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Moon, Jucheol, and Oliver Eulenstein. "Synthesizing large-scale species trees using the strict consensus approach." Journal of Bioinformatics and Computational Biology 15, no. 03 (April 20, 2017): 1740002. http://dx.doi.org/10.1142/s0219720017400029.
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Supertree problems are a standard tool for synthesizing large-scale species trees from a given collection of gene trees under some problem-specific objective. Unfortunately, these problems are typically NP-hard, and often remain so when their instances are restricted to rooted gene trees sampled from the same species. While a class of restricted supertree problems has been effectively addressed by the parameterized strict consensus approach, in practice, most gene trees are unrooted and sampled from different species. Here, we overcome this stringent limitation by describing efficient algorithms that are adopting the strict consensus approach to also handle unrestricted supertree problems. Finally, we demonstrate the performance of our algorithms in a comparative study with classic supertree heuristics using simulated and empirical data sets.
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Acevedo-Saenz, Liliana, Federico Perdomo-Celis, Carlos J. Montoya, and Paula A. Velilla. "Polyfunctional CD8+ T-Cell Response to Autologous Peptides from Protease and Reverse Transcriptase of HIV-1 Clade B." Current HIV Research 17, no. 5 (December 4, 2019): 350–59. http://dx.doi.org/10.2174/1570162x17666191017105910.
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Background: : The diversity of the HIV proteome influences the cellular response and development of an effective vaccine, particularly due to the generation of viral variants with mutations located within CD8+ T-cell epitopes. These mutations can affect the recognition of the epitopes, that may result in the selection of HIV variants with mutated epitopes (autologous epitopes) and different CD8+ T-cell functional profiles. Objective:: To determine the phenotype and functionality of CD8+ T-cell from HIV-infected Colombian patients in response to autologous and consensus peptides derived from HIV-1 clade B protease and reverse transcriptase (RT). Methods:: By flow cytometry, we compared the ex vivo CD8+ T-cell responses from HIV-infected patients to autologous and consensus peptides derived from HIV-1 clade B protease and RT, restricted by HLA-B*35, HLA-B*44 and HLA-B*51 alleles. Results:: Although autologous peptides restricted by HLA-B*35 and HLA-B*44 did not show any differences compared with consensus peptides, we observed the induction of a higher polyfunctional profile of CD8+ T-cells by autologous peptides restricted by HLA-B*51, particularly by the production of interferon-γ and macrophage inflammatory protein-1β. The response by different memory CD8+ T-cell populations was comparable between autologous vs. consensus peptides. In addition, the magnitude of the polyfunctional response induced by the HLA-B*51-restricted QRPLVTIRI autologous epitope correlated with low viremia. Conclusion:: Autologous peptides should be considered for the evaluation of HIV-specific CD8+ Tcell responses and to reveal some relevant epitopes that could be useful for therapeutic strategies aiming to promote polyfunctional CD8+ T-cell responses in a specific population of HIV-infected patients.
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Chen, Kairui, Chuance Yan, Qijun Ren, Xianxian Zeng, and Junwei Wang. "Mean Square Consensus of General Linear Multiagent Systems with Communication Noises under Switching Topologies." Complexity 2022 (August 13, 2022): 1–9. http://dx.doi.org/10.1155/2022/1337959.
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This paper investigates the distributed consensus problem of general linear multiagent systems (MASs) with communication noises under fixed and Markovian switching topologies, respectively. Each agent can obtain full state of itself and receive its neighbors’ state with noises, where intensities of noises are vector functions of relative states of agents. Bearing in mind the above constrains, a consensus protocol is proposed, where the gain matrix is obtained by the algebraic Riccati equation and the coupling strength is restricted in a given interval. By using the stochastic stability theorem, we show that mean square consensus is achieved in fixed topology case and switching topologies case, respectively. Furthermore, an estimation of the exponential convergence rate of consensus is given explicitly. Finally, simulation examples are given to show the correctness of the proposed results.
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Horiuchi, Masahiro, and Koichi Okita. "Blood Flow Restricted Exercise and Vascular Function." International Journal of Vascular Medicine 2012 (2012): 1–17. http://dx.doi.org/10.1155/2012/543218.
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It is established that regular aerobic training improves vascular function, for example, endothelium-dependent vasodilatation and arterial stiffness or compliance and thereby constitutes a preventative measure against cardiovascular disease. In contrast, high-intensity resistance training impairs vascular function, while the influence of moderate-intensity resistance training on vascular function is still controversial. However, aerobic training is insufficient to inhibit loss in muscular strength with advancing age; thus, resistance training is recommended to prevent sarcopenia. Recently, several lines of study have provided compelling data showing that exercise and training with blood flow restriction (BFR) leads to muscle hypertrophy and strength increase. As such, BFR training might be a novel means of overcoming the contradiction between aerobic and high-intensity resistance training. Although it is not enough evidence to obtain consensus about impact of BFR training on vascular function, available evidences suggested that BFR training did not change coagulation factors and arterial compliance though with inconsistence results in endothelial function. This paper is a review of the literature on the impact of BFR exercise and training on vascular function, such as endothelial function, arterial compliance, or other potential factors in comparison with those of aerobic and resistance training.
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Chen, Kairui, Junwei Wang, Yun Zhang, and Zhi Liu. "Second-order consensus of nonlinear multi-agent systems with restricted switching topology and time delay." Nonlinear Dynamics 78, no. 2 (June 17, 2014): 881–87. http://dx.doi.org/10.1007/s11071-014-1483-1.
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O’Donnell, Kevin, Kevin B. Freedman, and Fotios P. Tjoumakaris. "Rehabilitation Protocols After Isolated Meniscal Repair: A Systematic Review." American Journal of Sports Medicine 45, no. 7 (October 7, 2016): 1687–97. http://dx.doi.org/10.1177/0363546516667578.
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Background: Current postoperative rehabilitation protocols after isolated meniscal repair vary widely. No consensus exists with regard to the optimal amount of weightbearing, range of motion, or speed at which the patient progresses through the rehabilitation phases. Confounding factors including concomitant ligamentous or cartilaginous injuries have made studying isolated meniscal tears problematic. Purpose: To systematically review and evaluate the influence of range of motion and weightbearing status during the postoperative rehabilitation period after isolated meniscal repair on clinical efficacy and outcome scores. Study Design: Systematic review. Methods: A search of PubMed, Scopus, and Cochrane Central Register of Controlled Trials was conducted. The selection criteria for inclusion were English-language in vivo clinical studies reporting on isolated meniscal repairs utilizing an arthroscopically assisted technique that outlined the postoperative rehabilitation protocol and included at least a 2-year follow-up. Titles, abstracts, and articles were reviewed, and data concerning patient demographics, tear type, repair technique, postoperative protocol details, clinical failures, and outcome scores were extracted from the eligible studies. Rehabilitation protocols were divided into “accelerated,” “motion restricted,” “weight restricted,” and “dual restricted” according to the limitations placed on the treatment groups. Results: Fifteen studies, containing 17 different treatment groups, met the inclusion criteria. The 2 accelerated groups, 2 motion-restricted groups, 4 weight-restricted groups, and 9 dual-restricted groups showed similar efficacy in terms of clinical success and postoperative outcome scores. Early range of motion and weightbearing status showed no influence over clinical outcomes. Of the 17 groups, 13 reported a greater than 70% clinical success rate with significant variation in the tear type, fixation technique, and postoperative restrictions. Conclusion: Early range of motion and immediate postoperative weightbearing appear to have no detrimental effect on the chances for clinical success after isolated meniscal repair. Significant variation exists between postoperative protocols, with no current consensus on the ideal parameters for weightbearing and range of motion. Studies reporting outcomes regarding isolated meniscal repair are limited. Future research should include determining the ideal combination of weightbearing and range of motion for specific tear types.
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Altfeld, Marcus, Todd M. Allen, Elizabeth T. Kalife, Nicole Frahm, Marylyn M. Addo, Bianca R. Mothe, Almas Rathod, et al. "The Majority of Currently Circulating Human Immunodeficiency Virus Type 1 Clade B Viruses Fail To Prime Cytotoxic T-Lymphocyte Responses against an Otherwise Immunodominant HLA-A2-Restricted Epitope: Implications for Vaccine Design." Journal of Virology 79, no. 8 (April 15, 2005): 5000–5005. http://dx.doi.org/10.1128/jvi.79.8.5000-5005.2005.
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ABSTRACT Human immunodeficiency virus type 1 (HIV-1) mutates to escape immune selection pressure, but there is little evidence of selection mediated through HLA-A2, the dominant class I allele in persons infected with clade B virus. Moreover, HLA-A2-restricted responses are largely absent in the acute phase of infection as the viral load is being reduced, suggesting that circulating viruses may lack immunodominant epitopes targeted through HLA-A2. Here we demonstrate an A2-restricted epitope within Vpr (Vpr59-67) that is targeted by acute-phase HIV-1-specific CD8+ T cells, but only in a subset of persons expressing HLA-A2. Individuals in the acute stage of infection with viruses containing the most common current sequence within this epitope (consensus sequence) were unable to mount epitope-specific T-cell responses, whereas subjects infected with the less frequent I60L variant all developed these responses. The I60L variant epitope was a stronger binder to HLA-A2 and was recognized by epitope-specific T cells at lower peptide concentrations than the consensus sequence epitope. These data demonstrate that HLA-A2 is capable of contributing to the acute-phase cytotoxic T-lymphocyte response in infected subjects, but that most currently circulating viruses lack a dominant immunogenic epitope presented by this allele, and suggest that immunodominant epitopes restricted by common HLA alleles may be lost as the epidemic matures.
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Davenport, Eddie D., Thomas Syburra, Gary Gray, Rienk Rienks, Dennis Bron, Olivier Manen, Joanna d’Arcy, Norbert J. Guettler, and Edward D. Nicol. "Management of established coronary artery disease in aircrew with previous myocardial infarction or revascularisation." Heart 105, Suppl 1 (November 13, 2018): s31—s37. http://dx.doi.org/10.1136/heartjnl-2018-313055.
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This manuscript focuses on the broad aviation medicine considerations that are required to optimally manage aircrew with established coronary artery disease (CAD) without myocardial infarction (MI) or revascularisation (both pilots and non-pilot aviation professionals). It presents expert consensus opinion and associated recommendations and is part of a series of expert consensus documents covering all aspects of aviation cardiology.Aircrew may present with MI (both ST elevation MI (STEMI) and non-ST elevation MI (NSTEMI)) as the initial presenting symptom of obstructive CAD requiring revascularisation. Management of these individuals should be conducted according to published guidelines, ideally with consultation between the cardiologist, surgeon and aviation medical examiner. Return to restricted flight duties is possible in the majority of aircrew; however, they must have normal cardiac function, acceptable residual disease burden and no residual ischaemia. They must also be treated with aggressive cardiac risk factor modification. Aircrew should be restricted to dual pilot operations in non-high-performance aircraft, with return to flying no sooner than 6 months after the event. At minimum, annual follow-up with routine non-invasive cardiac evaluation is recommended.
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Josephs, Tracy M., Emma J. Grant, and Stephanie Gras. "Molecular challenges imposed by MHC-I restricted long epitopes on T cell immunity." Biological Chemistry 398, no. 9 (August 28, 2017): 1027–36. http://dx.doi.org/10.1515/hsz-2016-0305.
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Abstract It has widely been accepted that major histocompatibility complex class I molecules (MHC-I) are limited to binding small peptides of 8–10 residues in length. However, this consensus has recently been challenged with the identification of longer peptides (≥11 residues) that can also elicit cytotoxic CD8+ T cell responses. Indeed, a growing number of studies demonstrate that these non-canonical epitopes are important targets for the immune system. As long epitopes represent up to 10% of the peptide repertoire bound to MHC-I molecules, here we review their impact on antigen presentation by MHC-I, TCR recognition, and T cell immunity.
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Mei, Xuehui, Zhiyong Yu, Haijun Jiang, and Cheng Hu. "Consensus of high-order feed-forward non-linear systems with low gain and communication constraints." Transactions of the Institute of Measurement and Control 41, no. 4 (July 5, 2018): 1101–9. http://dx.doi.org/10.1177/0142331218780226.
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In this paper, the consensus problem of high-order multi-agent systems with inherent feed-forward delayed non-linear dynamics is investigated. First, a new kind of aperiodically intermittent communication strategy, which can be regarded as an extension of continuous communication, is proposed. The time-varying delay is considered in the multi-agent systems and the delay is not restricted to less than the communication width. Moreover, in order to reach a consensus, the effect of the feed-forward non-linearity and the time-varying delay is eliminated by designing a low-gain control protocol. Based on Lyapunov stability theory, graph theory and inequality techniques, some sufficient conditions related to the input gain and the communication width are obtained for achieving the consensus. Finally, a simulation example is presented to demonstrate the effectiveness of the proposed method.
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Khan, Misbah, Frank den Hartog, and Jiankun Hu. "A Survey and Ontology of Blockchain Consensus Algorithms for Resource-Constrained IoT Systems." Sensors 22, no. 21 (October 26, 2022): 8188. http://dx.doi.org/10.3390/s22218188.
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The basic properties of blockchain, such as decentralization, security, and immutability, show promising potential for IoT applications. The main feature—decentralization of blockchain technology—depends on the consensus. However, consensus algorithms are mostly designed to work in extensive computational and communication environments for network security and immutability, which is not desirable for resource-restricted IoT applications. Many solutions are proposed to address this issue with modified consensus algorithms based on the legacy consensus, such as the PoW, PoS, and BFT, and new non-linear data structures, such as DAG. A systematic classification and analysis of various techniques in the field will be beneficial for both researchers and industrial practitioners. Most existing relevant surveys provide classifications intuitively based on the domain knowledge, which are infeasible to reveal the intrinsic and complicated relationships among the relevant basic concepts and techniques. In this paper, a powerful tool of systematic knowledge classification and explanation is introduced to structure the survey on blockchain consensus algorithms for resource-constrained IoT systems. More specifically, an ontology was developed for a consensus algorithm apropos of IoT adaptability. The developed ontology is subdivided into two parts—CONB and CONIoT—representing the classification of generic consensus algorithms and the ones that are particularly proposed for IoT, respectively. Guided by this ontology, an in depth discussion and analysis are provided on the major consensus algorithms and their IoT compliance based on design and implementation targets. Open research challenges and future research directions are provided.
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Jones, Karen. "Quick and Smart? Modularity and the Pro-Emotion Consensus." Canadian Journal of Philosophy Supplementary Volume 32 (2006): 3–27. http://dx.doi.org/10.1353/cjp.2007.0031.
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Within both philosophy and psychology, a new pro-emotion consensus is replacing the old dogmas that emotions disrupt practical rationality, that they are at best arational, if not outright irrational, and that we can understand what is really central to human cognition without studying them. Emotions are now commonly viewed as evolved capacities that are integral to our practical rationality. An infinite mind, unencumbered by a body, might get along just fine without emotions; but we finite embodied creatures need them if we are to be capable of responding appropriately to our reasons and navigating in a risky world with poor information, limited attention, and restricted computational power. Emotions are clever design solutions to the problem of making fast decisions in response to significant practical problems posed by the natural and social worlds: we perceive a danger and fear immediately primes us to take protective action. On this view, the theory of emotions is an essential part of a theory of ecologically situated and constrained rationality - that is to say, of human rationality (Samuels et al. 1999; Gigerenzer 2000).
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Freeman, Michael. "Democracy and Dynamite: The Peoples' Right to Self-Determination." Political Studies 44, no. 4 (September 1996): 746–61. http://dx.doi.org/10.1111/j.1467-9248.1996.tb01754.x.
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The right to self-determination is a potent and paradoxical political concept. It is associated with democracy, xenophobia and anarchy. Its explosive potential was more or less held in check during the Cold War by an international consensus that restricted it to the context of decolonization. The unravelling of the Soviet Union and the break-up of Yugoslavia have demonstrated the inadequacy of the available theory and practice. Various recent approaches to self-determination are reviewed. These may be roughly classified as realist, liberal and communitarian. Although no approach is wholly satisfactory, the key issues can now be more clearly stated, an emerging consensus identified, and the agenda for further theoretical work proposed.
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Choi, Jong Han, Jee-Hyun Kang, and Suk Chon. "Comprehensive Understanding for Application in Korean Patients with Type 2 Diabetes Mellitus of the Consensus Statement on Carbohydrate-Restricted Diets by Korean Diabetes Association, Korean Society for the Study of Obesity, and Korean Society of Hypertension." Diabetes & Metabolism Journal 46, no. 3 (May 31, 2022): 377–90. http://dx.doi.org/10.4093/dmj.2022.0051.
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The Joint Committee of the Korean Diabetes Association, the Korean Society for the Study of Obesity, and the Korean Society of Hypertension announced a consensus statement on carbohydrate-restricted diets and intermittent fasting, representing an emerging and popular dietary pattern. In this statement, we recommend moderately-low-carbohydrate or low-carbohydrate diets, not a very-low-carbohydrate diet, for patients with type 2 diabetes mellitus. These diets can be considered a dietary regimen to improve glycemic control and reduce body weight in adults with type 2 diabetes mellitus. This review provides the detailed results of a meta-analysis and systematic literature review on the potential harms and benefits of carbohydrate-restricted diets in patients with diabetes. We expect that this review will help experts and patients by fostering an in-depth understanding and appropriate application of carbohydrate-restricted diets in the comprehensive management of diabetes.
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Kawase, Takakazu, Yoshiki Akatsuka, Hiroki Torikai, Satoko Morishima, Yoshihisa Kodera, Yasuo Morishima, Kiyotaka Kuzushima, and Toshitada Takahashi. "Alternative Splicing Due to an Intronic SNP Defines a Novel HLA-B44-Restricted-Hematopoiesis-Restricted Minor Histocompatibility Antigen." Blood 108, no. 11 (November 16, 2006): 3229. http://dx.doi.org/10.1182/blood.v108.11.3229.3229.
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Abstract Minor histocompatibility antigens (mHAgs) with expression limited to hematopoietic cells represent attractive targets for immunotherapy to induce selective graft-versus-leukemia (GVL) reactions. Here we report the identification of a novel mHAg which is recognized by an HLA-B*4403-restricted CTL clone. Microsatellite allele image analysis of two DNA pools generated from CTL-defined mHAg positive and mHAg negative groups was performed using microsatellite markers set at 100 kb intervals within the segment initially mapped by two-point genetic linkage analysis and detailed mapping of the chromosomal recombinant points. This approach defined a 0.53 Mbp region of chromosome 18q21–22 containing 12 candidate genes potentially encoding the mHAg, although the target gene could not be identified. Subsequently, cDNA expression cloning studies demonstrated that the CTL epitope of interest was encoded by a novel allelic splice variant of XM_209104, hereafter designated as XM_209104-av. Indeed, this gene was found to lie within the region predicted by microsatellite allele image analysis. The immunogenicity of the epitope was generated by differential protein expression due to alternative splicing, which was completely controlled by one intronic single nucleotide polymorphism (SNP) located in the consensus 5′ splice site adjacent to an exon. To our knowledge, this is the first example of a mHAg controlled by a SNP located in a region other than coding sequences. Because the CTL lysed also HLA-B*4402 positive, mHAg positive B-LCLs, this novel epitope peptide can bind to not only HLA-B*4403 but also HLA-B*4402 which is a relatively common HLA-B allele in Caucasian populations. Finally, the finding that the novel XM_209104-av showed low or no expression in normal tissues including resting hematopoietic cells, but significantly higher expression in primary acute leukemia cells, especially those of myeloid lineage, suggest that this novel epitope may be an attractive therapeutic target for immunotherapy not only as a minor H antigen but also as a leukemia-associated antigen.
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Zhang, Xiaoshuai, Chao Liu, Kok Keong Chai, and Stefan Poslad. "A Challenge-Response Assisted Authorisation Scheme for Data Access in Permissioned Blockchains." Sensors 20, no. 17 (August 19, 2020): 4681. http://dx.doi.org/10.3390/s20174681.
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Permissioned blockchains can be applied for sharing data among permitted users to authorise the data access requests in a permissioned blockchain. A consensus network constructed using pre-selected nodes should verify a data requester’s credentials to determine if he or she have the correct permissions to access the queried data. However, current studies do not consider how to protect users’ privacy for data authorisation if the pre-selected nodes become untrusted, e.g., the pre-selected nodes are manipulated by attackers. When a user’s credentials are exposed to pre-selected nodes in the consensus network during authorisation, the untrusted (or even malicious) pre-selected nodes may collect a user’s credentials and other private information without the user’s right to know. Therefore, the private data exposed to the consensus network should be tightly restricted. In this paper, we propose a challenge-response based authorisation scheme for permissioned blockchain networks named Challenge-Response Assisted Access Authorisation (CRA3) to protect users’ credentials during authorisation. In CRA3, the pre-selected nodes in the consensus network do not require users’ credentials to authorise data access requests to prevent privacy leakage when these nodes are compromised or manipulated by attackers. Furthermore, the computational burden on the consensus network for authorisation is reduced because the major computing work of the authorisation is executed by the data requester and provider in CRA3.
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Jacquet, Marie-Ange, Ricardo Ehrlich, and Claude Reiss. "In vivogene expression directed by synthetic promoter constructions restricted to the −10 and −35 consensus hexamers ofE.coli." Nucleic Acids Research 17, no. 8 (1989): 2933–45. http://dx.doi.org/10.1093/nar/17.8.2933.
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Jiang, Shi-Wen, Dinakar Desai, Sohail Khan, and Norman L. Eberhardt. "Cooperative Binding of TEF-1 to Repeated GGAATG-Related Consensus Elements with Restricted Spatial Separation and Orientation." DNA and Cell Biology 19, no. 8 (August 2000): 507–14. http://dx.doi.org/10.1089/10445490050128430.
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Deng, Kaiping, Robert J. Blick, Wei Liu, and Eric J. Hansen. "Identification of Francisella tularensis Genes Affected by Iron Limitation." Infection and Immunity 74, no. 7 (July 2006): 4224–36. http://dx.doi.org/10.1128/iai.01975-05.
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ABSTRACT Cells of an attenuated live vaccine strain (LVS) of F. tularensis grown under iron-restricted conditions were found to contain increased quantities of several proteins relative to cells of this same strain grown under iron-replete conditions. Mass spectrometric analysis identified two of these proteins as IglC and PdpB, both of which are encoded by genes located in a previously identified pathogenicity island in F. tularensis LVS. Regions with homology to the consensus Fur box sequence were located immediately in front of the iglC and pdpB open reading frames (ORFs), and in silico analysis of the F. tularensis Schu4 genome detected a number of predicted 5′ untranslated regions that contained putative Fur boxes. The putative Fur box preceding Francisella iron-regulated gene A (figA) had the highest degree of identity with the consensus Fur box sequence. DNA microarray analysis showed that nearly 80 of the genes in the F. tularensis LVS genome were up- or down-regulated at least twofold under iron-restricted growth conditions. When tested for possible siderophore production by means of the Chrome Azurol S assay, a wild-type F. novicida strain produced a large reaction zone whereas its figA mutant produced very little reactivity in this assay. In addition, a cross-feeding experiment demonstrated that this siderophore-like activity produced by the wild-type F. novicida strain could enhance the ability of the F. novicida figA mutant to grow under iron-restricted conditions. This study provides the first identification of iron-regulated genes in F. tularensis LVS and evidence for the production of a siderophore-like molecule by F. novicida.
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Wang, Xixi, and Yepeng Guan. "A Hierarchy Byzantine Fault Tolerance Consensus Protocol Based on Node Reputation." Sensors 22, no. 15 (August 6, 2022): 5887. http://dx.doi.org/10.3390/s22155887.
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A blockchain has been applied in many areas, such as cryptocurrency, smart cities and digital finance. The consensus protocol is the core part of the blockchain network, which addresses the problem of transaction consistency among the involved participants. However, the scalability, efficiency and security of the consensus protocol are greatly restricted with the increasing number of nodes. A Hierarchy Byzantine Fault Tolerance consensus protocol (HBFT) based on node reputation has been proposed. The two-layer hierarchy structure is designed to improve the scalability by assigning nodes to different layers. Each node only needs to exchange messages within its group, which deducts the communication complexity between nodes. Specifically, a reputation model is proposed to distinguish normal nodes from malicious ones by a punish and reward mechanism. It is applied to ensure that the malicious node merely existing in the bottom layer and the communication complexity in the high layer can be further lowered. Finally, a random selection mechanism is applied in the selection of the leader node. The mechanism can ensure the security of the blockchain network with the characteristics of unpredictability and randomicity. Some experimental results demonstrated that the proposed consensus protocol has excellent performance in comparison to some state-of-the-art models.
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Martorana, Margherita, Tobias Kuhn, Ronald Siebes, and Jacco van Ossenbruggen. "Aligning restricted access data with FAIR: a systematic review." PeerJ Computer Science 8 (July 20, 2022): e1038. http://dx.doi.org/10.7717/peerj-cs.1038.
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Understanding the complexity of restricted research data is vitally important in the current new era of Open Science. While the FAIR Guiding Principles have been introduced to help researchers to make data Findable, Accessible, Interoperable and Reusable, it is still unclear how the notions of FAIR and Openness can be applied in the context of restricted data. Many methods have been proposed in support of the implementation of the principles, but there is yet no consensus among the scientific community as to the suitable mechanisms of making restricted data FAIR. We present here a systematic literature review to identify the methods applied by scientists when researching restricted data in a FAIR-compliant manner in the context of the FAIR principles. Through the employment of a descriptive and iterative study design, we aim to answer the following three questions: (1) What methods have been proposed to apply the FAIR principles to restricted data?, (2) How can the relevant aspects of the methods proposed be categorized?, (3) What is the maturity of the methods proposed in applying the FAIR principles to restricted data?. After analysis of the 40 included publications, we noticed that the methods found, reflect the stages of the Data Life Cycle, and can be divided into the following Classes: Data Collection, Metadata Representation, Data Processing, Anonymization, Data Publication, Data Usage and Post Data Usage. We observed that a large number of publications used ‘Access Control‘ and ‘Usage and License Terms’ methods, while others such as ‘Embargo on Data Release’ and the use of ‘Synthetic Data’ were used in fewer instances. In conclusion, we are presenting the first extensive literature review on the methods applied to confidential data in the context of FAIR, providing a comprehensive conceptual framework for future research on restricted access data.
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Ko, L. J., and J. D. Engel. "DNA-binding specificities of the GATA transcription factor family." Molecular and Cellular Biology 13, no. 7 (July 1993): 4011–22. http://dx.doi.org/10.1128/mcb.13.7.4011-4022.1993.
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Members of the GATA family of transcription factors, which are related by a high degree of amino acid sequence identity within their zinc finger DNA-binding domains, each show distinct but overlapping patterns of tissue-restricted expression. Although GATA-1, -2, and -3 have been shown to recognize a consensus sequence derived from regulatory elements in erythroid cell-specific genes, WGATAR (in which W indicates A/T and R indicates A/G), the potential for more subtle differences in the binding preferences of each factor has not been previously addressed. By employing a binding selection and polymerase chain reaction amplification scheme with randomized oligonucleotides, we have determined the binding-site specificities of bacterially expressed chicken GATA-1, -2, and -3 transcription factors. Whereas all three GATA factors bind an AGATAA erythroid consensus motif with high affinity, a second, alternative consensus DNA sequence, AGATCTTA, is also recognized well by GATA-2 and GATA-3 but only poorly by GATA-1. These studies suggest that all three GATA factors are capable of mediating transcriptional effects via a common erythroid consensus DNA-binding motif. Furthermore, GATA-2 and GATA-3, because of their distinct expression patterns and broader DNA recognition properties, may be involved in additional regulatory processes beyond those of GATA-1. The definition of an alternative GATA-2-GATA-3 consensus sequence may facilitate the identification of new target genes in the further elucidation of the roles that these transcription factors play during development.
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Ko, L. J., and J. D. Engel. "DNA-binding specificities of the GATA transcription factor family." Molecular and Cellular Biology 13, no. 7 (July 1993): 4011–22. http://dx.doi.org/10.1128/mcb.13.7.4011.
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Members of the GATA family of transcription factors, which are related by a high degree of amino acid sequence identity within their zinc finger DNA-binding domains, each show distinct but overlapping patterns of tissue-restricted expression. Although GATA-1, -2, and -3 have been shown to recognize a consensus sequence derived from regulatory elements in erythroid cell-specific genes, WGATAR (in which W indicates A/T and R indicates A/G), the potential for more subtle differences in the binding preferences of each factor has not been previously addressed. By employing a binding selection and polymerase chain reaction amplification scheme with randomized oligonucleotides, we have determined the binding-site specificities of bacterially expressed chicken GATA-1, -2, and -3 transcription factors. Whereas all three GATA factors bind an AGATAA erythroid consensus motif with high affinity, a second, alternative consensus DNA sequence, AGATCTTA, is also recognized well by GATA-2 and GATA-3 but only poorly by GATA-1. These studies suggest that all three GATA factors are capable of mediating transcriptional effects via a common erythroid consensus DNA-binding motif. Furthermore, GATA-2 and GATA-3, because of their distinct expression patterns and broader DNA recognition properties, may be involved in additional regulatory processes beyond those of GATA-1. The definition of an alternative GATA-2-GATA-3 consensus sequence may facilitate the identification of new target genes in the further elucidation of the roles that these transcription factors play during development.
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Nakaseko, Chiaki, Daijiro Abe, Masahiro Takeuchi, Yusuke Takeda, Hiroaki Tanaka, Kayo Oda, Chikako Ohwada, et al. "Restricted Oligo-Clonal Usage of Monoclonal Immunoglobulin λ Light Chain Germline in POEMS Syndrome." Blood 110, no. 11 (November 16, 2007): 2483. http://dx.doi.org/10.1182/blood.v110.11.2483.2483.
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Abstract Background: POEMS syndrome (also known as Crow-Fukase or Takatsuki syndrome) is a rare plasma cell disorder characterized by peripheral neuropathy, a monoclonal plasma cell disorder, and other paraneoplastic features including organomegaly, endocrinopathy, skin changes, edema and effusions. High levels of vascular endothelial growth factor (VEGF) in the serum may contribute to pathology seen in this disease but exact pathogenetic mechanisms are still unclear. A unique feature of this syndrome is that the proliferating monoclonal plasma cells are virtually always λ-restricted. Here, we determined complete nucleotide sequences of monoclonal immunoglobulin λ light chain (IGL) variable regions in 10 patients with POEMS syndrome and found that Vλ germline usage is highly restricted to the Vλ1 family and oligoclonal germlines. Materials and methods: Total RNA was extracted from bone marrow mononuclear cells of patients with POEMS syndrome and the V-J region of the IGL gene was amplified by RT-PCR using 5′ degenerative primers for the Vλ consensus leader lesion (5′-ATGGCCKGSWYYSYTCTCCTC-3′) and 3′ primers matching the consensus upstream part of the cl exon (5′-CTCCCGGGTAGAGAAGTCACT-3′). Monoclonal bands were detected by heteroduplex analysis or TA cloning and subjected to nucleotide sequencing. Sequence data were analyzed using the International ImMunoGeneTics information system (IMGT, http://imgt.cines.fr) and mutations were identified by comparison with the germline sequence databases. Results: Of 13 POEMS syndrome patients with λ-type M protein, nucleotide sequencing of the IGL gene was successful in 10. The V-region of the IGL gene of all 10 patients was restricted to the Vλ1 family. Searching for homologies with IGL germlines revealed that only two were used, with an average homology of 90.1%. IGLV1-40*01 was used in 8 patients and IGLV1-44*01 in the remaining two. In the IGL-J region, the IGLJ3 gene was found in 9 of 10 patients and IGLJ2 in one (10%). All IGLV-J rearrangements were mutated with homologies to the germline sequence ranging from 77.66% to 96.10% (average homology: 90.1%). All CDR3 were composed of 11 amino acids, with identical acidic isoelectric point (pI) values (13.0) and similar molecular weights ranging from 1394.7 to 1552.8 (median, 1506.2). Conclusions: IGL-M protein in POEMS syndrome belongs to the Vλ1 family and is markedly restricted to specific oligoclonal germlines. Our results suggest that the restricted use of IGL plays an important role in the pathogenesis of POEMS syndrome. These data provide an important insight for elucidating the pathogenesis of POEMS syndrome. To the best of our knowledge, this the first report of restricted oligo-clonal usage of monoclonal immunoglobulin germlines in plasma cell disorders.
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Tan, Xiao, Jianjun Zhu, and Tong Wu. "Dynamic Reference Point-Oriented Consensus Mechanism in Linguistic Distribution Group Decision Making Restricted by Quantum Integration of Information." Group Decision and Negotiation 31, no. 2 (February 24, 2022): 491–528. http://dx.doi.org/10.1007/s10726-022-09775-0.
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Peluso, Augusto, Mads V. Damgaard, Marcelo A. S. Mori, and Jonas T. Treebak. "Age-Dependent Decline of NAD+—Universal Truth or Confounded Consensus?" Nutrients 14, no. 1 (December 27, 2021): 101. http://dx.doi.org/10.3390/nu14010101.
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Nicotinamide adenine dinucleotide (NAD+) is an essential molecule involved in various metabolic reactions, acting as an electron donor in the electron transport chain and as a co-factor for NAD+-dependent enzymes. In the early 2000s, reports that NAD+ declines with aging introduced the notion that NAD+ metabolism is globally and progressively impaired with age. Since then, NAD+ became an attractive target for potential pharmacological therapies aiming to increase NAD+ levels to promote vitality and protect against age-related diseases. This review summarizes and discusses a collection of studies that report the levels of NAD+ with aging in different species (i.e., yeast, C. elegans, rat, mouse, monkey, and human), to determine whether the notion that overall NAD+ levels decrease with aging stands true. We find that, despite systematic claims of overall changes in NAD+ levels with aging, the evidence to support such claims is very limited and often restricted to a single tissue or cell type. This is particularly true in humans, where the development of NAD+ levels during aging is still poorly characterized. There is a need for much larger, preferably longitudinal, studies to assess how NAD+ levels develop with aging in various tissues. This will strengthen our conclusions on NAD metabolism during aging and should provide a foundation for better pharmacological targeting of relevant tissues.
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Mihai, Radu, Gianluca Donatini, Oscar Vidal, and Laurent Brunaud. "Volume-outcome correlation in adrenal surgery—an ESES consensus statement." Langenbeck's Archives of Surgery 404, no. 7 (November 2019): 795–806. http://dx.doi.org/10.1007/s00423-019-01827-5.
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Abstract Background Published data in the last decade showed that a majority of adrenal operations are done by surgeons performing only one such case per year and based on the distribution of personal workloads ‘high-volume’ surgeons are defined as those doing 4 or more cases/year. Purpose This paper summarises literature data identified by a working group established by the European Society of Endocrine Surgeons (ESES). The findings were discussed during ESES-2019 conference and members agreed on a consensus statement. Results The annual of adrenal operations performed yearly in individual countries was reported to be 800/year in UK and over 1600/year in France. The learning curve of an individual surgeon undertaking laparoscopic, retroperitoneoscopic or robotic adrenalectomy is estimated to be 20–40 cases. Preoperative morbidity and length of stay are more favourable in high-volume centres. Conclusion The main recommendations are that adrenal surgery should continue only in centres performing at least 6 cases per year, surgery for adrenocortical cancer should be restricted to centres performing at least 12 adrenal operations per year, and an integrated multidisciplinary team should be established in all such centres. Clinical information regarding adrenalectomies should be recorded prospectively and contribution to the established EUROCRINE and ENSAT databases is strongly encouraged. Surgeons wishing to develop expertise in this field should seek mentorship and further training from established adrenal surgeons.
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Murnaghan, Chantelle D., Jordan W. Squair, Romeo Chua, J. Timothy Inglis, and Mark G. Carpenter. "Cortical contributions to control of posture during unrestricted and restricted stance." Journal of Neurophysiology 111, no. 9 (May 1, 2014): 1920–26. http://dx.doi.org/10.1152/jn.00853.2012.
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There is very little consensus regarding the mechanisms underlying postural control. Whereas some theories suggest that posture is controlled at lower levels (i.e., brain stem and spinal cord), other theories have proposed that upright stance is controlled using higher centers, including the motor cortex. In the current investigation, we used corticomuscular coherence (CMC) to investigate the relationship between cortical and shank muscle activity during conditions of unrestricted and restricted postural sway. Participants were instructed to stand as still as possible in an apparatus that allowed the center of mass to move freely (“Unlocked”) or to be stabilized (“Locked”) without subject awareness. EEG (Cz) and electromyography (soleus and lateral/medial gastrocnemii) were collected and used to estimate CMC over the Unlocked and Locked periods. Confirming our previous results, increases in center of pressure (COP) displacements were observed in 9 of 12 participants in the Locked compared with Unlocked condition. Across these 9 participants, CMC was low or absent in both the Unlocked and Locked conditions. The results from the current study suggest that this increase is not associated with an increase in the relationship between cortical and shank muscle activities. Rather, it may be that increases in COP displacement with locking are mediated by subcortical structures as a means of increasing sway to provide the central nervous system with a critical level of sensory information.
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Salloum, Shadi, Cesar Oniangue-Ndza, Christoph Neumann-Haefelin, Laura Hudson, Silvia Giugliano, Marc aus dem Siepen, Jacob Nattermann, et al. "Escape from HLA-B*08-Restricted CD8 T Cells by Hepatitis C Virus Is Associated with Fitness Costs." Journal of Virology 82, no. 23 (September 24, 2008): 11803–12. http://dx.doi.org/10.1128/jvi.00997-08.
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ABSTRACT The inherent sequence diversity of the hepatitis C virus (HCV) represents a major hurdle for the adaptive immune system to control viral replication. Mutational escape within targeted CD8 epitopes during acute HCV infection has been well documented and is one possible mechanism for T-cell failure. HLA-B*08 was recently identified as one HLA class I allele associated with spontaneous clearance of HCV replication. Selection of escape mutations in the immunodominant HLA-B*08-restricted epitope HSKKKCDEL1395-1403 was observed during acute infection. However, little is known about the impact of escape mutations in this epitope on viral replication capacity. Their previously reported reversion back toward the consensus residue in patients who do not possess the B*08 allele suggests that the consensus sequence in this epitope is advantageous for viral replication in the absence of immune pressure. The aim of this study was to determine the impact of mutational escape from this immunodominant epitope on viral replication. We analyzed it with a patient cohort with chronic HCV genotype 1b infection and in a single-source outbreak (genotype 1b). Sequence changes in this highly conserved region are rare and selected almost exclusively in the presence of the HLA-B*08 allele. When tested in the subgenomic replicon (Con1), the observed mutations reduce viral replication compared with the prototype sequence. The results provide direct evidence that escape mutations in this epitope are associated with fitness costs and that the antiviral effect of HLA-B*08-restricted T cells is sufficiently strong to force the virus to adopt a relatively unfavorable sequence.
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Chan, Alexandre, Matin M. Abdullah, Wan Zamaniah B. Wan Ishak, Annielyn B. Ong-Cornel, Antonio H. Villalon, and Ravindran Kanesvaran. "Applicability of the National Comprehensive Cancer Network/Multinational Association of Supportive Care in Cancer Guidelines for Prevention and Management of Chemotherapy-Induced Nausea and Vomiting in Southeast Asia: A Consensus Statement." Journal of Global Oncology 3, no. 6 (December 2017): 801–13. http://dx.doi.org/10.1200/jgo.2016.005728.
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A meeting of regional experts was convened in Manila, Philippines, to develop a resource-stratified chemotherapy-induced nausea and vomiting (CINV) management guideline. In patients treated with highly emetogenic chemotherapy in general clinical settings, triple therapy with a serotonin (5-hydroxytryptamine-3 [5-HT3]) antagonist (preferably palonosetron), dexamethasone, and aprepitant is recommended for acute CINV prevention. In resource-restricted settings, triple therapy is still recommended, although a 5-HT3 antagonist other than palonosetron may be used. In both general and resource-restricted settings, dual therapy with dexamethasone (days 2 to 4) and aprepitant (days 2 to 3) is recommended to prevent delayed CINV. In patients treated with moderately emetogenic chemotherapy, dual therapy with a 5-HT3 antagonist, preferably palonosetron, and dexamethasone is recommended for acute CINV prevention in general settings; any 5-HT3 antagonist can be combined with dexamethasone in resource-restricted environments. In general settings, for the prevention of delayed CINV associated with moderately emetogenic chemotherapy, corticosteroid monotherapy on days 2 and 3 is recommended. If aprepitant is used on day 1, it should be continued on days 2 and 3. Prevention of delayed CINV with corticosteroids is preferred in resource-restricted settings. The expert panel also developed CINV management guidelines for anthracycline plus cyclophosphamide combination schedules, multiday cisplatin, and chemotherapy with low or minimal emetogenic potential, and its recommendations are detailed in this review. Overall, these regional guidelines provide definitive guidance for CINV management in general and resource-restricted settings. These consensus recommendations are anticipated to contribute to collaborative efforts to improve CINV management in Southeast Asia.
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Schipper, Hyman M. "Biological Markers and Alzheimer Disease: A Canadian Perspective." International Journal of Alzheimer's Disease 2010 (2010): 1–7. http://dx.doi.org/10.4061/2010/978182.
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Decreased -amyloid1-42and increased phospho-tau protein levels in the cerebrospinal fluid (CSF) are currently the most accurate chemical neurodiagnostics of sporadic Alzheimer disease (AD). A report (2007) of the Third Canadian Consensus Conference on the Diagnosis and Treatment of Dementia (2006) recommended that biological markers shouldnotbe currently requisitioned by primary care physicians in the routine investigation of subjects with memory complaints. Consideration for such testing should prompt patient referral to a specialist engaged in dementia evaluations or a Memory Clinic. The specialist should consider having CSF biomarkers (-amyloid1-42and phospho-tau) measured at a reputable facility in restricted cases presenting with atypical features and diagnostic confusion, but not as a routine procedure in all individuals with typical sporadic AD phenotypes. We submit that developments in the field of AD biomarker discovery since publication of the 3rd CCCDTD consensus data do not warrant revision of the 2007 recommendations.
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Mukhtyar, C., L. Guillevin, M. C. Cid, B. Dasgupta, K. de Groot, W. Gross, T. Hauser, et al. "EULAR recommendations for the management of large vessel vasculitis." Annals of the Rheumatic Diseases 68, no. 3 (April 15, 2008): 318–23. http://dx.doi.org/10.1136/ard.2008.088351.
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Objectives:To develop European League Against Rheumatism (EULAR) recommendations for the management of large vessel vasculitis.Methods:An expert group (10 rheumatologists, 3 nephrologists, 2 immunolgists, 2 internists representing 8 European countries and the USA, a clinical epidemiologist and a representative from a drug regulatory agency) identified 10 topics for a systematic literature search through a modified Delphi technique. In accordance with standardised EULAR operating procedures, recommendations were derived for the management of large vessel vasculitis. In the absence of evidence, recommendations were formulated on the basis of a consensus opinion.Results:Seven recommendations were made relating to the assessment, investigation and treatment of patients with large vessel vasculitis. The strength of recommendations was restricted by the low level of evidence and EULAR standardised operating procedures.Conclusions:On the basis of evidence and expert consensus, management recommendations for large vessel vasculitis have been formulated and are commended for use in everyday clinical practice.
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Bursill, David, William J. Taylor, Robert Terkeltaub, Abhishek Abhishek, Alexander K. So, Ana Beatriz Vargas-Santos, Angelo Lino Gaffo, et al. "Gout, Hyperuricaemia and Crystal-Associated Disease Network (G-CAN) consensus statement regarding labels and definitions of disease states of gout." Annals of the Rheumatic Diseases 78, no. 11 (September 9, 2019): 1592–600. http://dx.doi.org/10.1136/annrheumdis-2019-215933.
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ObjectiveThere is a lack of standardisation in the terminology used to describe gout. The aim of this project was to develop a consensus statement describing the recommended nomenclature for disease states of gout.MethodsA content analysis of gout-related articles from rheumatology and general internal medicine journals published over a 5-year period identified potential disease states and the labels commonly assigned to them. Based on these findings, experts in gout were invited to participate in a Delphi exercise and face-to-face consensus meeting to reach agreement on disease state labels and definitions.ResultsThe content analysis identified 13 unique disease states and a total of 63 unique labels. The Delphi exercise (n=76 respondents) and face-to-face meeting (n=35 attendees) established consensus agreement for eight disease state labels and definitions. The agreed labels were as follows: ‘asymptomatic hyperuricaemia’, ‘asymptomatic monosodium urate crystal deposition’, ‘asymptomatic hyperuricaemia with monosodium urate crystal deposition’, ‘gout’, ‘tophaceous gout’, ‘erosive gout’, ‘first gout flare’ and ‘recurrent gout flares’. There was consensus agreement that the label ‘gout’ should be restricted to current or prior clinically evident disease caused by monosodium urate crystal deposition (gout flare, chronic gouty arthritis or subcutaneous tophus).ConclusionConsensus agreement has been established for the labels and definitions of eight gout disease states, including ‘gout’ itself. The Gout, Hyperuricaemia and Crystal-Associated Disease Network recommends the use of these labels when describing disease states of gout in research and clinical practice.
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Pina-Oliveira, Alfredo Almeida, Roseli Lana Moreira, Rosemary Aparecida Fracolli Pécora, and Anna Maria Chiesa. "Analysis of the process of translation of knowledge regarding early childhood at the undergraduate level." Revista da Escola de Enfermagem da USP 48, spe (August 2014): 160–67. http://dx.doi.org/10.1590/s0080-623420140000600023.
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Objective To analyze innovative contents on Early Child Development Promotion. Method This action-research involves nine faculties from four Higher Education Institutions at inner-state of São Paulo, Brazil.Data were collected by syllabi analyses (2009-2011), interviews and focus group. We have adopted an ECDP underpinning from international consensus, thus evaluating KT Results We have found relevant incorporation between teaching and extension in Nursing (87,5%) and Psychology (75%) undergraduate courses, while Pedagogy was restricted to teaching. Conclusion This KT evaluation has evinced innovative potential of extension, regardless teaching and research, for a better Early Childhood.
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Flamant, F., C. C. Gurin, and J. A. Sorge. "An embryonic DNA-binding protein specific for the promoter of the retrovirus long terminal repeat." Molecular and Cellular Biology 7, no. 10 (October 1987): 3548–53. http://dx.doi.org/10.1128/mcb.7.10.3548-3553.1987.
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Retrovirus expression is restricted in embryonal carcinoma (EC) cells but not in many differentiated cell lines. We used a very sensitive gel retardation assay to detect sequence-specific DNA-binding proteins in crude nuclear extracts obtained from EC and differentiated cells. Four binding sites were mapped in the noncoding sequences of the amphotropic murine leukemia virus. Strong binding to the CCAAT consensus sequence located in the promoter was specifically observed with EC nuclear extract. The binding protein is called EPBF (embryonal promoter-binding factor), and it is a candidate for the repressor of retrovirus transcription.
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Flamant, F., C. C. Gurin, and J. A. Sorge. "An embryonic DNA-binding protein specific for the promoter of the retrovirus long terminal repeat." Molecular and Cellular Biology 7, no. 10 (October 1987): 3548–53. http://dx.doi.org/10.1128/mcb.7.10.3548.
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Retrovirus expression is restricted in embryonal carcinoma (EC) cells but not in many differentiated cell lines. We used a very sensitive gel retardation assay to detect sequence-specific DNA-binding proteins in crude nuclear extracts obtained from EC and differentiated cells. Four binding sites were mapped in the noncoding sequences of the amphotropic murine leukemia virus. Strong binding to the CCAAT consensus sequence located in the promoter was specifically observed with EC nuclear extract. The binding protein is called EPBF (embryonal promoter-binding factor), and it is a candidate for the repressor of retrovirus transcription.
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Lazebnik, L. B., E. V. Golovanova, S. A. Alekseenko, A. O. Bueverov, E. Y. Plotnikova, A. I. Dolgushina, L. Y. Ilchenko, et al. "Russian Consensus on “Hyperammonemia in Adults”: The 2021 Version (in English)." Experimental and Clinical Gastroenterology, no. 12 (January 16, 2022): 154–72. http://dx.doi.org/10.31146/1682-8658-ecg-196-12-154-172.
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Hyperammonemia is an acute or chronic intoxication with ammonia and ammonium associated with elevated ammonia levels in serum due to either its increased production and/or decreased detoxification. Hyperammonemia can result from a variety of causes and clinically presents with unspecific signs and symptoms, including asthenia, encephalopathy, liver steatosis or fibrosis, and sarcopenia. With impaired liver function, hyperammonemia most frequently manifests in (micro)encephalopathy. Thus in case of unexpect change in mental status hyperammonemia must be excluded as fast as possible. An express method of photometric assay is informative enough to determine the ammonia levels. The following hyperammonemia classification is proposed: a) by ammonia levels (normal level: ≤ 60 μmol/L; mild (Grade 1): ≤ 100 μmol/L; moderate (Grade 2): ≤ 200 μmol/L; and severe (Grade 3): > 200 μmol/L); b) by etiopathogenesis (hereditary (congenital), functional (physiological), acquired (hepatic, extrahepatic, mixed)); c) by clinical presentation (transient, recurrent or persistent, constant (stable, without treatment), covert). Treatment for hyperammonemia is aimed at treating the primary disease and includes a diet that is restricted in animal protein but contains sufficient vegetable protein, limited physical activities, and use of intestinal non-absorbable antibiotics (rifaximin- alpha) as well as pre- and probiotics. L-ornithine- L-aspartate (LOLA) is a baseline therapeutic product administered in a number of scenarios to correct the level of hyperammonemia.
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Mukhtyar, C., L. Guillevin, M. C. Cid, B. Dasgupta, K. de Groot, W. Gross, T. Hauser, et al. "EULAR recommendations for the management of primary small and medium vessel vasculitis." Annals of the Rheumatic Diseases 68, no. 3 (April 15, 2008): 310–17. http://dx.doi.org/10.1136/ard.2008.088096.
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Objectives:To develop European League Against Rheumatism (EULAR) recommendations for the management of small and medium vessel vasculitis.Methods:An expert group (consisting of 10 rheumatologists, 3 nephrologists, 2 immunologists, 2 internists representing 8 European countries and the USA, a clinical epidemiologist and a representative from a drug regulatory agency) identified 10 topics for a systematic literature search using a modified Delphi technique. In accordance with standardised EULAR operating procedures, recommendations were derived for the management of small and medium vessel vasculitis. In the absence of evidence, recommendations were formulated on the basis of a consensus opinion.Results:In all, 15 recommendations were made for the management of small and medium vessel vasculitis. The strength of recommendations was restricted by low quality of evidence and by EULAR standardised operating procedures.Conclusions:On the basis of evidence and expert consensus, recommendations have been made for the evaluation, investigation, treatment and monitoring of patients with small and medium vessel vasculitis for use in everyday clinical practice.
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Cona, Sebastián, Claudio Cornejo, Sebastián Hernández, and Christian M. Ibáñez. "Combining morphological and molecular information to infer phylogenetic relationships of lamniform sharks." Revista de Biología Marina y Oceanografía 57, Especial (October 4, 2022): press. http://dx.doi.org/10.22370/rbmo.2022.57.especial.3339.
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Sharks of the order Lamniformes are restricted to 15 extant species grouped into 10 genera and 8 families. These species are characterized by two spine-less dorsal fins and a ring-shaped intestinal valve. Their phylogenetic relationships are not congruent among different methods and approaches, such as the use of morphological or molecular data. The present study evaluates the phylogenetic relationships of species of the order Lamniformes by means of phylogenetic reconstructions through Bayesian inference based on morphological and molecular data and using both datasets combined. The consensus tree of the morphological Bayesian reconstruction shows that Lamnidae and Alopiidae are monophyletic, while Odontaspididae is polyphyletic. Eight synapomorphies are detected in Alopiidae, six in Lamnidae, and one for Odontaspididae. In the Bayesian molecular reconstruction consensus tree, Lamnidae and Odontaspididae are monophyletic, and Alopiidae is polyphyletic. In the consensus tree of the Bayesian reconstruction of combined data, Lamnidae, Alopiidae and, Odontaspididae are monophyletic. The results obtained suggest that posterior probabilities increase when using combined characters in a Bayesian phylogenetic analysis, which is greatly advantageous for systematics of the order Lamniformes. Due to the presence of non-monophyletic groups, monotypic families, and the strong support for the division of lamniforms into two clades, a crucial review for the classification of species is needed.
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Moss, Stephana J., Henry T. Stelfox, Karla D. Krewulak, Sofia Ahmed, Melanie C. Anglin, Sean M. Bagshaw, Tavish Barnes, et al. "Impact of restricted visitation policies in hospitals on patients, family members and healthcare providers during the COVID-19 pandemic: a scoping review protocol." BMJ Open 11, no. 9 (September 2021): e048227. http://dx.doi.org/10.1136/bmjopen-2020-048227.
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IntroductionFlexible visitation policies in hospitals are an important component of care that contributes to reduced stress and increased satisfaction among patients and their family members. Early evidence suggests restricted visitation policies enacted in hospitals during the COVID-19 pandemic are having unintended consequences on patients, family members and healthcare providers. There is a need for a comprehensive summary of the impacts of restricted visitation policies on key stakeholders and approaches to mitigate that impact.Methods and analysisWe will conduct a scoping review as per the Arksey-O’Malley 5-stage scoping review method and the Scoping Review Methods Manual by the Joanna Briggs Institute. We will search relevant electronic databases (eg, CINAHL, MEDLINE, PsycINFO), grey literature and preprint repositories. We will include all study designs including qualitative and quantitative methodologies (excluding protocols) as well as reports, opinions and editorials, to identify the broad impact of restricted hospital visitation policies due to the COVID-19 pandemic on patients, family members or healthcare providers of hospitalised patients, and approaches taken or proposed to mitigate this impact. Two reviewers will calibrate the screening criteria and data abstraction form and will independently screen studies and abstract the data. Narrative synthesis with thematic analysis will be performed.Ethics and disseminationEthical approval is not applicable as this review will be conducted on published literature only. This scoping review will identify, describe and categorise impacts of restricted hospital visitation policies due to the COVID-19 pandemic on patients, family members and healthcare providers of hospitalised patients, and approaches that have been taken to mitigate impact. We will provide a comprehensive synthesis by developing a framework of restricted visitation policies and associated impacts. Our results will inform the development of consensus statements on restricted visitation policies to be implemented in future pandemics.PROSPERO registration numberCRD42020221662.
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Liang, Binhua, Ma Luo, T. Blake Ball, Steven J. M. Jones, and Francis A. Plummer. "QUASI analysis of host immune responses to Gag polyproteins of human immunodeficiency virus type 1 by a systematic bioinformatics approachThis paper is one of a selection of papers published in this special issue entitled “Second International Symposium on Recent Advances in Basic, Clinical, and Social Medicine” and has undergone the Journal's usual peer review process." Biochemistry and Cell Biology 88, no. 4 (August 2010): 671–81. http://dx.doi.org/10.1139/o10-002.
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There is a consensus that Gag-specific cytotoxic T lymphocyte (CTL) response plays a key role in the immune control of human immunodeficiency virus type 1 (HIV-1) infection. In this study, we analyzed all currently available gag sequences in the Los Alamos HIV sequence database and identified positive selection (PS) sites likely restricted by the host immune responses. We found that between 23.4% and 47.4% of PS sites were shared by clades A, B, and C of Gag, indicating similar positive selection pressure on Gag in different subtypes of HIV-1. Furthermore, a significant correlation was observed between the combined CTL and antibody responses and PS sites. The Gag regions of free from PS contained 9 CTL epitopes restricted by 11 HLA class I alleles associated with disease progression to acquired immune deficiency syndrome (AIDS). These analyses provide information important for the identification of cross-clade epitopes and development of a global HIV-1 vaccine.
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Brooks, Jill M., Robert A. Colbert, John P. Mear, Alison M. Leese, and Alan B. Rickinson. "HLA-B27 Subtype Polymorphism and CTL Epitope Choice: Studies with EBV Peptides Link Immunogenicity with Stability of the B27:Peptide Complex." Journal of Immunology 161, no. 10 (November 15, 1998): 5252–59. http://dx.doi.org/10.4049/jimmunol.161.10.5252.
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Abstract HLA-B27-restricted CTL responses to EBV are principally directed against two of the EBV nuclear Ags, EBNAs 3B and 3C. We have previously described a target epitope derived from EBNA 3C (residues 258–266, sequence RRIYDLIEL) that is immunodominant in the context of at least three different B27 subtypes, including B*2705 and B*2702. In this study, we show that this peptide binds well to B*2705 and B*2702 in a cell surface binding assay, and that the two B27:peptide complexes are relatively stable, with t1/2 of 20 and 37 h, respectively. We now identify another B27-restricted epitope derived from EBNA 3B (residues 243–253, sequence RRARSLSAERY), which again accords well with the B*2705/B*2702 consensus motifs, having an arginine residue at position 2 and a tyrosine residue at the carboxyl terminus. In this case, five of five B*2702-positive donors respond to the epitope, whereas there was no response in any B*2705-positive donor studied. This peptide binds at least as well to B*2705 as to its restriction element B*2702; however, the two class I:peptide complexes show marked differences in stability, with t1/2 of 9 and 42 h, respectively. Thus, the stability of B27:peptide complexes can vary markedly between different B27 subtypes in ways that may not be apparent from cell surface binding assays and cannot be predicted from currently known peptide consensus motifs, yet which may critically influence CTL epitope choice.
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Marecki, Sylvia, Michael L. Atchison, and Matthew J. Fenton. "Differential Expression and Distinct Functions of IFN Regulatory Factor 4 and IFN Consensus Sequence Binding Protein in Macrophages." Journal of Immunology 163, no. 5 (September 1, 1999): 2713–22. http://dx.doi.org/10.4049/jimmunol.163.5.2713.
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Abstract IFN regulatory factor 4 (IRF4) and IFN consensus sequence binding protein (ICSBP) are highly homologous members of the growing family of IRF proteins. ICSBP expression is restricted to lymphoid and myeloid cells, whereas IRF4 expression has been reported to be lymphoid-restricted. We present evidence that primary murine and human macrophages express IRF4, thereby extending its range of expression to myeloid cells. Here, we provide a comparative analysis of IRF4 and ICSBP expression and function in distinct cell types. These IRF proteins can form specific complexes with the Ets-like protein PU.1, and can activate transcription via binding to PU.1/IRF composite sequences. EMSA analysis revealed that murine macrophages contained both IRF4/PU.1 and ICSBP/PU.1 complexes, analogous to B cells. Over-expression of ICSBP in these macrophages activated transcription of a PU.1/IRF-dependent promoter, whereas over-expression of IRF4 had no effect on this promoter. In contrast, over-expression of either IRF4 or ICSBP in both macrophages and NIH-3T3 fibroblasts suppressed transcription of the PU.1-independent H-2Ld MHC class I promoter. In NIH-3T3 fibroblasts, IRF4 and ICSBP also synergized with exogenous PU.1 to activate transcription of a PU.1/IRF-dependent promoter. Furthermore, both IRF4 and ICSBP activated transcription of the IL-1β promoter in both cell types. While this promoter is PU.1-dependent, it lacks any known PU.1/IRF composite binding sites. Synergistic activation of the IL-1β promoter by these IRF proteins and PU.1 was found to require PU.1 serine 148. Together, these data demonstrate that IRF4 and ICSBP are dichotomous regulators of transcription in macrophages.
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Tapp, James, Fiona Warren, Chris Fife-Schaw, Derek Perkins, and Estelle Moore. "Essential elements of treatment and care in high secure forensic inpatient services: an expert consensus study." Journal of Forensic Practice 18, no. 3 (August 8, 2016): 189–203. http://dx.doi.org/10.1108/jfp-07-2015-0041.
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Purpose – The evidence base for what works with forensic patients in high-security inpatient settings has typically focused on outcome research and not included clinical expertise from practice-based experience, which is an important facet of evidence-based practice. The purpose of this paper is to establish whether experts with clinical and/or research experience in this setting could reach consensus on elements of high-security hospital services that would be essential to the rehabilitation of forensic patients. Design/methodology/approach – A three-round Delphi survey was conducted to achieve this aim. Experts were invited to rate agreement with elements of practice and interventions derived from existing research evidence and patient perspectives on what worked. Experts were also invited to propose elements of hospital treatment based on their individual knowledge and experience. Findings – In the first round 54 experts reached consensus on 27 (out of 39) elements that included physical (e.g. use of CCTV), procedural (e.g. managing restricted items) and relational practices (e.g. promoting therapeutic alliances), and to a lesser extent-specific medical, psychological and social interventions. In total, 16 additional elements were also proposed by experts. In round 2 experts (n=45) were unable to reach a consensus on how essential each of the described practices were. In round 3 (n=35), where group consensus feedback from round 2 was provided, consensus was still not reached. Research limitations/implications – Patient case complexity, interventions with overlapping outcomes and a chequered evidence base history for this population are offered as explanations for this finding alongside limitations with the Delphi method. Practical implications – Based on the consensus for essential elements derived from research evidence and patient experience, high-secure hospital services might consider those practices and interventions that experts agreed were therapeutic options for reducing risk of offending, improving interpersonal skills and therapeutic interactions with patients, and mental health restoration. Originality/value – The study triangulates what works research evidence from this type of forensic setting and is the first to use a Delphi survey in an attempt to collate this information.
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Hirscher, Timo. "Overly determined agents prevent consensus in a generalized Deffuant model on ℤ with dispersed opinions." Advances in Applied Probability 49, no. 3 (September 2017): 722–44. http://dx.doi.org/10.1017/apr.2017.19.
Full textAbstract:
Abstract During the last decades, quite a number of interacting particle systems have been introduced and studied in the crossover area of mathematics and statistical physics. Some of these can be seen as simplistic models for opinion formation processes in groups of interacting people. In the model introduced by Deffuant et al. (2000), agents that are neighbors on a given network graph, randomly meet in pairs and approach a compromise if their current opinions do not differ by more than a given threshold value θ. We consider the two-sided infinite path ℤ as the underlying graph and extend existing models to a setting in which opinions are given by probability distributions. Similar to what has been shown for finite-dimensional opinions, we observe a dichotomy in the long-term behavior of the model, but only if the initial narrow mindedness of the agents is restricted.
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Gévay, Gábor E., Juan Soto, and Volker Markl. "Handling Iterations in Distributed Dataflow Systems." ACM Computing Surveys 54, no. 9 (December 31, 2022): 1–38. http://dx.doi.org/10.1145/3477602.
Full textAbstract:
Over the past decade, distributed dataflow systems (DDS) have become a standard technology. In these systems, users write programs in restricted dataflow programming models, such as MapReduce, which enable them to scale out program execution to a shared-nothing cluster of machines. Yet, there is no established consensus that prescribes how to extend these programming models to support iterative algorithms. In this survey, we review the research literature and identify how DDS handle control flow, such as iteration, from both the programming model and execution level perspectives. This survey will be of interest for both users and designers of DDS.
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Mills, Ian N. "Pagan Readers of Christian Scripture: the Role of Books in Early Autobiographical Conversion Narratives." Vigiliae Christianae 73, no. 5 (October 9, 2019): 481–506. http://dx.doi.org/10.1163/15700720-12341396.
Full textAbstract:
Abstract Most scholars agree that “pagans” did not read Christian scripture. This critical consensus, however, places inordinate weight on a decontextualized quotation from Tertullian and neglects a body of evidence to the contrary. In particular, the role of books in early autobiographical conversion narratives suggests that early Christian authors and copyists could sometimes work with a reasonable expectation of pagan readership. Against traditional notions of the restricted appeal and circulation of Christian literature, pagan and Christian sources alike indicate that Christian writings found an audience among philo-barbarian thinkers and that certain Christians promoted their books in pagan circles.
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Ivanov, Hristo Y., Vili K. Stoyanova, Nikolay T. Popov, and Tihomir I. Vachev. "Autism Spectrum Disorder - A Complex Genetic Disorder." Folia Medica 57, no. 1 (March 1, 2015): 19–28. http://dx.doi.org/10.1515/folmed-2015-0015.
Full textAbstract:
Abstract Autism spectrum disorder is an entity that reflects a scientific consensus that several previously separated disorders are actually a single spectrum disorder with different levels of symptom severity in two core domains - deficits in social communication and interaction, and restricted repetitive behaviors. Autism spectrum disorder is diagnosed in all racial, ethnic and socioeconomic groups and because of its increased prevalence, reported worldwide through the last years, made it one of the most discussed child psychiatric disorders. In term of aetiology as several other complex diseases, Autism spectrum disorder is considered to have a strong genetic component.
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Zaman, Akhteruz. "Global Diffusion with Local Dimension: A Study of Iraq War News in South Asia." Media International Australia 113, no. 1 (November 2004): 87–97. http://dx.doi.org/10.1177/1329878x0411300111.
Full textAbstract:
The reporting of war has always been a tough challenge for journalists. Restricted access to information, lack of consensus about journalists' role during wartime and the process of news production make the task daunting. The media's vulnerability is manifested in the pattern of war coverage, which is directly related to a country's historic, social and cultural perspectives. This content analysis of the 2003 Iraq war coverage in the Bangladesh press shows that, despite the publications’ dependence on Western sources for war news, they rejected the Western definition of the war and echoed the opposing version of it harboured by the country's elite.
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Burke, Louise M., Linda M. Castell, Douglas J. Casa, Graeme L. Close, Ricardo J. S. Costa, Ben Desbrow, Shona L. Halson, et al. "International Association of Athletics Federations Consensus Statement 2019: Nutrition for Athletics." International Journal of Sport Nutrition and Exercise Metabolism 29, no. 2 (March 1, 2019): 73–84. http://dx.doi.org/10.1123/ijsnem.2019-0065.
Full textAbstract:
The International Association of Athletics Federations recognizes the importance of nutritional practices in optimizing an Athlete’s well-being and performance. Although Athletics encompasses a diverse range of track-and-field events with different performance determinants, there are common goals around nutritional support for adaptation to training, optimal performance for key events, and reducing the risk of injury and illness. Periodized guidelines can be provided for the appropriate type, amount, and timing of intake of food and fluids to promote optimal health and performance across different scenarios of training and competition. Some Athletes are at risk of relative energy deficiency in sport arising from a mismatch between energy intake and exercise energy expenditure. Competition nutrition strategies may involve pre-event, within-event, and between-event eating to address requirements for carbohydrate and fluid replacement. Although a “food first” policy should underpin an Athlete’s nutrition plan, there may be occasions for the judicious use of medical supplements to address nutrient deficiencies or sports foods that help the athlete to meet nutritional goals when it is impractical to eat food. Evidence-based supplements include caffeine, bicarbonate, beta-alanine, nitrate, and creatine; however, their value is specific to the characteristics of the event. Special considerations are needed for travel, challenging environments (e.g., heat and altitude); special populations (e.g., females, young and masters athletes); and restricted dietary choice (e.g., vegetarian). Ideally, each Athlete should develop a personalized, periodized, and practical nutrition plan via collaboration with their coach and accredited sports nutrition experts, to optimize their performance.