Rapid-INR: Storage Efficient CPU-free DNN Training Using Implicit Neural Representation

Implicit Neural Representation (INR) is an innovative approach for representing complex shapes or objects without explicitly defining their geometry or surface structure. Instead, INR represents objects as continuous functions. Previous research has demonstrated the effectiveness of using neural networks as INR for image compression, showcasing comparable performance to traditional methods such as JPEG. However, INR holds potential for various applications beyond image compression. This paper introduces Rapid-INR, a novel approach that utilizes INR for encoding and compressing images, thereby accelerating neural network training in computer vision tasks. Our methodology involves storing the whole dataset directly in INR format on a GPU, mitigating the significant data communication overhead between the CPU and GPU during training. Additionally, the decoding process from INR to RGB format is highly parallelized and executed on-the-fly. To further enhance compression, we propose iterative and dynamic pruning, as well as layer-wise quantization, building upon previous work. We evaluate our framework on the image classification task, utilizing the ResNet-18 backbone network and three commonly used datasets with varying image sizes. Rapid-INR reduces memory consumption to only 5% of the original dataset size and achieves a maximum 6$\times$ speedup over the PyTorch training pipeline, as well as a maximum 1.2x speedup over the DALI training pipeline, with only a marginal decrease in accuracy. Importantly, Rapid-INR can be readily applied to other computer vision tasks and backbone networks with reasonable engineering efforts. Our implementation code is publicly available at https://anonymous.4open.science/r/INR-4BF7.Comment: Submitted to ICCAD 2023, under revie

Effects of Copper Exchange Levels on Complexation of Ammonia in Cu (II)-exchanged X Zeolite

Copper (II)-exchanged faujasite-X zeolites at various loadings of copper per unit cell of zeolites were prepared and then exposed to ammonia. The copper ammine complexes of the various copper levels per unit cell were characterized and analyzed by a combination of diffuse reflectance, X-ray powder diffraction, FT-infrared spectroscopy, electron paramagnetic resonance and nuclear magnetic resonance spectroscopic methods. At low copper exchange levels (<5 copper atoms per unit cell), the major complex is [Cu(Ozeo)2(NH3)2]2+ and it is strongly bound to the zeolite framework walls at single four ring sites (site III). Above five copper atoms per unit cell, the major complex becomes [Cu(NH3)4]2+ and it is least interacting with the zeolite framework walls. The [Cu(NH3)4]2+ complex which was formed at higher copper levels per unit cell was most favoured by the presence of maximal amount of ammonia.Keywords: Cation Exchange, Catalysis, Copper, Complexation, Copper AmminesAttached PDF and Supplementary Fil

Superconductivity in iron telluride thin films under tensile stress

By realizing in thin films a tensile stress state, superconductivity of 13 K was introduced into FeTe, an non-superconducting parent compound of the iron pnictides and chalcogenides, with transition temperature higher than that of its superconducting isostructural counterpart FeSe. For these tensile stressed films, the superconductivity is accompanied by the softening of the first-order magnetic and structural phase transition; and also, the in-plane extension and out-of-plane contraction are universal in all FeTe films independent of sign of lattice mismatch, either positive or negative. Moreover, the correlations were found exist between the transition temperatures and the tetrahedra bond angles in these thin films.Comment: 4 pages, 4 figures, accepted by Physical Review Letter

Analysis of flavour compounds and prediction of sensory properties in sea buckthorn (Hippophae rhamnoides L.) berries

The aim of this study was to investigate sugars, organic acids, flavonol glycosides (FGs), proanthocyanidins and volatiles as flavour compounds in sea buckthorn (SB) berries of five cultivars and to predict the sensory properties of berries. The profiles of flavour compounds in SB berries varied significantly among the cultivars. Total proanthocyanidins and FGs were highest in 'Pertsik' and 'Raisa', respectively. Total volatiles were highest in 'Vorobyevskaya' and lowest in 'Raisa'. A previously established PLS model was used to predict the sensory properties of SB berries based on the non-volatile flavour compounds. The mouth-drying astringency can be predicted the most reliably, which has the highest regression coefficients with quinic acid, isorhamnetin-3-O-sophoroside-7-O-rhamnoside and total proanthocyanidins. Bitterness cannot be predicted using the model. 'Pertsik' berries were predicted to be more mouth-drying astringency and sour than those of 'Raisa'. The research supports the cultivar selection in cultivation and industry of SB berries

A Mechanical Mass Sensor with Yoctogram Resolution

Nanoelectromechanical systems (NEMS) have generated considerable interest as inertial mass sensors. NEMS resonators have been used to weigh cells, biomolecules, and gas molecules, creating many new possibilities for biological and chemical analysis [1-4]. Recently, NEMS-based mass sensors have been employed as a new tool in surface science in order to study e.g. the phase transitions or the diffusion of adsorbed atoms on nanoscale objects [5-7]. A key point in all these experiments is the ability to resolve small masses. Here we report on mass sensing experiments with a resolution of 1.7 yg (1 yg = 10^-24 g), which corresponds to the mass of one proton, or one hydrogen atom. The resonator is made of a ~150 nm long carbon nanotube resonator vibrating at nearly 2 GHz. The unprecedented level of sensitivity allows us to detect adsorption events of naphthalene molecules (C10H8) and to measure the binding energy of a Xe atom on the nanotube surface (131 meV). These ultrasensitive nanotube resonators offer new opportunities for mass spectrometry, magnetometry, and adsorption experiments.Comment: submitted version of the manuscrip

DNA binding induces active site conformational change in the human TREX2 3′-exonuclease

The TREX enzymes process DNA as the major 3′→5′ exonuclease activity in mammalian cells. TREX2 and TREX1 are members of the DnaQ family of exonucleases and utilize a two metal ion catalytic mechanism of hydrolysis. The structure of the dimeric TREX2 enzyme in complex with single-stranded DNA has revealed binding properties that are distinct from the TREX1 protein. The TREX2 protein undergoes a conformational change in the active site upon DNA binding including ordering of active site residues and a shift of an active site helix. Surprisingly, even when a single monomer binds DNA, both monomers in the dimer undergo the structural rearrangement. From this we have proposed a model for DNA binding and 3′ hydrolysis for the TREX2 dimer. The structure also shows how TREX proteins potentially interact with double-stranded DNA and suggest features that might be involved in strand denaturation to provide a single-stranded substrate for the active site

The CoQ oxidoreductase FSP1 acts parallel to GPX4 to inhibit ferroptosis.

Ferroptosis is a form of regulated cell death that is caused by the iron-dependent peroxidation of lipids1,2. The glutathione-dependent lipid hydroperoxidase glutathione peroxidase 4 (GPX4) prevents ferroptosis by converting lipid hydroperoxides into non-toxic lipid alcohols3,4. Ferroptosis has previously been implicated in the cell death that underlies several degenerative conditions2, and induction of ferroptosis by the inhibition of GPX4 has emerged as a therapeutic strategy to trigger cancer cell death5. However, sensitivity to GPX4 inhibitors varies greatly across cancer cell lines6, which suggests that additional factors govern resistance to ferroptosis. Here, using a synthetic lethal CRISPR-Cas9 screen, we identify ferroptosis suppressor protein 1 (FSP1) (previously known as apoptosis-inducing factor mitochondrial 2 (AIFM2)) as a potent ferroptosis-resistance factor. Our data indicate that myristoylation recruits FSP1 to the plasma membrane where it functions as an oxidoreductase that reduces coenzyme Q10 (CoQ) (also known as ubiquinone-10), which acts as a lipophilic radical-trapping antioxidant that halts the propagation of lipid peroxides. We further find that FSP1 expression positively correlates with ferroptosis resistance across hundreds of cancer cell lines, and that FSP1 mediates resistance to ferroptosis in lung cancer cells in culture and in mouse tumour xenografts. Thus, our data identify FSP1 as a key component of a non-mitochondrial CoQ antioxidant system that acts in parallel to the canonical glutathione-based GPX4 pathway. These findings define a ferroptosis suppression pathway and indicate that pharmacological inhibition of FSP1 may provide an effective strategy to sensitize cancer cells to ferroptosis-inducing chemotherapeutic agents

Utilization of a deoxynucleoside diphosphate substrate by HIV reverse transcriptase

Background: Deoxynucleoside triphosphates (dNTPs) are the normal substrates for DNA sysnthesis is catalyzed by polymerases such as HIV-1 reverse transcriptase (RT). However, substantial amounts of deoxynucleoside diphosphates (dNDPs) are also present in the cell. Use of dNDPs in HIV-1 DNA sysnthesis could have significant implications for the efficacy of nucleoside RT inhibitors such as AZT which are first line therapeutics fro treatment of HIV infection. Our earlier work on HIV-1 reverse transcriptase (RT) suggested that the interaction between the γ phosphate of the incoming dNTP and RT residue K65 in the active site is not essential for dNTP insertion, implying that this polymerase may be able to insert dNPs in addition to dNTPs. Methodology/Principal Findings: We examined the ability of recombinant wild type (wt) and mutant RTs with substitutions at residue K65 to utilize a dNDP substrate in primer extension reactions. We found that wild type HIV-1 RT indeed catalyzes incorporation of dNDP substrates whereas RT with mutations of residue K645 were unable to catalyze this reaction. Wild type HIV-1 RT also catalyzed the reverse reaction, inorganic phosphate-dependent phosphorolysis. Nucleotide-mediated phosphorolytic removal of chain-terminating 3′-terminal nucleoside inhibitors such as AZT forms the basis of HIV-1 resistance to such drugs, and this removal is enhanced by thymidine analog mutations (TAMs). We found that both wt and TAM-containing RTs were able to catalyze Pi-mediated phosphorolysis of 3′-terminal AZT at physiological levels of Pi with an efficacy similar to that for ATP-dependent AZT-excision. Conclusion: We have identified two new catalytic function of HIV-1 RT, the use of dNDPs as substrates for DNA synthesis, and the use of Pi as substrate for phosphorolytic removal of primer 3′-terminal nucleotides. The ability to insert dNDPs has been documented for only one other DNA polymerase The RB69 DNA polymerase and the reverse reaction employing inorganic phosphate has not been documented for any DNA polymerase. Importantly, our results show that Pi-mediated phosphorolysis can contribute to AZT resistance and indicates that factors that influence HIV resistance to AZT are more complex than previously appreciated. © 2008 Garforth et al