T1 (100), T2 (100), T3 (100), T4 (100), T5 (100), T6 (100), T7 (100)
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA769555 | ENA |
REPOSITORIES: ENA
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Project description:Metagenomic diversity of soil co-contaminated with lead and amended with microbes and root exudates
| PRJNA769188 | ENA
Project description:The main purpose was to investigate the differences of the esophageal motion (EM) and the internal target volume (ITV) margins for the esophagus between clinical T1-T3 (cT1-T3) and cT4 cases, using 4-dimensional computed tomography. A secondary purpose was to assess the metastatic lymph nodal motion (NM) and the ITV margins for lymph nodes (LNs) using the datasets of patients with nodal involvement pathologically defined.We analyzed patients with thoracic esophageal cancer consecutively treated with definitive chemoradiation, measuring the EM and the ITV margins in the left-right, anteroposterior, and superoinferior directions. All esophageal contours were divided at the carina. The EM and NM were measured from the displacement of the centroid point between 0% images (at the end of inhalation) and 50% images (at the end of exhalation). The ITV margins were defined as the maximum distance in each direction from the clinical target volume at the 4-dimensional computed tomography average images to the intersection of the clinical target volume at the 0% and 50% images of complete coverage in each patient.The EM below the carina in cT4 was significantly smaller than that in cT1-T2 in all directions (P < .01) and than that in cT3 in all directions (left-right: P = .03, anteroposterior and superoinferior: P < .01). The EM in the case of a cT4 tumor located below the carina was smaller than that in the case of cT4 tumor located above the carina. The NM of abdominal-LNs was much larger than that of cervicothoracic-LNs and the EM below the carina. These tendencies were similar in the ITV measurements.The EM and the ITV margins in cT4 were significantly smaller than those in cT1-T3. The NM and the ITV margins of abdominal LNs were much larger than those of cervicothoracic LNs and the esophagus. In clinical radiation therapy planning for esophageal cancer, we should take cT stage into consideration.
| S-EPMC5514169 | biostudies-other
Project description:Guidelines on T4?+?T3 combination therapy were published in 2012. This review investigates whether the issue is better understood 7 years later. Dissatisfaction with the outcome of T4 monotherapy remains high. Persistent symptoms consist mostly of fatigue, weight gain, problems with memory and thinking and mood disturbances. T4 monotherapy is associated with low serum T3 levels, which often require TSH-suppressive doses of L-T4 for normalization. Peripheral tissue thyroid function tests during T4 treatment indicate mild hyperthyroidism at TSH?<?0.03 mU/L and mild hypothyroidism at TSH 0.3-5.0 mU/L; tissues are closest to euthyroidism at TSH 0.03-0.3 mU/L. This is explained by the finding that whereas T4 is usually ubiquinated and targeted for proteasomal degradation, hypothalamic T4 is rather stable and less sensitive to ubiquination. A normal serum TSH consequently does not necessarily indicate a euthyroid state. Persistent symptoms in L-T4 treated patients despite a normal serum TSH remain incompletely understood. One hypothesis is that a SNP (Thr92Ala) in DIO2 (required for local production of T3 out of T4) interferes with its kinetics and/or action, resulting in a local hypothyroid state in the brain. Effective treatment of persistent symptoms has not yet realized. One may try T4?+?T3 combination treatment in selected patients as an experimental n?=?1 study. The 2012 ETA guidelines are still valid for this purpose. More well-designed randomized clinical trials in selected patients are key in order to make progress. In the meantime the whole issue has become rather complicated by commercial and political overtones, as evident from skyrocketing prices of T3 tablets, aggressive pressure groups and motions in the House of Lords.
| S-EPMC6794355 | biostudies-literature
Project description:In bacteriophage T4, there is a strong tendency for genes that encode interacting proteins to be clustered on the chromosome. There is 1.6 kb of DNA between the DNA helicase (gene 41) and the DNA primase (gene 61) genes of this virus. The DNA sequence of this region suggests that it contains five genes, designated as open reading frames (ORFs) 61.1 to 61.5, predicted to encode proteins ranging in size from 5.94 to 22.88 kDa. Are these ORFs actually genes? As one test, we compared the DNA sequence of this region in bacteriophages T2, T4, and T6 and found that ORFs 61.1, 61.3, 61.4, and 61.5 are highly conserved among the three closely related viruses. In contrast, ORF 61.2 is conserved between phages T4 and T6 yet is absent from phage T2, where it is replaced by another ORF, T2 ORF 61.2, which is not found in the T4 and T6 genomes. As a second, independent test for coding sequences, we calculated the codon base position preferences for all ORFs in this region that could encode proteins that contain at least 30 amino acids. Both the T4/T6 and T2 versions of ORF 61.2, as well as the other ORFs, have codon base position preferences that are indistinguishable from those of known T4 genes (coefficients of 0.81 to 0.94); the six other possible ORFs of at least 90 bp in this region are ruled out as genes by this test (coefficients less than zero). Thus, both evolutionary conservation and codon usage patterns lead us to conclude that ORFs 61.1 to 61.5 represent important protein-coding sequences for this family of bacteriophages. Because they are located between the genes that encode the two interacting proteins of the T4 primosome (DNA helicase plus DNA primase), one or more may function in DNA replication by modulating primosome function.
| S-EPMC240378 | biostudies-other
Project description:PurposeTo implement a free-breathing sequence for simultaneous quantification of T1 , T2 , and T2∗ for comprehensive tissue characterization of the myocardium in a single scan using a multi-gradient-echo readout with saturation and T2 preparation pulses.MethodsIn the proposed Saturation And T2 -prepared Relaxometry with Navigator-gating (SATURN) technique, a series of multi-gradient-echo (GRE) images with different magnetization preparations was acquired during free breathing. A total of 35 images were acquired in 26.5 ± 14.9 seconds using multiple saturation times and T2 preparation durations and with imaging at 5 echo times. Bloch simulations and phantom experiments were used to validate a 5-parameter fit model for accurate relaxometry. Free-breathing simultaneous T1 , T2 , and T2∗ measurements were performed in 10 healthy volunteers and 2 patients using SATURN at 3T and quantitatively compared to conventional single-parameter methods such as SASHA for T1 , T2 -prepared bSSFP, and multi-GRE for T2∗ .ResultsSimulations confirmed accurate fitting with the 5-parameter model. Phantom measurements showed good agreement with the reference methods in the relevant range for in vivo measurements. Compared to single-parameter methods comparable accuracy was achieved. SATURN produced in vivo parameter maps that were visually comparable to single-parameter methods. No significant difference between T1 , T2 , and T2∗ times acquired with SATURN and single-parameter methods was shown in quantitative measurements (SATURN T1=1573±86ms , T2=33.2±3.6ms , T2∗=25.3±6.1ms ; conventional methods: T1=1544±107ms , T2=33.2±3.6ms , T2∗=23.8±5.5ms ; P>.2 ) CONCLUSION: SATURN enables simultaneous quantification of T1 , T2 , and T2∗ in the myocardium for comprehensive tissue characterization with co-registered maps, in a single scan with good agreement to single-parameter methods.
| S-EPMC8252099 | biostudies-literature
Project description:Neuronal computation underlying detection of visual motion has been studied for more than a half-century. In Drosophila, direction-selective T4/T5 neurons show supralinear signal amplification in response to stimuli moving in their preferred direction, in agreement with the prediction made by the Hassenstein-Reichardt detector. Nevertheless, the molecular mechanism explaining how the Hassenstein-Reichardt model is implemented in T4/T5 cells has not been identified yet. In the present study, we utilized cell type-specific transcriptome profiling with RNA-seq to obtain a complete gene expression profile of T4/T5 neurons. We analyzed the expression of genes that affect neuronal computational properties and can underlie the molecular implementation of the core features of the Hassenstein-Reichardt model to the dendrites of T4/T5 neurons. Furthermore, we used the acquired RNA-seq data to examine the neurotransmitter system used by T4/T5 neurons. Surprisingly, we observed co-expression of the cholinergic markers and the vesicular GABA transporter in T4/T5 neurons. We verified the previously undetected expression of vesicular GABA transporter in T4/T5 cells using VGAT-LexA knock-in line. The provided gene expression dataset can serve as a useful source for studying the properties of direction-selective T4/T5 neurons on the molecular level.
| S-EPMC5042512 | biostudies-literature
Project description:To evaluate, at the molecular level, potential pathways involved in changes of PVB permeability, we dissected lateral CP tissues at all time points (T0, T1, T3, or T5) and performed transcriptional profiling by deep RNA-sequencing. We used a regression model-based method for the classification of co-regulated genes based on their temporal expression profiles and the identification of differentially expressed genes (DEGs).
2021-10-26 | GSE178750 | GEO
Project description:In the Drosophila visual system, T4/T5 neurons represent the first stage of computation of the direction of visual motion. T4 and T5 neurons exist in four subtypes, each responding to motion in one of the four cardinal directions and projecting axons into one of the four lobula plate layers. However, all T4/T5 neurons share properties essential for sensing motion. How T4/T5 neurons acquire their properties during development is poorly understood. We reveal that the transcription factors SoxN and Sox102F control the acquisition of properties common to all T4/T5 neuron subtypes, i.e. the layer specificity of dendrites and axons. Accordingly, adult flies are motion blind after disruption of SoxN or Sox102F in maturing T4/T5 neurons. We further find that the transcription factors Ato and Dac are redundantly required in T4/T5 neuron progenitors for SoxN and Sox102F expression in T4/T5 neurons, linking the transcriptional programmes specifying progenitor identity to those regulating the acquisition of morphological properties in neurons. Our work will help to link structure, function and development in a neuronal type performing a computation that is conserved across vertebrate and invertebrate visual systems.
| S-EPMC6361130 | biostudies-literature
Project description:Acanthamoeba keratitis (AK) is a rare but sight-threatening ocular infection. Outbreaks have been associated with contaminated water and contact lens wear. The epidemiology and pathology may be associated with unique genotypes. We determined the Rns genotype for 37 clinical isolates from 23 patients presenting at the University of Miami Bascom Palmer Eye Institute with confirmed AK infections in 2006 to 2008. The genus-specific ASA.S1 amplicon allowed for rapid genotyping of the nonaxenic cultures. Of the 37 isolates, 36 were of the T4 genotype. Within this group, 13 unique diagnostic fragment 3 sequences were identified, 3 of which were not in GenBank. The 37th isolate was a T5, the first in the United States and second worldwide to be found in AK. For five patients with isolates from the cornea and contact lens/case, identical sequences within each patient cluster were observed, confirming the link between contact lens contamination and AK infection. Genotyping is an important tool in the epidemiological study of AK. In this study, it allowed for the detection of new strains and provided an etiological link between source and infection. Additionally, it can allow for accurate categorizing of physiological differences, such as strain virulence, between isolates and clades.
| S-EPMC2681865 | biostudies-literature
Project description:The current study aimed to test whether the ratio of T1-weighted to T2-weighted signal intensity (T1W/T2W ratio: rT1/T2) derived from conventional MRI could act as a surrogate relaxation time predictive of IDH mutation status in histologically lower-grade gliomas. Strong exponential correlations were found between rT1/T2 and each of T1- and T2-relaxation times in eight subjects (rT1/T2 = 1.63exp-0.0005T1-relax + 0.30 and rT1/T2 = 1.27exp-0.0081T2-relax + 0.48; R2 = 0.64 and 0.59, respectively). In a test cohort of 25 patients, mean rT1/T2 (mrT1/T2) was significantly higher in IDHwt tumors than in IDHmt tumors (p < 0.05) and the optimal cut-off of mrT1/T2 for discriminating IDHmt was 0.666-0.677, (AUC = 0.75, p < 0.05), which was validated in an external domestic cohort of 29 patients (AUC = 0.75, p = 0.02). However, this result was not validated in an external international cohort derived from TCIA/TCGA (AUC = 0.63, p = 0.08). The t-Distributed Stochastic Neighbor Embedding analysis revealed a greater diversity in image characteristics within the TCIA/TCGA cohort than in the two domestic cohorts. The failure of external validation in the TCIA/TCGA cohort could be attributed to its wider variety of original imaging characteristics.
| S-EPMC9637175 | biostudies-literature