Critical assessment of pan-genomics of metagenome-assembled genomes

Background: Large scale metagenome assembly and binning to generate metagenome-assembled genomes (MAGs) has become possible in the past five years. As a result, millions of MAGs have been produced and increasingly included in pan-genomics workflow. However, pan-genome analyses of MAGs may suffer from the known issues with MAGs: fragmentation, incompleteness, and contamination, due to mis-assembly and mis-binning. Here, we conducted a critical assessment of including MAGs in pan-genome analysis, by comparing pan-genome analysis results of complete bacterial genomes and simulated MAGs. Results: We found that incompleteness led to more significant core gene loss than fragmentation. Contamination had little effect on core genome size but had major influence on accessory genomes. The core gene loss remained when using different pan-genome analysis tools and when using a mixture of MAGs and complete genomes. Importantly, the core gene loss was partially alleviated by lowering the core gene threshold and using gene prediction algorithms that consider fragmented genes, but to a less degree when incompleteness was higher than 5%. The core gene loss also led to incorrect pan-genome functional predictions and inaccurate phylogenetic trees. Conclusions: We conclude that lowering core gene threshold and predicting genes in metagenome mode (as Anvio does with Prodigal) are necessary in pan-genome analysis of MAGs to alleviate the accuracy loss. Better quality control of MAGs and development of new pan-genome analysis tools specifically designed for MAGs are needed in future studies.

Comment on “Evidence of humans in North America during the Last Glacial Maximum”

Bennett et al . (Reports, 24 September 2021, p. 1528) report human footprints from Lake Otero, New Mexico, USA ~22,000 years ago. Critical assessment suggests that their radiocarbon chronology may be inaccurate. Reservoir effects may have caused radiocarbon ages to appear thousands of years too old. Independent verification of the ages of the footprint horizons is imperative and is possible through other means.

A Critical Assessment of Pertinent Locus Standi Features of the Derivative Remedy under Zimbabwe's New Companies and Other Business Entities Act

The importance and contribution of derivative litigation to the effectiveness and credibility of a jurisdiction's corporate governance system is indisputable. There is a positive correlation between good corporate governance practices, which include shareholders’ rights, and investors’ return on their investments. On the one hand, an overly pro-shareholder derivative scheme is vulnerable to abuse and results in unnecessary interference with company management. This may, in turn, discourage directors from entrepreneurial risk-taking and undermine enterprise efficiency. On the other hand, a complex and ineffective system of derivative litigation protects errant directors and decreases investor confidence. This article is a critical assessment of Zimbabwe's recently adopted statutory derivative remedy. The analysis focuses on five locus standi-related aspects of the new statutory derivative regime. The article highlights some major weaknesses within Zimbabwe's statutory remedy and proposes pertinent legislative amendments.

The Simplification of Procedures in Portuguese Administrative Law

The present paper intends to provide an overview and a critical assessment of the administrative simplification policies implemented in Portugal over the past 20+ years. Throughout these decades, the major instruments for administrative simplification have been: (i) Decree-Law n. 135/99, of 22 April; (ii) the Simplex programme; (iii) the 2015 new Code of Administrative Procedure and its 2021 amendment; and (iv) the COVID-19 legislation. Although Decree-Law n. 135/99 (i) was the first attempt to specifically address simplification, it was a very thin one. The Simplex programme (ii), created in 2006, was the first cross-sectoral robust policy of simplification; its motto is “the simpler the better” and it encompassed reforms in all government areas aiming at cutting red tape, promoting administrative efficiency, and making the citizens’ and the corporations’ lives easier when dealing with State. The new Code of Administrative Procedure (iii), approved in 2015, brought about specific normative solutions to simplify procedures, namely, prior communications, administrative assistance, procedural conferences, and the electronic one-stop shop. Finally, the COVID-19 legislation (iv) was made necessary by the COVID-19 pandemic and by the fact that public health restrictions made it impossible for citizens to establish personal contact with the administration in many cases.

Self-Criticism in In-Work Poverty: The Mediating Role of Social Support in the Era of Flexibility

In-work poverty reflects situations of income below the poverty threshold among employed people, involving a deterioration of wellbeing. The International Labour Organization prioritises this situation, which in countries such as Spain, Germany or Italy reaches rates of 11.8%, 10.6% and 11.8%, respectively. Within a context of flexibility, the occupational situation tends to be understood as an individual responsibility, which is why this study analyses the increase in self-criticism in these situations, and the role of social support in this relationship. The mediation of social support in the manifestation of self-criticism among people experiencing in-work poverty is analysed. The participants were 1430 employed people, grouped into those in a situation of poverty and those who are not. The results show that people in a situation of in-work poverty present a higher score in self-criticism and lower in social support. Social support is a mediating variable that prevents the manifestation of self-criticism. Lastly, a gender analysis shows that women experience this relationship more intensely. These findings enable a critical assessment of the activation policies that only take an individual approach. As an alternative, we propose strengthening interventions that foster social support, particularly among women.

Immigrants on Chinese Television and Limitations of China’s Globalist Discourse

Traditionally perceived as a country of emigration, China has in recent years become an increasingly popular subject for immigration and diaspora studies, with an immigrant population that has been growing quietly and steadily since the 1990s. However, media representations of immigrants in China have not garnered much attention. This article provides a critical assessment of how immigrants and immigrant experience are portrayed on Chinese television, using the example of Foreigner in China (2013–19), the first-ever program on a national platform to tackle this topic. It argues that, while the program paints a rather insightful and entertaining picture of contemporary immigrant life in China, its representation of immigrants is restricted by not only the internal contradiction of the Xi administration’s globalist discourse, but also the exclusive, ethnocentric conception of Chinese nationhood, which remains the norm in a more heterogenous and globally conscious Chinese society.

An Inclusive Teaching Program From the Socio-Intercultural Entrepreneurship Approach

This chapter aims to elaborate a critical assessment of socio-intercultural entrepreneurship. The study is supported on the assumption that culture and social entrepreneurship are limited and that a framework analysis that helps to improve the understanding of the socio-economic realities is necessary. The research methodology employed were the exploratory and analytical instruments based on literature review and the transference of findings to a specific case on a postgraduate program in economy and international business at the Autonomous Indigenous University of Mexico. It's concluded that socio-intercultural entrepreneurship presents a methodological frame that allows entrepreneurs to have a major perception of global and local realities.

Critical assessment of genome-scale metabolic models of Arabidopsis thaliana

Genome-scale metabolic models (GSMMs) have enabled researchers to perform systems-level studies of living organisms. As a constraint-based technique, flux balance analysis (FBA) aids computation of reaction fluxes and prediction of...

Conceptualising fairness: three pillars for medical algorithms and health equity

ObjectivesFairness is a core concept meant to grapple with different forms of discrimination and bias that emerge with advances in Artificial Intelligence (eg, machine learning, ML). Yet, claims to fairness in ML discourses are often vague and contradictory. The response to these issues within the scientific community has been technocratic. Studies either measure (mathematically) competing definitions of fairness, and/or recommend a range of governance tools (eg, fairness checklists or guiding principles). To advance efforts to operationalise fairness in medicine, we synthesised a broad range of literature.MethodsWe conducted an environmental scan of English language literature on fairness from 1960-July 31, 2021. Electronic databases Medline, PubMed and Google Scholar were searched, supplemented by additional hand searches. Data from 213 selected publications were analysed using rapid framework analysis. Search and analysis were completed in two rounds: to explore previously identified issues (a priori), as well as those emerging from the analysis (de novo).ResultsOur synthesis identified ‘Three Pillars for Fairness’: transparency, impartiality and inclusion. We draw on these insights to propose a multidimensional conceptual framework to guide empirical research on the operationalisation of fairness in healthcare.DiscussionWe apply the conceptual framework generated by our synthesis to risk assessment in psychiatry as a case study. We argue that any claim to fairness must reflect critical assessment and ongoing social and political deliberation around these three pillars with a range of stakeholders, including patients.ConclusionWe conclude by outlining areas for further research that would bolster ongoing commitments to fairness and health equity in healthcare.