Letter to the Editor: Detection of EML4-ALK and Other ALK Fusion Genes in Lung Cancer: A Lesson from the Leukemia Fusion Gene Analysis and Future Application

We read with interest the article “EML4-ALK Fusion Gene in Korean Non-Small Cell Lung Cancer ” in a recent issue of the Journal of Korean Medical Science by Jin et al. (1). In this study, EML4-ALK fusion gene was detected in 10 of 167 non-small cell lung cancer (NSCLC) patients by using reverse transcriptase-polymerase chain reaction (RT-PCR) as a basic screening technique instead of fluorescence in situ hybridization (FISH) method. The frequency of EML4-ALK fusion gene in this study (6.0%) was not largely different from a previous study that used the FISH method on Korean NSCLC patients (4.2%) (2), while it did not diverge from the results in previous studies on a general NSCLC patient population that yielded 3%-7 % ratios as well. Based on the experience of detecting leukemia fusion genes with several new molecular methods during the diagnosis of leukemia (3-6), we would like to mention the pros and cons of such methods i

Impact of meteorological variation on hospital visits of patients with tree pollen allergy

<p>Abstract</p> <p>Background</p> <p>Climate change could affect allergic diseases, especially due to pollen. However, there has been no epidemiologic study to demonstrate the relationship between meteorological factors, pollen, and allergic patients. We aimed to investigate the association between meteorological variations and hospital visits of patients with tree pollen allergy.</p> <p>Methods</p> <p>The study subjects were adult patients who received skin prick tests between April and July from 1999 to 2008. We reviewed the medical records for the test results of 4,715 patients. Patients with tree pollen allergy were defined as those sensitized to more than 1 of 12 tree pollen allergens. We used monthly means of airborne tree pollen counts and meteorological factors: maximum/average/minimum temperature, relative humidity, and precipitation. We analyzed the correlations between meteorological variations, tree pollen counts, and the patient numbers. Multivariable logistic regression analyses were used to investigate the associations between meteorological factors and hospital visits of patients.</p> <p>Results</p> <p>The minimum temperature in March was significantly and positively correlated with tree pollen counts in March/April and patient numbers from April through July. Pollen counts in March/April were also correlated with patient numbers from April through July. After adjusting for confounders, including air pollutants, there was a positive association between the minimum temperature in March and hospital visits of patients with tree pollen allergy from April to July(odds ratio, 1.14; 95% CI 1.03 to 1.25).</p> <p>Conclusions</p> <p>Higher temperatures could increase tree pollen counts, affecting the symptoms of patients with tree pollen allergy, thereby increasing the number of patients visiting hospitals.</p

Investigation of drought propagation in South Korea using drought index and conditional probability

Meteorological drought commonly originates from precipitation deficit and is then propagated to agricultural and hydrological droughts. Since drought impacts are more directly related to agricultural and hydrological systems of human society, it is important to understand the drought propagation process for reducing drought impacts. This study investigated the propagation of meteorological droughts through the hydrological system in South Korea. We performed comparative analyses between a meteorological drought indicator [Standardized Precipitation Index (SPI) at various timescales] and a hydrological drought indicator [Palmer Hydrological Drought Index (PHDI)], and pooled the mutually dependent drought events from the indicators. The results indicated that most hydrological droughts occurred following meteorological droughts, and drought events became fewer and longer when moving from 3- and 6-month SPI to PHDI. In addition, when we investigated the meteorological conditions, about 70 - 80% of 3- and 6-month SPI corresponding to the onset of hydrological drought (PHDI ⤠-2) were less than -1.0. We also calculated the propagation probability using the conditional probability theory with 33% (3-month SPI) and 48% (6-month SPI) of meteorological droughts propagated to hydrological drought. We concluded that even though the frequency of hydrological drought in South Korea was less than that of meteorological drought, the severity of hydrological drought was greater than that of meteorological drought

Microfluidic static droplet array for analyzing microbial communication on a population gradient

Quorum sensing (QS) is a type of cell-cell communication using signal molecules that are released and detected by cells, which respond to changes in their population density. A few studies explain that QS may operate in a density-dependent manner; however, due to experimental challenges, this fundamental hypothesis has never been investigated. Here, we present a microfluidic static droplet array (SDA) that combines a droplet generator with hydrodynamic traps to independently generate a bacterial population gradient into a parallel series of droplets under complete chemical and physical isolation. The SDA independently manipulates both a chemical concentration gradient and a bacterial population density. In addition, the bacterial population gradient in the SDA can be tuned by a simple change in the number of sample plug loading. Finally, the method allows the direct analysis of complicated biological events in an addressable droplet to enable the characterization of bacterial communication in response to the ratio of two microbial populations, including two genetically engineered QS circuits, such as the signal sender for acyl-homoserine lactone (AHL) production and the signal receiver bacteria for green fluorescent protein (GFP) expression induced by AHL. For the first time, we found that the population ratio of the signal sender and receiver indicates a significant and potentially interesting partnership between microbial communities. Therefore, we envision that this simple SDA could be a useful platform in various research fields, including analytical chemistry, combinatorial chemistry, synthetic biology, microbiology, and molecular biology.close4

ACCORD: an assessment tool to determine the orientation of homodimeric coiled-coils

The coiled-coil (CC) domain is a very important structural unit of proteins that plays critical roles in various biological functions. The major oligomeric state of CCs is a dimer, which can be either parallel or antiparallel. The orientation of each α-helix in a CC domain is critical for the molecular function of CC-containing proteins, but cannot be determined easily by sequence-based prediction. We developed a biochemical method for assessing differences between parallel and antiparallel CC homodimers and named it ACCORD (Assessment tool for homodimeric Coiled-Coil ORientation Decision). To validate this technique, we applied it to 15 different CC proteins with known structures, and the ACCORD results identified these proteins well, especially with long CCs. Furthermore, ACCORD was able to accurately determine the orientation of a CC domain of unknown directionality that was subsequently confirmed by X-ray crystallography and small angle X-ray scattering. Thus, ACCORD can be used as a tool to determine CC directionality to supplement the results of in silico prediction. © The Author(s) 20171101sciescopu

Identifying and extracting bark key features of 42 tree species using convolutional neural networks and class activation mapping

© 2022, The Author(s).The significance of automatic plant identification has already been recognized by academia and industry. There were several attempts to utilize leaves and flowers for identification; however, bark also could be beneficial, especially for trees, due to its consistency throughout the seasons and its easy accessibility, even in high crown conditions. Previous studies regarding bark identification have mostly contributed quantitatively to increasing classification accuracy. However, ever since computer vision algorithms surpassed the identification ability of humans, an open question arises as to how machines successfully interpret and unravel the complicated patterns of barks. Here, we trained two convolutional neural networks (CNNs) with distinct architectures using a large-scale bark image dataset and applied class activation mapping (CAM) aggregation to investigate diagnostic keys for identifying each species. CNNs could identify the barks of 42 species with &gt; 90% accuracy, and the overall accuracies showed a small difference between the two models. Diagnostic keys matched with salient shapes, which were also easily recognized by human eyes, and were typified as blisters, horizontal and vertical stripes, lenticels of various shapes, and vertical crevices and clefts. The two models exhibited disparate quality in the diagnostic features: the old and less complex model showed more general and well-matching patterns, while the better-performing model with much deeper layers indicated local patterns less relevant to barks. CNNs were also capable of predicting untrained species by 41.98% and 48.67% within the correct genus and family, respectively. Our methodologies and findings are potentially applicable to identify and visualize crucial traits of other plant organs.Y

Robot-assisted laparoscopic intracorporeal urachal mass resection and partial cystectomy for a huge urachal adenocarcinoma: a case report and review of literature

Urachal adenocarcinoma is rare, accounting for only 10% of adenocarcinomas of the bladder and the prognosis of urachal adenocarcinomas is poor since most cases are detected late. Since urachal adenocarcinoma is a rare disease, no effective standard treatment has yet been established. However, in recent studies, resection of carcinoma is considered the only treatment considered for non-metastatic cases. Although for large sized urachal adenocarcinoma, open surgery or laparoscopic surgery is usually considered, we have recently experienced huge urachal carcinoma by robotic surgery. We used cystoscopy and the robot to assess the cancer margins and safely perform the operation. A 71-year-old man with a medical history of hypertension and arrhythmia visited our urology department with urachal cancer detected by computed tomography (CT). CT showed a lobulated low-density mass, most likely urachal carcinoma, abutting the anterior dome of the bladder and anterior abdominal wall. We performed preoperative cystoscopy to assess the extent of the protrusion of the urachal cancer into the bladder wall and the area requiring resection during surgery. We confirmed the size and extent of the mass protruding into the anterior wall of the urinary bladder and Robot-assisted laparoscopic intracorporeal urachal mass resection and partial cystectomy using cystoscopy together was performed. After one month, the patient has no complications and no complaining symptoms complaints without any abnormal finding of follow up imaging test. Although more procedures must be performed to ensure the safety of robotic surgery as a treatment strategy for large urachal carcinomas, we confirm that robotic surgery can replace open or laparoscopic surgery for such tumors