TPMD: a database and resources of microsatellite marker genotyped in Taiwanese populations

Taiwan Polymorphic Marker Database (TPMD) (http://tpmd.nhri.org.tw/) is a marker database designed to provide experimental details and useful marker information allelotyped in Taiwanese populations accompanied by resources and technical supports. The current version deposited more than 372 000 allelotyping data from 1425 frequently used and fluorescent-labeled microsatellite markers with variation types of dinucleotide, trinucleotide and tetranucleotide. TPMD contains text and map displays with searchable and retrievable options for marker names, chromosomal location in various human genome maps and marker heterozygosity in populations of Taiwanese, Japanese and Caucasian. The integration of marker information in map display is useful for the selection of high heterozygosity and commonly used microsatellite markers to refine mapping of diseases locus followed by identification of disease gene by positional candidate cloning. In addition, our results indicated that the number of markers with heterozygosity over 0.7 in Asian populations is lower than that in Caucasian. To increase accuracy and facilitate genetic studies using microsatellite markers, we also list markers with genotyping difficulty due to ambiguity of allele calling and recommend an optimal set of microsatellite markers for genotyping in Taiwanese, and possible extension of genotyping in other Mongoloid populations

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Genome-wide association study of lung adenocarcinoma in East Asia and comparison with a European population

Lung adenocarcinoma is the most common type of lung cancer. Known risk variants explain only a small fraction of lung adenocarcinoma heritability. Here, we conducted a two-stage genome-wide association study of lung adenocarcinoma of East Asian ancestry (21,658 cases and 150,676 controls; 54.5% never-smokers) and identified 12 novel susceptibility variants, bringing the total number to 28 at 25 independent loci. Transcriptome-wide association analyses together with colocalization studies using a Taiwanese lung expression quantitative trait loci dataset (n = 115) identified novel candidate genes, including FADS1 at 11q12 and ELF5 at 11p13. In a multi-ancestry meta-analysis of East Asian and European studies, four loci were identified at 2p11, 4q32, 16q23, and 18q12. At the same time, most of our findings in East Asian populations showed no evidence of association in European populations. In our studies drawn from East Asian populations, a polygenic risk score based on the 25 loci had a stronger association in never-smokers vs. individuals with a history of smoking (P interaction  = 0.0058). These findings provide new insights into the etiology of lung adenocarcinoma in individuals from East Asian populations, which could be important in developing translational applications

Genome-wide association study of lung adenocarcinoma in East Asia and comparison with a European population.

Lung adenocarcinoma is the most common type of lung cancer. Known risk variants explain only a small fraction of lung adenocarcinoma heritability. Here, we conducted a two-stage genome-wide association study of lung adenocarcinoma of East Asian ancestry (21,658 cases and 150,676 controls; 54.5% never-smokers) and identified 12 novel susceptibility variants, bringing the total number to 28 at 25 independent loci. Transcriptome-wide association analyses together with colocalization studies using a Taiwanese lung expression quantitative trait loci dataset (n = 115) identified novel candidate genes, including FADS1 at 11q12 and ELF5 at 11p13. In a multi-ancestry meta-analysis of East Asian and European studies, four loci were identified at 2p11, 4q32, 16q23, and 18q12. At the same time, most of our findings in East Asian populations showed no evidence of association in European populations. In our studies drawn from East Asian populations, a polygenic risk score based on the 25 loci had a stronger association in never-smokers vs. individuals with a history of smoking (Pinteraction = 0.0058). These findings provide new insights into the etiology of lung adenocarcinoma in individuals from East Asian populations, which could be important in developing translational applications

Influence of Changing the Diameter of the Bubble Generator Bottle and Expiratory Limb on Bubble CPAP: An in vitro Study

The noisy component of bubble continuous positive airway pressure (CPAP) is thought to contribute to breathing efficiency and lung volume recruitment, mainly because of stochastic resonance. The magnitude and frequency of the superimposed noise are vital to this process. We wanted to evaluate the in vitro effect of changing various parameters of the bubble CPAP circuit regarding the magnitude and frequency of pressure oscillations transmitted to the lung model. Methods: In a bubble CPAP lung model, we immersed different sizes (3.0∼12.5 mm) of the expiratory limb of the CPAP circuit into different depths under water (2.0∼10.0 cm) and used various diameters (2.9∼9.0 cm) of bubble generator bottles. We also varied the compliance of the model lung. We measured the changes in mean, magnitude, and frequency of pressure oscillations transmitted to the lung model at three different flow rates (namely 4, 8, and 12 L/minute). Results: Increasing the size and submergence depth of the expiratory limb of a CPAP circuit and decreasing the diameter of the bubble generator bottle intensified the magnitude but diminished the frequency of noise transmitted to the lung model. Decreasing compliance of the lung model intensified both the magnitude and frequency content of pressure oscillations in the model lung. Conclusion: The size and submergence depth of an expiratory limb of a CPAP circuit, the diameter of the bubble generator bottle, and the compliance of the model lung all influence the magnitude and frequency of the transmitted pressure waveform. Therefore, these factors may affect lung volume recruitment and breathing efficiency in bubble CPAP

High Resolution Ultrasonography of Ganglion in the Left Common Peroneal Nerve

Intraneural ganglion is uncommon. We report a 49-year-old man with numbness of the left lower leg and foot drop for 1 month. High resolution ultrasonography (HRUS) showed a fusiform hypoechoic cystic structure, 5 × 0.5 cm in size, in the left lateral popliteal fossa which extended to below the fibula head region and which was encased by the epineurium of the left common peroneal nerve. Histology was compatible with ganglion. After operation, the patient recovered very well. This was correlated to a previous report in which the outcome essentially depended on the resectability of the lesion without nerve damage and the duration of symptoms. HRUS has the advantage of no radiation exposure, good resolution and high mobility. HRUS could be a valuable screening tool for soft tissue neoplasm and to differentiate it from the surrounding structure

Use of sonography in assessing elbow medial collateral ligament injury after arm wrestling

Medial collateral ligament injury is an infrequent occurrence in arm wrestlers. We report here a male patient who injured his left elbow while arm wrestling. Ultrasonography showed a medial collateral ligament tear. We assessed both elbows using ultrasonography at his 3-year follow-up visit. Dynamic ultrasonography showed a decreased gap at the ulnotrochlear joint space in his left elbow. A medial collateral ligament tear in his right elbow was also evident using ultrasonography. This case report shows the advantages of ultrasonography, especially dynamic ultrasonography, in the evaluation of elbow injury. Ultrasonography provides more information than valgus stress radiography, arthrography, and magnetic resonance imaging in the assessment of medial collateral ligament injury. In addition, the contralateral side can readily be assessed for comparison during ultrasonography

Acquired Duodenal Obstruction in Children

Traumatic intramural hematoma of the duodenum is a rare cause of acquired duodenal obstruction in children, and a high degree of suspicion is therefore required to make an early and accurate diagnosis. We report a 6-year-old boy whose epigastrium was impacted by the handlebar of his bicycle during a traffic accident. The boy then experienced epigastralgia. Six days later, progressive bilious vomiting suggestive of gastrointestinal obstruction was noted. Imaging studies revealed a large hematoma extending from the fourth portion of the duodenum to the jejunum. Conservative methods of treatment failed to manage his condition. He underwent laparoscopic surgery to evacuate the hematoma. We also report a case of duodenal obstruction in a previously healthy 2-year-old girl who presented for the first time with acute symptoms of proximal intestinal obstruction. Contrast examinations showed apparent barium retention over the stomach and proximal duodenum. She underwent surgery due to persistent obstruction, and a mushroom-like foreign body was detected embedded in the orifice of the windsock duodenal web. After duodenoduodenostomy and removal of the bezoar, she had a smooth recovery and tolerated feeding well. We conclude that blunt abdominal trauma and incomplete duodenal obstruction, such as that caused by duodenal web, should be considered as possible causes of acquired proximal gastrointestinal obstruction in previously healthy children, despite their rarity