218 research outputs found
FlyNet 2.0: Drosophila heart 3D (2D + time) segmentation in optical coherence microscopy images using a convolutional long short-term memory neural network
A custom convolutional neural network (CNN) integrated with convolutional long short-term memory (LSTM) achieves accurate 3D (2D + time) segmentation in cross-sectional videos of the Drosophila heart acquired by an optical coherence microscopy (OCM) system. While our previous FlyNet 1.0 model utilized regular CNNs to extract 2D spatial information from individual video frames, convolutional LSTM, FlyNet 2.0, utilizes both spatial and temporal information to improve segmentation performance further. To train and test FlyNet 2.0, we used 100 datasets including 500,000 fly heart OCM images. OCM videos in three developmental stages and two heartbeat situations were segmented achieving an intersection over union (IOU) accuracy of 92%. This increased segmentation accuracy allows morphological and dynamic cardiac parameters to be better quantified
Activation of BNIP3-mediated mitophagy protects against renal ischemia-reperfusion injury
Acute kidney injury (AKI) is a syndrome of abrupt loss of renal functions. The underlying pathological mechanisms of AKI remain largely unknown. BCL2-interacting protein 3 (BNIP3) has dual functions of regulating cell death and mitophagy, but its pathophysiological role in AKI remains unclear. Here, we demonstrated an increase of BNIP3 expression in cultured renal proximal tubular epithelial cells following oxygen-glucose deprivation-reperfusion (OGD-R) and in renal tubules after renal ischemia-reperfusion (IR)-induced injury in mice. Functionally, silencing Bnip3 by specific short hairpin RNAs in cultured renal tubular cells reduced OGD-R-induced mitophagy, and potentiated OGD-R-induced cell death. In vivo, Bnip3 knockout worsened renal IR injury, as manifested by more severe renal dysfunction and tissue injury. We further showed that Bnip3 knockout reduced mitophagy, which resulted in the accumulation of damaged mitochondria, increased production of reactive oxygen species, and enhanced cell death and inflammatory response in kidneys following renal IR. Taken together, these findings suggest that BNIP3-mediated mitophagy has a critical role in mitochondrial quality control and tubular cell survival during AKI
Chemisorption Induced Formation of Biphenylene Dimer on Surfaces
We report an example that demonstrates the clear interdependence between
surface-supported reactions and molecular adsorption configurations. Two
biphenyl-based molecules with two and four bromine substituents, i.e.
2,2-dibromo-biphenyl (DBBP) and 2,2,6,6-tetrabromo-1,1-biphenyl (TBBP), show
completely different reaction pathways on a Ag(111) surface, leading to the
selective formation of dibenzo[e,l]pyrene and biphenylene dimer, respectively.
By combining low-temperature scanning tunneling microscopy, synchrotron
radiation photoemission spectroscopy, and density functional theory
calculations, we unravel the underlying reaction mechanism. After
debromination, a bi-radical biphenyl can be stabilized by surface Ag adatoms,
while a four-radical biphenyl undergoes spontaneous intramolecular annulation
due to its extreme instability on Ag(111). Such different chemisorption-induced
precursor states between DBBP and TBBP consequently lead to different reaction
pathways after further annealing. In addition, using bond-resolving scanning
tunneling microscopy and scanning tunneling spectroscopy, we determine the bond
length alternation of biphenylene dimer product with atomic precision, which
contains four-, six-, and eight-membered rings. The four-membered ring units
turn out to be radialene structures
Identification and validation of an immune-related gene prognostic signature for clear cell renal carcinoma
Clear Cell Renal Carcinoma (ccRCC) accounts for nearly 80% of renal carcinoma cases, and immunotherapy plays an important role in ccRCC therapy. However, the responses to immunotherapy and overall survival for ccRCC patients are still hard to predict. Here, we constructed an immune-related predictive signature using 19 genes based on TCGA datasets. We also analyzed its relationships between disease prognosis, infiltrating immune cells, immune subtypes, mutation load, immune dysfunction, immune escape, etc. We found that our signature can distinguish immune characteristics and predict immunotherapeutic response for ccRCC patients with better prognostic prediction value than other immune scores. The expression levels of prognostic genes were determined by RT-qPCR assay. This signature may help to predict overall survival and guide the treatment for patients with ccRCC
Effect of Grain Coalescence on Dislocation and Stress Evolution of GaN Films Grown on Nanoscale Patterned Sapphire Substrates
Two types of nucleation layers (NLs), including in-situ low-temperature grown
GaN (LT-GaN) and ex-situ sputtered physical vapor deposition AlN (PVD-AlN), are
applied on cone-shaped nanoscale patterned sapphire substrate (NPSS). The
initial growth process of GaN on these two NLs is comparably investigated by a
series of growth interruptions. The coalescence process of GaN grains is
modulated by adjusting the three-dimensional (3D) temperatures. The results
indicate that higher 3D temperatures reduce the edge dislocation density while
increasing the residual compressive stress in GaN films. Compared to the LT-GaN
NLs, the PVD-AlN NLs effectively resist Ostwald ripening and facilitate the
uniform growth of GaN grains on NPSS. Furthermore, GaN films grown on NPSS with
PVD-AlN NLs exhibit a reduction of over 50% in both screw and edge dislocation
densities compared to those grown on LT-GaN NLs. Additionally, PVD-AlN NLs
result in an increase of about 0.5 GPa in the residual compressive stress
observed in GaN films
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