Analysis of CATMA transcriptome data identifies hundreds of novel functional genes and improves gene models in the Arabidopsis genome

<p>Abstract</p> <p>Background</p> <p>Since the finishing of the sequencing of the <it>Arabidopsis thaliana </it>genome, the Arabidopsis community and the annotator centers have been working on the improvement of gene annotation at the structural and functional levels. In this context, we have used the large CATMA resource on the Arabidopsis transcriptome to search for genes missed by different annotation processes. Probes on the CATMA microarrays are specific gene sequence tags (GSTs) based on the CDS models predicted by the Eugene software. Among the 24 576 CATMA v2 GSTs, 677 are in regions considered as intergenic by the TAIR annotation. We analyzed the cognate transcriptome data in the CATMA resource and carried out data-mining to characterize novel genes and improve gene models.</p> <p>Results</p> <p>The statistical analysis of the results of more than 500 hybridized samples distributed among 12 organs provides an experimental validation for 465 novel genes. The hybridization evidence was confirmed by RT-PCR approaches for 88% of the 465 novel genes. Comparisons with the current annotation show that these novel genes often encode small proteins, with an average size of 137 aa. Our approach has also led to the improvement of pre-existing gene models through both the extension of 16 CDS and the identification of 13 gene models erroneously constituted of two merged CDS.</p> <p>Conclusion</p> <p>This work is a noticeable step forward in the improvement of the Arabidopsis genome annotation. We increased the number of Arabidopsis validated genes by 465 novel transcribed genes to which we associated several functional annotations such as expression profiles, sequence conservation in plants, cognate transcripts and protein motifs.</p

Stroke

Background and Purpose-The aim of the present study was to evaluate the relationship between normal-appearing white matter (NAWM) integrity and postischemic stroke recovery in 4 main domains including cognition, mood, gait, and dependency. Methods-A prospective study was conducted, including patients diagnosed for an ischemic supratentorial stroke on a 3T brain MRI performed 24 to 72 hours after symptom onset. Clinical assessment 1 year after stroke included a Montreal Cognitive Assessment, an Isaacs set test, a Zazzo cancelation task, a Hospital Anxiety and Depression scale, a 10-meter walking test, and a modified Rankin Scale (mRS). Diffusion tensor imaging parameters in the NAWM were computed using FMRIB (Functional Magnetic Resonance Imaging of the Brain) Diffusion Toolbox. The relationships between mean NAWM diffusion tensor imaging parameters and the clinical scores were assessed using linear and ordinal regression analyses, including the volumes of white matter hyperintensities, gray matter, and ischemic stroke as radiological covariates. Results-Two hundred seven subjects were included (66±13 years old; 67% men; median National Institutes of Health Stroke Scale score, 3; interquartile range, 2-6). In the models including only radiological variables, NAWM fractional anisotropy was associated with the mRS and the cognitive scores. After adjusting for demographic confounders, NAWM fractional anisotropy remained a significant predictor of mRS (β=-0.24; P=0.04). Additional path analysis showed that NAWM fractional anisotropy had a direct effect on mRS (β=-0.241; P=0.001) and a less important indirect effect mediating white matter hyperintensity burden. Similar results were found with mean diffusivity, axial diffusivity, and radial diffusivity. In further subgroup analyses, a relationship between NAWM integrity in widespread white matter tracts, mRS, and Isaacs set test was found in right hemispheric strokes. Conclusions-NAWM diffusion tensor imaging parameters measured early after an ischemic stroke are independent predictors of functional outcome and may be additional markers to include in studies evaluating poststroke recovery. © 2020 Lippincott Williams and Wilkins. All rights reserved.Translational Research and Advanced Imaging Laborator

Radiology

Background: A target mismatch profile can identify good clinical response to recanalization after acute ischemic stroke, but does not consider region specificities. Purpose: To test whether location-weighted infarction core and mismatch, determined from diffusion and perfusion MRI performed in patients with acute stroke, could improve prediction of good clinical response to mechanical thrombectomy compared with a target mismatch profile. Materials and Methods: In this secondary analysis, two prospectively collected independent stroke data sets (2012–2015 and 2017–2019) were analyzed. From the brain before stroke (BBS) study data (data set 1), an eloquent map was computed through voxel-wise associations between the infarction core (based on diffusion MRI on days 1–3 following stroke) and National Institutes of Health Stroke Scale (NIHSS) score. The French acute multimodal imaging to select patients for mechanical thrombectomy (FRAME) data (data set 2) consisted of large vessel occlusion–related acute ischemic stroke successfully recanalized. From acute MRI studies (performed on arrival, prior to thrombectomy) in data set 2, target mismatch and eloquent (vs noneloquent) infarction core and mismatch were computed from the intersection of diffusion- and perfusion-detected lesions with the coregistered eloquent map. Associations of these imaging metrics with early neurologic improvement were tested in multivariable regression models, and areas under the receiver operating characteristic curve (AUCs) were compared. Results: Data sets 1 and 2 included 321 (median age, 69 years [IQR, 58–80 years]; 207 men) and 173 (median age, 74 years [IQR, 65–82 years]; 90 women) patients, respectively. Eloquent mismatch was positively and independently associated with good clinical response (odds ratio [OR], 1.14; 95% CI: 1.02, 1.27; P =.02) and eloquent infarction core was negatively associated with good response (OR, 0.85; 95% CI: 0.77, 0.95; P =.004), while noneloquent mismatch was not associated with good response (OR, 1.03; 95% CI: 0.98, 1.07; P =.20). Moreover, adding eloquent metrics improved the prediction accuracy (AUC, 0.73; 95% CI: 0.65, 0.81) compared with clinical variables alone (AUC, 0.65; 95% CI: 0.56, 0.73; P =.01) or a target mismatch profile (AUC, 0.67; 95% CI: 0.59, 0.76; P =.03). Conclusion: Location-weighted infarction core and mismatch on diffusion and perfusion MRI scans improved the identification of patients with acute stroke who would benefit from mechanical thrombectomy compared with the volume-based target mismatch profile. © RSNA, 2022.Translational Research and Advanced Imaging Laborator

Facteurs prédictifs et pronostiques des transformations hémorragiques des infarctus cérébraux traités par thrombolyse

Les transformations hémorragiques (TH) sont les complications les plus redoutées de la thrombolyse des infarctus cérébraux. Savoir caractériser les TH graves et en identifier les facteurs de risque permettrait d améliorer l innocuité de ce traitement. Les dossiers de 124 patients ayant fait une TH post-thrombolyse ont été comparés à ceux de 80 patients indemnes de saignement. Trois méthodes pour caractériser une TH associée à un mauvais pronostic ont été étudiées : le volume du saignement, le caractère symptomatique de la TH et la classification radiologique ECASS. La reproductibilité inter-observateur de la classification ECASS a été étudiée sur un sous-groupe de patients. Les facteurs de risque des TH graves ainsi définies ont été recherchés. Le volume de saignement supérieur à 15 ml (OR ajusté=21,5, IC=3,2-144,6, p=0,001), le caractère symptomatique de l hémorragie (OR ajusté=31,6, IC=3,6-280, p=0,002) et le classement radiologique en hématome parenchymateux (PH1 et PH2) (OR ajusté=8,1, IC=1,9-34,2, p=0,004) sont corrélés à un score de Rankin >= à 4 à 3 mois. La reproductibilité inter-observateur de la classification ECASS est bonne pour la séquence T2* mais médiocre pour les autres séquences IRM et le TDM. Les facteurs de risque indépendants des TH graves précédemment définies sont l âge et la baisse de l ADC (< 400X10-6 mm /s) au cœur de l infarctus. En conclusion, la mesure du volume du saignement pourrait être la meilleure méthode pour prédire la gravité d une TH post-thrombolyse. L âge et la baisse d ADC au cœur du foyer ischémique sont les seules variables significativement corrélées au risque de TH grave dans cette série.PARIS6-Bibl.Pitié-Salpêtrie (751132101) / SudocPARIS-BIUM (751062103) / SudocSudocFranceF

Anesth Reanim

Les accidents vasculaires cérébraux (AVC) sont très liés à l’hypertension artérielle (HTA). Le traitement de l’HTA doit être envisagé avant, pendant et après la survenue d’un évènement aigu, les objectifs thérapeutiques variant en fonction du type d’AVC et/ou des autres stratégies mises en œuvre. Une nouvelle entité, qui est la variabilité de la pression artérielle (VPA), émerge dans la littérature et sera probablement une cible thérapeutique supplémentaire à l’avenir.Stroke is strongly associated with high blood pressure (hypertension). Treatment of hypertension must be considered before, during and after the occurrence of an acute event, with therapeutic objectives varying according to the type of stroke and/or other strategies implemented. A new entity, blood pressure variability (BPV), is emerging in the literature and is likely to be an additional therapeutic target in the future

Pharmacy-Based Opportunistic Atrial Fibrillation Screening at a Community Level: A Real-Life Study

Purpose: Opportunistic pharmacy-based screening of atrial fibrillation (AF) appears effective, but the proportion of detected citizens is unknown. The aim of our real-life study was to determine rates of screening in a community population according to age group and gender. Methods: We conducted four community campaigns of pharmacy-based single-time point AF screening that involved individuals ≥65 years. We used a single-lead and hand-held device MyDiagnostick (6229 EV Maastricht, The Netherlands) that generates a 60-s ECG trace. All pharmacies of the communities (n = 54) were involved. Rates of screening were assessed on the base of the French National Institute for Statistics and Economic Studies data and were expressed as percentage and 95% Confidence interval (CI). Results: We screened 4208 individuals (Mean age, 74.2 ± 6.6 years; females, 60.2%). The screening rate in citizens aged ≥65 years was 17.2% (16.6–17.7), and higher in females than in males (17.9% [17.3–18.6] versus 16.0 [15.3–16.8], p p = 0.04), male sex (OR: 4.30 [2.33–7.92], p p = 0.0008) were independent predictors of unknown AF. Conclusion: Single-lead AF detection performed in community pharmacies result in screening one in six elderly citizens. Although male sex and elderly predicted unknown AF diagnosis, they were less involved in such designed campaigns

Transcriptome dynamics of a susceptible wheat upon Fusarium head blight reveals that molecular responses to Fusarium graminearum infection fit over the grain development processes

In many plant/pathogen interactions, host susceptibility factors are key determinants of disease development promoting pathogen growth and spreading in plant tissues. In the Fusarium head blight (FHB) disease, the molecular basis of wheat susceptibility is still poorly understood while it could provide new insights into the understanding of the wheat/Fusarium graminearum (Fg) interaction and guide future breeding programs to produce cultivars with sustainable resistance. To identify the wheat grain candidate genes, a genome-wide gene expression profiling was performed in the French susceptible wheat cultivar, Recital. Gene-specific two-way ANOVA of about 40 K transcripts at five grain developmental stages identified 1309 differentially expressed genes. Out of these, 536 were impacted by the Fg effect alone. Most of these Fg-responsive genes belonged to biological and molecular functions related to biotic and abiotic stresses indicating the activation of common stress pathways during susceptibility response of wheat grain to FHB. This analysis revealed also 773 other genes displaying either specific Fg-responsive profiles along with grain development stages or synergistic adjustments with the grain development effect. These genes were involved in various molecular pathways including primary metabolism, cell death, and gene expression reprogramming. An increasingly complex host response was revealed, as was the impact of both Fg infection and grain ontogeny on the transcription of wheat genes. This analysis provides a wealth of candidate genes and pathways involved in susceptibility responses to FHB and depicts new clues to the understanding of the susceptibility determinism in plant/pathogen interactions

Association between neurological outcome and poststroke comorbid mood and anxiety disorders: A real‐life experience

Abstract Introduction Poststroke depression (PSD) and anxiety (PSA) are prevalent and have a strong impact on functional outcome. Beside stroke severity, little is known on their clinical determinants. This study investigated the association between stroke mechanism, neurological poststroke complications and remaining vascular risk factors and the presence of comorbid PSD and PSA, termed poststroke emotional distress (PSED). Methods This was a retrospective analysis of a prospectively compiled medical records database of consecutive patients evaluated during a follow‐up visit 3‐ to 4‐month poststroke. HAD scale was used to define PSED category (PSD+PSA vs. NoPSD+NoPSA). Stroke mechanism and poststroke complications were identified clinically or using appropriate scales. Their association with PSED was tested using a multivariate logistic regression model. Results The sample included 2,300 patients (male: 64.8%); 19% had a PSED and 56.39% were free of any depression or anxiety. The most frequent poststroke complications were fatigue/fatigability (58.4%), sleep problems (26.7%), and pain (20.4%). While no association was observed between PSED and stroke mechanism, higher functional disability (OR:1.572), lower cognitive abilities (OR:0.953), sleep problems (OR:2.334), pain (OR:1.478), fatigue/fatigability (OR:2.331), and abnormal movements (OR:2.380) were all independent risk factors. Persisting tobacco consumption (OR:1.360) was the only vascular significant risk factor. Conclusions The frequency of comorbid PSED remains high (1/5 patient) despite improved awareness of these conditions. The association between poststroke complications and the presence of PSED emphasizes the need for standardized neurological and psychological evaluations at follow‐up. These results foster the need to improve the management of addictive behaviors to reduce the burden of PSED