scholarly journals Validation analysis of EMDB entries

2021 ◽  
Author(s):  
Zhe Wang ◽  
Ardan Patwardhan ◽  
Gerard J Kleywegt
Keyword(s):  
Protein Data Bank ◽  
Data Bank ◽  
Tier 2 ◽  
Volume Data ◽  
Validation Metrics ◽  
Web Resource ◽  
Tier 1 ◽  
Tiered System ◽  
Tier 3

The Electron Microscopy Data Bank (EMDB) is the central archive of the electron cryo-microscopy (cryo-EM) community for storing and disseminating volume maps and tomograms. With input from the community, EMDB has developed new resources for validation of cryo-EM structures, focussing on the quality of the volume data alone and that of the fit of any models, themselves archived in the Protein Data Bank (PDB), to the volume data. Based on recommendations from community experts, the validation resources are developed in a three-tiered system. Tier 1 covers an extensive and evolving set of validation metrics, including tried and tested as well as more experimental ones, which are calculated for all EMDB entries and presented in the Validation Analysis (VA) web resource. This system is particularly useful for cryo-EM experts, both to validate individual structures and to assess the utility of new validation metrics. Tier 2 comprises a subset of the validation metrics covered by the VA resource that have been subjected to extensive testing and are considered to be useful for specialists as well as non-specialists. These metrics are presented on the entry-specific web pages for the entire archive on the EMDB website. As more experience is gained with the metrics included in the VA resource, it is expected that consensus will emerge in the community regarding a subset that is suitable for inclusion in the tier 2 system. Tier 3, finally, consists of the validation reports and servers that are produced by the Worldwide Protein Data Bank (wwPDB) Consortium. Successful metrics from tier 2 will be proposed for inclusion in the wwPDB validation pipeline and reports. We describe the details of the new resource, with an emphasis on the tier 1 system. The output of all three tiers is publicly available, either through the EMDB website (tiers 1 and 2) or through the wwPDB ftp sites (tier 3), although the content of all three will evolve over time (fastest for tier 1 and slowest for tier 3). It is our hope that these validation resources will help the cryo-EM community to get a better understanding of the quality, and the best ways to assess the quality of cryo-EM structures in EMDB and PDB.

scholarly journals Worldwide Protein Data Bank validation information: usage and trends

2018 ◽  
Vol 74 (3) ◽  
pp. 237-244 ◽  
Author(s):  
Oliver S. Smart ◽  
Vladimír Horský ◽  
Swanand Gore ◽  
Radka Svobodová Vařeková ◽  
Veronika Bendová ◽  
...  
Keyword(s):  
Protein Data Bank ◽  
Three Dimensional ◽  
Data Bank ◽  
Resonance Spectroscopy ◽  
X Ray ◽  
Validation Metrics ◽  
Task Forces ◽  
X Ray Crystallography ◽  
Structure Properties

Realising the importance of assessing the quality of the biomolecular structures deposited in the Protein Data Bank (PDB), the Worldwide Protein Data Bank (wwPDB) partners established Validation Task Forces to obtain advice on the methods and standards to be used to validate structures determined by X-ray crystallography, nuclear magnetic resonance spectroscopy and three-dimensional electron cryo-microscopy. The resulting wwPDB validation pipeline is an integral part of the wwPDB OneDep deposition, biocuration and validation system. The wwPDB Validation Service webserver (https://validate.wwpdb.org) can be used to perform checks prior to deposition. Here, it is shown how validation metrics can be combined to produce an overall score that allows the ranking of macromolecular structures and domains in search results. The ValTrendsDBdatabase provides users with a convenient way to access and analyse validation information and other properties of X-ray crystal structures in the PDB, including investigating trends in and correlations between different structure properties and validation metrics.

scholarly journals Evaluating Diet Quality of Canadian Adults Using Health Canada’s Surveillance Tool Tier System: Findings from the 2015 Canadian Community Health Survey-Nutrition

Nutrients ◽  
2020 ◽  
Vol 12 (4) ◽  
pp. 1113
Author(s):  
Salma Hack ◽  
Mahsa Jessri ◽  
Mary R. L’Abbé
Keyword(s):  
Food Choices ◽  
Canadian Community Health Survey ◽  
Dietary Intakes ◽  
Tier 2 ◽  
Dietary Recommendations ◽  
Tier System ◽  
Tier 1 ◽  
Community Health Survey ◽  
Tier 3

The 2014 Health Canada’s Surveillance Tool, Tier System (HCST) is a nutrient profiling model developed to evaluate adherence of food choices to dietary recommendations. With the recent release of the nationally representative Canadian Community Health Survey-Nutrition (CCHS-N) 2015, this study used HCST to evaluate nutritional quality of the dietary intakes of Canadians in the CCHS-N. Dietary intakes were ascertained using 24-hour dietary recalls from Canadians adults ≥19 years (N = 13,605). Foods were categorized into four Tiers based on degree of adherence to dietary recommendations according to thresholds for sodium, total fat, saturated fats, and sugars. Tier 1 and Tier 2 represented “recommended foods”, Tier 3 represents foods to “choose less often”, and Tier 4 represented foods “not recommended”. Across all dietary reference intakes (DRI) groups, most foods were categorized as Tier 1 for Vegetable and Fruits (2.2–3.8 servings/day), Tier 2 for Grain Products (2.9–3.4 servings/day), Tier 3 for Milk and Alternatives (0.7–1 serving/day) or for Meat and Alternatives (1.1–1.6 servings/day). Consumption of foods from Tier 4 and “other foods” such as high fat/sugary foods, sugar-sweetened beverages, and alcohol, represented 24–26% and 21–23% kcal/day, for males and females, respectively. Canadians are eating more foods categorized as Tier 1–3, rather than Tier 4. Adults with the highest intakes of Tier 4 and “other foods” had lower intakes of macronutrients and increased body mass index. These findings can be used by policy makers to assist in identifying targets for food reformulation at the nutrient level and quantitative guidance to support healthy food choices.

scholarly journals Frequency and neural correlates related to psychosis in motor neurone disease

2021 ◽  
Author(s):  
Alicia Wilcox ◽  
James Rowe ◽  
P Simon Jones ◽  
Rhys Clwyd Roberts
Keyword(s):  
White Matter ◽  
Grey Matter ◽  
Psychotic Disorders ◽  
Neural Correlates ◽  
Motor Neurone ◽  
Motor Neurone Disease ◽  
Tier 2 ◽  
Tier 1 ◽  
Tiered System ◽  
Tier 3

Psychosis is a challenging feature of the syndromes motor neurone disease (MND), frontotemporal dementia and their overlap. Clinically evident psychosis affects 5-10% of patients, and more in those with C9orf72 expansions. However, subthreshold psychosis features may be overlooked in the context of overriding concern for physical impairment. This prospective study aimed to establish the prevalence and severity of psychosis features in a population-representative sample of MND, and to identify the neural correlates of psychosis by structural magnetic resonance imaging. A three-tiered system was applied to recruit people with MND, with cognitive and psychosis screening (Tier 1: N=111 with the Edinburgh ALS Cognitive and Behavioural Screen), in-depth neuropsychiatric assessment (Tier 2: N=60) and imaging (Tier 3: N=30). Age, education and sex-matched healthy controls were recruited to Tier 2 (N=30) and Tier 3 (N=20). Overt psychosis was identified in 10% of the Tier 1 cohort, whilst 46% showed milder and diverse neuropsychiatric change. Grey matter correlates of psychosis included atrophy of the cingulate cortex and the hippocampus. White matter correlates included compromised integrity along frontotemporal and temporal-parietal association pathways, especially those connecting the anterior temporal lobe. These grey and white matter changes in MND represent vulnerability to psychosis and are qualitatively similar to volumetric and white matter abnormalities observed in other primary psychotic disorders. Neuropsychiatric features are common, even though overt psychosis is identified in a minority of people with motor neurone disease.

scholarly journals Reverse logistics of Indian E-Commerce Industry- Consumer Perspective and Ways to Improve

2020 ◽  
Vol 4 (12) ◽  
pp. 41-49
Keyword(s):  
Supply Chain ◽  
Distribution Center ◽  
Business Success ◽  
Tier 2 ◽  
Logistics Industry ◽  
Tier 1 ◽  
Reverse Logistic ◽  
Consumer Perspective ◽  
Tier 3

The modern supply chain has become complex and multi-locational, and efficient movement of material contributing to business success. The industry that deals with the movement of goods from one point to another is known as the logistics industry. Reverse logistic is a process of moving materials back from their consumer destination to their point of manufacturer or the distribution center in order to recapture their value for redistribution, or to dispose them properly. The movement of goods backwards in the supply chain is as important as the movement of goods forward in the supply chain. With the introduction of ecommerce and increase in the footprint of digitalization, the expectations of the consumers and the industries have reached an all-time high. We have used customer survey to know their perspective and then we have analyzed and visualized the data using Tableau. This research paper will focus on the Indian ecommerce industry and how end-consumers think differently than the industry, and how the gap in the quality of service is too wide between tier-1 cities and tier-2 or tier- 3 cities. We have used our data to analyze and find how can big data and blockchain help these industries in finding modern day solutions.

Optimal Timing for Launching Installation of Tier 2 and 3 Systems of School-Wide Positive Behavioral Interventions and Supports

2021 ◽  
pp. 109830072199608
Author(s):  
Angus Kittelman ◽  
Sterett H. Mercer ◽  
Kent McIntosh ◽  
Robert Hoselton
Keyword(s):  
Longitudinal Study ◽  
Behavioral Interventions ◽  
Structural Equation ◽  
Equation Modeling ◽  
Optimal Timing ◽  
First Year ◽  
Tier 2 ◽  
Positive Behavioral Interventions ◽  
Tier 1 ◽  
Tier 3

The purpose of this longitudinal study was to examine patterns in implementation of Tier 2 and 3 school-wide positive behavioral interventions and supports (SWPBIS) systems to identify timings of installation that led to higher implementation of advanced tiers. Extant data from 776 schools in 27 states reporting on the first 3 years of Tier 2 implementation and 359 schools in 23 states reporting on the first year of Tier 3 implementation were analyzed. Using structural equation modeling, we found that higher Tier 1 implementation predicted subsequent Tier 2 and Tier 3 implementation. In addition, waiting 2 or 3 years after initial Tier 1 implementation to launch Tier 2 systems predicted higher initial Tier 2 implementation (compared with implementing the next year). Finally, we found that launching Tier 3 systems after Tier 2 systems, compared with launching both tiers simultaneously, predicted higher Tier 2 implementation in the second and third year, so long as Tier 3 systems were launched within 3 years of Tier 2 systems. These findings provide empirical guidance for when to launch Tier 2 and 3 systems; however, we emphasize that delays in launching advanced systems should not equate to delays in more intensive supports for students.

scholarly journals Global Inland Capture and Culture Finfisheries Follow Different Trends When Evaluated by the Human Development Index

2021 ◽  
Vol 13 (15) ◽  
pp. 8420
Author(s):  
Peter W. Sorensen ◽  
Maria Lourdes D. Palomares
Keyword(s):  
Socioeconomic Factors ◽  
Human Development ◽  
Human Development Index ◽  
Developed Countries ◽  
Global Scale ◽  
Tier 2 ◽  
Development Index ◽  
Tier 1 ◽  
Catch Reconstruction ◽  
Tier 3

To assess whether and how socioeconomic factors might be influencing global freshwater finfisheries, inland fishery data reported to the FAO between 1950 and 2015 were grouped by capture and culture, country human development index, plotted, and compared. We found that while capture inland finfishes have greatly increased on a global scale, this trend is being driven almost entirely by poorly developed (Tier-3) countries which also identify only 17% of their catch. In contrast, capture finfisheries have recently plateaued in moderately-developed (Tier-2) countries which are also identifying 16% of their catch but are dominated by a single country, China. In contrast, reported capture finfisheries are declining in well-developed (Tier-1) countries which identify nearly all (78%) of their fishes. Simultaneously, aquacultural activity has been increasing rapidly in both Tier-2 and Tier-3 countries, but only slowly in Tier-1 countries; remarkably, nearly all cultured species are being identified by all tier groups. These distinctly different trends suggest that socioeconomic factors influence how countries report and conduct capture finfisheries. Reported rapid increases in capture fisheries are worrisome in poorly developed countries because they cannot be explained and thus these fisheries cannot be managed meaningfully even though they depend on them for food. Our descriptive, proof-of-concept study suggests that socioeconomic factors should be considered in future, more sophisticated efforts to understand global freshwater fisheries which might include catch reconstruction.

Incorporation of plasma-based next-generation sequencing to improve guideline-concordant molecular testing in patients with newly diagnosed metastatic nonsquamous non-small cell lung cancer.

2021 ◽  
Vol 39 (28_suppl) ◽  
pp. 14-14
Author(s):  
Charu Aggarwal ◽  
Melina Elpi Marmarelis ◽  
Wei-Ting Hwang ◽  
Dylan G. Scholes ◽  
Aditi Puri Singh ◽  
...  
Keyword(s):  
Clinical Practice ◽  
Practice Change ◽  
Molecular Testing ◽  
Tier 2 ◽  
Newly Diagnosed ◽  
Next Generation ◽  
First Line ◽  
Tier 1 ◽  
Tier 3 ◽  
The Impact

14 Background: Current NCCN guidelines recommend comprehensive molecular profiling for all newly diagnosed patients with metastatic non-squamous NSCLC to enable the delivery of personalized medicine. We have previously demonstrated that incorporation of plasma based next-generation gene sequencing (NGS) improves detection of clinically actionable mutations in patients with advanced NSCLC (Aggarwal et al, JAMA Oncology, 2018). To increase rates of comprehensive molecular testing at our institution, we adapted our clinical practice to include concurrent use of plasma (P) and tissue (T) based NGS upon initial diagnosis. P NGS testing was performed using a commercial 74 gene assay. We analyzed the impact of this practice change on guideline concordant molecular testing at our institution. Methods: A retrospective cohort study of patients with newly diagnosed metastatic non-squamous NSCLC following the implementation of this practice change in 12/2018 was performed. Tiers of NCCN guideline concordant testing were defined, Tier 1: complete EGFR, ALK, BRAF, ROS1, MET, RET, NTRK testing, Tier 2: included above, but with incomplete NTRK testing, Tier 3: > 2 genes tested, Tier 4: single gene testing, Tier 5: no testing. Proportion of patients with comprehensive molecular testing by modality (T NGS vs. T+P NGS) were compared using one-sided Fisher’s exact test. Results: Between 01/2019, and 12/2019, 170 patients with newly diagnosed metastatic non-Sq NSCLC were treated at our institution. Overall, 98.2% (167/170) patients underwent molecular testing, Tier 1: n = 100 (59%), Tier 2: n = 39 (23%), Tier 3/4: n = 28 (16.5%), Tier 5: n = 3 (2%). Amongst these patients, 43.1% (72/167) were tested with T NGS alone, 8% (15/167) with P NGS alone, and 47.9% (80/167) with T+P NGS. A higher proportion of patients underwent comprehensive molecular testing (Tiers 1+2) using T+P NGS: 95.7% (79/80) compared to T alone: 62.5% (45/72), p < 0.0005. Prior to the initiation of first line treatment, 72.4% (123/170) patients underwent molecular testing, Tier 1: n = 73 (59%), Tier 2: n = 27 (22%) and Tier 3/4: n = 23 (18%). Amongst these, 39% (48/123) were tested with T NGS alone, 7% (9/123) with P NGS alone and 53.6% (66/123) with T+P NGS. A higher proportion of patients underwent comprehensive molecular testing (Tiers 1+2) using T+P NGS, 100% (66/66) compared to 52% (25/48) with T NGS alone (p < 0.0005). Conclusions: Incorporation of concurrent T+P NGS testing in treatment naïve metastatic non-Sq NSCLC significantly increased the proportion of patients undergoing guideline concordant molecular testing, including prior to initiation of first-line therapy at our institution. Concurrent T+P NGS should be adopted into institutional pathways and routine clinical practice.

scholarly journals Initial Experience in Predicting the Risk of Hospitalization of 496 Outpatients with COVID-19 Using a Telemedicine Risk Assessment Tool

2020 ◽  
Author(s):  
James B O'Keefe ◽  
Elizabeth J Tong ◽  
Thomas H Taylor ◽  
Ghazala D Datoo O'Keefe ◽  
David C Tong
Keyword(s):  
Risk Assessment ◽  
Assessment Tool ◽  
Cox Regression ◽  
Risk Assessment Tool ◽  
Individual Risk ◽  
Tier 2 ◽  
Tier 1 ◽  
Risk Patients ◽  
Tier 3

Objective: To determine whether a risk prediction tool developed and implemented in March 2020 accurately predicts subsequent hospitalizations. Design: Retrospective cohort study, enrollment from March 24 to May 26, 2020 with follow-up calls until hospitalization or clinical improvement (final calls until June 19, 2020) Setting: Single center telemedicine program managing outpatients from a large medical system in Atlanta, Georgia Participants: 496 patients with laboratory-confirmed COVID-19 in isolation at home. Exclusion criteria included: (1) hospitalization prior to telemedicine program enrollment, (2) immediate discharge with no follow-up calls due to resolution. Exposure: Acute COVID-19 illness Main Outcome and Measures: Hospitalization was the outcome. Days to hospitalization was the metric. Survival analysis using Cox regression was used to determine factors associated with hospitalization. Results: The risk-assessment rubric assigned 496 outpatients to risk tiers as follows: Tier 1, 237 (47.8%); Tier 2, 185 (37.3%); Tier 3, 74 (14.9%). Subsequent hospitalizations numbered 3 (1%), 15 (7%), and 17 (23%) and for Tiers 1-3, respectively. From a Cox regression model with age ≥ 60, gender, and self-reported obesity as covariates, the adjusted hazard ratios using Tier 1 as reference were: Tier 2 HR=3.74 (95% CI, 1.06-13.27; P=0.041); Tier 3 HR=10.87 (95% CI, 3.09-38.27; P<0.001). Tier was the strongest predictor of time to hospitalization. Conclusions and Relevance: A telemedicine risk assessment tool prospectively applied to an outpatient population with COVID-19 identified both low-risk and high-risk patients with better performance than individual risk factors alone. This approach may be appropriate for optimum allocation of resources.

SFBT Within the Tier 2 Framework

2017 ◽  
Author(s):  
Michael S. Kelly ◽  
Johnny S. Kim ◽  
Cynthia Franklin
Keyword(s):  
Classroom Climate ◽  
Tier 2 ◽  
Social Emotional ◽  
Prevention Services ◽  
Coaching Intervention ◽  
Tier 1 ◽  
American Schools ◽  
Tier 2 Intervention ◽  
Tier 3 ◽  
Teacher Coaching

The educational policy changes of the past 20 years have increased the focus on the provision of prevention services within schools, both for individual students and for social-emotional programming delivered in their classroom. Whether characterized as Response to Intervention (RTI), Positive Behavior Intervention and Supports (PBIS), or Multi-Tiered Systems of Supports (MTSS), the focus on a 3-tier framework of universal (Tier 1), selective (Tier 2) and indicated (Tier 3) has become one of the largest evidence-based framework ever scaled up within American schools, with over 19,000 schools across all 50 states having implemented PBIS by this writing. This chapter focuses on an example of a SFBT Tier 2 intervention, the Working on What Works (WOWW) teacher coaching intervention, that strives to create a better classroom climate for teachers and their students.

TIER-2 IN EAST ASIA1: CHALLENGES AND ANSWERS

2008 ◽  
Vol 2008 (1) ◽  
pp. 49-55
Author(s):  
Alexander Nicolau
Keyword(s):  
Media Coverage ◽  
Oil Spills ◽  
Oil Industry ◽  
Government Agencies ◽  
Tier 2 ◽  
International Media ◽  
The Past ◽  
Tier 1 ◽  
Tier 3 ◽  
And Training

ABSTRACT On numerous occasions, East Asia has been affected by marine oil spills incidents, originating from tankers and other types of ships. Important spills incidents that involved the IOPC Funds in the last decade (e.g. Nakhodka, Evoikos, Natuna Sea and Solar 1 …) indicate an average occurrence of one spill per year. This figure remains significantly high when considering that some States in the region are still not parties to international compensation regimes. In addition, numerous incidents do not benefit of international media coverage, thus making them often unnoticed. Lower scale incidents (within the range of hundreds of tonnes) occur on a more frequent basis and may appear trivial to respond to. Nevertheless, they represent the same range of difficulties experienced during larger scale incidents (logistics, suitable means to apply dispersants promptly and effectively, availability of temporary storage, lack of plan and training …) In terms of response, the ultimate authority in the coordination of spill response activities is in the hands of Government Agencies. However, the equipment and manpower available belong in various proportions to both Government Agencies and the Oil Industry. The latter operates numerous oil terminals and offshore facilities and is responsible to respond to minor spills defined as Tier 1. In the case of a large spill that exceeds the on-site capability, Tier 3 Cooperatives funded by the vast majority of major companies were created to assist and complement the local response, by offering access to a large range of special supplementary resources and services, such as the Airborne Dispersant Delivery System. Whilst Tiers 1 and 3 are well defined and are respectively synonyms of small and huge oil spill incidents, there is a lack of clarity and consistency in-between, thus making the Tier 2 response difficult to define. This gap that is often underestimated and may result in a preparedness weakness leading to unfortunate consequences. The aim of this paper is to analyse the Tier-2 response requirements and to discuss on the challenges of implementing effective measures in a region where the only imports of crude oil of China have more than doubled in the past five years.

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