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SET Domain

The SET Domain is a protein domain that plays a critical role in the epigenetic regulation of gene expression.
This conserved motif is found in various proteins involved in histone methyltransferase activity, chromatin remodeling, and transcriptional control.
The SET Domain mediates the transfer of methyl groups to specific lysine residues on histone tails, thereby influencing chromatin structure and accessibility.
Researchers investigating the SET Domain can utilize advanced AI-driven platforms like PubCompare.ai to streamline their investigations, effortlessly locate relevant protocols, and leverage intelligent comparisons to identify the most effective research strategies.
This cutting-edeg technolgy can help optimize SET Domain research and advance our understanding of epigenetic mechanisms underlying diverse biological processes.

Most cited protocols related to «SET Domain»

Cognitive domain and test selection were based on a combination of methods evolving from regular meetings of the CTF. A subcommittee was formed to specifically undertake the design of the neuropsychological test battery, to bring essential issues to the larger group and to interface with the ADCs. Three overriding criteria governed decisions for selecting domains and tests. The first was the mandate for the UDS to initially focus on cognitive markers of aging and of dementia associated with AD, the second was to minimize burden on the ADCs and their subjects, and the third was to accommodate the continuity of measures that ADCs have previously collected. A fourth principle that emerged after an initial set of domains and tests was identified was the need to overlap with other ADC initiatives such as the Late Onset Alzheimer’s Disease (LOAD) Genetics study and the Alzheimer’s Disease Neuroimaging Initiative (ADNI). Because of the need to focus on the cognitive continuum from aging without dementia, to MCI, to AD, cognitive domains were selected for their sensitivity to age-related change in cognition [17 (link)–29 (link)] sensitivity to the demonstrated primary cognitive impairments in AD [30 –36 (link)], ability to measure change over time and to stage AD [37 (link)], and ability to predict progression from MCI to AD [38 (link)–41 ]. Additional criteria for test selection included applicability of the measures to different educational levels, to diverse racial/ethnic minority groups and to Spanish-speaking populations. A Spanish translation of the UDS has been completed and is available on the NACC website (https://www.alz.washington.edu).
The minimization of burden, an issue of feasibility, had to figure centrally in test selection. Many ADCs have been conducting research for over 20 years. Well-established protocols and longitudinal research projects could be disrupted by the need to significantly alter assessment and enrollment methods, notwithstanding the added time burden for subjects and their study partners. Thus, with input from the ADCs, the CTF concluded that the neuropsychological battery should not add more than 30 minutes to existing protocols at each Center. One implication of this principle was that tests already in use by all or most ADCs would be high on the list of candidates for inclusion.
The CTF conducted several surveys of the ADCs to gather data about their ongoing assessment practices including, among other variables: 1) cognitive domains tested; 2) specific instruments and versions, for tests with multiple forms; 3) populations of subjects followed (i.e., disease and control groups; clinic and/or community samples); 4) frequency of subject visits. Once these data were acquired, the most commonly tested domains and the most commonly used specific measures were identified and comments and approval were solicited from the ADCs.
Publication 2009
Cognition Disease Progression Disorders, Cognitive Ethnic Minorities Hispanic or Latino Hypersensitivity Neuropsychological Tests Population Group Presenile Dementia Racial Groups SET Domain
The revised FIQ (the FIQR) has 21 individual questions (Table 1). All questions are based on an 11-point numeric rating scale of 0 to 10, with 10 being 'worst'. As in the FIQ, all questions are framed in the context of the past 7 days. Following the convention used in the FIQ, the FIQR is divided into three linked sets of domains: (a) 'function' (contains 9 questions versus 11 in the FIQ), (b) 'overall impact' (contains 2 questions, as in the FIQ) but the questions now relate to the overall impact of FM on functioning and the overall impact symptom severity, and (c) 'symptoms' (contains 10 questions versus 7 in the FIQ); one original FIQ symptom was dropped: 'When you worked, how much did pain or other symptoms of your fibromyalgia interfere with your ability to do your work, including housework?' The symptom domain contains four new questions relating to memory, tenderness, balance, and environmental sensitivity (to loud noises, bright lights, odors, and cold temperatures). The 'time' dimension is the same as the FIQ; that is, all questions relate to the impact of FM over the course of the past 7 days. The scoring of the FIQR is much simpler than the FIQ: namely, the summed score for function (range 0 to 90) is divided by 3, the summed score for overall impact (range 0 to 20) is not changed, and the summed score for symptoms (range 0 to 100) is divided by 2. The total FIQR is the sum of the three modified domain scores. The weighting of these three domains is different from the FIQ in that 30% of the total score is ascribed to 'function' as opposed to 10% in the FIQ, 50% is ascribed to 'symptoms' as opposed to 70% in the FIQ, and 'overall impact' remains the same as the FIQ at 20%. The total maximal score of the FIQR remains the same as the FIQ, namely 100.
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Publication 2009
BAD protein, human Cold Temperature Conferences Fibromyalgia Hypersensitivity Light Memory Odors Pain SET Domain

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Publication 2010
Acyltransferase Amino Acids Anabolism brevianamide F CSF2RB protein, human Dehydrogenase, Aminoadipate-Semialdehyde Dimethylallyltranstransferase Enzymes Genes Genes, Fungal Genome Genome, Fungal Hybrids Lyngbya Toxins Nitric Oxide Synthase non-ribosomal peptide synthase Proteins Protein Subunits SET Domain short chain trans-2-enoyl-CoA reductase Synthase, Polyketide tryptophan dimethylallyltransferase Tyrosine Vertebral Column
We assembled three sets of domain-specific genomic tRNA sequences from a total of over 4000 genomes using existing tRNAscan-SE 1.3 predictions in GtRNAdb Release 15 (4 (link)) plus additional predictions (also from tRNAscan-SE 1.3 for species not yet represented in GtRNAdb), representing a broad diversity of eukaryotes, bacteria, and archaea (Table 1 and Supplementary Figure S1). Before using these tRNA sequences as training sets for building domain-specific covariance models, multiple filtering steps were used to maximize quality. To avoid the inclusion of common tRNA-derived repetitive elements that exist in many eukaryotic genomes, especially those in mammals (33–35 (link)), we first selected only the eukaryotic tRNAs with a COVE score >50 bits, a threshold reflecting more conserved, canonical tRNA features. We then selected only the top 50 scoring tRNAs for each isotype per organism to avoid overrepresentation of high-scoring tRNA-derived repetitive elements which are abundant in some species (e.g. elephant shark has over 9500 tRNAAla scoring over 50 bits). For the bacterial tRNA training set, all genes having potential self-splicing introns were excluded to eliminate large alignment gaps (i.e. mostly over 200 nt) which can hinder efficient model creation. Similarly for archaea, pre-processing of sequence training sets was necessary. Some species within the phyla Crenarchaeota and Thaumarchaeota contain tRNA genes that are known to have multiple noncanonical introns (5 (link),36 (link),37 (link)). Atypical tRNAs such as trans-spliced tRNAs and circularized permuted tRNAs have also previously been discovered in Crenarchaeota and Nanoarchaeota (12 (link),38 (link),39 (link)). To accommodate these special archaeal features without sacrificing performance, both mature tRNA sequences (without introns) and selected atypical genes with multiple introns at different locations were included in the archaeal tRNA training sets. As a last step, anticodons of tRNA sequences in all training sets were replaced with NNN and aligned to the corresponding original domain-specific tRNA covariance models using Infernal (20 (link)). The resulting alignments were then used to generate the new set of domain-specific tRNA covariance models with Infernal.
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Publication 2021
Alanine-Specific tRNA Anticodon Archaea Bacteria Crenarchaeota Elephants Eukaryota Genes Genome Immunoglobulin Isotypes Introns Mammals Multiple Birth Offspring Nanoarchaeota Repetitive Region SET Domain Sharks Strains Transfer RNA
pHMMs (25 ,26 (link)) are a widely used probabilistic representation of protein domain families and can conveniently be used to search for known domains in given protein sequences. pHMMs are versatile: First, models are publicly available, e.g. from the Pfam protein family database (27 (link)). This database contains various prebuilt models of protein domains associated with the process of retrotransposition. Secondly, pHMMs can easily be built from custom multiple sequence alignments. Due to this flexibility, pHMMs were chosen to model protein domains in LTR retrotransposon candidates. For the analyses performed in this work, collections of protein domain models associated with LTR retrotransposons were compiled (Supplementary Data 1, Tables B1 and B2). Given such a user-configurable set D of domain models in HMMER format, LTRdigest searches for all models in the translations of all six reading frames of a LTR retrotransposon candidate sequence. In the case of frame shifts, it is possible to obtain multiple partial hits per protein domain occurring in different reading frames. If more than one hit per domain model is found in a candidate, individual hits are combined using a chaining algorithm adapted from the gene prediction software GenomeThreader (28 ). This algorithm is able to find an optimal sequence of individual hits representing the model-sequence alignment best. Finally, the amino acid start and end positions in the translated sequences of all hits in the optimal chain below a user-defined E-value threshold are mapped back to the respective coordinates in the DNA sequence before they are reported.
Publication 2009
Amino Acids Amino Acid Sequence DNA Sequence Genes Protein Domain Reading Frames Retrotransposons Sequence Alignment SET Domain

Most recents protocols related to «SET Domain»

The PROM/PREM implemented in this project were those proposed in the PCB set: questionnaires at two moments during pregnancy (T1: first trimester, T2: early third trimester) and three postpartum (T3: maternity week, T4: 6 weeks postpartum, T5: 6 months postpartum). The PCB set was developed internationally and subsequently translated to the Dutch setting, both phases involving all stakeholders, including care professionals and patients [18 (link), 29 (link)]. An overview of the PCB set’s patient-reported domains and timeline for completion is provided in Additional file 1: Fig. S1. The set’s PROM/PREM were implemented for two purposes. First, individual-level PROM/PREM were implemented in clinic: reviewing N = 1 scores with patients during a regular care contact after completing a questionnaire. The timeline of collection, workflow, and follow-up services (including scoring and alert values) were organized as described in the national pilot project [30 (link)]. Second, the same PROM/PREM outcomes would be used at group-level in network-broad QI sessions. Despite the complexity of combining these purposes, findings in our pre-implementation research amongst care professionals, patients and other stakeholders in perinatal care suggested both goals could also reinforce each other [8 (link)]. Direct usability in clinical practice could, for instance, motivate care professionals and patients to comply, thereby generating data for group-level use (and vice-versa). Likewise, other previous findings from our pre-implementation analysis and feasibility pilot [8 (link), 28 (link)], were used to design the initial implementation strategy. Important elements for individual-level use included visual alerts to support care professionals in interpreting the answers and offering patients a choice whether their care professional had insight in their individual PREM answers. During the action research project, this initial implementation strategy (Fig. 1) was continuously refined guided by action research principles in iterative cycles of planning and executing implementation activities, data generation, and reflection on these data to refine subsequent activities. These cycles were conducted jointly by researchers and care professionals. The researchers developed the baseline strategy for project organization and education (e.g. identified possible IT-systems, developed an e-learning and kick-off meeting), provided materials and support for its execution (e.g. patient information folder, for working protocol for care professionals), and facilitated data generation for its refinement (e.g. organized focus groups, sent out the survey). The project teams designed and coordinated local implementation (e.g. adapt instruction material to local workflow, chose the IT system that best fitted local needs and resources) and participated in data generation and reflections (e.g. survey results were discussed in project team meetings, participation in focus groups). Three OCN started implementation sequentially to be able to learn from previous experiences, exchanged via the researchers and directly between care professionals from different OCN. After the one-year implementation period, project teams reported their experiences to their OCN and advised future steps in an end-evaluation.

Timeline of implementation and data generation activities. PROM, patient-reported outcome measure. PREM, patient-reported experience measure. QI, quality improvement. OCN, obstetric care network. CP, care professional. VHBC, value-based healthcare

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Publication 2023
CARE protocol Patients Perinatal Care Pregnancy Reflex SET Domain TimeLine
Content analysis was performed to assess the impact of the H&P 360 template. For purposes of qualitative comparison of note content, research coordinators collected and deidentified all of the H&P 360 notes and a sample of the traditional notes. The sample of traditional notes was drawn by attempting relatively balanced representation across students. Specifically, each student could contribute no more than 5 traditional notes to the total sample; for those with more than 5 traditional notes, a random subsample was selected for inclusion.
The content analysis team was composed of three internists involved in medical education (JWT, VGP, IJA) and one medical student (EYR). Throughout the process of analysis, team members discussed their preconceived notions and biases from their roles in education and patient care. The team began with a set of a priori content domains based on the H&P 360 template (eg, mental health, behavioral health, social support). The team members independently reviewed a set of notes—four from the H&P 360 group and four from the traditional group—to clarify the definition of the content domains, add additional de novo content domains as needed, and improve consistency between coders. Subsequently, for each of the notes, two team members extracted relevant text and entered it into a Research Electronic Data Capture (REDCap) template under the appropriate content domain. Discrepancies in coding were reviewed and resolved through email correspondence. The text from each content domain was then aggregated into a document and reviewed by two members of the team to identify themes within each content domain and to assess whether there were qualitative differences in the content between the H&P 360 and traditional templated notes. Each content domain was discussed at the weekly group video meeting. The number of notes categorized under each content domain was counted for the H&P 360 and traditional templated groups.
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Publication 2023
6H,8H-3,4-dihydropyrimido(4,5-c)(1,2)oxazin-7-one Education, Medical Mental Health SET Domain Student Students, Medical
We define transfer learning as in the following clear and simple statements:
"Transfer learning and domain adaptation refer to the situation where what has been learned in one setting (e.g., distributionP1) is exploited to improve generalization in another setting (say, distributionP2)”49 ;
"Given a source domainDSand learning taskTS, a target domainDTand learning taskTT, transfer learning aims to help improve the learning of the target predictive functionfT( ⋅ ) in DTusing the knowledge inDSandTS, whereDS ≠ DTandTS ≠ TT50 (link).
In our study the source and the target tasks are the same, i.e. TS ≡ TT. The task is always to perform sleep staging with the same set of sleep classes/stages. We want to transfer the knowledge about the previously learned sleep recordings (e.g., different hardware, different subject distributions with different sleep disorders) and the knowledge about the sleep scoring-rules (i.e., inter-scorer variability in the different data centers). The process generally involves overwriting a knowledge from a small-sized database to a previous big-sized knowledge (result of a long training process). One big concern is to avoid ending up in what the data scientists call catastrophic forgetting: “Also known as catastrophic interference, it is the tendency of an artificial neural network to completely and abruptly forget previously learned information upon learning new information” as defined in51 . Even if it is conceptually easy to understand, avoiding its occurrence is not trivial. To partially bypass this phenomena we fine-tune the architecture on the target domain using a smaller learning rate.
In our experiments we first pre-train the architecture on the data-source domain S (e.g., a set of different domains/databases {SDB1,SDB2,...,SDBn} ), then we fine-tune the model on the data-target domain T. Formally, we first minimize the loss function LS, resulting in the learned parameters θ: argminθ=(x,y)DSLS(x,P(yx),Pθ(y,x))
The parameters θ of the pre-trained model are used as the starting point on the data-target domain T. To transfer the learning on the new domain T, we fine-tune all the pre-trained parameters θ=θ (i.e., the entire network is further trained on the new data domain T): argminθ=θ=(x,y)DTLT(x,P(yx),Pθ(y,x))
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Publication 2023
Acclimatization Conditioning, Psychology Generalization, Psychological SET Domain Sleep Sleep Disorders
To determine if ASTADs were enriched for particular genomic features, we performed enrichment analysis using LOLA (v1.22) [67 (link)]. ASTAD enrichment was tested against a background set of all identified TAD domains in a given cell line. To facilitate cell line comparison, only autosomal regions were tested for enrichment. A full list of genomic features tested and enrichment status is available in Additional file 1: Table S5.
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Publication 2023
Cell Lines Genome SET Domain
In order to determine the secretory signal peptides, SignalP v4.1 (Nielsen, 2017 (link))4 was used to examine the 16,179 predicted proteins of F. udum. Further, TMHMM v2.0 was used to predict the protein sets with the existence of transmembrane domains (Krogh et al., 2001 (link)) and GPI (glycosylphosphatidyl inositol)-anchor using PredGPI (Pierleoni et al., 2008 (link)). Proteins including one transmembrane domain situated within the N-terminal signal peptide and no transmembrane domain overall were chosen. The predicted secretory proteins’ cysteine content was examined. In order to functionally annotate the predicted secretome, BLAST2GO was used to assign GO keywords (Altschul et al., 1990 (link)). The dbCAN HMMs 5.0 (Yin et al., 2012 (link)) was used to find carbohydrate metabolism active enzymes (CAZymes) based on the CAZy database in the F. udum secretome.
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Publication 2023
Carbohydrate Metabolism Cysteine Enzymes Glycosylphosphatidylinositols Hypertelorism, Severe, With Midface Prominence, Myopia, Mental Retardation, And Bone Fragility Proteins secretion Secretome SET Domain Signal Peptides

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More about "SET Domain"

The SET (Suppressor of variegation, Enhancer of zeste, and Trithorax) Domain is a highly conserved protein motif that plays a critical role in the epigenetic regulation of gene expression.
This domain is found in a variety of proteins involved in histone methyltransferase activity, chromatin remodeling, and transcriptional control.
The SET Domain facilitates the transfer of methyl groups to specific lysine residues on histone tails, which can influence chromatin structure and accessibility, ultimately affecting gene expression.
Researchers investigating the SET Domain can utilize advanced AI-driven platforms like PubCompare.ai to streamline their research efforts.
This cutting-edge technology can help researchers effortlessly locate relevant protocols from the literature, preprints, and patents, and leverage intelligent comparisons to identify the most effective research strategies.
PubCompare.ai can also assist in optimizing SET Domain research by providing access to a wide range of related technologies, such as SYPRO Orange for protein thermal stability analysis, COMSOL Multiphysics for computational modeling, and GBlocks for gene synthesis.
Additionally, researchers may find 3H-AdoMet, a radioactive S-adenosylmethionine analog, useful for studying the enzymatic activity of SET Domain-containing proteins.
The Lipofectamine CRISPRMAX reagent can be employed for efficient delivery of CRISPR-Cas9 components, including the Cas9 PLUS Reagent, to investigate the role of the SET Domain in cellular processes.
The CFX96 Touch Real-Time PCR Detection System can be utilized for quantitative analysis of gene expression, while the PhyML web server can aid in phylogenetic analysis of SET Domain-containing proteins.
Furthermore, transfection reagents like FuGENE HD can be employed to introduce SET Domain-encoding plasmids into cell lines, and the TRC-50DX retinal camera can be used for in vivo imaging of epigenetic modifications mediated by the SET Domain in animal models.
By leveraging the power of these technologies and the insights provided by PubCompare.ai, researchers can optimize their SET Domain investigations and advance our understanding of the epigenetic mechanisms underlying diverse biological processes.