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)

Atypical Presentation of Disseminated Intravascular Coagulation with Synchronous Peripheral Venous Thromboembolism and Arterial Gangrene in a Pancreatic Cancer Patient: A Case Report

Context Cancer is a prothrombotic state and anticancer therapies are often complicated by vascular events. The risk of developing thromboembolic events is substantially increased in patients with pancreatic cancer. One possible presentation of vascular events in pancreatic cancer is disseminated intravascular coagulation (DIC). Case report In our case a patient with a diagnosis of pancreatic cancer initially presented with thrombosis and received low molecular weight heparin (LMWH) in addition to standard chemotherapy regimen. He was thought to have DIC by assessment of clinical and laboratory findings. Conclusion Clinically, thrombosis was first located in the left femoral vein and encountered at right femoral artery after three weeks. This pattern was an unusual presentation of DIC. Subclinical DIC is common in patients presenting with pancreatic cancer and is considered a ‘poor’ prognostic factor. Acute DIC, on the other hand is a potentially mortal condition.Image: The legs 7 weeks after diagnosis

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