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Biological soil crusts represent a rich habitat for diverse and complex eukaryotic microbial communities. A unique but extremely common habitat is the urban sidewalk and its cracks that collect detritus. While these habitats are ubiquitous across the globe, little to no work has been conducted to characterize protists found there. Amoeboid protists are major predators of bacteria and other microbial eukaryotes in these microhabitats and therefore play a substantial ecological role. From sidewalk crack soil crusts, we have isolated three naked amoebae with finely tapered subpseudopodia, and a simple life cycle consisting of a trophic amoeba and a cyst stage. Using a holistic approach including light, electron, and fluorescence microscopy as well as phylogenetics using the ribosomal small subunit rRNA gene and phylogenomics using 230 nuclear genes, we find that these amoeboid organisms fail to match any previously described eukaryote genus. However, we determined the amoebae belong to the amoebozoan lineage Variosea based on phylogenetics. The molecular analyses place our isolates in two novel genera forming a grade at the base of the variosean group Protosteliida. These three novel varioseans among two novel genera and species are herein named “Kanabo kenzan” and “Parakanabo toge.”

 

PhyloFisher is a software package written primarily in Python3 that can be used for the creation, analysis, and visualization of phylogenomic datasets that consist of protein sequences from eukaryotic organisms. Unlike many existing phylogenomic pipelines, PhyloFisher comes with a manually curated database of 240 protein‐coding genes, a subset of a previous phylogenetic dataset sampled from 304 eukaryotic taxa. The software package can also utilize a user‐created database of eukaryotic proteins, which may be more appropriate for shallow evolutionary questions. PhyloFisher is also equipped with a set of utilities to aid in running routine analyses, such as the prediction of alternative genetic codes, removal of genes and/or taxa based on occupancy/completeness of the dataset, testing for amino acid compositional heterogeneity among sequences, removal of heterotachious and/or fast‐evolving sites, removal of fast‐evolving taxa, supermatrix creation from randomly resampled genes, and supermatrix creation from nucleotide sequences. © 2024 Wiley Periodicals LLC.

Basic Protocol 1: Constructing a phylogenomic dataset

Basic Protocol 2: Performing phylogenomic analyses

Support Protocol 1: Installing PhyloFisher

Support Protocol 2: Creating a custom phylogenomic database

 

Multiple studies report the benefits of authentic research experiences in STEM education. While most of them focus either on course-based research projects or on undergraduate students’ experiences, few document authentic learning experiences unfolding in real time among and between graduate students in research laboratories. Therefore, we situate our study in the context of authentic research experiences in research laboratories and focus on documenting learning processes as they unfold during daily practices in the laboratories. Specifically, the goal of our study is to observe and document how graduate students, and other lab members, learn from one another within the cultural space of the laboratory, and what aspects of laboratory culture facilitate and what impede learning. To that end, we use cognitive ethnography, an ethnographic approach combined with cognitive science to study cognitive processes through participant-observation of two engineering research laboratories. We identified the following themes pertaining to learning experiences: scaffolding (structured activities or apprenticeship), peer-to-peer learning, self-directed and self-regulated learning, and independence in research activities. While in many respects the two laboratories are similar, the presence and role of a leader-mentor in daily activities is what set them apart. In this report, we analyze the impact of leadership-mentorship on learning and professional formation. We argue that the degree to which a leader-mentor is consistently active in the laboratory’s life presents advantages and disadvantages with respect to different aspects of learning and professional formation. On one hand, professional development of students may be hindered by the absence of direct oversight from an in-laboratory professional mentor, resulting in delayed graduation for example. On another, absence of direct oversight can compel students to independently seek out mentors who have important expertise to help complete projects in a timely manner, an important professional skill. In the first case, students benefit from the expertise of mentors, so having mentors consistently present in the laboratory helps students efficiently conduct their projects. In the second case, students learn that they cannot always rely on only one person to provide direction and will need to seek help from other quarters. 

Protosteloid amoebae are a paraphyletic assemblage of amoeboid protists found exclusively in the eukaryotic assemblage Amoebozoa. These amoebae can facultatively form a dispersal structure known as a fruiting body, or more specifically, a sporocarp, from a single amoeboid cell. Sporocarps consist of one to a few spores atop a noncellular stalk. Protosteloid amoebae are known in two out of three well-established major assemblages of Amoebozoa. Amoebae with a protosteloid life cycle are known in the major Amoebozoa lineages Discosea and Evosea but not in Tubulinea. To date, only one genus, which is monotypic, lacks sequence data and, therefore, remains phylogenetically homeless. To further clarify the evolutionary milieu of sporocarpic fruiting we used single-cell transcriptomics to obtain data from individual sporocarps of isolates of the protosteloid amoeba Microglomus paxillus. Our phylogenomic analyses using 229 protein coding markers suggest that M. paxillus is a member of the Discosea lineage of Amoebozoa most closely related to Mycamoeba gemmipara. Due to the hypervariable nature of the SSU rRNA sequence we were unable to further resolve the phylogenetic position of M. paxillus in taxon rich datasets using only this marker. Regardless, our results widen the known distribution of sporocarpy in Discosea and stimulate the debate between a single or multiple origins of sporocarpic fruiting in Amoebozoa. 

An experiment was performed to investigate a modified pooling method for use in convolutional neural networks for image recognition. This algorithm–Variable Stride–allows the user to segment an image and change the amount of subsampling in each region. This control allows for the user to maintain a higher amount of data retention in more important regions of the image, while more aggressively subsampling the less important regions to increase training speed. Three Variable Stride methods were compared to the preexisting pooling algorithms, Maximum Pool and Average Pool, in three different network configurations tasked with classifying Diabetic Retinopathy images between its early and advanced stages. Each combination was run multiple times and the AUC, Validation Loss, Validation Accuracy, and number of training epochs until convergence of each run was all collected. Maximum Pool and Average Pool were both found to be superior to Variable Stride when deployed in these scenarios. 

How has recent AI Ethics literature addressed topics such as fairness and justice in the context of continued social and structural power asymmetries? We trace both the historical roots and current landmark work that have been shaping the field and categorize these works under three broad umbrellas: (i) those grounded in Western canonical philosophy, (ii) mathematical and statistical methods, and (iii) those emerging from critical data/algorithm/information studies. We also survey the field and explore emerging trends by examining the rapidly growing body of literature that falls under the broad umbrella of AI Ethics. To that end, we read and annotated peer-reviewed papers published over the past four years in two premier conferences: FAccT and AIES. We organize the literature based on an annotation scheme we developed according to three main dimensions: whether the paper deals with concrete applications, use-cases, and/or people’s lived experience; to what extent it addresses harmed, threatened, or otherwise marginalized groups; and if so, whether it explicitly names such groups. We note that although the goals of the majority of FAccT and AIES papers were often commendable, their consideration of the negative impacts of AI on traditionally marginalized groups remained shallow. Taken together, our conceptual analysis and the data from annotated papers indicate that the field would benefit from an increased focus on ethical analysis grounded in concrete use-cases, people’s experiences, and applications as well as from approaches that are sensitive to structural and historical power asymmetries. 

Electronic waste is a global issue brought about by the short lifespan of electronics. Viable methods to relieve the inundated disposal system by repurposing the enormous amount of electronic waste remain elusive. Inspired by the need for sustainable solutions, this study resulted in a multifaceted approach to upcycling compact discs. The once-ubiquitous plates can be transformed into stretchable and flexible biosensors. Our experiments and advanced prototypes show that effective, innovative biosensors can be developed at a low-cost. An affordable craft-based mechanical cutter allows pre-determined patterns to be scored on the recycled metal, an essential first step for producing stretchable, wearable electronics. The active metal harvested from the compact discs was inert, cytocompatible, and capable of vital biopotential measurements. Additional studies examined the material’s resistive emittance, temperature sensing, real-time metabolite monitoring performance, and moisture-triggered transience. This sustainable approach for upcycling electronic waste provides an advantageous research-based waste stream that does not require cutting-edge microfabrication facilities, expensive materials, and high-caliber engineering skills.