Balanced Group Convolution: An Improved Group Convolution Based on Approximability Estimates

The performance of neural networks has been significantly improved by increasing the number of channels in convolutional layers. However, this increase in performance comes with a higher computational cost, resulting in numerous studies focused on reducing it. One promising approach to address this issue is group convolution, which effectively reduces the computational cost by grouping channels. However, to the best of our knowledge, there has been no theoretical analysis on how well the group convolution approximates the standard convolution. In this paper, we mathematically analyze the approximation of the group convolution to the standard convolution with respect to the number of groups. Furthermore, we propose a novel variant of the group convolution called balanced group convolution, which shows a higher approximation with a small additional computational cost. We provide experimental results that validate our theoretical findings and demonstrate the superior performance of the balanced group convolution over other variants of group convolution.Comment: 26pages, 2 figure

Parareal Neural Networks Emulating a Parallel-in-time Algorithm

As deep neural networks (DNNs) become deeper, the training time increases. In this perspective, multi-GPU parallel computing has become a key tool in accelerating the training of DNNs. In this paper, we introduce a novel methodology to construct a parallel neural network that can utilize multiple GPUs simultaneously from a given DNN. We observe that layers of DNN can be interpreted as the time step of a time-dependent problem and can be parallelized by emulating a parallel-in-time algorithm called parareal. The parareal algorithm consists of fine structures which can be implemented in parallel and a coarse structure which gives suitable approximations to the fine structures. By emulating it, the layers of DNN are torn to form a parallel structure which is connected using a suitable coarse network. We report accelerated and accuracy-preserved results of the proposed methodology applied to VGG-16 and ResNet-1001 on several datasets

Loss of p53 tumor suppression function drives invasion and genomic instability in models of murine pancreatic cancer

Pancreatic ductal adenocarcinoma (PDA) is a deadly disease with few treatment options. There is an urgent need to better understand the molecular mechanisms that drive disease progression, with the ultimate aim of identifying early detection markers and clinically actionable targets. To investigate the transcriptional and morphological changes associated with pancreatic cancer progression, we analyzed the KrasLSLG12D/+; Trp53LSLR172H/+; Pdx1-Cre (KPC) mouse model. We have identified an intermediate cellular event during pancreatic carcinogenesis in the KPC mouse model of PDA that is represented by a subpopulation of tumor cells that express KrasG12D, p53R172H and one allele of wild-type Trp53. In vivo, these cells represent a histological spectrum of pancreatic intraepithelial neoplasia (PanIN) and acinar-to-ductal metaplasia (ADM) and rarely proliferate. Following loss of wild-type p53, these precursor lesions undergo malignant de-differentiation and acquire invasive features. We have established matched organoid cultures of pre-invasive and invasive cells from murine PDA. Expression profiling of the organoids led to the identification of markers of the pre-invasive cancer cells in vivo and mechanisms of disease aggressiveness

Self-Isolated Dual-Mode High-Pass Birdcage RF Coil for Proton and Sodium MR Imaging at 7 T MRI

This study presents the feasibility of a dual-mode high-pass birdcage RF coil to acquire MR images at both 1H and 23Na frequencies at ultra-high-field MR scanner, 7 T. A dual-mode circuit (DMC) in the dual-mode birdcage (DMBC) RF coil operates at two frequencies, addressing the limitations of sensitivity reduction and isolation between two frequencies as in traditional dual-tuned RF coil. Finite-difference time-domain (FDTD) based electromagnetic (EM) simulations were performed to verify the RF coil at each frequency on the three-dimensional human head model. The DMBC RF coil resonated at proton (1H) and sodium (23Na) frequencies, and also single-tuned high-pass birdcage RF coils were constructed for both 1H and 23Na frequencies. The bench test performance of the RF coils was evaluated using network analysis parameters, including the measurement of scattering parameters (S-parameters) and quality factors (Q-factors). Q-factor of the DMBC coil at 1H port was 10.2% lower than that of 1H single-tuned birdcage (STBC) coil, with a modest SNR reduction of 6.5%. Similarly, the Q-factor for the DMBC coil at 23Na port was 12.3% less than that of 23Na STBC coil, and the SNR showed a minimal reduction of 5.4%. Utilizing the DMBC coil, promising 1H and 23Na MR images were acquired compared to those by using STBC coils. In conclusion, deploying a DMBC 1H/23Na coil has been demonstrated to overcome traditional constraints associated with dual-tuned RF coils, achieving this with only nominal signal attenuation across both nuclei operational frequencies

Akt Determines Replicative Senescence and Oxidative or Oncogenic Premature Senescence and Sensitizes Cells to Oxidative Apoptosis

SummaryAkt deficiency causes resistance to replicative senescence, to oxidative stress- and oncogenic Ras-induced premature senescence, and to reactive oxygen species (ROS)-mediated apoptosis. Akt activation induces premature senescence and sensitizes cells to ROS-mediated apoptosis by increasing intracellular ROS through increased oxygen consumption and by inhibiting the expression of ROS scavengers downstream of FoxO, particularly sestrin 3. This uncovers an Achilles' heel of Akt, since in contrast to its ability to inhibit apoptosis induced by multiple apoptotic stimuli, Akt could not inhibit ROS-mediated apoptosis. Furthermore, treatment with rapamycin that led to further Akt activation and resistance to etoposide hypersensitized cancer cells to ROS-mediated apoptosis. Given that rapamycin alone is mainly cytostatic, this constitutes a strategy for cancer therapy that selectively eradicates cancer cells via Akt activation

Reading Single DNA with DNA Polymerase Followed by Atomic Force Microscopy

The importance of DNA sequencing in the life sciences and personalized medicine is continually increasing. Single-molecule sequencing methods have been developed to analyze DNA directly without the need for amplification. Here, we present a new approach to sequencing single DNA molecules using atomic force microscopy (AFM). In our approach, four surface conjugated nucleotides were examined sequentially with a DNA polymerase immobilized AFM tip. By observing the specific rupture events upon examination of a matching nucleotide, we could determine the template base bound in the polymerase's active site. The subsequent incorporation of the complementary base in solution enabled the next base to be read. Additionally, we observed that the DNA polymerase could incorporate the surface-conjugated dGTP when the applied force was controlled by employing the force-clamp mode.X1114Ysciescopu

Spectrum of movement disorders in GNAO1 encephalopathy: in-depth phenotyping and case-by-case analysis

Background GNAO1 encephalopathy is a rare neurodevelopmental disorder characterized by distinct movement presentations and early onset epileptic encephalopathy. Here, we report the in-depth phenotyping of genetically confirmed patients with GNAO1 encephalopathy, focusing on movement presentations. Results Six patients who participated in Korean Undiagnosed Disease Program were diagnosed to have pathogenic or likely pathogenic variants in GNAO1 using whole exome sequencing. All medical records and personal video clips were analyzed with a literature review. Three of the 6 patients were male. Median follow-up duration was 41 months (range 7–78 months) and age at last examination was 7.4 years (range 3.3–16.9 years). Initial complaints were hypotonia or developmental delay in 5 and right-hand clumsiness in 1 patient, which were noticed at median age of 3 months (range 0–75 months). All patients showed global developmental delay and 4 had severely retarded development. Five patients (5/6, 83.3%) had many different movement symptoms with various onset and progression. The symptoms included stereotyped hands movement, non-epileptic myoclonus, dyskinesia, dystonia and choreoathetosis. Whole exome sequencing identified 6 different variants in GNAO1. Three were novel de novo variants and atypical presentation was noted in a patient. One variant turned out to be inherited from patients mother who had mosaic variant. Distinct and characteristics movement phenotypes in patients with variant p.Glu246Lys and p.Arg209His were elucidated by in-depth phenotyping and literature review. Conclusions We reported 6 patients with GNAO1 encephalopathy showing an extremely diverse clinical spectrum on video. Some characteristic movement features identified by careful inspection may also provide important diagnostic insight and practice guidelines.This study was supported by a research program funded by the Korea Centers for Disease Control and Prevention (Grant No. 2018-ER6901-02)

Exosomes neutralize synaptic-plasticity-disrupting activity of Aβ assemblies in vivo

Background: Exosomes, small extracellular vesicles of endosomal origin, have been suggested to be involved in both the metabolism and aggregation of Alzheimer’s disease (AD)-associated amyloid β-protein (Aβ). Despite their ubiquitous presence and the inclusion of components which can potentially interact with Aβ, the role of exosomes in regulating synaptic dysfunction induced by Aβ has not been explored. Results: We here provide in vivo evidence that exosomes derived from N2a cells or human cerebrospinal fluid can abrogate the synaptic-plasticity-disrupting activity of both synthetic and AD brain-derived Aβ. Mechanistically, this effect involves sequestration of synaptotoxic Aβ assemblies by exosomal surface proteins such as PrPC rather than Aβ proteolysis. Conclusions: These data suggest that exosomes can counteract the inhibitory action of Aβ, which contributes to perpetual capability for synaptic plasticity

Oncogenic KRAS engages an RSK1/NF1 pathway to inhibit wild-type RAS signaling in pancreatic cancer.

Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy with limited treatment options. Although activating mutations of the KRAS GTPase are the predominant dependency present in >90% of PDAC patients, targeting KRAS mutants directly has been challenging in PDAC. Similarly, strategies targeting known KRAS downstream effectors have had limited clinical success due to feedback mechanisms, alternate pathways, and dose-limiting toxicities in normal tissues. Therefore, identifying additional functionally relevant KRAS interactions in PDAC may allow for a better understanding of feedback mechanisms and unveil potential therapeutic targets. Here, we used proximity labeling to identify protein interactors of active KRAS in PDAC cells. We expressed fusions of wild-type (WT) (BirA-KRAS4B), mutant (BirA-KRAS4BG12D), and nontransforming cytosolic double mutant (BirA-KRAS4BG12D/C185S) KRAS with the BirA biotin ligase in murine PDAC cells. Mass spectrometry analysis revealed that RSK1 selectively interacts with membrane-bound KRASG12D, and we demonstrate that this interaction requires NF1 and SPRED2. We find that membrane RSK1 mediates negative feedback on WT RAS signaling and impedes the proliferation of pancreatic cancer cells upon the ablation of mutant KRAS. Our findings link NF1 to the membrane-localized functions of RSK1 and highlight a role for WT RAS signaling in promoting adaptive resistance to mutant KRAS-specific inhibitors in PDAC

Distinct populations of inflammatory fibroblasts and myofibroblasts in pancreatic cancer

Pancreatic stellate cells (PSCs) differentiate into cancer-associated fibroblasts (CAFs) that produce desmoplastic stroma, thereby modulating disease progression and therapeutic response in pancreatic ductal adenocarcinoma (PDA). However, it is unknown whether CAFs uniformly carry out these tasks or if subtypes of CAFs with distinct phenotypes in PDA exist. We identified a CAF subpopulation with elevated expression of alpha-smooth muscle actin (alphaSMA) located immediately adjacent to neoplastic cells in mouse and human PDA tissue. We recapitulated this finding in co-cultures of murine PSCs and PDA organoids, and demonstrated that organoid-activated CAFs produced desmoplastic stroma. The co-cultures showed cooperative interactions and revealed another distinct subpopulation of CAFs, located more distantly from neoplastic cells, which lacked elevated alphaSMA expression and instead secreted IL6 and additional inflammatory mediators. These findings were corroborated in mouse and human PDA tissue, providing direct evidence for CAF heterogeneity in PDA tumor biology with implications for disease etiology and therapeutic development