Critical assessment of protein intrinsic disorder prediction (CAID) - Results of round 2

Protein intrinsic disorder (ID) is a complex and context-dependent phenomenon that covers a continuum between fully disordered states and folded states with long dynamic regions. The lack of a ground truth that fits all ID flavors and the potential for order-to-disorder transitions depending on specific conditions makes ID prediction challenging. The CAID2 challenge aimed to evaluate the performance of different prediction methods across different benchmarks, leveraging the annotation provided by the DisProt database, which stores the coordinates of ID regions when there is experimental evidence in the literature. The CAID2 challenge demonstrated varying performance of different prediction methods across different benchmarks, highlighting the need for continued development of more versatile and efficient prediction software. Depending on the application, researchers may need to balance performance with execution time when selecting a predictor. Methods based on AlphaFold2 seem to be good ID predictors but they are better at detecting absence of order rather than ID regions as defined in DisProt. The CAID2 predictors can be freely used through the CAID Prediction Portal, and CAID has been integrated into OpenEBench, which will become the official platform for running future CAID challenges

CAID prediction portal: A comprehensive service for predicting intrinsic disorder and binding regions in proteins

Intrinsic disorder (ID) in proteins is well-established in structural biology, with increasing evidence for its involvement in essential biological processes. As measuring dynamic ID behavior experimentally on a large scale remains difficult, scores of published ID predictors have tried to fill this gap. Unfortunately, their heterogeneity makes it difficult to compare performance, confounding biologists wanting to make an informed choice. To address this issue, the Critical Assessment of protein Intrinsic Disorder (CAID) benchmarks predictors for ID and binding regions as a community blind-test in a standardized computing environment. Here we present the CAID Prediction Portal, a web server executing all CAID methods on user-defined sequences. The server generates standardized output and facilitates comparison between methods, producing a consensus prediction highlighting high-confidence ID regions. The website contains extensive documentation explaining the meaning of different CAID statistics and providing a brief description of all methods. Predictor output is visualized in an interactive feature viewer and made available for download in a single table, with the option to recover previous sessions via a private dashboard. The CAID Prediction Portal is a valuable resource for researchers interested in studying ID in proteins. The server is available at the URL: https://caid.idpcentral.org

Resistance effects due to magnetic guiding orbits

The Hall and magnetoresistance of a two dimensional electron gas subjected to a magnetic field barrier parallel to the current direction is studied as function of the applied perpendicular magnetic field. The recent experimental results of Nogaret {\em et al.} [Phys. Rev. Lett. {\bf 84}, 2231 (2000)] for the magneto- and Hall resistance are explained using a semi-classical theory based on the Landauer-B\"{u}ttiker formula. The observed positive magnetoresistance peak is explained as due to a competition between a decrease of the number of conducting channels as a result of the growing magnetic field, from the fringe field of the ferromagnetic stripe as it becomes magnetized, and the disappearance of snake orbits and the subsequent appearance of cycloidlike orbits.Comment: 7 pages, 7 figure

The repetitive structure of DNA clamps: An overlooked protein tandem repeat

Structured tandem repeats proteins (STRPs) are a specific kind of tandem repeat proteins characterized by a modular and repetitive three-dimensional structure arrangement. The majority of STRPs adopt solenoid structures, but with the increasing availability of experimental structures and high-quality predicted structural models, more STRP folds can be characterized. Here, we describe “Box repeats”, an overlooked STRP fold present in the DNA sliding clamp processivity factors, which has eluded classification although structural data has been available since the late 1990s. Each Box repeat is a β⍺βββ module of about 60 residues, which forms a class V “beads-on-a-string” type STRP. The number of repeats present in processivity factors is organism dependent. Monomers of PCNA proteins in both Archaea and Eukarya have 4 repeats, while the monomers of bacterial beta-sliding clamps have 6 repeats. This new repeat fold has been added to the RepeatsDB database, which now provides structural annotation for 66 Box repeat proteins belonging to different organisms, including viruses

Metamaterials proposed as perfect magnetoelectrics

Magnetoelectric susceptibility of a metamaterial built from split ring resonators have been investigated both experimentally and within an equivalent circuit model. The absolute values have been shown to exceed by two orders of magnitude that of classical magnetoelectric materials. The metamaterial investigated reaches the theoretically predicted value of the magnetoelectric susceptibility which is equal to the geometric average of the electric and magnetic susceptibilities.Comment: 5 pages, 3 figure

From public health policy to impact for COVID-19: a multi-country case study in Switzerland, Spain, Iran and Pakistan

Objectives: With the application of a systems thinking lens, we aimed to assess the national COVID-19 response across health systems components in Switzerland, Spain, Iran, and Pakistan. Methods: We conducted four case studies on the policy response of national health systems to the early phase of the COVID-19 pandemic. Selected countries include different health system typologies. We collected data prospectively for the period of January-July 2020 on 17 measures of the COVID-19 response recommended by the WHO that encompassed all health systems domains (governance, financing, health workforce, information, medicine and technology and service delivery). We further monitored contextual factors influencing their adoption or deployment. Results: The policies enacted coincided with a decrease in the COVID-19 transmission. However, there was inadequate communication and a perception that the measures were adverse to the economy, weakening political support for their continuation and leading to a rapid resurgence in transmission. Conclusion: Social pressure, religious beliefs, governance structure and level of administrative decentralization or global economic sanctions played a major role in how countries' health systems could respond to the pandemic

Ground state properties of ferromagnetic metal/conjugated polymer interfaces

We theoretically investigate the ground state properties of ferromagnetic metal/conjugated polymer interfaces. The work is partially motivated by recent experiments in which injection of spin polarized electrons from ferromagnetic contacts into thin films of conjugated polymers was reported. We use a one-dimensional nondegenerate Su-Schrieffer-Heeger (SSH) Hamiltonian to describe the conjugated polymer and one-dimensional tight-binding models to describe the ferromagnetic metal. We consider both a model for a conventional ferromagnetic metal, in which there are no explicit structural degrees of freedom, and a model for a half-metallic ferromagnetic colossal magnetoresistance (CMR) oxide which has explicit structural degrees of freedom. The Fermi energy of the magnetic metallic contact is adjusted to control the degree of electron transfer into the polymer. We investigate electron charge and spin transfer from the ferromagnetic metal to the organic polymer, and structural relaxation near the interface. Bipolarons are the lowest energy charge state in the bulk polymer for the nondegenerate SSH model Hamiltonian. As a result electrons (or holes) transferred into the bulk of the polymer form spinless bipolarons. However, there can be spin density in the polymer localized near the interface.Comment: 7 figure

Virtual karyotyping with SNP microarrays reduces uncertainty in the diagnosis of renal epithelial tumors

<p>Abstract</p> <p>Background</p> <p>Renal epithelial tumors are morphologically, biologically, and clinically heterogeneous. Different morphologic subtypes require specific management due to markedly different prognosis and response to therapy. Each common subtype has characteristic chromosomal gains and losses, including some with prognostic value. However, copy number information has not been readily accessible for clinical purposes and thus has not been routinely used in the diagnostic evaluation of these tumors. This information can be useful for classification of tumors with complex or challenging morphology. 'Virtual karyotypes' generated using SNP arrays can readily detect characteristic chromosomal lesions in paraffin embedded renal tumors and can be used to correctly categorize the common subtypes with performance characteristics that are amenable for routine clinical use.</p> <p>Methods</p> <p>To investigate the use of virtual karyotypes for diagnostically challenging renal epithelial tumors, we evaluated 25 archived renal neoplasms where sub-classification could not be definitively rendered based on morphology and other ancillary studies. We generated virtual karyotypes with the Affymetrix 10 K 2.0 mapping array platform and identified the presence of genomic lesions across all 22 autosomes.</p> <p>Results</p> <p>In 91% of challenging cases the virtual karyotype unambiguously detected the presence or absence of chromosomal aberrations characteristic of one of the common subtypes of renal epithelial tumors, while immunohistochemistry and fluorescent in situ hybridization had no or limited utility in the diagnosis of these tumors.</p> <p>Conclusion</p> <p>These results show that virtual karyotypes generated by SNP arrays can be used as a practical ancillary study for the classification of renal epithelial tumors with complex or ambiguous morphology.</p

Supporting the Identification, Monitoring and Preservation of Government Data Resources: Findings from DataLumos Outreach Efforts

This report documents the findings of “Identification, Monitoring, and Preservation of Government Data Resources”, an 18-month project involving outreach to government data producers, users, and intermediaries. Through this project, the Inter-university Consortium for Political and Social Research (ICPSR) sought to identify stakeholders’ most-used government datasets that they perceive to be potentially less accessible in the future, among other goals. Interviews and less formal interactions with data advocates and intermediaries, government data producers, and a variety of data users provided insights into the use of government data and perceptions of these data’s future accessibility. The most important source of data to these stakeholders is the Census Bureau, and several of its products were identified as being critical to stakeholders’ work. Data from other major statistical agencies, non-statistical federal agencies, and state and local data sources were also cited. The federal government data most used by stakeholders—and specifically the data of greatest importance to AECF-funded work—are perceived as accessible for future use. All of the federal datasets that stakeholders perceived to be potentially at risk were assessed and added to the DataLumos archive. A noteworthy finding from these interactions is that data created or collected by KIDS COUNT grantees, National Neighborhood Indicators Partnership (NNIP) participants, and other data intermediaries may not have a long-term data archiving or sharing plan. The analysts at these organizations spend significant effort gathering, aggregating, and analyzing data for their products, but they generally have no mechanism to archive or share these data. Given the investment in this work and the potential value of these data to community organizations, researchers, and even local and regional government agencies, there is a real opportunity for data intermediaries to store and share these data in a secure manner for the long term. Recommendations based on the project’s findings can be grouped into two major categories: advocacy and data sharing. Data users, intermediaries, and funders should continue to advocate that the Census Bureau and other principal statistical agencies provide access to the data products needed to successfully complete their work. Advocacy is also needed at the state and local levels, with the goals of targeting the creation of transparency laws and sunshine clauses, budget line items for data sharing, and infrastructural investments like open data portals and data application programming interfaces (APIs). Beyond traditional advocacy work, sustained and increased collaboration between government data producers and data users, intermediaries, and advocates is needed. As for data sharing, we recommend that data creators and intermediaries like KIDS COUNT grantees and NNIP partners work with data repositories like ICPSR to make their data available to others now and in the future. The archiving of these data would require both the infrastructure of a secure data repository as well as specialized curation and technical assistance related to sharing these types of data. The creation of an archive for data intermediaries’ data would extend the value of intermediaries’ important work, creating new resources for community members, institutions, and researchers.Annie E. Casey Foundationhttps://deepblue.lib.umich.edu/bitstream/2027.42/148837/1/Supporting the Identification, Monitoring and Preservation of Government Data Resources.pdfDescription of Supporting the Identification, Monitoring and Preservation of Government Data Resources.pdf : Repor