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Small RNA biology is systems biology

  • Jost, Daniel;Nowojewski, Andrzej;Levine, Erel
    • BMB Reports
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    • v.44 no.1
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    • pp.11-21
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    • 2011
  • During the last decade small regulatory RNA (srRNA) emerged as central players in the regulation of gene expression in all kingdoms of life. Multiple pathways for srRNA biogenesis and diverse mechanisms of gene regulation may indicate that srRNA regulation evolved independently multiple times. However, small RNA pathways share numerous properties, including the ability of a single srRNA to regulate multiple targets. Some of the mechanisms of gene regulation by srRNAs have significant effect on the abundance of free srRNAs that are ready to interact with new targets. This results in indirect interactions among seemingly unrelated genes, as well as in a crosstalk between different srRNA pathways. Here we briefly review and compare the major srRNA pathways, and argue that the impact of srRNA is always at the system level. We demonstrate how a simple mathematical model can ease the discussion of governing principles. To demonstrate these points we review a few examples from bacteria and animals.

Spectrum of Pulmonary Fibrosis from Interstitial Lung Abnormality to Usual Interstitial Pneumonia: Importance of Identification and Quantification of Traction Bronchiectasis in Patient Management

  • Takuya Hino;Kyung Soo Lee;Joungho Han;Akinori Hata;Kousei Ishigami;Hiroto Hatabu
    • Korean Journal of Radiology
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    • v.22 no.5
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    • pp.811-828
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    • 2021
  • Following the introduction of a novel pathological concept of usual interstitial pneumonia (UIP) by Liebow and Carrington in 1969, diffuse interstitial pneumonia has evolved into UIP, nonspecific interstitial pneumonia (NSIP), and interstitial lung abnormality (ILA); the histopathological and CT findings of these conditions reflect the required multidisciplinary team approach, involving pulmonologists, radiologists, and pathologists, for their diagnosis and management. Concomitantly, traction bronchiectasis and bronchiolectasis have been recognized as the most persistent and important indices of the severity and prognosis of fibrotic lung diseases. The traction bronchiectasis index (TBI) can stratify the prognoses of patients with ILAs. In this review, the evolutionary concepts of UIP, NSIP, and ILAs are summarized in tables and figures, with a demonstration of the correlation between CT findings and pathologic evaluation. The CT-based UIP score is being proposed to facilitate a better understanding of the spectrum of pulmonary fibrosis, from ILAs to UIP, with emphasis on traction bronchiectasis/bronchiolectasis.

The impact of major league baseball on the incidence of operative hand and facial trauma at a level 1 trauma center

  • Ricci, Joseph A.;Vargas, Christina R.;Ho, Olivia A.;Lin, Samuel J.;Lee, Bernard T.
    • Archives of Plastic Surgery
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    • v.46 no.3
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    • pp.198-203
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    • 2019
  • Background Professional affiliation between medical centers and professional sports teams can be mutually beneficial in the provision of healthcare and marketing strategy. Anecdotal evidence suggests a link between trauma volume and sporting events; however, there is limited data. This study aims to characterize the incidence of operative hand and facial trauma during professional baseball home games. Methods A retrospective review of surgical cases for traumatic hand or facial injuries at a level 1 center between 1999 and 2012 was performed. Demographic information including date of injury, admission status, and operative repair were collected. Patients were grouped based on whether their trauma occurred on the date of a home game. Results Operative hand and facial trauma occurred at a rate of 33.4 injuries per 100 days with home games, compared to 22.2 injuries per 100 days (incidence rate ratios, 1.50; 95% confidence interval, 1.34-1.69). When home games were played, patients were more likely to present as a result of motorcycle accidents (3.1% vs. 1.5%; P=0.04) or bicycle accidents (5.0% vs. 2.6%; P=0.01). Other mechanisms of trauma were not statistically different. There was an increase incidence of injuries during home games in August; weekly variability showed an increased incidence during the weekends. Conclusions There was an increased rate of operative hand and facial injuries on dates with professional home games. The incidence of injuries during home games was higher in the late summer and on the weekends. Further analysis may allow improved resource allocation and strategies for injury prevention and treatment.

QSO Selections Using Time Variability and Machine Learning

  • Kim, Dae-Won;Protopapas, Pavlos;Byun, Yong-Ik;Alcock, Charles;Khardon, Roni
    • The Bulletin of The Korean Astronomical Society
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    • v.36 no.2
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    • pp.64-64
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    • 2011
  • We present a new quasi-stellar object (QSO) selection algorithm using a Support Vector Machine, a supervised classification method, on a set of extracted time series features including period, amplitude, color, and autocorrelation value. We train a model that separates QSOs from variable stars, non-variable stars, and microlensing events using 58 known QSOs, 1629 variable stars, and 4288 non-variables in the MAssive Compact Halo Object (MACHO) database as a training set. To estimate the efficiency and the accuracy of the model, we perform a cross-validation test using the training set. The test shows that the model correctly identifies ~80% of known QSOs with a 25% false-positive rate. The majority of the false positives are Be stars. We applied the trained model to the MACHO Large Magellanic Cloud (LMC) data set, which consists of 40 million lightcurves, and found 1620 QSO candidates. During the selection, none of the 33,242 known MACHO variables were misclassified as QSO candidates. In order to estimate the true false-positive rate, we crossmatched the candidates with astronomical catalogs including the Spitzer Surveying the Agents of a Galaxy's Evolution (SAGE) LMC catalog and a few X-ray catalogs. The results further suggest that the majority of the candidates, more than 70%, are QSOs.

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The Role of Magnetic Topology in the Heating of Active Region Coronal Loops

  • Lee, Jin-Yi;Barnes, Graham;Leka, K.D.;Reeves, Katharine K.;Korreck, K.E.;Golub, L.;Deluca, E.E.
    • The Bulletin of The Korean Astronomical Society
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    • v.36 no.2
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    • pp.86.2-86.2
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    • 2011
  • We investigate the evolution of coronal loop emission in the context of the coronal magnetic field topology. New modeling techniques allow us to investigate the magnetic field structure and energy release in active regions (ARs). Using these models and high-resolution multi-wavelength coronal observations from the Transition Region and Coronal Explorer and the X-ray Telescope on Hinode, we are able to establish a relationship between the light curves of coronal loops and their associated magnetic topologies for NOAA AR 10963. We examine loops that show both transient and steady emission, and we find that loops that show many transient brightenings are located in domains associated with a high number of separators. This topology provides an environment for continual impulsive heating events through magnetic reconnection at the separators. A loop with relatively constant X-ray and EUV emission, on the other hand, is located in domains that are not associated with separators. This result implies that larger-scale magnetic field reconnections are not involved in heating plasma in these regions, and the heating in these loops must come from another mechanism, such as smallscale reconnections (i.e., nanoflares) or wave heating. Additionally, we find that loops that undergo repeated transient brightenings are associated with separators that have enhanced free energy. In contrast, we find one case of an isolated transient brightening that seems to be associated with separators with a smaller free energy.

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