Augmenting Chest X-ray Datasets with Non-Expert Annotations

The advancement of machine learning algorithms in medical image analysis requires the expansion of training datasets. A popular and cost-effective approach is automated annotation extraction from free-text medical reports, primarily due to the high costs associated with expert clinicians annotating chest X-ray images. However, it has been shown that the resulting datasets are susceptible to biases and shortcuts. Another strategy to increase the size of a dataset is crowdsourcing, a widely adopted practice in general computer vision with some success in medical image analysis. In a similar vein to crowdsourcing, we enhance two publicly available chest X-ray datasets by incorporating non-expert annotations. However, instead of using diagnostic labels, we annotate shortcuts in the form of tubes. We collect 3.5k chest drain annotations for CXR14, and 1k annotations for 4 different tube types in PadChest. We train a chest drain detector with the non-expert annotations that generalizes well to expert labels. Moreover, we compare our annotations to those provided by experts and show "moderate" to "almost perfect" agreement. Finally, we present a pathology agreement study to raise awareness about ground truth annotations. We make our annotations and code available

Proximal 21q deletion as a result of a <i>de novo </i>unbalanced t(12;21) translocation in a patient with dysmorphic features, hepatomegaly, thick myocardium and delayed psychomotor development

BACKGROUND: IInterstitial 21q deletions can cause a wide spectrum of symptoms depending on the size and the location of the deletion. It has previously been suggested that the long arm of chromosome 21 can be divided into three regions based on the clinical severity of the patients and deletion of the region from 32.3 Mb to 37.1 Mb was more crucial than the deletion of other regions. CASE PRESENTATION: In this study we describe a female patient with dysmorphic features, hepatomegaly, thick myocardium and psychomotor delay. Conventional karyotyping was initially interpreted as full monosomy 21, but subsequent chromosome microarray analysis suggested an approximately 18 Mb partial monosomy. Re-evaluation of the karyotype and fluorescence in situ hybridization revealed deletion of the proximal 21q11.2-q22.11 segment and insertion of 21q22.11-qter to 12qter. The deletion of the present case overlaps with two of the proposed regions including part of the proposed crucial region. CONCLUSIONS: This report emphasizes the relevance of investigating suspected full monosomies with high resolution methods and FISH in order to investigate the extent of the deletion and the presence of more complex rearrangements

24-hour access outpatient clinic for patients with exacerbation of chronic disease: a before-after cohort study of differences in acute healthcare utilisation

Abstract Background Chronic diseases are becoming more common due to an increasing ageing population. Patients with chronic conditions managed in outpatient clinics account for a large share of healthcare costs. We developed a 24-h access outpatient clinic offering 24-h telephone support and triaged access to the hospital for patients with acute exacerbation of four selected chronic diseases. The aim of this study was to conduct a 1-year before-after study of the acute healthcare utilisation in patients offered the 24-h access outpatient clinic intervention. Methods The study was conducted as an observational register-based cohort study. Data from the patient administrative register and the Danish National Health Service Register were extracted 12 months before and 12 months after implementation of the 24-h access intervention. Patients with chronic obstructive pulmonary disease, chronic liver disease, inflammatory bowel disease and heart failure managed in hospital outpatient clinics were enrolled in the study. Differences in healthcare utilisation were analysed for all patients, including the subgroup of high-risk patients with at least one acute admission in the year before enrolment. Results Length-of-stay remained unchanged for all diagnostic groups, except for patients with heart failure in whom a statistically significant reduction was observed. Statistically significant reductions of length of stay and acute admissions were observed in all high-risk groups, except for patients with chronic liver disease. A statistically significant reduction in the number of contacts to out-of-hours primary care was seen in patients with chronic obstructive pulmonary disease, whereas the level remained unchanged in the other diagnostic groups. Similar patterns were also seen in high-risk patients. Conclusions The 24-h access outpatient clinic did not increase the use of acute healthcare services inpatients with chronic disease. Significant reductions in hospital utilisation were seen in high-risk patients. These preliminary results should be interpreted with caution due to the observational before-after design of the study

DanTok: Domain Beats Language for Danish Social Media POS Tagging

Language from social media remains challenging to process automatically, especially for non-English languages. In this work, we introduce the first NLP dataset for TikTok comments and the first Danish social media dataset with part-of-speech annotation. We further supply annotations for normalization, code-switching, and annotator uncertainty. As transferring models to such a highly specialized domain is non-trivial, we conduct an extensive study into which source data and modeling decisions most impact the performance. Surprisingly, transferring from in-domain data, even from a different language, outperforms in-language, out-of-domain training. These benefits nonetheless rely on the underlying language models having been at least partially pre-trained on data from the target language. Using our additional annotation layers, we further analyze how normalization, code-switching, and human uncertainty affect the tagging accuracy

UPF2 is a critical regulator of liver development, function and regeneration

BACKGROUND: Nonsense-mediated mRNA decay (NMD) is a post-transcriptional RNA surveillance process that facilitates the recognition and destruction of mRNAs bearing premature terminations codons (PTCs). Such PTC-containing (PTC+) mRNAs may arise from different processes, including erroneous processing and expression of pseudogenes, but also from more regulated events such as alternative splicing coupled NMD (AS-NMD). Thus, the NMD pathway serves both as a silencer of genomic noise and a regulator of gene expression. Given the early embryonic lethality in NMD deficient mice, uncovering the full regulatory potential of the NMD pathway in mammals will require the functional assessment of NMD in different tissues. METHODOLOGY/PRINCIPAL FINDINGS: Here we use mouse genetics to address the role of UPF2, a core NMD component, in the development, function and regeneration of the liver. We find that loss of NMD during fetal liver development is incompatible with postnatal life due to failure of terminal differentiation. Moreover, deletion of Upf2 in the adult liver results in hepatosteatosis and disruption of liver homeostasis. Finally, NMD was found to be absolutely required for liver regeneration. CONCLUSION/SIGNIFICANCE: Collectively, our data demonstrate the critical role of the NMD pathway in liver development, function and regeneration and highlights the importance of NMD for mammalian biology