The correct typification of Tradescantia crassula (Commelinaceae).
Ontology highlight
ABSTRACT:
SUBMITTER: Hassemer G
PROVIDER: S-EPMC5543610 | biostudies-other | 2017
REPOSITORIES: biostudies-other
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Project description:Interventions: The intervention is based on cognitive behavior therapy (CBT) and consists of blended therapy, a combination of face-to-face CBT with a self-management interactive website. The intervention lasts four months and compromises of five individual face-to-face sessions, supplemented by three telephone contacts. Patients will have daily access to the self-management website. The CBT protocol is directed at changing cognitions and behavior related to distress. Treatment will be individually-tailored based on the presenting problems identified during clinical assessment and and the data gathered during baseline assessment. The intervention consists of one generic module and three optional modules. Three different types of distress will be addressed in the modules: 1) distress caused by physical consequences (e.g. post-cancer fatigue, gastrointestinal problems, urinary incontinence and sexual dysfunction), 2) anxiety and fear of recurrence, 3) depressive mood.
Primary outcome(s): Psychological distress as measured by the Brief Symptom Inventory (BSI-18)
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2007-08-16 | GSE8744 | GEO
Project description:Correct formation of disulfide bonds is critical for protein folding. We find that cells lacking protein disulfide isomerases (PDIs) can use alternative mechanisms for correct disulfide bond formation. By linking correct disulfide bond formation to antibiotic resistance, we selected mutants that catalyze correct disulfide formation in the absence of DsbC, Escherichia coli's PDI. Most of our mutants massively overproduce the disulfide oxidase DsbA and change its redox status. They enhance DsbA's ability to directly form the correct disulfides by increasing the level of mixed disulfides between DsbA and substrate proteins. One mutant operates via a different mechanism; it contains mutations in DsbB and CpxR that alter the redox environment of the periplasm and increases the level of the chaperone/protease DegP, allowing DsbA to gain disulfide isomerase ability in vivo. Thus, given the proper expression level, redox status, and chaperone assistance, the oxidase DsbA can readily function in vivo to catalyze the folding of proteins with complex disulfide bond connectivities. Our selection reveals versatile strategies for correct disulfide formation in vivo. Remarkably, our evolution of new pathways for correct disulfide bond formation in E. coli mimics eukaryotic PDI, a highly abundant partially reduced protein with chaperone activity.
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Project description:BackgroundThe prediction of protein structure can be facilitated by the use of constraints based on a knowledge of functional sites. Without this information it is still possible to predict which residues are likely to be part of a functional site and this information can be used to select model structures from a variety of alternatives that would correspond to a functional protein.ResultsUsing a large collection of protein-like decoy models, a score was devised that selected those with predicted functional site residues that formed a cluster. When tested on a variety of small alpha/beta/alpha type proteins, including enzymes and non-enzymes, those that corresponded to the native fold were ranked highly. This performance held also for a selection of larger alpha/beta/alpha proteins that played no part in the development of the method.ConclusionThe use of predicted site positions provides a useful filter to discriminate native-like protein models from non-native models. The method can be applied to any collection of models and should provide a useful aid to all modelling methods from ab initio to homology based approaches.
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Project description:MotivationSequence similarity searches performed with BLAST, SSEARCH and FASTA achieve high sensitivity by using scoring matrices (e.g. BLOSUM62) that target low identity (<33%) alignments. Although such scoring matrices can effectively identify distant homologs, they can also produce local alignments that extend beyond the homologous regions.ResultsWe measured local alignment start/stop boundary accuracy using a set of queries where the correct alignment boundaries were known, and found that 7% of BLASTP and 8% of SSEARCH alignment boundaries were overextended. Overextended alignments include non-homologous sequences; they occur most frequently between sequences that are more closely related (>33% identity). Adjusting the scoring matrix to reflect the identity of the homologous sequence can correct higher identity overextended alignment boundaries. In addition, the scoring matrix that produced a correct alignment could be reliably predicted based on the sequence identity seen in the original BLOSUM62 alignment. Realigning with the predicted scoring matrix corrected 37% of all overextended alignments, resulting in more correct alignments than using BLOSUM62 alone.
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Project description:Falkenstein et al. (1991) first described a negative wave occurring just after an erroneous response in choice Reaction time tasks ("Error Negativity"-Ne or "Error Related Negativity"-ERN). Thanks to Laplacian transform of the data, Vidal et al. (2000, 2003a) described a wave on correct trials with similar topography and latency, although of smaller amplitude compared to the errors. A critical question is whether the Ne observed on errors and the negativity reported on correct trials reflect the same (modulated) activity, or whether they reflect completely different mechanisms. These two alternative possibilities were tested thanks to Independent Component Analysis (ICA) and source localization. ICA results showed that the waves recorded on errors and correct trials can be accounted for by the same independent component, corresponding to a dipolar source located within the Rostral Cingulate Zone. Source localization on the raw data also confirmed a common generator for correct and error trials. These data suggest that the waves on errors and correct trials reflect the same brain activity, whose amplitude varies as a function of the correctness of the response. The implications of this result for cognitive control are discussed.
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Project description:OBJECTIVE: To evaluate the impact of follicle rupture on pregnancy rate in intrauterine insemination. MATERIAL AND METHOD: Retrospective cohort study. Evidence of follicle rupture was assessed by transvaginal ultrasonography following IUI. Two hundred ninety-six couples with unexplained infertility and 121 couples with male factor subfertility were included. Results of 578 cycles were analyzed here. RESULT: Clinical pregnancy rate was 23.5% (64/272) in the group when follicle rupture was evident by transvaginal ultrasonography, while it was only 8.8% (27/306) when follicle rupture was not evident (p < 0.001). CONCLUSION: Postponing IUI until observation of follicle rupture may yield a higher pregnancy rate.
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Project description:Comparison of genome binding/occupancy profiling of the cohesin subunit Rec8 by high throughput sequencing in WT and ctf19-9A strains in meiotic prophase I.
2024-01-28 | GSE254215 | GEO
Project description:BACKGROUND: Although individual occurrence is rare, syndromic obesity with mental retardation has been reported in conjunction with 140 different diseases. CASE PRESENTATION: The patient was born at term after a pregnancy complicated by threatened miscarriage. A diagnosis of Bardet-Biedl syndrome (BBS; OMIM #209900) was made in another hospital when she was 8 years old, but other clinical problems emerged subsequently. She came to our attention for the first time when she was 14 years old. The clinical picture, characterized by the presence of ophthalmological, renal, endocrinological, and liver disorders associated with a peculiar weight growth pattern, was more suggestive for Alström syndrome (ALMS; OMIM #203800); consequently, a genetic study was performed. Genetic analysis revealed a novel compound heterozygous frameshift mutation on exon 8 of ALMS1 (c. [3251_3258delCTGACCAG] and c. [6731delA]), which has not previously been described. CONCLUSION: Early onset of retinal degeneration associated with obesity represents a diagnostic challenge in paediatric and genetic practice, although the absence of skeletal abnormalities and developmental delay could help in addressing the clinical diagnosis. Confirmation of clinical suspicion by genetic analysis has been diriment in this case, since only a single gene is known to cause ALMS.
| S-EPMC4230022 | biostudies-literature
Project description:MOTIVATION:Protein-protein interactions are a key in virtually all biological processes. For a detailed understanding of the biological processes, the structure of the protein complex is essential. Given the current experimental techniques for structure determination, the vast majority of all protein complexes will never be solved by experimental techniques. In lack of experimental data, computational docking methods can be used to predict the structure of the protein complex. A common strategy is to generate many alternative docking solutions (atomic models) and then use a scoring function to select the best. The success of the computational docking technique is, to a large degree, dependent on the ability of the scoring function to accurately rank and score the many alternative docking models. RESULTS:Here, we present ProQDock, a scoring function that predicts the absolute quality of docking model measured by a novel protein docking quality score (DockQ). ProQDock uses support vector machines trained to predict the quality of protein docking models using features that can be calculated from the docking model itself. By combining different types of features describing both the protein-protein interface and the overall physical chemistry, it was possible to improve the correlation with DockQ from 0.25 for the best individual feature (electrostatic complementarity) to 0.49 for the final version of ProQDock. ProQDock performed better than the state-of-the-art methods ZRANK and ZRANK2 in terms of correlations, ranking and finding correct models on an independent test set. Finally, we also demonstrate that it is possible to combine ProQDock with ZRANK and ZRANK2 to improve performance even further. AVAILABILITY AND IMPLEMENTATION:http://bioinfo.ifm.liu.se/ProQDock CONTACT:bjornw@ifm.liu.se SUPPLEMENTARY INFORMATION:Supplementary data are available at Bioinformatics online.
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