•We classify high-quality articles using other topics’ articles.•Our classifiers by trained on articles having common properties improve the AUC.•Our method can reduce the labor required for the new ...systematic reviews.
To determine whether SVM-based classifiers, which are trained on a combination of inclusion and common exclusion articles, are useful to experts reviewing journal articles for inclusion during new systematic reviews.
Test collections were built using the annotated reference files from 19 procedure and 4 drug systematic reviews. The classifiers were trained by balanced data sets, which were sampled using random sampling. This approach compared two balanced data sets, one with a combination of included and commonly excluded articles and one with a combination of included and excluded articles. AUCs were used as evaluation metrics.
The AUCs of the classifiers, which were trained on the balanced data set with included and commonly excluded articles, were significantly higher than those of the classifiers, which were trained on the balanced data set with included and excluded articles.
Automatic, high-quality article classifiers using machine learning could reduce the workload of experts performing systematic reviews when topic-specific data are scarce. In particular, when used as training data, a combination of included and commonly excluded articles is more helpful than a combination of included and excluded articles.
► CHFR mediates the ubiquitination of the major components of the SWI/SNF complex. ► CHFR mediated-ubiquitination induces the degradation of the major components. ► SRG3 stabilizes the SWI/SNF-like ...BAF complex by blocking the CHFR activity.
The murine SWI/SNF-like BAF complex is an ATP-dependent chromatin remodeling complex that functions as a transcriptional regulator in cell proliferation, differentiation and development. The SWI/SNF-like BAF complex consists of several components including core subunits such as BRG1, BAF155/SRG3, BAF47/SNF5/INI1, and BAF170. We have previously shown that the interaction between SRG3/mBAF155 and other components of the complex stabilizes them by attenuating their proteasomal degradation. However, it has not been known how the major components of the SWI/SNF-like BAF complex such as BRG1, SNF5, and BAF60a are targeted for the ubiquitination and degradation, and how SRG3/mBAF155 protects them from the degradation process. Here we report that CHFR interacts with BRG1, SNF5, and BAF60a of the SWI/SNF-like BAF complex and ubiquitinates them to target for degradation through a proteasome-mediated pathway, and that SRG3/mBAF155 stabilizes these components by blocking their interaction with CHFR.
Improving the retrieval accuracy of MEDLINE documents is still a challenging issue due to low retrieval precision. Focusing on a query expansion technique based on pseudo-relevance feedback (PRF), ...this paper addresses the problem by systematically examining the effects of expansion term selection and adjustment of the term weights of the expanded query using a set of MEDLINE test documents called OHSUMED. Implementing a baseline information retrieval system based on the Okapi BM25 retrieval model, we compared six well-known term ranking algorithms for useful expansion term selection and then compared traditional term reweighting algorithms with our new variant of the standard Rocchio’s feedback formula, which adopts a group-based weighting scheme. Our experimental results on the OHSUMED test collection showed a maximum improvement of 20.2% and 20.4% for mean average precision and recall measures over unexpanded queries when terms were expanded using a co-occurrence analysis-based term ranking algorithm in conjunction with our term reweighting algorithm (
p-value
<
0.05). Our study shows the behaviors of different query reformulation techniques that can be utilized for more effective MEDLINE document retrieval.
The remarkable regenerative capacity of the lung suggests that stem cells could be of therapeutic importance in diverse lung diseases; however, the successful exploitation of lung stem cell biology ...has long been hampered by our inability to maintain and expand adult lung stem cells while retaining their multi-lineage potential in vitro. Recently, advances in our understanding of stem cell niches and the role of key signalling modulators in controlling stem cell maintenance and differentiation have fuelled the development of new in vitro three-dimensional (3D) culture technologies that sustain the stem cell-driven formation of near-physiological, self-organizing structures called organoids. Here we review basic approaches to organoid model systems and highlight recent achievements in the generation of organoids from adult stem and progenitor cells of both the murine and human lungs. We evaluate current applications in studying cellular changes in proliferation, differentiation, plasticity, and cell polarity, and cellular and molecular crosstalk of epithelial cells with stroma. Advantages and limitations of organoids for clinical use are also discussed.
•Adult lung epithelial progenitor cells are capable of generating self-organizing structure in 3D culture.•Lung organoids have the capacity for clonal propagation and multi-lineage differentiation.•Lung organoids recapitulate the regenerative process proposed from in vivo study.•Lung organoid co-culture provides a platform to study niche functions in adult stem cell regulation.
The purpose of this study was to compare fracture resistances of K3 nickel-titanium files made from different thermal treatments. K3 (SybronEndo, Orange, CA), K3XF (SybronEndo), and experimentally ...heat treated K3 (K3H) were used. For the cyclic fatigue test, the samples were rotated with up-and-down motion in the artificial canal with the curvature of 60 degrees until the fracture occurred. The number of cycles to fracture (NCF) was measured. For the torsional fracture test, the samples were tightly bound and rotated until the fracture occurred. Elastic modulus (EM), ultimate torsional strength (UTS), and angle of rotation to fracture (ARF) were measured. The results were statistically analyzed by one-way ANOVA. The NCF of K3H was higher than those of K3 and K3XF ( P < 0.05 ). The EM of K3XF and K3H was lower than that of K3 ( P < 0.05 ). There was no significant difference in UTS. The ARF of K3XF was higher than that of K3 ( P < 0.05 ). K3XF and K3H showed more flexibility than K3. The maximum torsional angle of K3XF was higher than that of K3, but there was no significant difference on the UTS in all three groups.
The purpose of this study was to investigate the effects of query expansion algorithms for MEDLINE retrieval within a pseudo-relevance feedback framework.
A number of query expansion algorithms were ...tested using various term ranking formulas, focusing on query expansion based on pseudo-relevance feedback. The OHSUMED test collection, which is a subset of the MEDLINE database, was used as a test corpus. Various ranking algorithms were tested in combination with different term re-weighting algorithms.
Our comprehensive evaluation showed that the local context analysis ranking algorithm, when used in combination with one of the reweighting algorithms - Rocchio, the probabilistic model, and our variants - significantly outperformed other algorithm combinations by up to 12% (paired t-test; p < 0.05). In a pseudo-relevance feedback framework, effective query expansion would be achieved by the careful consideration of term ranking and re-weighting algorithm pairs, at least in the context of the OHSUMED corpus.
Comparative experiments on term ranking algorithms were performed in the context of a subset of MEDLINE documents. With medical documents, local context analysis, which uses co-occurrence with all query terms, significantly outperformed various term ranking methods based on both frequency and distribution analyses. Furthermore, the results of the experiments demonstrated that the term rank-based re-weighting method contributed to a remarkable improvement in mean average precision.
The purpose of this study is to validate a method that uses multiple queries to create a set of relevance judgments used to indicate which documents are pertinent to each query when forming a ...biomedical test collection.
The aspect query is the major concept of this research; it can represent every aspect of the original query with the same informational need. Manually generated aspect queries created by 15 recruited participants where run using the BM25 retrieval model in order to create aspect query based relevance sets (QRELS). In order to demonstrate the feasibility of these QRELSs, The results from a 2004 genomics track run supported by the National Institute of Standards and Technology (NIST) were used to compute the mean average precision (MAP) based on Text Retrieval Conference (TREC) QRELSs and aspect-QRELSs. The rank correlation was calculated using both Kendall's and Spearman's rank correlation methods.
We experimentally verified the utility of the aspect query method by combining the top ranked documents retrieved by a number of multiple queries which ranked the order of the information. The retrieval system correlated highly with rankings based on human relevance judgments.
Substantial results were shown with high correlations of up to 0.863 (p < 0.01) between the judgment-free gold standard based on the aspect queries and the human-judged gold standard supported by NIST. The results also demonstrate that the aspect query method can contribute in building test collections used for medical literature retrieval.
Interpretation of noncoding disease variants, which comprise the vast majority of Genome-wide association studies (GWAS) hits, remains a momentous challenge due to haplotype structure and our limited ...understanding of the mechanisms and physiological contexts of noncoding elements. GWAS have identified loci underlying human diseases, but assigning the causal nucleotide changes still remain a controversial issue. Here we addressed these issues through the combination of high-density genotyping and epigenomic data using a random forest model to discover the noncoding causal variants. Focusing on autoimmune diseases, we triaged putative causal variants for atopic dermatitis and inflammatory bowel diseases. Making a filtering pipeline, we found three interesting single nucleotide polymorphisms (rs1800630, rs1799964 and rs4796793) in the upstream site of TNF and STAT3 genes, two frequent genes shared in some autoimmune diseases, and show how those variants affect on TNF and STAT3 expression levels. All data and source codes related to this manuscript are available at https://github.com/jieunjung511/Autoimmune-research.
•We looked for shared noncoding causal genetic loci for autoimmune diseases•A random forest model was trained on genetic and epigenetic features of pathogenic variants.•Our model encompassed both promoter and enhancer sites by considering the associations between them.•We identified three SNPs (rs1800630, rs1799964 and rs4796793) in the upstream regions of TNF and STAT3 genes as the putative causal variants for atopic dermatitis and inflammatory bowel diseases.
Acquiring temporal information is important because knowledge in clinical narratives is time-sensitive. In this paper, we describe an approach that can be used to extract the temporal information ...found in Korean clinical narrative texts.
We developed a two-stage system, which employs an exhaustive text analysis phase and a temporal expression recognition phase. Since our target document may include tokens that are made up of both Korean and English text joined together, the minimal semantic units are analyzed and then separated from the concatenated phrases and linguistic derivations within a token using a corpus-based approach to decompose complex tokens. A finite state machine is then used on the minimal semantic units in order to find phrases that possess time-related information.
In the experiment, the temporal expressions within Korean clinical narratives were extracted using our system. The system performance was evaluated through the use of 100 discharge summaries from Seoul National University Hospital containing a total of 805 temporal expressions. Our system scored a phrase-level precision and recall of 0.895 and 0.919, respectively.
Finding information in Korean clinical narrative is challenging task, since the text is written in both Korean and English and frequently omits syntactic elements and word spacing, which makes it extremely noisy. This study presents an effective method that can be used to aquire the temporal information found in Korean clinical documents.
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