196,746 research outputs found
Algorithms for building and evaluating multiple sequence alignments
No full textThe alignment of biological sequences is crucial for the transfer of annotation from model organisms to humans. Pairwise alignment of sequences can reveal homology while multiple alignments are used to characterize protein families and elucidate their evolutionary history.We developed several software packages to create, evaluate and visualize multiple alignments. Our alignment program Kalign combines excellent accuracy with unparalleled computational benefits. The initial publication outlines the algorithm and innovations introduced to the field, while the second introduced several key improvements and additions to the original algorithm. The accuracy of Kalign is high for both protein and nucleotide alignments and Kalign can thus be used for a wide range of applications in genomics, including homology detection, protein and RNA structure prediction, phylogenetic analysis and promoter prediction.The assessment of alignment quality is a tough problem the field. While alignment programs can be tested on benchmark sets to reveal their overall performance, determining the accuracy of individual alignments is next to impossible. We approached this problem by analyzing several alignments of the same sequences and applying a consensus principle: if different methods arrive at the same conclusion it is more likely to be correct than when methods disagree. Our program MUMSA can thus diagnose faulty alignments which is critical in high throughput genomics application.Both Kalign and Mumsa can be freely accessed at our website http://msa.cgb.ki.se which also features Kalignvu, a lightweight alignment viewer.List of scientific papersI. Lassmann T, Sonnhammer EL (2002). "Quality assessment of multiple alignment programs" FEBS Lett 529(1): 126-30 https://pubmed.ncbi.nlm.nih.gov/12354624II. Lassmann T, Sonnhammer EL (2005). Kalign--an accurate and fast multiple sequence alignment algorithm. BMC Bioinformatics. 6: 298. https://pubmed.ncbi.nlm.nih.gov/16343337III. Lassmann T (2006). Kalign2 - a scalable approach for the alignment of protein and nucleotide sequences. [Submitted]IV. Lassmann T, Sonnhammer EL (2005). Automatic assessment of alignment quality. Nucleic Acids Res. 33(22): 7120-8. https://pubmed.ncbi.nlm.nih.gov/16361270V. Lassmann T, Sonnhammer EL (2006). "Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment. Nucleic Acids Res. 34 (Web Server issue): W596-9. https://pubmed.ncbi.nlm.nih.gov/16845078VI. Finn RD, Mistry J, Schuster-Bockler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, Eddy SR, Sonnhammer EL, Bateman A (2006). Pfam: clans, web tools and services. Nucleic Acids Res. 34 (Database issue): D247-51. https://pubmed.ncbi.nlm.nih.gov/16381856</p
Myths surrounding vertical dimension of occlusion in restorative dentistry: A scoping review
No full textObjective: This scoping review aims to clarify the concept of vertical dimension of occlusion (VDO) in prosthetic dentistry, addressing prevalent myths, and controversies regarding its clinical management and impact on the stomatognathic system. Methods: This paper critically examines common beliefs about VDO alteration and its effects on temporomandibular disorders (TMD) through an extensive literature review and an international survey. The survey included 862 general dentists and prosthodontists and explored their approaches to altering VDO and their perceptions of the clinical implications. The literature review provided a thorough analysis of existing research on VDO modification techniques, the adaptability of the stomatognathic system, and the relationship between VDO changes and TMD. Results: The survey revealed insights into dentists' perspectives on VDO, showing that while many practitioners test a new VDO due to concerns about patient adaptation, a significant majority observed that patients typically adjust well to a new VDO regardless of the technique used. The survey highlighted differing beliefs about the need for a gradual process and trial phase for VDO alteration, as well as the stability of modified VDO. Literature review suggests the stability and adaptability of VDO changes due to muscle adaptability and indicates no direct causal or curative link between VDO changes and TMD. Traditional methods for determining VDO in complete dentures may not be suitable for worn dentition, underscoring the need for tailored approaches. Conclusion: This paper suggests that the traditional belief in the need for a prolonged trial phase for VDO alterations may be reconsidered in light of evidence supporting the adaptability of the stomatognathic system. Moreover, it emphasizes the importance of distinguishing between methods suitable for complete dentures and those for managing cases of worn dentition. The purported link between VDO alterations and TMD is also found to lack scientific evidence, highlighting the need for individualized patient care based on current evidence and clinical judgment
Gut Bless Your Pain—Roles of the Gut Microbiota, Sleep, and Melatonin in Chronic Orofacial Pain and Depression
No full textBackground. Increased attention has been paid to the gut–brain axis recently, but little is known so far regarding how this translates into pain susceptibility. Aim. The aim of this review is to determine whether gastroenterological disorders and sleep disorders (directly or indirectly) contribute to an increased susceptibility to depression and chronic orofacial pain. Method. A search was performed in the U.S. National Library of Medicine (PubMed) database in order to find studies published before 19 December 2021. We used the following terms: gut microbiome, OR sleep quality, OR melatonin, OR GERD, OR IBS, AND: depression OR chronic pain, in different configurations. Only papers in English were selected. Given the large number of papers retrieved in the search, their findings were described and organized narratively. Results. A link exists between sleep disorders and gastroenterological disorders, which, by adversely affecting the psyche and increasing inflammation, disturb the metabolism of tryptophan and cause excessive microglial activation, leading to increased susceptibility to pain sensation and depression. Conclusions. Pain therapists should pay close attention to sleep and gastrointestinal disorders in patients with chronic pain and depression
Dr. Duane M. Jackson, Morehouse College, July 2011
No full textThis video is a conversation with Dr. Duane M. Jackson. Dr. Jackson talks about his paper, "Recall and the Serial Position Effect: The Role of Primacy and Recency on Accounting Students' Performance." Jackie Daniel, AUC Woodruff Library, is the interviewer
The neuroprotective effect of inflammation: Implications for the therapy of multiple sclerosis
No full text"Reflections on the subject of Emigration from Europe with a view to Settlement in the United States" By M. Carey.
No full text"Reflections on the subject of Emigration from Europe with a view to Settlement in the United States: containing bried sketches of the moral and political character of those states.
By M. Carey, member of the American philosophical, and of the American Antiquarian Society, and author of The Olive Branch, Cindiciae Hibernicae, essays on banking, on political economy, and on internal improvement.
To which are now added the English editor's comments on the subject; together with Important Advice to Emigrants, and Cautions Against Impositions Practiced in the Outports
Dispelling the Myths Behind First-author Citation Counts
No full textWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
Dr. Glendon Swarthout
No full textHosted by Roger M. Busfield, MSU Assistant Professor of Speech and Theater, Meet the Author is designed to introduce a general audience to a contemporary author and their work through in-depth interviews. This episode features a conversation between Dr. Glendon Swarthout, prolific author and English professor at MSU, and assistant professors Sam S. Baskett and Theodore B. Strandness
Simulation of thermal plant optimization and hydraulic aspects of thermal distribution loops for large campuses
No full textFollowing an introduction, the author describes Texas A&M University and its utilities system. After that, the author presents how to construct simulation models for chilled water and heating hot water distribution systems. The simulation model was used in a $2.3 million Ross Street chilled water pipe replacement project at Texas A&M University. A second project conducted at the University of Texas at San Antonio was used as an example to demonstrate how to identify and design an optimal distribution system by using a simulation model. The author found that the minor losses of these closed loop thermal distribution systems are significantly higher than potable water distribution systems. In the second part of the report, the author presents the latest development of software called the Plant Optimization Program, which can simulate cogeneration plant operation, estimate its operation cost and provide optimized operation suggestions. The author also developed detailed simulation models for a gas turbine and heat recovery steam generator and identified significant potential savings. Finally, the author also used a steam turbine as an example to present a multi-regression method on constructing simulation models by using basic statistics and optimization algorithms. This report presents a survey of the author??s working experience at the Energy Systems Laboratory (ESL) at Texas A&M University during the period of January 2002 through March 2004. The purpose of the above work was to allow the author to become familiar with the practice of engineering. The result is that the author knows how to complete a project from start to finish and understands how both technical and nontechnical aspects of a project need to be considered in order to ensure a quality deliverable and bring a project to successful completion. This report concludes that the objectives of the internship were successfully accomplished and that the requirements for the degree of Degree of Engineering have been satisfied
The role of fibroblast growth factor 9 in multiple sclerosis: inhibition of myelination and induction of pro-inflammatory environment
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