Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

The Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP) Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. The consortium generated over 427 million long-read sequences from cDNA and direct RNA datasets, encompassing human, mouse, and manatee species, using different protocols and sequencing platforms. These data were utilized by developers to address challenges in transcript isoform detection and quantification, as well as de novo transcript isoform identification. The study revealed that libraries with longer, more accurate sequences produce more accurate transcripts than those with increased read depth, whereas greater read depth improved quantification accuracy. In well-annotated genomes, tools based on reference sequences demonstrated the best performance. When aiming to detect rare and novel transcripts or when using reference-free approaches, incorporating additional orthogonal data and replicate samples are advised. This collaborative study offers a benchmark for current practices and provides direction for future method development in transcriptome analysis

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

The Long-read RNA-Seq Genome Annotation Assessment Project Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. Using different protocols and sequencing platforms, the consortium generated over 427 million long-read sequences from complementary DNA and direct RNA datasets, encompassing human, mouse and manatee species. Developers utilized these data to address challenges in transcript isoform detection, quantification and de novo transcript detection. The study revealed that libraries with longer, more accurate sequences produce more accurate transcripts than those with increased read depth, whereas greater read depth improved quantification accuracy. In well-annotated genomes, tools based on reference sequences demonstrated the best performance. Incorporating additional orthogonal data and replicate samples is advised when aiming to detect rare and novel transcripts or using reference-free approaches. This collaborative study offers a benchmark for current practices and provides direction for future method development in transcriptome analysis

Early mobilisation in critically ill COVID-19 patients: a subanalysis of the ESICM-initiated UNITE-COVID observational study

Background Early mobilisation (EM) is an intervention that may improve the outcome of critically ill patients. There is limited data on EM in COVID-19 patients and its use during the first pandemic wave. Methods This is a pre-planned subanalysis of the ESICM UNITE-COVID, an international multicenter observational study involving critically ill COVID-19 patients in the ICU between February 15th and May 15th, 2020. We analysed variables associated with the initiation of EM (within 72 h of ICU admission) and explored the impact of EM on mortality, ICU and hospital length of stay, as well as discharge location. Statistical analyses were done using (generalised) linear mixed-effect models and ANOVAs. Results Mobilisation data from 4190 patients from 280 ICUs in 45 countries were analysed. 1114 (26.6%) of these patients received mobilisation within 72 h after ICU admission; 3076 (73.4%) did not. In our analysis of factors associated with EM, mechanical ventilation at admission (OR 0.29; 95% CI 0.25, 0.35; p = 0.001), higher age (OR 0.99; 95% CI 0.98, 1.00; p ≤ 0.001), pre-existing asthma (OR 0.84; 95% CI 0.73, 0.98; p = 0.028), and pre-existing kidney disease (OR 0.84; 95% CI 0.71, 0.99; p = 0.036) were negatively associated with the initiation of EM. EM was associated with a higher chance of being discharged home (OR 1.31; 95% CI 1.08, 1.58; p = 0.007) but was not associated with length of stay in ICU (adj. difference 0.91 days; 95% CI − 0.47, 1.37, p = 0.34) and hospital (adj. difference 1.4 days; 95% CI − 0.62, 2.35, p = 0.24) or mortality (OR 0.88; 95% CI 0.7, 1.09, p = 0.24) when adjusted for covariates. Conclusions Our findings demonstrate that a quarter of COVID-19 patients received EM. There was no association found between EM in COVID-19 patients' ICU and hospital length of stay or mortality. However, EM in COVID-19 patients was associated with increased odds of being discharged home rather than to a care facility. Trial registration ClinicalTrials.gov: NCT04836065 (retrospectively registered April 8th 2021)

The evaluation of the sensitivity and specificity of wrist examination indings for predicting fractures (vol 36, pg 425, 2018)

[No Abstract Available

Could pulmonary thromboembolism be associated with air pollution ?

SUNER, ASLI/0000-0002-6872-9901WOS:000606501407108[No Abstract Available

A prospective cohort study: can advanced ultrasonography replace magnetic resonance imaging in the diagnosis of placental adhesion disorders?

Objectives: To define and compare the diagnostic accuracy of ultrasonography (USG) and magnetic resonance imaging (MRI) for the placental adhesive disorder (PAD). Methods: A prospective study was conducted between January 2019 and February 2020 in a tertiary referral university hospital. A total of 115 placenta previa cases were included in the study during the third trimester of gestation. USG examination was performed, and the placenta was scanned in a systematic manner using gray-scale ultrasound, color Doppler flow mapping, and 3-D imaging for each participant. Thereafter, all participants underwent an MRI examination. USG and MRI findings were compared with histopathological findings. Results: Loss of the retroplacental sonolucent zone (71% [95% CI 47-88]) and an irregular retroplacental sonolucent zone (71% [95% CI 47-88]) were the most sensitive USG parameters. For MRI, the uterine bulging parameter was the most sensitive (60% [95% CI 36-80]) and specific (91% [95% CI 83-96]) findings, and it had the highest accuracy rate (85% [95% CI 77-91]). Overall, the USG sensitivity, specificity, and accuracy rates were 77% (95% CI 54-92), 87% (95% CI 79-93), and 85% (95% CI 77-91), respectively. The MRI sensitivity, specificity, and accuracy rates for all participants were 81% (95% CI 59-94), 85% (95% CI 76-92), and 84% (95% CI 76-90), respectively. Conclusions: In the diagnosis of PAD, the specificity and accuracy of USG are higher than that of MRI, whereas the sensitivity of MRI is better than that of USG

Importance of HER2 Work-Up and Treatment Even in Patients with Poor Performance Status: A Case Report

Gastric cancer is one of most common types of cancers. Metastatic gastric cancer has a poor prognosis and is accepted as incurable at this stage. Treatment of metastatic gastric cancer did not progress substantially until new targeted agents have come out. Recently published ToGA trial showed promising results in HER2 overexpressing metastatic gastric cancer. In this case we present a case with an excellent complete response with anti-HER2 treatment. Most importantly, we wanted to emphasize (1) the importance of early determination of HER2 overexpression, and (2) to draw attention of anti-HER2 agents in the first line treatment even in patients with a poor performance status

The evaluation of the sensitivity and specificity of wrist examination findings for predicting fractures

WOS: 000428231100016PubMed ID: 28912085Background: The aim of this study was to evaluate the sensitivity and specificity of physical examination findings and functional tests in adult acute wrist trauma patients who presented to the emergency department (ED) and to create a reliable and practical clinical decision rule for determining the necessity of radiography in wrist trauma. Methods: This prospective observational study was conducted in a tertiary ED. Each patient was checked for 18 physical examination findings and functional tests. Patients with suspected fracture were enrolled consecutively. Antero-posterior and lateral wrist views were performed for each patient. All radiographical studies were interpreted by an orthopedic surgeon. The prevalence, sensitivity and specificity, negative and positive predictive values of each finding were calculated. A modeling for predicting fractures was created using computer. Results: 207 patients were evaluated and 69 patients (33.3%) had fractures. The most common encounterd fracture site was distal radius (29.5%). The most sensitive examination finding was pain in dorsiflexion (95.7%) and the most specific finding was ecchymosis (97.8%). Wrist edema, deformity and pain aggravated by pronation were found to be strong predictors of fracture. The area under the receiver operating characteristic curve at internal validation for a prediction model based on these three predictors was 0.88 (95% CI: 0.83-0,93). The overall sensitivity and specificity of this model were 94% (95% CI: 85-98%) and 51% (95% CI 43-60%) respectively. According to the model created in this study, 34% of acute blunt wrist trauma patients do not require any X-ray imaging. Conclusions: This triple modeling may be used as an effective decision rule for predicting all wrist fractures in the ED and in the disaster setting. (c) 2017 Elsevier Inc. All rights reserved