Hardware-only stream prediction + cache prefetching + dynamic access ordering

Journal ArticleThe speed gap between processors and memory system is becoming the performance bottleneck for many applications, and computations with strided access patterns are among those that suffer most. The vectors used in such applications lack temporal and often spatial locality, and are usually too large to cache. In spite of their poor cache behavior, these access patterns have the advantage of being, predictable, which can be exploited to improve the efficiency of the memory subsystem. As a promising technique to relieve memory system bottleneck, prefetching has been studied in its various forms, and so is dynamic memory scheduling. This study builds on these results, combining a stride-based reference prediction table, a mechanism that prefetches L2 cache lines, and a memory controller that dynamically schedules accesses to a Direct Rambus memory subsystem. We find that such a system delivers impressive speedups for scientific applications with regular access patterns (reducing execution time by almost a factor of two) without negatively affecting the performance of non-streaming programs

Data set for cloning and characterization of heterologous transporters in Saccharomyces cerevisiae and identification of important amino acids for xylose utilization

AbstractThe efficient uptake is important for the xylose utilization by Saccharomyces cerevisiae. A heterogenous transporter Mgt05196p was cloned from Meyerozyma guilliermondii and expressed in Saccharomyces cerevisiae [1]. This data article contains the transport characteristics of Mgt05196p in S. cerevisiae. The fluorescence of fusion protein Mgt05196p-GFP expressing strain was located on the cell surface demonstrated that the heterogenous transporter Mgt05196p was targeted to the plasma membrane of S. cerevisiae. The expressing of Mgt05196p in the hxt null S. cerevisiae endowed the strain with the glucose and d-xylose absorption capacity, as well as expressing the native d-xylose transporter Gal2p. The transmembrane domains of Mgt05196p were predicted and compared with the XylEp, whose crystal structure was revealed. And then, the homologous modeling of Mgt05196p was built basing on the XylEp to find out the crucial amino acid residues for sugars binding and transport

Effects of rice or wheat residue retention on the quality of milled japonica rice in a rice–wheat rotation system in China

AbstractIn rice–wheat rotation systems, crop straw is usually retained in the field at land preparation in every, or every other, season. We conducted a 3-year-6-season experiment in the middle–lower Yangtze River Valley to compare the grain qualities of rice under straw retained after single or double seasons per year. Four treatments were designed as: both wheat and rice straw retained (WR), only rice straw retained (R), only wheat straw retained (W), and no straw retained (CK). The varieties were Yangmai 16 wheat and Wuyunjing 23 japonica rice. The results showed contrasting effects of W and R on rice quality. Amylopectin content, peak viscosity, cool viscosity, and breakdown viscosity of rice grain were significantly increased in W compared to the CK, whereas gelatinization temperature, setback viscosity, and protein content significantly decreased. In addition, the effect of WR on rice grain quality was similar to that of W, although soil fertility was enhanced in WR due to straw being retained in two cycles. The differences in protein and starch contents among the treatments might result from soil nitrogen supply. These results indicate that wheat straw retained in the field is more important for high rice quality than rice straw return, and straw from both seasons is recommended for positive effects on soil fertility

Biomechanical analysis of sandwich vertebrae in osteoporotic patients: finite element analysis

ObjectiveThe aim of this study was to investigate the biomechanical stress of sandwich vertebrae (SVs) and common adjacent vertebrae in different degrees of spinal mobility in daily life.Materials and methodsA finite element model of the spinal segment of T10-L2 was developed and validated. Simultaneously, T11 and L1 fractures were simulated, and a 6-ml bone cement was constructed in their center. Under the condition of applying a 500-N axial load to the upper surface of T10 and immobilizing the lower surface of L2, moments were applied to the upper surface of T10, T11, T12, L1, and L2 and divided into five groups: M-T10, M-T11, M-T12, M-L1, and M-L2. The maximum von Mises stress of T10, T12, and L2 in different groups was calculated and analyzed.ResultsThe maximum von Mises stress of T10 in the M-T10 group was 30.68 MPa, 36.13 MPa, 34.27 MPa, 33.43 MPa, 26.86 MPa, and 27.70 MPa greater than the maximum stress value of T10 in the other groups in six directions of load flexion, extension, left and right lateral bending, and left and right rotation, respectively. The T12 stress value in the M-T12 group was 29.62 MPa, 32.63 MPa, 30.03 MPa, 31.25 MPa, 26.38 MPa, and 26.25 MPa greater than the T12 stress value in the other groups in six directions. The maximum stress of L2 in M-T12 in the M-L2 group was 25.48 MPa, 36.38 MPa, 31.99 MPa, 31.07 MPa, 30.36 MPa, and 32.07 MPa, which was greater than the stress value of L2 in the other groups. When the load is on which vertebral body, it is subjected to the greatest stress.ConclusionWe found that SVs did not always experience the highest stress. The most stressed vertebrae vary with the degree of curvature of the spine. Patients should be encouraged to avoid the same spinal curvature posture for a long time in life and work or to wear a spinal brace for protection after surgery, which can avoid long-term overload on a specific spine and disrupt its blood supply, resulting in more severe loss of spinal quality and increasing the possibility of fractures

Integrated mRNA-seq and miRNA-seq analysis of goat fibroblasts response to Brucella Melitensis strain M5-90

Brucellosis is a globally zoonotic bacterial disease of humans and various animals including goats, sheep, and cattle. Brucella melitensis M5-90, a live attenuated vaccine strain, has been widely used to prevent brucellosis in goats and sheep. However, the molecular mechanisms governing protective immunity response in non-professional phagocytes infected with B. melitensis M5-90 have not been fully investigated, especially in goats. In our research, goat fibroblasts were used as in vitro models to determine these mechanisms by transcriptome analysis. After incubating with B. melitensis M5-90 3 h, the infected goat fibroblasts were collected at 0 h, 4 h, 24 h, 48 h and 72 h for RNA-seq. The results indicated that there were totally 11,819 differentially expressed genes (DEGs) and 777 differentially expressed (DE) miRNAs found in experiment groups compared with the control groups (|log2(Foldchange)|≥1, FDR<0.05). GO and KEGG enrichment analyses revealed that down-regulated genes were involved in the riboflavin metabolism and positive regulation of IL-8 secretion pathway. The up-regulated genes were mainly involved in adaptive immunity, including TNF signaling pathway, MAPK signaling pathway and JAK/STAT pathway. Additionally, cytokine-cytokine receptor interaction, natural killer cell mediated cytotoxicity and toll-like receptor signaling pathway, which associated with innate immunity pathways, were also induced. Based on the Pearson correlation coefficients and prediction results of TargetScan and miRanda, the miRNA-mRNA networks of NFKB1, IFNAR2 and IL10RB were constructed and verified in goat fibroblasts by qPCR, which demonstrated that goat fibroblasts displayed immunomodulatory properties. Our findings provide a deeper insight into the host miRNA-driven B. melitensis defense mechanism and reveal the transcriptome changes involved in the innate and adaptive immune response of the goats to B. melitensis infection

Genome-wide analysis of circular RNAs in goat skin fibroblast cells in response to Orf virus infection

Orf, caused by Orf virus (ORFV), is a globally distributed zoonotic disease responsible for serious economic losses in the agricultural sector. However, the mechanism underlying ORFV infection remains largely unknown. Circular RNAs (circRNAs), a novel type of endogenous non-coding RNAs, play important roles in various pathological processes but their involvement in ORFV infection and host response is unclear. In the current study, whole transcriptome sequencing and small RNA sequencing were performed in ORFV-infected goat skin fibroblast cells and uninfected cells. A total of 151 circRNAs, 341 messenger RNAs (mRNAs), and 56 microRNAs (miRNAs) were differently expressed following ORFV infection. Four circRNAs: circRNA1001, circRNA1684, circRNA3127 and circRNA7880 were validated by qRT-PCR and Sanger sequencing. Gene ontology (GO) analysis indicated that host genes of differently expressed circRNAs were significantly enriched in regulation of inflammatory response, epithelial structure maintenance, positive regulation of cell migration, positive regulation of ubiquitin-protein transferase activity, regulation of ion transmembrane transport, etc. The constructed circRNA-miRNA-mRNA network suggested that circRNAs may function as miRNA sponges indirectly regulating gene expression following ORFV infection. Our study presented the first comprehensive profiles of circRNAs in response to ORFV infection, thus providing new clues for the mechanisms of interactions between ORFV and the host

Qwen Technical Report

Large language models (LLMs) have revolutionized the field of artificial intelligence, enabling natural language processing tasks that were previously thought to be exclusive to humans. In this work, we introduce Qwen, the first installment of our large language model series. Qwen is a comprehensive language model series that encompasses distinct models with varying parameter counts. It includes Qwen, the base pretrained language models, and Qwen-Chat, the chat models finetuned with human alignment techniques. The base language models consistently demonstrate superior performance across a multitude of downstream tasks, and the chat models, particularly those trained using Reinforcement Learning from Human Feedback (RLHF), are highly competitive. The chat models possess advanced tool-use and planning capabilities for creating agent applications, showcasing impressive performance even when compared to bigger models on complex tasks like utilizing a code interpreter. Furthermore, we have developed coding-specialized models, Code-Qwen and Code-Qwen-Chat, as well as mathematics-focused models, Math-Qwen-Chat, which are built upon base language models. These models demonstrate significantly improved performance in comparison with open-source models, and slightly fall behind the proprietary models.Comment: 59 pages, 5 figure