Storage Codes with Flexible Number of Nodes

This paper presents flexible storage codes, a class of error-correcting codes that can recover information from a flexible number of storage nodes. As a result, one can make a better use of the available storage nodes in the presence of unpredictable node failures and reduce the data access latency. Let us assume a storage system encodes $k\ell$ information symbols over a finite field $\mathbb{F}$ into $n$ nodes, each of size $\ell$ symbols. The code is parameterized by a set of tuples $\{(R_j,k_j,\ell_j): 1 \le j \le a\}$, satisfying $k_1\ell_1=k_2\ell_2=...=k_a\ell_a$ and $k_1>k_2>...>k_a = k, \ell_a=\ell$, such that the information symbols can be reconstructed from any $R_j$ nodes, each node accessing $\ell_j$ symbols. In other words, the code allows a flexible number of nodes for decoding to accommodate the variance in the data access time of the nodes. Code constructions are presented for different storage scenarios, including LRC (locally recoverable) codes, PMDS (partial MDS) codes, and MSR (minimum storage regenerating) codes. We analyze the latency of accessing information and perform simulations on Amazon clusters to show the efficiency of presented codes

Spontaneous excitation of an accelerated hydrogen atom coupled with electromagnetic vacuum fluctuations

We consider a multilevel hydrogen atom in interaction with the quantum electromagnetic field and separately calculate the contributions of the vacuum fluctuation and radiation reaction to the rate of change of the mean atomic energy of the atom for uniform acceleration. It is found that the acceleration disturbs the vacuum fluctuations in such a way that the delicate balance between the contributions of vacuum fluctuation and radiation reaction that exists for inertial atoms is broken, so that the transitions to higher-lying states from ground state are possible even in vacuum. In contrast to the case of an atom interacting with a scalar field, the contributions of both electromagnetic vacuum fluctuations and radiation reaction to the spontaneous emission rate are affected by the acceleration, and furthermore the contribution of the vacuum fluctuations contains a non-thermal acceleration-dependent correction, which is possibly observable.Comment: 8 pages, Revtex4, accepted for publication in PR

Intra-cluster coalescing to reduce GPU NoC pressure

GPUs continue to increase the number of streaming multiprocessors (SMs) to provide increasingly higher compute capabilities. To construct a scalable crossbar network-on-chip (NoC) that connects the SMs to the memory controllers, a cluster structure is introduced in modern GPUs in which several SMs are grouped together to share a network port. Because of network port sharing, clustered GPUs face severe NoC congestion, which creates a critical performance bottleneck. In this paper, we target redundant network traffic to mitigate GPU NoC congestion. In particular, we observe that in many GPU-compute applications, different SMs in a cluster access shared data. Issuing redundant requests to access the same memory location wastes valuable NoC bandwidth - we find on average 19.4% (and up to 48%) of the requests to be redundant. To reduce redundant NoC traffic, we propose intracluster coalescing (ICC) to merge memory requests from different SMs in a cluster. Our evaluation results show that ICC achieves an average performance improvement of 9.7% (and up to 33%) over a conventional design

Dexmedetomidine pretreatment alleviates ischemia reperfusion injury-induced inflammatory reaction via inhibition of TLR-4/NF-ΚB signaling pathway

Purpose: To study the effect of dexmedetomidine on ischemia-reperfusion injury (IRI)–induced inflammatory response, as well as its underlying mechanism of action. Methods: Three groups of healthy adult Sprague Dawley (SD) rats (mean weight, 275 ± 10 g): control, IRI and treatment groups were used. With the exception of control group, ligation was performed on left anterior descending coronary arteries for 30 min and blood perfusion was restored within 100 min to establish IRI. Control group rats were without left ligation. Rats in control and IRI groups received normal saline intraperitoneally 30 min prior to surgery, while the treatment group received 100 μg/kg dexmedetomidine via intraperitoneal injection 30 min before operation. Infarct volume was determined using triphenyl tetrazolium chloride (TTC) staining. IL-6) and TNF-α levels of myocardial tissues and serum were determined using enzyme-linked immunosorbent assay (ELISA). Western blotting was used to determine protein expressions of NF-ΚB and TLR-4 in myocardial tissues. Results: Pretreatment with dexmedetomidine markedly decreased infarct volume caused by IRI (p < 0.05). Serum and myocardial TNF-α and IL-6 were significantly upregulated in IRI group, relative to control group, but were downregulated by pretreatment with dexmedetomidine (p < 0.05). There was marked upregulation of NF-ΚB and TLR-4 proteins in IRI rats, relative to untreated rats (p < 0.05). Dexmedetomidine also down-regulated the expressions of these proteins (p < 0.05). Conclusion: Pretreatment with dexmedetomidine alleviates IRI-induced inflammatory reaction via suppression of TLR-4/NF-ΚB signaling pathway. This finding provides a basis for large-scale clinical trials with dexmedetomidine

Modeling emerging memory-divergent GPU applications

Analytical performance models yield valuable architectural insight without incurring the excessive runtime overheads of simulation. In this work, we study contemporary GPU applications and find that the key performance-related behavior of such applications is distinct from traditional GPU applications. The key issue is that these GPU applications are memory-intensive and have poor spatial locality, which implies that the loads of different threads commonly access different cache blocks. Such memory-divergent applications quickly exhaust the number of misses the L1 cache can process concurrently, and thereby cripple the GPU's ability to use Memory-Level Parallelism (MLP) and Thread-Level Parallelism (TLP) to hide memory latencies. Our Memory Divergence Model (MDM) is able to accurately represent this behavior and thereby reduces average performance prediction error by 14x compared to the state-of-the-art GPUMech approach across our memory-divergent applications

Pipeline for phylogenetic analysis of the GlcDEF, GOX/LOX, and tsar genes conducted as part of "Community context and pCO2 impact the transcriptome of the "helper" bacterium Alteromonas in co-culture with picocyanobacteria"

Dataset: Pipeline for phylogenetic analysis of the GlcDEF, GOX/LOX, and tsar genesPipeline for phylogenetic analysis of the GlcDEF, GOX/LOX, and tsar genes conducted as part of "Community context and pCO2 impact the transcriptome of the "helper" bacterium Alteromonas in co-culture with picocyanobacteria" (Barreto Filho et al., 2022). The provided code, documentation, input and output files include all the information needed to replicate our findings. The following results abstract describes these data along with related datasets which can be accessed from the "Related Datasets" section of this page. Many microbial photoautotrophs depend on heterotrophic bacteria for accomplishing essential functions. Environmental changes, however, could alter or eliminate such interactions. We investigated the effects of changing pCO2 on gene expression in co-cultures of 3 strains of picocyanobacteria (Synechococcus strains CC9311 and WH8102 and Prochlorococcus strain MIT9312) paired with the ‘helper’ bacterium Alteromonas macleodii EZ55. Co-culture with cyanobacteria resulted in a much higher number of up- and down-regulated genes in EZ55 than pCO2 by itself. Pathway analysis revealed significantly different expression of genes involved in carbohydrate metabolism, stress response, and chemotaxis, with different patterns of up- or down-regulation in co-culture with different cyanobacterial strains. Gene expression patterns of organic and inorganic nutrient transporter and catabolism genes in EZ55 suggested resources available in the culture media were altered under elevated (800 ppm) pCO2 conditions. Altogether, changing expression patterns were consistent with the possibility that the composition of cyanobacterial excretions changed under the two pCO2 regimes, causing extensive ecophysiological changes in both members of the co-cultures. Additionally, significant downregulation of oxidative stress genes in MIT9312/EZ55 cocultures at 800 ppm pCO2 were consistent with a link between the predicted reduced availability of photorespiratory byproducts (i.e., glycolate/2PG) under this condition and observed reductions in internal oxidative stress loads for EZ55, providing a possible explanation for the previously observed lack of “help” provided by EZ55 to MIT9312 under elevated pCO2. The data and code stored in this archive will allow the reconstruction of our analysis pipelines. Additionally, we provide annotation mapping files and other resources for conducting transcriptomic analyses with Alteromonas sp. EZ55. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/882970NSF Division of Ocean Sciences (NSF OCE) OCE-185108

Intra-cluster coalescing and distributed-block scheduling to reduce GPU NoC pressure

GPUs continue to boost the number of streaming multiprocessors (SMs) to provide increasingly higher compute capabilities. To construct a scalable crossbar network-on-chip (NoC) that connects the SMs to the memory controllers, a cluster structure is introduced in modern GPUs in which several SMs are grouped together to share a network port. Because of network port sharing, clustered GPUs face severe NoC congestion, which creates a critical performance bottleneck. In this paper, we target redundant network traffic to mitigate GPU NoC congestion. In particular, we observe that in many GPU-compute applications, different SMs in a cluster access shared data. Sending redundant requests to access the same memory location wastes valuable NoC bandwidth-we find on average 19 percent (and up to 48 percent) of the requests to be redundant. To remove redundant NoC traffic, we propose distributed-block scheduling, intra-cluster coalescing (ICC) and the coalesced cache (CC) to coalesce L1 cache misses within and across SMs in a cluster, respectively. Our evaluation results show that distributed-block scheduling, ICC and CC are complementary and improve both performance and energy consumption. We report an average performance improvement of 15 percent (and up to 67 percent) while at the same time reducing system energy by 6 percent (and up to 19 percent) and improving the energy-delay product (EDP) by 19 percent on average (and up to 53 percent), compared to state-of-the-art distributed CTA scheduling

Pipelines for transcriptome analyses conducted as part of "Community context and pCO2 impact the transcriptome of the "helper" bacterium Alteromonas in co-culture with picocyanobacteria"

Dataset: Pipelines for transcriptome analysesPipelines for transcriptome analyses conducted as part of "Community context and pCO2 impact the transcriptome of the "helper" bacterium Alteromonas in co-culture with picocyanobacteria" (Barreto Filho et al., 2022). The provided code, documentation, input and output files include all the information needed to replicate our findings. The following results abstract describes these data along with related datasets which can be accessed from the "Related Datasets" section of this page. Many microbial photoautotrophs depend on heterotrophic bacteria for accomplishing essential functions. Environmental changes, however, could alter or eliminate such interactions. We investigated the effects of changing pCO2 on gene expression in co-cultures of 3 strains of picocyanobacteria (Synechococcus strains CC9311 and WH8102 and Prochlorococcus strain MIT9312) paired with the ‘helper’ bacterium Alteromonas macleodii EZ55. Co-culture with cyanobacteria resulted in a much higher number of up- and down-regulated genes in EZ55 than pCO2 by itself. Pathway analysis revealed significantly different expression of genes involved in carbohydrate metabolism, stress response, and chemotaxis, with different patterns of up- or down-regulation in co-culture with different cyanobacterial strains. Gene expression patterns of organic and inorganic nutrient transporter and catabolism genes in EZ55 suggested resources available in the culture media were altered under elevated (800 ppm) pCO2 conditions. Altogether, changing expression patterns were consistent with the possibility that the composition of cyanobacterial excretions changed under the two pCO2 regimes, causing extensive ecophysiological changes in both members of the co-cultures. Additionally, significant downregulation of oxidative stress genes in MIT9312/EZ55 cocultures at 800 ppm pCO2 were consistent with a link between the predicted reduced availability of photorespiratory byproducts (i.e., glycolate/2PG) under this condition and observed reductions in internal oxidative stress loads for EZ55, providing a possible explanation for the previously observed lack of “help” provided by EZ55 to MIT9312 under elevated pCO2. The data and code stored in this archive will allow the reconstruction of our analysis pipelines. Additionally, we provide annotation mapping files and other resources for conducting transcriptomic analyses with Alteromonas sp. EZ55. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/881942NSF Division of Ocean Sciences (NSF OCE) OCE-185108