Beyond Images: An Integrative Multi-modal Approach to Chest X-Ray Report Generation

Image-to-text radiology report generation aims to automatically produce radiology reports that describe the findings in medical images. Most existing methods focus solely on the image data, disregarding the other patient information accessible to radiologists. In this paper, we present a novel multi-modal deep neural network framework for generating chest X-rays reports by integrating structured patient data, such as vital signs and symptoms, alongside unstructured clinical notes.We introduce a conditioned cross-multi-head attention module to fuse these heterogeneous data modalities, bridging the semantic gap between visual and textual data. Experiments demonstrate substantial improvements from using additional modalities compared to relying on images alone. Notably, our model achieves the highest reported performance on the ROUGE-L metric compared to relevant state-of-the-art models in the literature. Furthermore, we employed both human evaluation and clinical semantic similarity measurement alongside word-overlap metrics to improve the depth of quantitative analysis. A human evaluation, conducted by a board-certified radiologist, confirms the model's accuracy in identifying high-level findings, however, it also highlights that more improvement is needed to capture nuanced details and clinical context

Öğretmen Eğitimi Programları ve Paradigmalarının Karşılaştırmalı Analizi

Bu çalışmanın amacı  New York, Singapur, Finlandiya, ve Türkiye’de benimsenen öğretmen yetiştirme programlarını ülkelerde baskın olan paradigmalar doğrultusunda incelemek ve araştırma sonuçlarından yola çıkarak Türkiye’de yapılacak olan yeniliklere katkıda bulunmaktır. Tarama modelinde desenlenen çalışmada ölçüt örneklem tekniği kullanılmıştır. Araştırmada nitel analiz teknikleri kullanımıştır. Araştırma sonucunda Finlandiya ve A.B.D’de öğretmen yetiştiren kurumların kendi programlarını belirlemede etkin oldukları, buna karşın Türkiye ve Singapur’da programların merkezi otoriteler tarafından belirlendiği ve bu durumun önemli bir zayıflık olduğu bulunmuştur.  Diğer yandan öğretmen eğitimi paradigması olarak A.B.D, Singapur ve Türkiye’de politika düzeyinde reformist paradigmaların vurgulanmasına karşın uygulamada rekabetçi ve yararlı bilgi paradigmasının baskın olduğu sonucuna ulaşılmıştır. Finlandiya ise işbirliği, araştırma temelli bilgi ve gelenekten ayrılma paradigmaları gibi reformist paradigmaların  gerek politika gerekse uygulama düzeyinde etkin olarak benimsendiği bir ülke konumundadır

Novelty detection for topic tracking

Multisource web news portals provide various advantages such as richness in news content and an opportunity to follow developments from different perspectives. However, in such environments, news variety and quantity can have an overwhelming effect. New-event detection and topic-tracking studies address this problem. They examine news streams and organize stories according to their events; however, several tracking stories of an event/topic may contain no new information (i.e., no novelty). We study the novelty detection (ND) problem on the tracking news of a particular topic. For this purpose, we build a Turkish ND test collection called BilNov-2005 and propose the usage of three ND methods: a cosine-similarity (CS)-based method, a language-model (LM)-based method, and a cover-coefficient (CC)-based method. For the LM-based ND method, we show that a simpler smoothing approach, Dirichlet smoothing, can have similar performance to a more complex smoothing approach, Shrinkage smoothing. We introduce a baseline that shows the performance of a system with random novelty decisions. In addition, a category-based threshold learning method is used for the first time in ND literature. The experimental results show that the LM-based ND method significantly outperforms the CS- and CC-based methods, and categorybased threshold learning achieves promising results when compared to general threshold learning. © 2011 ASIS&T

Probing Spatial Myeloid Heterogeneity in Glioblastoma

https://openworks.mdanderson.org/sumexp22/1015/thumbnail.jp

Semantic argument frequency-based Multi-Document Summarization

Semantic Role Labeling (SRL) aims to identify the constituents of a sentence, together with their roles with respect to the sentence predicates. In this paper, we introduce and assess the idea of using SRL on generic Multi-Document Summarization (MDS). We score sentences according to their inclusion of frequent semantic phrases and form the summary using the top-scored sentences. We compare this method with a term-based sentence scoring approach to investigate the effects of using semantic units instead of single words for sentence scoring. We also integrate our scoring metric as an auxiliary feature to a cutting edge summarizer with the intention of examining its effects on the performance. The experiments using datasets from the Document Understanding Conference (DUC) 2004 show that the SRL-based summarization outperforms the term-based approach as well as most of the DUC participants. © 2009 IEEE

Mutualist-Provisioned Resources Impact Vector Competency

ABSTRACT Many symbionts supplement their host’s diet with essential nutrients. However, whether these nutrients also enhance parasitism is unknown. In this study, we investigated whether folate (vitamin B9) production by the tsetse fly (Glossina spp.) essential mutualist, Wigglesworthia, aids auxotrophic African trypanosomes in completing their life cycle within this obligate vector. We show that the expression of Wigglesworthia folate biosynthesis genes changes with the progression of trypanosome infection within tsetse. The disruption of Wigglesworthia folate production caused a reduction in the percentage of flies that housed midgut (MG) trypanosome infections. However, decreased folate did not prevent MG trypanosomes from migrating to and establishing an infection in the fly’s salivary glands, thus suggesting that nutrient requirements vary throughout the trypanosome life cycle. We further substantiated that trypanosomes rely on symbiont-generated folate by feeding this vitamin to Glossina brevipalpis, which exhibits low trypanosome vector competency and houses Wigglesworthia incapable of producing folate. Folate-supplemented G. brevipalpis flies were significantly more susceptible to trypanosome infection, further demonstrating that this vitamin facilitates parasite infection establishment. Our cumulative results provide evidence that Wigglesworthia provides a key metabolite (folate) that is “hijacked” by trypanosomes to enhance their infectivity, thus indirectly impacting tsetse species vector competency. Parasite dependence on symbiontderived micronutrients, which likely also occurs in other arthropod vectors, represents a relationship that may be exploited to reduce disease transmission. IMPORTANCE Parasites elicit several physiological changes in their host to enhance transmission. Little is known about the functional association between parasitism and microbiota-provisioned resources typically dedicated to animal hosts and how these goods may be rerouted to optimize parasite development. This study is the first to identify a specific symbiont-generated metabolite that impacts insect vector competence by facilitating parasite establishment and, thus, eventual transmission. Specifically, we demonstrate that the tsetse fly obligate mutualist Wigglesworthia provisions folate (vitamin B9) that pathogenic African trypanosomes exploit in an effort to successfully establish an infection in the vector’s MG. This process is essential for the parasite to complete its life cycle and be transmitted to a new vertebrate host. Disrupting metabolic contributions provided by the microbiota of arthropod disease vectors may fuel future innovative control strategies while also offering minimal nontarget effects

Is loss of sense of smell a diagnostic marker in COVID-19: A Systematic Review and Meta-analysis

Aims: To systematically review the currently available evidence investigating the association between olfactory dysfunction (OD) and the novel coronavirus (COVID-19). To analyse the prevalence of OD in patients who have tested positive on polymerase chain reaction (PCR) for COVID-19. To perform a meta-analysis of patients presenting with olfactory dysfunction, during the pandemic, and to investigate the positive predictive value for a COVID-19-positive result in this population. To assess whether olfactory dysfunction could be used as a diagnostic marker for COVID-19 positivity and aid public health approaches in tackling the current outbreak. Methods: We systematically searched MedLine (PubMed), Embase, Health Management Information Consortium (HMIC), Medrxiv, the Cochrane Library, the Cochrane COVID-19 Study Register, NIHR Dissemination centre, Clinical Evidence, National Health Service Evidence and the National Institute of Clinical Excellence to identify the current published evidence which associates coronaviridae or similar RNA viruses with anosmia. The initial search identified 157 articles. A total of 145 papers were excluded following application of our exclusion criteria. The 12 remaining articles that presented evidence on the association between COVID-19 and olfactory dysfunction were critically analysed. Results: Olfactory dysfunction has been shown to be the strongest predictor of COVID-19 positivity when compared to other symptoms in logistic regression analysis. In patients who had tested positive for COVID-19, there was a prevalence of 62% of OD. In populations of patients who are currently reporting OD, there is a positive predictive value of 61% for a positive COVID-19 result. Conclusion: Our review has shown that there is already significant evidence which demonstrates an association between OD and the novel coronavirus—COVID-19. It is unclear if this finding is unique to this coronavirus as individual viral phenotypes rarely present in such concentrated large numbers. We have demonstrated that OD is comparatively more predictive for COVID-19 positivity compared to other associated symptoms. We recommend that people who develop OD during the pandemic should be self-isolate and this guidance should be adopted internationally to prevent transmission