Integrative analysis of relative abundance data and presence-absence data of the microbiome using the LDM

We previously developed LDM for testing hypotheses about the microbiome that performs the test at both the community level and the individual taxon level. LDM can be applied to relative abundance data and presence-absence data separately, which work well when associated taxa are abundant and rare, respectively. Here we propose an omnibus test based on LDM that allows simultaneous consideration of data at different scales, thus offering optimal power across scenarios with different association mechanisms. The omnibus test is available for the wide range of data types and analyses that are supported by LDM. The omnibus test has been added to the R package LDM, which is available on GitHub at https://github.com/yijuanhu/LDM .

Speculation Made Material: Experimental Archaeology & Maker’s Knowledge

Experimental archaeology is often understood both as testing hypotheses about processes shaping the archaeological record and as generating tacit knowledge. Considering lithic technologies, I examine the relationship between these conceptions. Experimental archaeology is usefully understood via ‘maker’s knowledge’: archaeological experiments generate embodied know-how enabling archaeological hypotheses to be grasped and challenged, further well-positioning archaeologists to generate integrated interpretations. Finally, experimental archaeology involves ‘material speculation’: the constraints and affordances of archaeologists and their materials shape productive exploration of the capacities of objects and human skill in ways relevant to archaeological questions.

Dataset of antiarch placoderms (the most basal jawed vertebrates) throughout Middle Paleozoic

Antiarch placoderms, the most basal jawed vertebrates, have the potential to enlighten the origin of the last common ancestor of jawed vertebrates. Quantitative study based on credible data is more convincing than qualitative study. To reveal the antiarch distribution in space and time, we created a comprehensive structured dataset of antiarchs comprising 64 genera and 6025 records. This dataset, which includes associated chronological and geographic information, has been digitalized from academic publications manually into the DeepBone database as a dateset. We implemented the paleogeographic map marker to visualize the biogeography of antiarchs. The comprehensive data of Antiarcha allow us to generate its biodiversity and variation rate changes throughout its duration. Structured data of antiarchs has tremendous research potential, including testing hypotheses in the fields of the biodiversity changes, distribution, differentiation,population and community composition. Also, it will be easily accessible by the other tools to generate new understanding on the evolution of early vertebrates. The data file described in this paper is available on https://doi.org/10.5281/zenodo.5639529 (Pan and Zhu, 2021).

Testing hypotheses about the harm that capitalism causes to the mind and brain: a theoretical framework for neuroscience research

This article reviews and discusses the part of neuroscience relevant to mental health within the contemporary capitalist context, and suggests ways in which the effects of this context on the nervous system can be reconceptualised and researched in the future. Firstly, the principal components of neoliberal capitalism are presented together with how it has historically influenced neuroscience. We then argue in favour of a neurodiversity perspective, as opposed to the dominant model of conceptualising neural (mal-)functioning, brain plasticity and potential for change and adaptation. We review the available empirical research indicating that the socio-economic environment is harmful to minds and brains. Lastly, we set out a theoretical framework that can generate neuroscientific hypotheses with regards to the effects of the capitalist context on brains and minds, as well as a frame for post-capitalist research.

An Early Framework for a Cognitive Neuroscience of Visual Aesthetics

In the early 2000s, no framework within which to investigate the biology of aesthetics had been articulated. The author believes that a componential framework, as was common in cognitive psychology, applied to neuroaesthetics made sense. Such frameworks were commonly applied to complex cognitive domains, such as in language, emotion processing, or visual processing research. As such, the author proposes a “box and arrow” model which incorporated levels of visual processing, emotions, attention, and decision-making. The advantage of such a framework is that specific experiments could be placed in the context of testing hypotheses of parts of a larger system deployed for aesthetic processing. The framework has held up well over the years, although the author believes he did not sufficiently emphasize the role of the motor system and the rich contribution of semantics in aesthetic experiences.

Arrested Friendships? Justice Involvement and Interpersonal Exclusion among Rural Youth

Objectives: We examine the impacts of adolescent arrest on friendship networks. In particular, we extend labeling theory by testing hypotheses for three potential mechanisms of interpersonal exclusion related to the stigma of arrest: rejection, withdrawal, and homophily. Method: We use longitudinal data on 48 peer networks from PROSPER, a study of rural youth followed through middle and high school. We test our hypotheses using stochastic actor–based models. Results: Our findings suggest that arrested youth are less likely to receive friendship ties from school peers and are also less likely to extend them. Moreover, these negative associations are attenuated by higher levels of risky behaviors among peers, suggesting that results are driven by exclusion from normative rather than nonnormative friendships. We find evidence of homophily on arrest but it appears to be driven by other selection mechanisms rather than a direct preference for similarity on arrest. Conclusions: Overall, our findings speak to how an arrest may foster social exclusion in rural schools, thereby limiting social capital for already disadvantaged youth.