The Digital-Forward Writing Course

First-year writing and composition courses can be major roadblocks for students as their success in later courses often hinges on their abilities to construct a quality written document. Students enter composition courses with broad variation in their abilities and yet must all meet the same standards of completion. In order to address this inequity, greater opportunities for writing and in receiving feedback are paramount. Yet such opportunities would place a high burden on writing instructors in a traditional course. This chapter proposes the digital-forward writing course that draws on a combination of a number of digital tools and pedagogical strategies that can increase writing opportunities while maintaining or even reducing instructors' time commitment. This information is drawn from a workshop held in 2020 that asked writing instructors, instructional designers, developers, and other educators to ideate on meeting the challenges of the entire student writing journey. Specific tools and a discussion of the value of adaptive courseware are included.

The life cycle in late Paleozoic eryopid temnospondyls: developmental variation, plasticity and phylogeny

Eryopid temnospondyls were large apex predators in Carboniferous and Permian stream and lake habitats. The eryopid life cycle is exemplified by Onchiodon labyrinthicus from Niederhäslich (Saxony, Germany), which is represented by numerous size classes from small larvae to heavily ossified adults. Morphometric and principal component analyses provide new insights into ontogenetic changes in O. labyrinthicus, and comparison with adults of other eryopids documents phylogenetic patterns in the occupation of morphospace. Compared with small specimens of Sclerocephalus spp., immature O. labyrinthicus occupies a neighboring but much larger space, corresponding to a broader range of variation. Adults of Actinodon frossardi map with some juveniles of O. labyrinthicus, whereas other juveniles of the latter lie close to adults of O. thuringiensis, Glaukerpeton avinoffi and Osteophorus roemeri. Morphospace occupation of adult eryopids is partly consistent with cladistic tree topology, which gives the following branching pattern: Actinodon frossardi forms the basalmost eryopid, followed by Osteophorus roemeri, Glaukerpeton avinoffi and the genus Onchiodon (O. labyrinthicus + O. thuringiensis); then Clamorosaurus nocturnus; and finally the monophyletic genus Eryops. The presumably juvenile skull of Eryops anatinus falls well outside the domains of both adult eryopids and immature O. labyrinthicus, showing a unique combination of juvenile and adult features. Instead, Onchiodon langenhani and the Ruprechtice specimens referred to O. labyrinthicus map within the domain of immature O. labyrinthicus. Raised levels of variation in O. labyrinthicus coincide with evidence of a stressed habitat, in which limiting factors were fluctuating salinity, absence of fishes, enhanced competition and seasonal algal blooms. The documented broad variation was possibly caused by developmental plasticity responding to fluctuations in lake hydrology and nutrients in this small, short-lived water body.

Predicting base editing outcomes with an attention-based deep learning algorithm trained on high-throughput target library screens

Base editors are chimeric ribonucleoprotein complexes consisting of a DNA-targeting CRISPR-Cas module and a single-stranded DNA deaminase. They enable transition of C•G into T•A base pairs and vice versa on genomic DNA. While base editors have great potential as genome editing tools for basic research and gene therapy, their application has been hampered by a broad variation in editing efficiencies on different genomic loci. Here we perform an extensive analysis of adenine- and cytosine base editors on a library of 28,294 lentivirally integrated genetic sequences and establish BE-DICT, an attention-based deep learning algorithm capable of predicting base editing outcomes with high accuracy. BE-DICT is a versatile tool that in principle can be trained on any novel base editor variant, facilitating the application of base editing for research and therapy.

A Low Dark Current 160 dB Logarithmic Pixel with Low Voltage Photodiode Biasing

Extending CMOS Image Sensors’ dynamic range is of fundamental importance in applications, such as automotive, scientific, or X-ray, where a broad variation of incoming light should be measured. The typical logarithmic pixels suffer from poor performance under low light conditions due to a leakage current, usually referred to as the dark current. In this paper, we propose a logarithmic pixel design capable of reducing the dark current through low-voltage photodiode biasing, without introducing any process modifications. The proposed pixel combines a high dynamic range with a significant improvement in the dark response compared to a standard logarithmic pixel. The reported experimental results show this architecture to achieve an almost 35 dB improvement at the expense of three additional transistors, thereby achieving an unprecedented dynamic range higher than 160 dB.

Broad variation in rates of polyploidy and dysploidy across flowering plants is correlated with lineage diversification

Changes in chromosome number are considered an important driver of diversification in angiosperms. Single chromosome number changes caused by dysploidy may produce strong reproductive barriers leading to speciation. Polyploidy, or whole genome duplication, yields new species that are often reproductively isolated from progenitors and may exhibit novel morphology or ecology that may further facilitate diversification. Here, we examined the rates of polyploidy, dysploidy, and diversification across the angiosperms. Our analyses of nearly 30,000 taxa representing 46 orders and 147 families found that rates of polyploidy and dysploidy differed by two to three orders of magnitude. The rates of polyploidy and dysploidy were positively correlated with diversification rates, but relative importance analyses indicated that variation in polyploidy was better correlated with diversification rates than dysploidy. Our results provide an overview of angiosperm chromosomal evolution and a roadmap for future research on the complex relationships among polyploidy, dysploidy, and diversification.

The Geodiversity of Brazil: quantification, distribution, and implications for conservation areas

<p>Research related to the assessment of Geodiversity is highly relevant both at the international and national levels, especially in the last 20 years. These researches aim at valuing abiotic aspects as inseparable components of natural heritage and, thus, as well as Biodiversity, must be understood and valued through the ordering of their use and Geoconservation. Geodiversity studies are developed on the basis of several approaches, from the broadest ones, which contemplate the measurement of abiotic elements in a full way, to those that assess Geoheritage through the values ​​of Geodiversity. The present research follows the broader approach of the evaluation and analysis of the entire Geodiversity, applying the measurement of abiotic elements without their valuation, with the purpose of the spatialization of areas with greater and lesser density of the selected elements related in this research to lithology, relief and soil. For this purpose, bases produced by systematic surveys of national research institutions such as the Brazilian Institute of Geography and Statistics (IBGE) and the Geological Survey of Brazil (CPRM) were used. As a result, the mapping of the subindexes was obtained pointing from the division into 5 classes, the areas that present greater and lesser diversity of each element, as well as the synthesis map for the indexes of Geodiversity elements in Brazil, considering the three elements selected for this mapping. A spatial analysis was also carried out between the Geodiversity Index Map and the Brazilian Conservation Units, as well as the areas where Geopark Projects are being developed. The majority of the Brazilian territory presents low Geodiversity index (32%), followed by medium (28%), very low (17%), high (15%) and very high (8%). The higher indexes are found in ancient Orogenic Belts, associated with Crystalline Basement that shows broad variation of rocks, in some cases linked with soil and relief elements. Areas of medium diversity are concentrated in Cratons and Sedimentary Basins borders, and low diversity areas are found in the central regions of large Sedimentary Basins, as well as in the Pantanal Floodplain. The Conservation Units present the following percentage of Geodiversity index: very high: 12%; high:10%; medium 16%; low: 23%; very low 22%. The analysis was done taking into account the categories of Conservation Units as well, and the higher indexes were found in Natural Monuments and Wildlife Refuges (38 and 43% respectively). 8 geopark projects have predominance of very high and high Geodiversity indexes; 7 presents medium index and only one amongst the 16 presents predominance of low index. No geopark project has very low index predominant in territory. The analysis of the spatialization of the indexes was carried out from a descriptive and genetic perspective, aiming at clarifying the causes of the distribution of the abiotic elements in the Brazilian territory, being able to provide subindexes for studies in the scope of environmental services, nature and territory conservation planning.</p>

IUPACpal: efficient identification of inverted repeats in IUPAC-encoded DNA sequences

Background An inverted repeat is a DNA sequence followed downstream by its reverse complement, potentially with a gap in the centre. Inverted repeats are found in both prokaryotic and eukaryotic genomes and they have been linked with countless possible functions. Many international consortia provide a comprehensive description of common genetic variation making alternative sequence representations, such as IUPAC encoding, necessary for leveraging the full potential of such broad variation datasets. Results We present IUPACpal, an exact tool for efficient identification of inverted repeats in IUPAC-encoded DNA sequences allowing also for potential mismatches and gaps in the inverted repeats. Conclusion Within the parameters that were tested, our experimental results show that IUPACpal compares favourably to a similar application packaged with EMBOSS. We show that IUPACpal identifies many previously unidentified inverted repeats when compared with EMBOSS, and that this is also performed with orders of magnitude improved speed.

Lack of standardization in the use of road counts for surveying raptors

Examination of population trends for raptors is a research priority, especially given recent concern for their conservation status. Road counts—in which raptors are counted from a motorized vehicle moving along the ground—might be an effective method to expand the monitoring of raptor populations and estimation of trends. Here, we review past methods used to perform road counts of raptors and present revised recommendations to aid collaboration, data transfer, and interpretation of results across monitoring programs. We performed a standardized keyword search of online literature databases to obtain 148 past road count studies. The number of studies employing road counts increased per year since the 1970s. Most of these studies occurred in North America. The times of day during which road counts were conducted ranged from sunrise to sunset, and maximum speeds ranged from 10 to 113 km hr–1. The number of observers ranged from 1 (the driver) to 5. Most (93) of the studies used unlimited-width transects and fixed-width transects ranging from 0.02 to 2.50 km wide. Sixteen percent of studies calculated or corrected for the probability of detection. Such broad variation in the methodology used during road counts, coupled with infrequent correction for detection, hampers the interpretation of results across road survey programs. We suggest that road count practitioners should emphasize the collection of data, such as speed, number of observers, and distance to observed raptors, which would allow for the calculation of detection-corrected estimates. Such correction would likely improve trend estimation. Recent technology, including mobile apps, allows researchers to collect such data relatively easily, conducting their own studies while contributing to a broader raptor monitoring initiative. Road counts will likely become more useful as statistical analysis of road count data improves and researchers pool their data in a global effort to monitor raptors.