpiece is a series of summaries of the QTD Working Group’s final reports. Drawing on a series of public, online conversations that unfolded at www.qualtd.net, the reports unpack transparency’s promise, practicalities, risks, and limitations in relation to different qualitative methodologies, forms of evidence, and research contexts. Taken as a whole, these reports offer practical guidance to scholars designing and implementing qualitative research, and to editors, reviewers, and funders seeking to develop criteria of evaluation that are appropriate – as understood by relevant research communities – to the forms of inquiry being assessed.

Genomic selection (GS) is a breeding tool, which is rapidly gaining popularity for plant breeding, particularly for traits that are difficult to measure. One such trait is ascochyta blight resistance in pea (Pisum sativum L.), which is difficult to assay because it is strongly influenced by the environment and depends on the natural occurrence of multiple pathogens. Here we report a study of the efficacy of GS for predicting ascochyta blight resistance in pea, as represented by ascochyta blight disease score (ASC), and using nucleotide polymorphism data acquired through genotyping-by-sequencing. The effects on prediction accuracy of different GS models and different thresholds for missing genotypic data (which modified the number of single nucleotide polymorphisms used in the analysis) were compared using cross-validation. Additionally, the inclusion of marker × environment interactions in a genomic best linear unbiased prediction (GBLUP) model was evaluated. Finally, different ways of combining trait data from two field trials using bivariate, spatial, and single-stage analyses were compared to results obtained using a mean value. The best prediction accuracy achieved for ASC was 0.56, obtained using GBLUP analysis with a mean value for ASC and data quality threshold of 70% (i.e., missing SNP data in

RÉSUMÉUne population vieillissante et la croissance de la population sur la base de l’immigration nécessitent que la recherche, la pratique et la politique doivent se concentrer sur la santé mentale des immigrants âgés, surtout parce que leur santé mentale semble se détériorer au fil du temps. Cette revue se concentre sur: Qu’est-ce que l’on sait sur les déterminants sociaux de la santé mentale chez les immigrants âgés, et quels sont les obstacles à l’accès aux services de santé mentale confrontés par les immigrants âgés? Les résultats révèlent que (1) les déterminants sociaux décisifs de la santé mentale sont la culture, le sexe et les services de santé; (2) que les immigrants plus âgés utilisent les services de santé mentale de moins que leurs homologues nés au Canada à cause des obstacles tels que, par exemple, les croyances et les valeurs culturelles, un manque de services culturellement et linguistiquement appropriées, des difficultés financières, et l’âgisme; et (3) quelles que soient les sous-catégories dans cette population, les immigrants âgés éprouvent des inégalités en matière de la santé mentale. La preuve des recherches disponibles indique que de combler les lacunes des service de santé mentale devrait devenir une priorité pour la politique et la pratique du système de soins de santé au Canada.

Although Sequence-Characterized Amplified Region (SCAR) markers linked to the potato H1 locus, which confers resistance to pathotypes Ro1 and Ro4 of the potato cyst nematode (PCN) Globodera rostochiensis, have been reported, robust markers that enable estimation of allele dosage would improve the quality of information obtained from genotyping parental accessions (cultivars/breeding lines) and progeny populations within breeding programmes. With this in mind, we have developed single nucleotide polymorphism (SNP)-based molecular markers flanking the H1 resistance gene, using genomic re-sequence data from five elite tetraploid accessions. The published TG689 and 57R primer sequences were used in a Basic Local Alignment Search Tool (BLAST) examination of the reference potato genome, and SNPs within the vicinity of these primer regions were identified and targeted for designing probe-based High Resolution Melting (HRM) SNP assays. Evaluation of the subsequently developed HRM markers, TG689_1P and 57R_1P, against the publicly available SCAR markers, TG689 and 57R, indicated that the HRM markers enabled more reliable marker-trait association than the SCARs. Additionally, allelic dosage estimates for the H1 locus were also derived using the TG689_1P marker, providing a tool to optimise parental and progeny selections in PCN resistance breeding.