matOptimize: A parallel tree optimization method enables online phylogenetics for SARS-CoV-2

Phylogenetic tree optimization is necessary for precise analysis of evolutionary and transmission dynamics, but existing tools are inadequate for handling the scale and pace of data produced during the COVID-19 pandemic. One transformative approach, online phylogenetics, aims to incrementally add samples to an ever-growing phylogeny, but there are no previously-existing approaches that can efficiently optimize this vast phylogeny under the time constraints of the pandemic. Here, we present matOptimize, a fast and memory-efficient phylogenetic tree optimization tool based on parsimony that can be parallelized across multiple CPU threads and nodes, and provides orders of magnitude improvement in runtime and peak memory usage compared to existing state-of-the-art methods. We have developed this method particularly to address the pressing need during the COVID-19 pandemic for daily maintenance and optimization of a comprehensive SARS-CoV-2 phylogeny. Thus, our approach addresses an important need for daily maintenance and refinement of a comprehensive SARS-CoV-2 phylogeny.

Stress conditions promote Leishmania hybridization in vitro marked by expression of the ancestral gamete fusogen HAP2 as revealed by single-cell RNAseq

Leishmania are protozoan parasites transmitted by the bite of sand fly vectors producing a wide spectrum of diseases in their mammalian hosts. These diverse clinical outcomes are directly associated with parasite strain and species diversity. Although Leishmania reproduction is mainly clonal, a cryptic sexual cycle capable of producing hybrid genotypes has been inferred from population genetic studies, and directly demonstrated by laboratory crosses. Experimentally, mating competence has been largely confined to promastigotes developing in the sand fly midgut. The ability to hybridize culture promastigotes in vitro has been limited so far to low efficiency crosses between two L. tropica strains, L747 and MA37, that mate with high efficiency in flies. Here, we show that exposure of promastigote cultures to DNA damage stress produces a remarkably enhanced efficiency of in vitro hybridization of the L. tropica strains, and extends to other species, including L. donovani, L. infantum, and L. braziliensis, a capacity to generate intra- and interspecific hybrids. Whole genome sequencing and total DNA content analyses indicate that the hybrids are in each case full genome, mostly tetraploid hybrids. Single-cell RNA sequencing of the L747 and MA37 parental lines highlights the transcriptome heterogeneity of culture promastigotes and reveals discrete clusters that emerge post-irradiation in which genes potentially involved in genetic exchange are expressed, including the ancestral gamete fusogen HAP2. By generating reporter constructs for HAP2, we could select for promastigotes that could either hybridize or not in vitro. Overall, this work reveals that there are specific populations involved in Leishmania hybridization associated with a discernible transcriptomic signature, and that stress facilitated in vitro hybridization can be a transformative approach to generate large numbers of hybrid genotypes between diverse species and strains.

Natural language processing in psychiatry: the promises and perils of a transformative approach

A person's everyday language can indicate patterns of thought and emotion predictive of mental illness. Here, we discuss how natural language processing methods can be used to extract indicators of mental health from language to help address long-standing problems in psychiatry, along with the potential hazards of this new technology.

Systems biology–the transformative approach to integrate sciences across disciplines

Life science is the study of living organisms, including bacteria, plants, and animals. Given the importance of biology, chemistry, and bioinformatics, we anticipate that this chapter may contribute to a better understanding of the interdisciplinary connections in life science. Research in applied biological sciences has changed the paradigm of basic and applied research. Biology is the study of life and living organisms, whereas science is a dynamic subject that as a result of constant research, new fields are constantly emerging. Some fields come and go, whereas others develop into new, well-recognized entities. Chemistry is the study of composition of matter and its properties, how the substances merge or separate and also how substances interact with energy. Advances in biology and chemistry provide another means to understand the biological system using many interdisciplinary approaches. Bioinformatics is a multidisciplinary or rather transdisciplinary field that encourages the use of computer tools and methodologies for qualitative and quantitative analysis. There are many instances where two fields, biology and chemistry have intersection. In this chapter, we explain how current knowledge in biology, chemistry, and bioinformatics, as well as its various interdisciplinary domains are merged into life sciences and its applications in biological research.

Incorporating Awareness of English as a Lingua Franca into Teacher Education for Secondary School Japanese Teachers of English

This article discusses the obstacles and potential solutions for the incorporation and increased awareness of English as a lingua franca (ELF) into teacher education programs for secondary school Japanese teachers of English (JTEs). While a nationally standardized “Core Curriculum” (CC) for secondary school JTEs’ learning guidelines and models in teacher education reflects relatively positive attitudes towards ELF, the integration of an ELF perspective into teacher education programs is considered a low priority. Recent literature explores the barriers to ELF-aware curriculum design and suggests that teachers carry out ELF-based action research, both to promote teachers’ critical awareness of ELF and to gain insights that will encourage a wider transformative approach to their beliefs. The authors here conclude that for a more effective and innovative ELF-aware curriculum implementation, it is important to consider the broader context of the current landscape of English use and language teaching. この論文は、中等教育に携わる日本人英語教師のための教師教育プログラムに、国際共通語としての英語(ELF)の理念を取り入れ認識を深めてもらうことへの障壁と、それに対する解決策を論じる。中等教育に携わる日本人英語教師の教師教育における学習ガイドラインおよびモデルである全国共通「コア・カリキュラム」では、ELFに対して比較的前向きな見解を示している。一方で、ELFの観点を教師教育プログラムに取り入れることは優先順位が低いと考えられている。最近の文献では、ELFを意識したカリキュラム考案の障壁が調査されており、教師がELFに基づいたアクション・リサーチを行うことを提案している。それにより、教師が批判的な視点でELFを捉えることを促し、また、教師の信念をより大きく変革するアプローチを促進するための洞察が得られるであろう。結論として、ELFを意識した教師教育プログラムをより効果的かつ革新的に実施するためには、現在の英語の使用状況や言語教育に関して幅広く見ていくことが重要である。

Conflict capability e mediazione: un approccio preventivo alla radicalizzazione e ai comportamenti antisociali in contesti familiari e microsociali

Understanding conflict dynamics among individuals and within society, and devising appropriate intervention strategies offer a relevant perspective for the prevention of radicalization processes. The article outlines an overview of some concrete instruments of analysis and intervention in microsocial conflicts, with special reference to family. We choose as a starting point the notion of “conflict capability”, the ability of human beings of appropriately handling conflict.The model presented here is based on a systemic understanding of social conflict and a transformative approach to foster human capabilities, and specifically women, of dealing with conflict. Friedrich Glasl’s “escalation model” offers a solid foundation in order to define conflict dynamics which is crucial for devising appropriate, context-specific interventions. For the family and microsocial context, we propose as intervention tools empathic communication and “problem solving without losers” proposed by Thomas Gordon, as well as a “systemic transformative” approach to mediation. The article also reflects on the importance of conflict capability in order to reinforce the practice of democracy, building on the contribution of authors such as Chantal Mouffe and Axel Honneth.

Health promotion for immigrant mothers of children with developmental disabilities: Towards a transformative approach

Background: High societal expectations that involve idealized and labour-intensive mothering are a source of stress, anxiety, guilt and frustration for women. Immigrant mothers caring for children with developmental disabilities are disproportionately burdened with health inequities. Study goals: The overall goal of our study was to examine health promotion practices of immigrant mothers with children with developmental disabilities using the Health Promotion Activities Scale (HPAS). Methods: Twenty-eight mothers of children with developmental disabilities were interviewed using the HPAS. A grounded theory approach was utilized to analyze the qualitative data. Results: Immigrant mothers of children with developmental disabilities’ engagement in health promoting activities is influenced by their role as primary caregivers, the gendered nature of mothering, non-Western views on health promotion, mothers’ burden from inequities and structural barriers pertaining to funding, disability, and migration status. The responses on the HPAS also underscore motherhood as a social construct with embedded assumptions and social expectations related to role and responsibilities that requires them to be “good” mothers. Discussion and Conclusion: There is need to incorporate transformative health promotion approaches in research and practice that consider mothers’ multicultural contexts. The intersections of motherhood, disability, gendered role expectations and migration need to be taken into account.

“I Assumed It Was a Much Safer Place Than It Really Is”: Nonbinary Educators’ Strategies for Finding School Jobs

People who are nonbinary—one of many kinds of trans identity that do not fit neatly within a man/woman binary—face particular challenges when seeking employment in P–12 schools, which have historically been places where rigid gender norms are strictly enforced. This paper draws on semistructured interviews conducted in 2018 to explore how 16 nonbinary educators navigated the process of finding, securing, and keeping jobs in Canadian and American schools. I found that most participants were concerned about securing a job or potentially losing their job or their safety at work because others might be inhospitable to their gender identity or expression. At the same time, participants had strategies to ensure that they found and kept jobs they were comfortable with, such as investigating a school’s support for queer and trans people, forging positive relationships with administrators and staff, and presenting their gender in particular ways during the hiring process. This study illustrates the limitations of individualistic, tokenizing forms of trans inclusion and reveals the continued prevalence of gender normativity in schools, despite a rapidly shifting gender landscape. While trans inclusion, at least on the surface, may be a selling point for some schools, trans people continue to face barriers when the underlying structures that privilege White, middle-class, cisgender, and heteronormative gender expression remain intact. I argue that, if trans people are to be fully supported in the education workplace, an intersectional and broadly transformative approach to gender justice is necessary.