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This research explored the relationships among inner peace and character strengths, both of which are understood to contribute to wellbeing, using a cross-sectional design. In Study One (N = 25,302), we examined individuals’ perceptions of the strengths most relevant to fostering a sense of inner peace. In Study Two (N = 21,201), we examined relationships among individuals’ scores on the 24 character strengths and serenity and harmony in life. Interestingly, the strengths individuals believed to be important for fostering innerpeace (in Study One) were different from those found to actually correlate with measures of inner peace (in Study Two). Hope was most strongly associated with facets of serenity (inner haven, trust, and acceptance) and harmony in life. Our findings indicate that, hope, zest, and gratitude are likely primary facets of inner peace, with spirituality and forgiveness acting as secondary facets for inner peace. Implications and future directions are discussed.

Since 2005, the Pathogen–Host Interactions Database (PHI-base) has manually curated experimentally verified pathogenicity, virulence and effector genes from fungal, bacterial and protist pathogens, which infect animal, plant, fish, insect and/or fungal hosts. PHI-base (www.phi-base.org) is devoted to the identification and presentation of phenotype information on pathogenicity and effector genes and their host interactions. Specific gene alterations that did not alter the in host interaction phenotype are also presented. PHI-base is invaluable for comparative analyses and for the discovery of candidate targets in medically and agronomically important species for intervention. Version 4.12 (September 2021) contains 4387 references, and provides information on 8411 genes from 279 pathogens, tested on 228 hosts in 18, 190 interactions. This provides a 24% increase in gene content since Version 4.8 (September 2019). Bacterial and fungal pathogens represent the majority of the interaction data, with a 54:46 split of entries, whilst protists, protozoa, nematodes and insects represent 3.6% of entries. Host species consist of approximately 54% plants and 46% others of medical, veterinary and/or environmental importance. PHI-base data is disseminated to UniProtKB, FungiDB and Ensembl Genomes. PHI-base will migrate to a new gene-centric version (version 5.0) in early 2022. This major development is briefly described.

The fission yeast Schizosaccharomyces japonicus has recently emerged as a powerful system for studying the evolution of essential cellular processes, drawing on similarities as well as key differences between S. japonicus and the related, well-established model Schizosaccharomyces pombe. We have deployed the open-source, modular code and tools originally developed for PomBase, the S. pombe model organism database (MOD), to create JaponicusDB (www.japonicusdb.org), a new MOD dedicated to S. japonicus. By providing a central resource with ready access to a growing body of experimental data, ontology-based curation, seamless browsing and querying, and the ability to integrate new data with existing knowledge, JaponicusDB supports fission yeast biologists to a far greater extent than any other source of S. japonicus data. JaponicusDB thus enables S. japonicus researchers to realise the full potential of studying a newly emerging model species, and illustrates the widely applicable power and utility of harnessing reusable PomBase code to build a comprehensive, community-maintainable repository of species-relevant knowledge.

Valérie de Crécy-Lagard: et al., Over the last 25 years, biology has entered the genomic era and is becoming a science of 'big data'. Most interpretations of genomic analyses rely on accurate functional annotations of the proteins encoded by more than 500 000 genomes sequenced to date. By different estimates, only half the predicted sequenced proteins carry an accurate functional annotation, and this percentage varies drastically between different organismal lineages. Such a large gap in knowledge hampers all aspects of biological enterprise and, thereby, is standing in the way of genomic biology reaching its full potential. A brainstorming meeting to address this issue funded by the National Science Foundation was held during 3-4 February 2022. Bringing together data scientists, biocurators, computational biologists and experimentalists within the same venue allowed for a comprehensive assessment of the current state of functional annotations of protein families. Further, major issues that were obstructing the field were identified and discussed, which ultimately allowed for the proposal of solutions on how to move forward., National Science Foundation (grant MCB-2129768) to V.d.C.-L; National Institutes of Health Intramural Research Program, National Library of Medicine (Z.L.).

According to SAMHSA (2014), 1 of the 10 domains of a trauma-informed approach to child welfare relates to universal screening; however, costs of installation and implementation models are often unc...

There are thousands of distinct disease entities and concepts, each of which are known by different and sometimes contradictory names. The lack of a unified system for managing these entities poses a major challenge for both machines and humans that need to harmonize information to better predict causes and treatments for disease. The Mondo Disease Ontology is an open, community-driven ontology that integrates key medical and biomedical terminologies, supporting disease data integration to improve diagnosis, treatment, and translational research. Mondo records the sources of all data and is continually updated, making it suitable for research and clinical applications that require up-to-date disease knowledge.

Motivation The conventional methods to detect homologous protein pairs use the comparison of protein sequences. But the sequences of two homologous proteins may diverge significantly and consequently may be undetectable by standard approaches. The release of the AlphaFold 2.0 software enables the prediction of highly accurate protein structures and opens many opportunities to advance our understanding of protein functions, including the detection of homologous protein structure pairs. Results In this proof-of-concept work, we search for the closest homologous protein pairs using the structure models of five model organisms from the AlphaFold database. We compare the results with homologous protein pairs detected by their sequence similarity and show that the structural matching approach finds a similar set of results. In addition, we detect potential novel homologs solely with the structural matching approach, which can help to understand the function of uncharacterized proteins and make previously overlooked connections between well-characterized proteins. We also observe limitations of our implementation of the structure-based approach, particularly when handling highly disordered proteins or short protein structures. Our work shows that high accuracy protein structure models can be used to discover homologous protein pairs, and we expose areas for improvement of this structural matching approach. Availability and Implementation Information to the discovered homologous protein pairs can be found at the following URL: https://doi.org/10.17863/CAM.87873. The code can be accessed here: https://github.com/VivianMonzon/Reciprocal_Best_Structure_Hits. Supplementary information Supplementary data are available at Bioinformatics Advances online.

PomBase (www.pombase.org), the model organism database (MOD) for the fission yeast Schizosaccharomyces pombe, supports research within and beyond the S. pombe community by integrating and presenting genetic, molecular, and cell biological knowledge into intuitive displays and comprehensive data collections. With new content, novel query capabilities, and biologist-friendly data summaries and visualisation, PomBase also drives innovation in the MOD community.

A better understanding of how to support resource (foster, kinship, and adoptive caregivers) is needed to ensure high-quality home-based care for children who cannot reside safely in their homes. U...

The standard of care treatment for locally advanced nasopharyngeal carcinoma (NPC) includes both chemotherapy and definitive radiation. However, there are limited data on the optimal management of stage II NPC. We performed a retrospective analysis of the National Cancer Database to analyze the treatment patterns and role of chemotherapy in patients with stage II NPC. We identified 611 patients diagnosed with T1‐2, N0‐1, M0 NPC, from 2004 to 2013. Five‐year survival was calculated using Kaplan Meier (KM) analysis. Multivariable analysis and propensity matched analysis were performed to analyze the impact of chemotherapy on overall survival. Of the 611 patients, 527 underwent concurrent chemoradiation (CCRT) and 84 received radiation only. Unadjusted KM analysis showed improved 5‐year survival in the CCRT group compared to radiation only (80.5% vs 65.7%; P = 0.0021). Multivariable analysis also showed improved survival with the addition of chemotherapy (Hazard ratio [HR] 0.59; 95 CI 0.39‐0.89; P = 0.0124). Propensity matched analysis confirmed a significant clinical benefit from the addition of chemotherapy to radiation. Age ≥ 65 years (HR 2.41; 95% CI 1.71‐3.4; P = 1 (HR 2.82; 95% CI 1.49‐5.31; P = 0.0014) and positive lymph node status (HR 1.6; 95% CI 1.04‐2.46; P = 0.0340) were associated with worse survival. In this retrospective analysis, patients with stage II NPC had improved survival with CCRT compared to definitive radiation only. Elderly patients with comorbidities had worse outcomes.

Biological processes are accomplished by the coordinated action of gene products. Gene products often participate in multiple processes, and can therefore be annotated to multiple Gene Ontology (GO) terms. Nevertheless, processes that are functionally, temporally, and/or spatially distant may have few gene products in common, and co-annotation to unrelated processes likely reflects errors in literature curation, ontology structure, or automated annotation pipelines. We have developed an annotation quality control workflow that uses rules based on mutually exclusive processes to detect annotation errors, based on and validated by case studies including the three we present here: fission yeast protein-coding gene annotations over time; annotations for cohesin complex subunits in human and model species; and annotations using a selected set of GO biological process terms in human and five model species. For each case study, we reviewed available GO annotations, identified pairs of biological processes which are unlikely to be correctly co-annotated to the same gene products (e.g., amino acid metabolism and cytokinesis), and traced erroneous annotations to their sources. To date we have generated 107 quality control rules, and corrected 289 manual annotations in eukaryotes and over 2.5 million automatically propagated annotations across all taxa.

PomBase (www.pombase.org) is a new model organism database established to provide access to comprehensive, accurate, and up-to-date molecular data and biological information for the fission yeast Schizosaccharomyces pombe to effectively support both exploratory and hypothesis-driven research. PomBase encompasses annotation of genomic sequence and features, comprehensive manual literature curation and genome-wide data sets, and supports sophisticated user-defined queries. The implementation of PomBase integrates a Chado relational database that houses manually curated data with Ensembl software that supports sequence-based annotation and web access. PomBase will provide user-friendly tools to promote curation by experts within the fission yeast community. This will make a key contribution to shaping its content and ensuring its comprehensiveness and long-term relevance.

Maximizing the impact and value of scientific research requires efficient knowledge distribution, which increasingly depends on the integration of standardized published data into online databases. To make data integration more comprehensive and efficient for fission yeast research, PomBase has pioneered a community curation effort that engages publication authors directly in FAIR-sharing of data representing detailed biological knowledge from hypothesis-driven experiments. Canto, an intuitive online curation tool that enables biologists to describe their detailed functional data using shared ontologies, forms the core of PomBase’s system. With 8 years’ experience, and as the author response rate reaches 50%, we review community curation progress and the insights we have gained from the project. We highlight incentives and nudges we deploy to maximize participation, and summarize project outcomes, which include increased knowledge integration and dissemination as well as the unanticipated added value arising from co-curation by publication authors and professional curators.

Introduction: The importance of both character and resilience for critical occupations (military, emergency medicine, first responders, and correctional officers) has been emphasized at the highest levels of military leadership. No studies to date have examined the relationship between character strengths and resilience within military populations. The purpose of this study was to evaluate the perceived importance of character strengths for Canadian military cadet success, the top strengths endorsed by cadets, and, in a subset of cadets, the relationships among core strengths and resilience. In line with previous research on character strengths in military populations, we predicted that bravery, honesty, perseverance, and teamwork might be included in the five most frequent signature strengths. Methods: A total of 360 Naval/Officer Cadets from a Canadian Military College were invited to participate in a study during two training sessions. Participants (n = 153) first completed a survey comprised of a resilience measure and demographic items. Then, one month later, students (n=134) were asked to complete a Values in Action (VIA) character strengths profile, and a survey with questions related to character strengths (their personal top-five character strengths, and strengths they believed were important for military-related stressors and leadership, academic success, resilience, and completion of military challenge). We were only able to match responses for a subset of participants, allowing a final sample of 94 participants. Results: Findings indicated that military cadets consider perseverance, judgment, teamwork, perspective, and self-regulation to be most critical for bouncing back from stressors. However, in line with our predictions, the most frequently endorsed strengths that characterized cadets were bravery, honesty, and perseverance. Finally, perseverance (p = .029), bravery (p = .01), and humor = .01) were positively correlated with cadet resilience, while endorsement of love was negatively correlated with resilience (p = .002). Conclusion: Focus on character strengths in military cadets can enhance academic and physical performance. Resilience assessment could be important for the purposes of military selection, performance, and well-being. Our findings indicate perseverance, bravery, and humor in particular might be relevant indicators of cadet resilience.

Multitasking-the performance of several tasks at the same time-is becoming increasingly prevalent in workplaces. Multitasking is known to disrupt performance, particularly in complex and dynamic si ...

Group cohesion and affective commitment have shown to have critical relevance to military organizations in particular. The relationship between cohesion and affective commitment is established, and...

BackgroundCochlear implantation is a highly successful intervention that, despite remarkable improvements in hardware and software, continues to show a high degree of variability in outcomes. Performance in adult patients can potentially be affected by the integrity of spiral ganglion neurons or by the performance of the central auditory system. Prolonged deafness and dementia are conditions that affect the central auditory system and can negatively impact cochlear implant outcomes. Central auditory test batteries can evaluate the central component of hearing in patients that have significant residual hearing, but cannot be effectively used in most cochlear implant patients. A wide variety of recent studies have shown that decline in olfaction predates and often predicts a variety of central nervous system degenerative disorders. We set out to evaluate if olfaction testing could predict hearing results after cochlear implantation.Material and MethodsAdult cochlear implant candidates were recruited and olfaction measured with the University of Pennsylvania smell identification test (UPSIT). Testing variables in the analysis include patient age, UPSIT score, AzBio +10 dB score at 6 months post activation, and change in AzBio +10 dB score from preoperative to post-activation testing timesResultsLower olfaction (UPSIT) scores correlated with poorer hearing outcomes (AzBio +10 dB) at 6 months post activation. Patients with lower UPSIT scores also showed less change in AzBio +10 dB scores over a 6-month period.ConclusionsOlfactory testing may be useful in preoperative evaluation of cochlear implant patients. Identification of patients at risk for central auditory system dysfunction may be possible by evaluation of patients’ olfactory function.

The pathogen–host interactions database (PHI-base) is available at www.phi-base.org. PHI-base contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen–host interactions reported in peer reviewed research articles. PHI-base also curates literature describing specific gene alterations that did not affect the disease interaction phenotype, in order to provide complete datasets for comparative purposes. Viruses are not included, due to their extensive coverage in other databases. In this article, we describe the increased data content of PHI-base, plus new database features and further integration with complementary databases. The release of PHI-base version 4.8 (September 2019) contains 3454 manually curated references, and provides information on 6780 genes from 268 pathogens, tested on 210 hosts in 13,801 interactions. Prokaryotic and eukaryotic pathogens are represented in almost equal numbers. Host species consist of approximately 60% plants (split 50:50 between cereal and non-cereal plants), and 40% other species of medical and/or environmental importance. The information available on pathogen effectors has risen by more than a third, and the entries for pathogens that infect crop species of global importance has dramatically increased in this release. We also briefly describe the future direction of the PHI-base project, and some existing problems with the PHI-base curation process.

The Gene Ontology (GO) is a comprehensive resource of computable knowledge regarding the functions of genes and gene products. As such, it is extensively used by the biomedical research community for the analysis of -omics and related data. Our continued focus is on improving the quality and utility of the GO resources, and we welcome and encourage input from researchers in all areas of biology. In this update, we summarize the current contents of the GO knowledgebase, and present several new features and improvements that have been made to the ontology, the annotations and the tools. Among the highlights are 1) developments that facilitate access to, and application of, the GO knowledgebase, and 2) extensions to the resource as well as increasing support for descriptions of causal models of biological systems and network biology. To learn more, visit http://geneontology.org/.

Background The purpose of this study was to further define the impact of primary surgery in the management of oropharyngeal squamous cell carcinoma (SCC). Methods Two hundred ninety-six patients with oropharyngeal SCC treated with primary surgery were included. Multivariable analysis and recursive partitioning analysis (RPA) identified predictors of survival and gastrostomy tube presence. Results Multivariable analysis identified that HPV negativity (p = .0002), presence of extranodal extension (p = .0025), and advanced T classification (p = .0081) were independent predictors of survival. For HPV-positive patients, surgical approach (p = .0111) and margin status (p = .0287) were significant predictors of survival. For HPV-negative patients, extranodal extension (p = .0021) and advanced T classification (p = .0342) were significant predictors of survival. Smoking status and advanced neck disease did not impact survival, and the addition of adjuvant chemotherapy did not confer survival benefit in HPV-positive or HPV-negative subgroups. Conclusion Independent predictors of survival are unique in patients with oropharyngeal SCC treated with primary surgery. © 2015 Wiley Periodicals, Inc. Head Neck 38: E1794–E1802, 2016

High-throughput studies constitute an essential and valued source of information for researchers. However, high-throughput experimental workflows are often complex, with multiple data sets that may contain large numbers of false positives. The representation of high-throughput data in the Gene Ontology (GO) therefore presents a challenging annotation problem, when the overarching goal of GO curation is to provide the most precise view of a gene's role in biology. To address this, representatives from annotation teams within the GO Consortium reviewed high-throughput data annotation practices. We present an annotation framework for high-throughput studies that will facilitate good standards in GO curation and, through the use of new high-throughput evidence codes, increase the visibility of these annotations to the research community.

PomBase (www.pombase.org), the model organism database for the fission yeast Schizosaccharomyces pombe, has undergone a complete redevelopment, resulting in a more fully integrated, better-performing service. The new infrastructure supports daily data updates as well as fast, efficient querying and smoother navigation within and between pages. New pages for publications and genotypes provide routes to all data curated from a single source and to all phenotypes associated with a specific genotype, respectively. For ontology-based annotations, improved displays balance comprehensive data coverage with ease of use. The default view now uses ontology structure to provide a concise, non-redundant summary that can be expanded to reveal underlying details and metadata. The phenotype annotation display also offers filtering options to allow users to focus on specific areas of interest. An instance of the JBrowse genome browser has been integrated, facilitating loading of and intuitive access to, genome-scale datasets. Taken together, the new data and pages, along with improvements in annotation display and querying, allow users to probe connections among different types of data to form a comprehensive view of fission yeast biology. The new PomBase implementation also provides a rich set of modular, reusable tools that can be deployed to create new, or enhance existing, organism-specific databases.

The fission yeast Schizosaccharomyces pombe has become well established as a model species for studying conserved cell-level biological processes, especially the mechanics and regulation of cell division. PomBase integrates the S. pombe genome sequence with traditional genetic, molecular, and cell biological experimental data as well as the growing body of large datasets generated by emerging high-throughput methods. This chapter provides insight into the curation philosophy and data organization at PomBase, and provides a guide to using PomBase for infrequent visitors and anyone considering exploring S. pombe in their research.

The Gene Ontology resource (GO; http://geneontology.org) provides structured, computable knowledge regarding the functions of genes and gene products. Founded in 1998, GO has become widely adopted in the life sciences, and its contents are under continual improvement, both in quantity and in quality. Here, we report the major developments of the GO resource during the past two years. Each monthly release of the GO resource is now packaged and given a unique identifier (DOI), enabling GO-based analyses on a specific release to be reproduced in the future. The molecular function ontology has been refactored to better represent the overall activities of gene products, with a focus on transcription regulator activities. Quality assurance efforts have been ramped up to address potentially out-of-date or inaccurate annotations. New evidence codes for high-throughput experiments now enable users to filter out annotations obtained from these sources. GO-CAM, a new framework for representing gene function that is more expressive than standard GO annotations, has been released, and users can now explore the growing repository of these models. We also provide the ‘GO ribbon’ widget for visualizing GO annotations to a gene; the widget can be easily embedded in any web page. This is an open access article distributed under the terms of the Creative Commons CC BY license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

The fission yeast Schizosaccharomyces pombe has become well established as a model species for studying conserved cell-level biological processes, especially the mechanics and regulation of cell division. PomBase integrates the S. pombe genome sequence with traditional genetic, molecular, and cell biological experimental data as well as the growing body of large datasets generated by emerging high-throughput methods. This chapter provides insight into the curation philosophy and data organization at PomBase, and provides a guide to using PomBase for infrequent visitors and anyone considering exploring S. pombe in their research.

RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences, collating information on ncRNA sequences of all types from a broad range of organisms. We have recently added a new genome mapping pipeline that identifies genomic locations for ncRNA sequences in 296 species. We have also added several new types of functional annotations, such as tRNA secondary structures, Gene Ontology annotations, and miRNA-target interactions. A new quality control mechanism based on Rfam family assignments identifies potential contamination, incomplete sequences, and more. The RNAcentral database has become a vital component of many workflows in the RNA community, serving as both the primary source of sequence data for academic and commercial groups, as well as a source of stable accessions for the annotation of genomic and functional features. These examples are facilitated by an improved RNAcentral web interface, which features an updated genome browser, a new sequence feature viewer, and improved text search functionality. RNAcentral is freely available at https://rnacentral.org.

The first decade of genome sequencing stimulated an explosion in the characterization of unknown proteins. More recently, the pace of functional discovery has slowed, leaving around 20% of the proteins even in well-studied model organisms without informative descriptions of their biological roles. Remarkably, many uncharacterized proteins are conserved from yeasts to human, suggesting that they contribute to fundamental biological processes. To fully understand biological systems in health and disease, we need to account for every part of the system. Unstudied proteins thus represent a collective blind spot that limits the progress of both basic and applied biosciences.We use a simple yet powerful metric based on Gene Ontology (GO) biological process terms to define characterized and uncharacterized proteins for human, budding yeast, and fission yeast. We then identify a set of conserved but unstudied proteins in S. pombe, and classify them based on a combination of orthogonal attributes determined by large-scale experimental and comparative methods. Finally, we explore possible reasons why these proteins remain neglected, and propose courses of action to raise their profile and thereby reap the benefits of completing the catalog of proteins’ biological roles.

Motivation: To provide consistent computable descriptions of phenotype data, PomBase is developing a formal ontology of phenotypes observed in fission yeast. Results: The fission yeast phenotype ontology (FYPO) is a modular ontology that uses several existing ontologies from the open biological and biomedical ontologies (OBO) collection as building blocks, including the phenotypic quality ontology PATO, the Gene Ontology and Chemical Entities of Biological Interest. Modular ontology development facilitates partially automated effective organization of detailed phenotype descriptions with complex relationships to each other and to underlying biological phenomena. As a result, FYPO supports sophisticated querying, computational analysis and comparison between different experiments and even between species. Availability: FYPO releases are available from the Subversion repository at the PomBase SourceForge project page (https://sourceforge.net/p/pombase/code/HEAD/tree/phenotype_ontology/). The current version of FYPO is also available on the OBO Foundry Web site (http://obofoundry.org/). Contact: mah79@cam.ac.uk or vw253@cam.ac.uk

Modern biomedical research depends critically on access to databases that house and disseminate genetic, genomic, molecular, and cell biological knowledge. Even as the explosion of available genome sequences and associated genome-scale data continues apace, the sustainability of professionally maintained biological databases is under threat due to policy changes by major funding agencies. Here, we focus on model organism databases to demonstrate the myriad ways in which biological databases not only act as repositories but actively facilitate advances in research. We present data that show that reducing financial support to model organism databases could prove to be not just scientifically, but also economically, unsound.

The Gene Ontology (GO) (http://www.geneontology.org) is a community bioinformatics resource that represents gene product function through the use of structured, controlled vocabularies. The number of GO annotations of gene products has increased due to curation efforts among GO Consortium (GOC) groups, including focused literature-based annotation and ortholog-based functional inference. The GO ontologies continue to expand and improve as a result of targeted ontology development, including the introduction of computable logical definitions and development of new tools for the streamlined addition of terms to the ontology. The GOC continues to support its user community through the use of e-mail lists, social media and web-based resources.

Genome annotation is a synthesis of computational prediction and experimental evidence. Small genes are notoriously difficult to detect because the patterns used to identify them are often indistinguishable from chance occurrences, leading to an arbitrary cutoff threshold for the length of a protein-coding gene identified solely by in silico analysis. We report a systematic reappraisal of the Schizosaccharomyces pombe genome that ignores thresholds. A complete six-frame translation was compared to a proteome data set, the Pfam domain database, and the genomes of six other fungi. Thirty-nine novel loci were identified. RT-PCR and RNA-Seq confirmed transcription at 38 loci; 33 novel gene structures were delineated by 5′ and 3′ RACE. Expression levels of 14 transcripts fluctuated during meiosis. Translational evidence for 10 genes, evolutionary conservation data supporting 35 predictions, and distinct phenotypes upon ORF deletion (one essential, four slow-growth, two delayed-division phenotypes) suggest that all 39 predictions encode functional proteins. The popularity of S. pombe as a model organism suggests that this augmented annotation will be of interest in diverse areas of molecular and cellular biology, while the generality of the approach suggests widespread applicability to other genomes.

e18088Background: Concurrent chemotherapy with definitive radiation is the standard of care treatment for locally advanced NPC. However, there is limited data on the optimal management of stage II ...

We report the construction and analysis of 4,836 heterozygous diploid deletion mutants covering 98.4% of the fission yeast genome. This resource provides a powerful tool for biotechnological and eukaryotic cell biology research. Comprehensive gene dispensability comparisons with budding yeast, the first time such studies have been possible between two eukaryotes, revealed that 83% of single copy orthologues in the two yeasts had conserved dispensability. Gene dispensability differed for certain pathways between the two yeasts, including mitochondrial translation and cell cycle checkpoint control. We show that fission yeast has more essential genes than budding yeast and that essential genes are more likely than non-essential genes to be single copy, broadly conserved and to contain introns. Growth fitness analyses determined sets of haploinsufficient and haploproficient genes for fission yeast, and comparisons with budding yeast identified specific ribosomal proteins and RNA polymerase subunits, which may act more generally to regulate eukaryotic cell growth.

The Athabaskan languages have a particularly rich series of stop contrasts, plain stops and affricates, each exhibiting a three-way laryngeal contrast, unaspirated, aspirated and ejective. Several aspects of this inventory are interesting to phonetic and phonological studies, among them the length and ‘heaviness’ of the releases on the aspirated plain stops, the temporal properties of the ejectives, and the richness of the stop contrast set, approximately 21 distinct segments. This paper is an investigation of the phonetic realization of the stops in five Athabaskan languages: Dene Sųline (CL), Dene Sųline (FC), Dogrib, North Slavey, and Tsilhqut’in, compared with data from Navajo from McDonough [(2003). The Navajo sound system . Kluwer: Dordrecht]. Based on the phonetic patterns in the data, we argue that, among the consonants, the primary organizing feature of the contrasts is a temporal distinction, which we model as simplex–complex contrast, based on Laver [(1994). Principles of phonetics . Cambridge: Cambridge University Press], in which the temporal properties of medial phase of the segment's articulation play a significant role in the contrast. This classification represents a major divide in the inventory between the unaspirated plain stops (orthographically ( b ) , d, g, ( q )) and the rest of the stops in the inventory. These data suggest first that aspirated plain stops (orthographically t, k ) are mislabeled. Instead, in keeping with much of the early literature on the Athabaskan languages, the t and k phonemes are the affricates /tx, kx/. Second, related to this, long release periods are a characteristic feature of all but the unaspirated stops in the inventory. As such they represent a feature of a larger grouping in the Athabaskan inventory, realized in a temporal domain and persistent in the family, in a pattern likely inherited from the parent language. We model this temporal distinction as a simplex–complex distinction, which separates out the ‘unaspirated’ plain stops, as simplex segments with short offsets, from the rest of the stops, including the plain ‘aspirated’ stops and ejectives, which have complex medial phases with long release periods. Furthermore, the proposal suggests that the languages have exploited the sets of simplex stops and fricatives to build their rich inventories of complex segments, as several linguists have observed. The analysis serves as a basis for understanding sound change and alternation patterns in the family.