Usage-pattern-based scheduling schemes for power optimization in multi-core systems

This thesis discusses the scheduling schemes with app usage pattern awareness for power dissipation optimization in mobile multi-core computing systems. The power dissipation of mobile multi-core computing systems becomes crucial as the power wall symptom arises. One way to resolve the power wall issue is to manage the system resource with power awareness focus. Three main areas of work are presented in the thesis to address the power dissipation issues. First, three scheduling schemes are proposed to decompose the instantaneous power dissipation into different components to model the redundancies in application inflicted power dissipation. The decomposition identifies the manageable power components as the Thread Interference Power which exists among the context switching of multithreading applications. Different amounts of Thread Interference Power dissipate between different combinations of adjacent threads. In this thesis the application combination and power dissipation relationship is studied, identified at system runtime. Application thread scheduling schemes are designed based on the assumption that the usage pattern of a mobile system user is periodical, hence the future application sequence and possible power dissipation are predictable based on the past performance recorded. The scheduling schemes presenting in the thesis make scheduling decisions based on the instantaneous system application combinations and the possible incoming application predicted. The scheduler reorders the application threads according to the amount of Thread Interference Power dissipated. The scheduler is testified in a simulated environment built with GEM5 and McPAT. The simulation results show that the adoption of usage pattern aware scheduling method is capable of reducing the total system power dissipation up to 19% compared to the total system power dissipated without applying the proposed method. To incorporate the proposed scheduling schemes in a Linux scheduler, the quantization method of the Thread Interference Power dissipation with system monitored performance events is studied. Multiple power dissipation related problems are studied to generalize the function of the scheduling schemes as functions of a scheduler. Mutual cache evictions or invalidations by parallel processes, corresponding data movements, context switching overheads and code serialization bottlenecks due to unfortunate scheduled synchronization / locking mechanisms on shared access resources are major contributors to the excessive computing power dissipation of modern chip multiprocessor (CMP) architectures. The proposed Linux scheduler manages above mentioned problems based on user-specific application usage pattern identified in the Thread Interference Power model. To extend the scheduling capacity of the proposed scheduler, novel Dynamic Voltage and Frequency Scaling (DVFS) techniques are developed for ARM asymmetrical System-on-Chip (SoC) designs and tested in a three clustered CPU setup. The result of the proposed scheduler shows a maximum of 22.2% improvement in the power dissipation reduction over the native Global Task Scheduler (GTS). Last but not least, to better the prediction based power dissipation monitoring mechanism in the proposed scheduler, neural network algorithms are adopted to solve the problem with non-parametric assumption. Each power component is sampled individually over a period of time and undergoes analysis as a time series. Thread Interference Power components are then identified and isolated from the time series power dissipation with the aid of a system of neural network algorithms including Autoencoder, Restricted Boltzmann Machine and recurrent neural network. With the aid of the neural network implementation the proposed scheduler reduced the computation overhead by 73.3% and power dissipated by a maximum of 8.1%.Doctor of Philosophy (EEE

The complete chloroplast genome sequence of Michelia compressa

Michelia compressa is an evergreen ornamental tree species. The high-throughput sequencing technology was used to sequence and assemble the chloroplast genome of Michelia compressa. Results showed that the chloroplast genome is 160,061 bp in length, of which the inverted repeats sequence (IRs) is 26,581 bp, the large single-copy region (LSC) and the small single copy region (SSC) are 88,097 bp and 18,802 bp, respectively. The GC content of the plastome was 39.2%, with 43.2%, 37.9% and 34.2% in IRs, LSC and SSC, respectively. A total of 132 genes are annotated, 86 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. This study enriched the Michelia compressa genomic information which provides the basis for rational exploitation and utilization of germplasm resources

Changes in Reference Evapotranspiration over Southwest China during 1960–2018: Attributions and Implications for Drought

Reference evapotranspiration (ET0) is important to the global energy balance and to hydrological cycling. However, the extent to which ET0 changes, the main driving factors, and especially the implications of its shift for drought in Southwest China are not clear. In this study, trends in Penman–Monteith ET0 and other climatic parameters at 79 stations in Southwest China from 1960 to 2018 were investigated by using the Mann–Kendall test. Furthermore, partial correlation analysis and multiple linear regression were used to determine the dominant climate driving factors in changes in ET0. The relative contribution of precipitation and ET0 to drought duration was also quantified based on spatial multiple linear regression. Results revealed that annual ET0 decreased significantly (p < 0.01) at a rate of 14.1 mm per decade from 1960 to 2000, and this decrease disappeared around 2000. For the entire study period, the sunshine duration (Tsun) was the most closely correlated with and played a dominant role in the variations in ET0 at both annual and seasonal (summer and autumn) timescales, whereas the relative humidity was the most dominant factor in the spring and winter. Trends in the Standardized Precipitation Evapotranspiration Index revealed that drought has become more serious in Southwest China, and ET0 has made a greater contribution to the duration of drought than precipitation. Our findings highlight that more attention should be paid to the impacts of ET0 changes on drought in Southwest China. Furthermore, these results can provide a reference for the allocation of water resources and the implementation of countermeasures to climate change

Research Progress for Targeting Deubiquitinases in Gastric Cancers

Gastric cancers (GCs) are malignant tumors with a high incidence that threaten global public health. Despite advances in GC diagnosis and treatment, the prognosis remains poor. Therefore, the mechanisms underlying GC progression need to be identified to develop prognostic biomarkers and therapeutic targets. Ubiquitination, a post-translational modification that regulates the stability, activity, localization, and interactions of target proteins, can be reversed by deubiquitinases (DUBs), which can remove ubiquitin monomers or polymers from modified proteins. The dysfunction of DUBs has been closely linked to tumorigenesis in various cancer types, and targeting certain DUBs may provide a potential option for cancer therapy. Multiple DUBs have been demonstrated to function as oncogenes or tumor suppressors in GC. In this review, we summarize the DUBs involved in GC and their associated upstream regulation and downstream mechanisms and present the benefits of targeting DUBs for GC treatment, which could provide new insights for GC diagnosis and therapy

Characterization and expression of the ABC family (G group) in ‘Dangshansuli’ pear (Pyrus bretschneideri Rehd.) and its russet mutant

Abstract The plant genes encoding ABCGs that have been identified to date play a role in suberin formation in response to abiotic and biotic stress. In the present study, 80 ABCG genes were identified in ‘Dangshansuli’ Chinese white pear and designated as PbABCGs. Based on the structural characteristics and phylogenetic analysis, the PbABCG family genes could be classified into seven main groups: classes A-G. Segmental and dispersed duplications were the primary forces underlying the PbABCG gene family expansion in ‘Dangshansuli’ pear. Most of the PbABCG duplicated gene pairs date to the recent whole-genome duplication that occurred 30~45 million years ago. Purifying selection has also played a critical role in the evolution of the ABCG genes. Ten PbABCG genes screened in the transcriptome of ‘Dangshansuli’ pear and its russet mutant ‘Xiusu’ were validated, and the expression levels of the PbABCG genes exhibited significant differences at different stages. The results presented here will undoubtedly be useful for better understanding of the complexity of the PbABCG gene family and will facilitate the functional characterization of suberin formation in the russet mutant

A Selective Fluorescent l-Lactate Biosensor Based on an l-Lactate-Specific Transcription Regulator and Förster Resonance Energy Transfer

Selective detection of l-lactate levels in foods, clinical, and bacterial fermentation samples has drawn intensive attention. Many fluorescent biosensors based on non-stereoselective recognition elements have been developed for lactate detection. Herein, the allosteric transcription factor STLldR from Salmonella enterica serovar Typhimurium LT2 was identified to be stereo-selectively respond to l-lactate. Then, STLldR was combined with Förster resonance energy transfer (FRET) to construct a fluorescent l-lactate biosensor FILLac. FILLac was further optimized by truncating the N- and C-terminal amino acids of STLldR between cyan and yellow fluorescent proteins. The optimized biosensor FILLac10N0C exhibited a maximum emission ratio change (ΔRmax) of 33.47 ± 1.91%, an apparent dissociation constant (Kd) of 6.33 ± 0.79 μM, and a limit of detection of 0.68 μM. FILLac10N0C was applied in 96-well microplates to detect l-lactate in bacterial fermentation samples and commercial foods such as Jiaosu and yogurt. The quantitation results of FILLac10N0C exhibited good agreement with that of a commercial l-lactate biosensor SBA-40D bioanalyzer. Thus, the biosensor FILLac10N0C compatible with high-throughput detection may be a potential choice for quantitation of l-lactate in different biological samples

Characterization and expression of the ABC family (G group) in ‘Dangshansuli’ pear (Pyrus bretschneideri Rehd.) and its russet mutant

<div><p>Abstract The plant genes encoding ABCGs that have been identified to date play a role in suberin formation in response to abiotic and biotic stress. In the present study, 80 ABCG genes were identified in ‘Dangshansuli’ Chinese white pear and designated as PbABCGs. Based on the structural characteristics and phylogenetic analysis, the PbABCG family genes could be classified into seven main groups: classes A-G. Segmental and dispersed duplications were the primary forces underlying the PbABCG gene family expansion in ‘Dangshansuli’ pear. Most of the PbABCG duplicated gene pairs date to the recent whole-genome duplication that occurred 30~45 million years ago. Purifying selection has also played a critical role in the evolution of the ABCG genes. Ten PbABCG genes screened in the transcriptome of ‘Dangshansuli’ pear and its russet mutant ‘Xiusu’ were validated, and the expression levels of the PbABCG genes exhibited significant differences at different stages. The results presented here will undoubtedly be useful for better understanding of the complexity of the PbABCG gene family and will facilitate the functional characterization of suberin formation in the russet mutant.</p></div

Control of Temperature on Microbial Community Structure in Hot Springs of the Tibetan Plateau

<div><p>The Tibetan Plateau in Northwest China hosts a number of hot springs that represent a biodiversity hotspot for thermophiles, yet their diversity and relationship to environmental conditions are poorly explored in these habitats. In this study we investigated microbial diversity and community composition in 13 Tibetan hot springs with a wide range of temperatures (22.1–75°C) and other geochemical conditions by using the 16S rRNA gene pyrosequencing approach. <i>Bacteria</i> (10⁸–10¹¹ copy/g; 42 bacterial phyla) in Tibetan hot springs were more abundant and far more diverse than <i>Archaea</i> (10⁷–10¹⁰ copy/g; 5 archaeal phyla). The dominant bacterial phyla systematically varied with temperature. Moderate temperatures (75–66°C) favored Aquificae, GAL35, and novel <i>Bacteria</i>, whereas low temperatures (60–22.1°C) selected for Deinococcus-Thermus, Cyanobacteria, and Chloroflexi. The relative abundance of Aquificae was correlated positively with temperature, but the abundances of Deinococcus-Thermus, Cyanobacteria, and Chloroflexi were negatively correlated with temperature. Cyanobacteria and Chloroflexi were abundant in Tibetan hot springs and their abundances were positively correlated at low temperatures (55–43°C) but negatively correlated at moderate temperatures (75–55°C). These correlation patterns suggest a complex physiological relationship between these two phyla. Most archaeal sequences were related to Crenarchaeota with only a few related to Euryarchaeota and Thaumarchaeota. Despite the fact that microbial composition in Tibetan hot springs was strongly shaped by temperature, microbial diversity (richness, evenness and Shannon diversity) was not significantly correlated with temperature change. The results of this study expand our current understanding of microbial ecology in Tibetan hot springs and provide a basis for a global comparison.</p></div

Primer sets used for qPCR.

<p>Primer sets used for qPCR.</p