ORCID Profile
0000-0002-1800-7935
Current Organisations
Universidade Federal de Viçosa
,
University of Washington
Does something not look right? The information on this page has been harvested from data sources that may not be up to date. We continue to work with information providers to improve coverage and quality. To report an issue, use the Feedback Form.
Publisher: Oxford University Press (OUP)
Date: 07-05-2022
DOI: 10.1093/NAR/GKAC323
Abstract: Proteins are essential macromolecules for the maintenance of living systems. Many of them perform their function by interacting with other molecules in regions called binding sites. The identification and characterization of these regions are of fundamental importance to determine protein function, being a fundamental step in processes such as drug design and discovery. However, identifying such binding regions is not trivial due to the drawbacks of experimental methods, which are costly and time-consuming. Here we propose GRaSP-web, a web server that uses GRaSP (Graph-based Residue neighborhood Strategy to Predict binding sites), a residue-centric method based on graphs that uses machine learning to predict putative ligand binding site residues. The method outperformed 6 state-of-the-art residue-centric methods (MCC of 0.61). Also, GRaSP-web is scalable as it takes 10-20 seconds to predict binding sites for a protein complex (the state-of-the-art residue-centric method takes 2-5h on the average). It proved to be consistent in predicting binding sites for bound/unbound structures (MCC 0.61 for both) and for a large dataset of multi-chain proteins (4500 entries, MCC 0.61). GRaSPWeb is freely available at grasp.ufv.br.
Publisher: BMJ
Date: 12-2022
DOI: 10.1136/BMJOPEN-2022-066564
Abstract: Reporting guidelines can improve dissemination and application of findings and help avoid research waste. Recent studies reveal opportunities to improve primary care (PC) reporting. Despite increasing numbers of guidelines, none exists for PC research. This study aims to prioritise candidate reporting items to inform a reporting guideline for PC research. Delphi study conducted by the Consensus Reporting Items for Studies in Primary Care (CRISP) Working Group. International online survey. Interdisciplinary PC researchers and research users. We drew potential reporting items from literature review and a series of international, interdisciplinary surveys. Using an anonymous, online survey, we asked participants to vote on and whether each candidate item should be included, required or recommended in a PC research reporting guideline. Items advanced to the next Delphi round if they received % votes to include. Analysis used descriptive statistics plus synthesis of free-text responses. 98/116 respondents completed round 1 (84% response rate) and 89/98 completed round 2 (91%). Respondents included a variety of healthcare professions, research roles, levels of experience and all five world regions. Round 1 presented 29 potential items, and 25 moved into round 2 after rewording and combining items and adding 2 new items. A majority of round 2 respondents voted to include 23 items (90%–100% for 11 items, 80%–89% for 3 items, 70%–79% for 3 items, 60%–69% for 3 items and 50%–59% for 3 items). Our Delphi study identified items to guide the reporting of PC research that has broad endorsement from the community of producers and users of PC research. We will now use these results to inform the final development of the CRISP guidance for reporting PC research.
Publisher: Oxford University Press (OUP)
Date: 21-05-2022
DOI: 10.1093/BIB/BBAC178
Abstract: Metals are present in >30% of proteins found in nature and assist them to perform important biological functions, including storage, transport, signal transduction and enzymatic activity. Traditional and experimental techniques for metal-binding site prediction are usually costly and time-consuming, making computational tools that can assist in these predictions of significant importance. Here we present Genetic Active Site Search (GASS)-Metal, a new method for protein metal-binding site prediction. The method relies on a parallel genetic algorithm to find candidate metal-binding sites that are structurally similar to curated templates from M-CSA and MetalPDB. GASS-Metal was thoroughly validated using homologous proteins and conservative mutations of residues, showing a robust performance. The ability of GASS-Metal to identify metal-binding sites was also compared with state-of-the-art methods, outperforming similar methods and achieving an MCC of up to 0.57 and detecting up to 96.1% of the sites correctly. GASS-Metal is freely available at gassmetal.unifei.edu.br. The GASS-Metal source code is available at androizidoro/gassmetal-local.
Publisher: Wiley
Date: 16-05-2020
DOI: 10.1111/EJN.14750
Abstract: Parkinson's disease is a neurodegenerative disease affecting the supply of dopamine to basal ganglia nuclei, leading to pathological beta band (13–35 Hz) oscillations in the subthalamic nucleus (STN). STN and beta activity are recognized in motoric functions but their role in cognitive functions remains elusive. We examined single unit and beta local field potential (LFP) activity in the STN during a visual choice preference task in PD patients ( n = 12) undergoing deep brain stimulation surgery. Patients viewed 2 of 5 possible animal picture‐pairs and were instructed to choose their favorite (“ fav ”) picture by clicking the left or right mouse key. A block of trials consisted of 50–75 picture‐pair presentations. Single unit histograms and LFP spectrograms were aligned to picture presentation and point of decision for pairs that included the fav and non‐fav pictures, respectively. A total of 58 neurons from 26 blocks of trials were analyzed. Thirty of 58 neurons showed a selective change in spiking activity 0.20–0.65 s to fav picture presentation, which preceded the shortest recorded reaction time (=0.7 s), and 17/58 neurons showed no significant response in our task. Beta LFP significantly desynchronized in response to fav but not non‐fav pictures in all trials, and in 14/26 blocks of trials, the desynchronization was followed by a “beta burst” and r ‐up to baseline activity. Neurons with choice preference responses were found throughout the dorsoventral extent of the STN. STN single units and beta activity are modulated during visual choice preference, and this suggests a role for STN beta activity in cognitive processing.
Publisher: Oxford University Press (OUP)
Date: 18-02-2021
Abstract: Despite broad efforts to improve the reporting of biomedical research, no reporting guideline exists for primary care (PC) research. Little is known about current reporting practices or how well reports meet the needs of varied users in PC. To map the published literature on PC research reporting: quality, strengths and weaknesses, recommendations and efforts to improve reporting. Scoping review of literature across seven major databases and search engines to identify all articles on PC research reporting published in English, 2000–20. An additional secondary search of references of these 25 articles and consideration of expert panel suggestions. Structured data extraction by multiple reviewers using a predetermined form. Search yielded 2847 unique titles, of which 126 underwent full-text review and 25 met inclusion criteria. Publications included opinion pieces (9), systematic reviews (5), methods articles (2), literature reviews (4), qualitative studies (4) and surveys (1). Studies focussed on a variety of topics and research methods. All publications identified the need for improved reporting and recommended items to include in reports. Most commonly, publications cited the need for more detailed reporting on the context of study interventions, clinical settings and health care systems. Most publications endorsed the use of reporting guidelines and recognized the unique needs of PC research reporting. Published research and opinion identify unique needs for PC research reports and support new guidance to improve the validity, generalizability and application of study findings.
Publisher: Wiley
Date: 13-02-2022
DOI: 10.1002/MDS.28953
Abstract: Patients with Parkinson's disease might develop treatment-resistant axial dysfunction after bilateral subthalamic stimulation. To study whether lateralized stimulation (unilateral 50% litude reduction) for ≥21 days results in ≥0.13 m/s faster gait velocity in the dopaminergic ON state in these patients, and its effects on motor and axial function, quantitative gait and speech measures, quality of life, and selected cognitive tasks. Randomized, double-blinded, double-crossover trial. In 22 participants (51-79 years old, 15 women), there were no significant changes in gait velocity, quality of life, cognitive, and speech measures. Reducing left-sided litude resulted in a 2.5-point improvement in axial motor Movement Disorder Society Unified Parkinson's Disease Rating Scale (MDS-UPDRS) (P = 0.005, uncorrected) and a 1.9-point improvement in the Freezing of Gait Questionnaire (P = 0.024, uncorrected). Lateralized subthalamic stimulation does not result in meaningful improvement in gait velocity in patients with Parkinson's disease who develop treatment-resistant axial dysfunction after bilateral subthalamic stimulation. Left subthalamic overstimulation may contribute to axial deterioration in these patients. © 2022 International Parkinson and Movement Disorder Society.
Location: United States of America
No related grants have been discovered for Tameem Al-Ozzi.