How can we biochemically validate protein function predictions with the deoxycytidine kinase family? - Associated data

<p>This is the data that accompanies the pub "<a href="https://doi.org/10.57844/arcadia-1e5d-e272">How can we biochemically validate ProteinCartography with the deoxycytydine kinase family?</a>" It's part of a group of pubs focused on validating ProtienCartography that begins with "<a href="https://doi.org/10.57844/arcadia-cae9-96c4">A strategy to validate protein functions <em>in vitro</em></a><a href="https://doi.org/10.57844/arcadia-cae9-96c4">." </a></p> <p>For this repository, we ran ProteinCartography <a href="https://github.com/Arcadia-Science/ProteinCartography/releases/tag/v0.5.0">v0.5.0</a> on the deoxycytidine kinase (dCK) using human dCK as our input (UniProt ID: <a href="https://www.uniprot.org/uniprotkb/P27707/entry">P27707</a>). We asked for 3,000 Foldseek hits and 7,000 BLAST hits for a total of 10,000 structures. The updated configuration file is in the zipped folder in this repository. Also included in the zipped folder are the inputs, structures of all hits, and all ProteinCartography results. </p> <p>Finally, we created a custom overlay for the protein map using this <a href="https://github.com/Arcadia-Science/2023-actin-embedding/blob/main/notebooks/3_plotting_overlays.ipynb">notebook</a> and the manually annotated TSV file in this repository, where we denoted which group of substrates a protein is predicted to act on based on its annotation from UniProt.</p&gt

A strategy to validate protein function predictions in vitro - accompanying data

<p>This repository contains the ProteinCartography analyses that accompany the pub "<a href="https://doi.org/10.57844/arcadia-cae9-96c4">A strategy to validate protein function predictions <em>in vitro</em></a><a href="https://doi.org/10.57844/arcadia-cae9-96c4">."</a> These proteins were selected from a list of the 200 most studied human proteins in the Protein Data Bank (PDB) which was published in <a href="https://onlinelibrary.wiley.com/doi/10.1002/pro.4038">Liu and Buck, 2021</a>. </p> <p>Each analysis was done using <a href="https://github.com/Arcadia-Science/ProteinCartography/releases/tag/v0.5.0">v0.5.0</a> of ProteinCartography using the standard configuration parameters. Each analysis is in its own zipped file corresponding to the protein name. The zipped files contain inputs, configuration files, all the structures, and all ProteinCartography results. Additionally, for a handful of the proteins, we ran a scaled-up version of ProteinCartography asking for 10,000 hit proteins instead of the standard. These are also included with the file prefix "Scaled-up_". </p> <p>Finally, we've decided to move forward with 2 protein families for validation of our tool, ProteinCartography. These protein families are <a href="https://doi.org/10.57844/arcadia-1e5d-e272">deoxycytidine kinase</a> and <a href="https://doi.org/10.57844/arcadia-74ad-345f">Ras GTPase</a>. For more about these two protein families, visit the mentioned pubs! </p&gt

How can we biochemically validate protein function predictions with the Ras GTPase family? - Associated data

<p>This is the data that accompanies the pub "<a href="https://doi.org/10.57844/arcadia-74ad-345f">How can we biochemically validate ProteinCartography with the Ras GTPase family?</a>" It's part of a group of pubs focused on validating ProtienCartography that begins with "<a href="https://doi.org/10.57844/arcadia-cae9-96c4">A strategy to validate protein functions <em>in vitro</em></a><a href="https://doi.org/10.57844/arcadia-cae9-96c4">." </a></p> <p>For this repository, we ran ProteinCartography <a href="https://github.com/Arcadia-Science/ProteinCartography/releases/tag/v0.5.0">v0.5.0</a> using human HRas and KRas as our inputs for a single run (UniProt ID: <a href="https://www.uniprot.org/uniprotkb/P01112/entry">P01112</a> and <a href="https://www.uniprot.org/uniprotkb/P01116/entry">P01116</a>). We asked for 3,000 Foldseek hits and 7,000 BLAST hits for a total of 10,000 structures. The updated configuration file is in the zipped folder in this repository. Also included in the zipped folder are the inputs, structures of all hits, and all ProteinCartography results. </p> <p>Finally, we created a custom overlay for the protein map using this <a href="https://github.com/Arcadia-Science/2023-actin-embedding/blob/main/notebooks/3_plotting_overlays.ipynb">notebook</a> and the manually annotated TSV file in this repository, where we denoted which group of substrates a protein is predicted to act on based on its annotation from UniProt.</p&gt

The treatise on the astrolabe;

"Appendix: reprints of papers on the astronomy of Chaucer in 'The Canterbury tales' with additional notes; essays: On the meaning of Chaucer's prime, On the Carrenare, On shippes opposteres": p. [63]-108.Mode of access: Internet

Far From Home: An Examination of the Juvenile Visitation Experience and the Barriers to Getting There

Despite a growing body of research on prison visitation, very few studies have examined visitation among committed juvenile offenders. As a result, we have little understanding of how youth experience visits and why some never receive them. This article fills these gaps. Using surveys collected from 1,202 youth released from residential facilities in Florida, we found that among youth who were visited, they had positive experiences with visits and that families went to great lengths to visit. For those youth who were not visited, the most common barrier was distance from home. However, some youth were not visited because they refused visits or because families withheld visits as punishment. Moreover, despite the possibility that lack of visitation is harmful, we found that most not-visited youth had positive perceptions of their future success. Policy implications and directions for research are discussed. </jats:p

The elusive actin cytoskeleton of a green alga expressing both conventional and divergent actins

The green alga Chlamydomonas reinhardtii is a leading model system to study photosynthesis, cilia, and the generation of biological products. The cytoskeleton plays important roles in all of these cellular processes, but to date, the filamentous actin network within Chlamydomonas has remained elusive. By optimizing labeling conditions, we can now visualize distinct linear actin filaments at the posterior of the nucleus in both live and fixed vegetative cells. Using in situ cryo-electron tomography, we confirmed this localization by directly imaging actin filaments within the native cellular environment. The fluorescently labeled structures are sensitive to the depolymerizing agent latrunculin B (Lat B), demonstrating the specificity of our optimized labeling method. Interestingly, Lat B treatment resulted in the formation of a transient ring-like filamentous actin structure around the nucleus. The assembly of this perinuclear ring is dependent upon a second actin isoform, NAP1, which is strongly up-regulated upon Lat B treatment and is insensitive to Lat B–induced depolymerization. Our study combines orthogonal strategies to provide the first detailed visual characterization of filamentous actins in Chlamydomonas, allowing insights into the coordinated functions of two actin isoforms expressed within the same cell.</jats:p

Are Adverse Childhood Experiences Associated With Deficits in Self-Control? A Test Among Two Independent Samples of Youth

A large body of research links both a lack of self-control and adverse childhood experiences (ACEs) to a variety of negative health and behavior outcomes, including delinquent and criminal behavior. To date, relatively little research considers whether experiencing a greater variety of ACEs is associated with lower self-control. We advance this area of research by first articulating potential mechanisms through which ACEs may impact self-control. We then investigate whether experiencing more ACEs is inversely associated with self-control in separate samples of youth from Michigan and Florida. For both samples, results indicate that experiencing a greater variety of ACEs is negatively associated with self-control. Exploratory analyses also indicate that ACEs reflecting interpersonal maltreatment are more strongly associated with deficits in self-control than ACEs pertaining to aspects of household dysfunction.</jats:p

Online_Supplementary_Appendix_A – Supplemental material for Are Adverse Childhood Experiences Associated With Deficits in Self-Control? A Test Among Two Independent Samples of Youth

Supplemental material, Online_Supplementary_Appendix_A for Are Adverse Childhood Experiences Associated With Deficits in Self-Control? A Test Among Two Independent Samples of Youth by Ryan C. Meldrum, Brae Campion Young, Sadhika Soor, Carter Hay, Jennifer E. Copp, Madison Trace, Joanne P. Smith-Darden and Poco D. Kernsmith in Criminal Justice and Behavior</p

Management of Uveal Melanoma: Updated Cancer Care Alberta Clinical Practice Guideline

Objective: The purpose of this guideline update is to reassess and update recommendations in the prior guideline from 2016 on the appropriate management of patients with uveal melanoma. Methods: In 2021, a multidisciplinary working group from the Provincial Cutaneous Tumour Team, Cancer Care Alberta, Alberta Health Services was convened to update the guideline. A comprehensive review of new research evidence in PubMed as well as new clinical practice guidelines from prominent oncology groups informed the update. An enhancement in methodology included adding levels of evidence and strength of recommendations. The updated guideline was circulated to all members of the Provincial Cutaneous Tumour Team for review and endorsement. Results: New and modified recommendations address provider training requirements, diagnostic imaging for the detection of metastases, neo-adjuvant pre-enucleation radiotherapy, intravitreal anti-vascular endothelial growth factor agents for radiation retinopathy, genetic prognostic testing, surveillance following definitive local therapy, and systemic therapy for patients with metastatic uveal melanoma. Discussion: The recommendations represent evidence-based standards of care agreed to by a large multidisciplinary group of healthcare professionals