There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality.

Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

I and i

Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

QIIME 2 development was primarily funded by NSF Awards 1565100 to J.G.C. and 1565057 to R.K. Partial support was also provided by the following: grants NIH U54CA143925 (J.G.C. and T.P.) and U54MD012388 (J.G.C. and T.P.); grants from the Alfred P. Sloan Foundation (J.G.C. and R.K.); ERCSTG project MetaPG (N.S.); the Strategic Priority Research Program of the Chinese Academy of Sciences QYZDB-SSW-SMC021 (Y.B.); the Australian National Health and Medical Research Council APP1085372 (G.A.H., J.G.C., Von Bing Yap and R.K.); the Natural Sciences and Engineering Research Council (NSERC) to D.L.G.; and the State of Arizona Technology and Research Initiative Fund (TRIF), administered by the Arizona Board of Regents, through Northern Arizona University. All NCI coauthors were supported by the Intramural Research Program of the National Cancer Institute. S.M.G. and C. Diener were supported by the Washington Research Foundation Distinguished Investigator Award.

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Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Reactive oxygen species and antioxidant machinery in abiotic stress tolerance in crop plants

The recent advent of DNA sequencing technologies facilitates the use of genome sequencing data that provide means for more informative and precise classification and identification of members of the Bacteria and Archaea. Because the current species definition is based on the comparison of genome sequences between type and other strains in a given species, building a genome database with correct taxonomic information is of paramount need to enhance our efforts in exploring prokaryotic diversity and discovering novel species as well as for routine identifications. Here we introduce an integrated database, called EzBioCloud, that holds the taxonomic hierarchy of the Bacteria and Archaea, which is represented by quality-controlled 16S rRNA gene and genome sequences. Whole-genome assemblies in the NCBI Assembly Database were screened for low quality and subjected to a composite identification bioinformatics pipeline that employs gene-based searches followed by the calculation of average nucleotide identity. As a result, the database is made of 61 700 species/phylotypes, including 13 132 with validly published names, and 62 362 whole-genome assemblies that were identified taxonomically at the genus, species and subspecies levels. Genomic properties, such as genome size and DNA G+C content, and the occurrence in human microbiome data were calculated for each genus or higher taxa. This united database of taxonomy, 16S rRNA gene and genome sequences, with accompanying bioinformatics tools, should accelerate genome-based classification and identification of members of the Bacteria and Archaea. The database and related search tools are available at www.ezbiocloud.net/.

Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies.

This paper describes EagleEye, which is an intelligent system that provides business intelligence through advanced data mining and text analytics. Unlike traditional search engines, EagleEye is entity oriented, and an entity can be an organization, a person, or a place. Given an entity name, the basic function of EagleEye is to generate a consolidated view of the entity information it gathers from many disparate data sources and to organize and categorize it, and automatically detect entity relationships. EagleEye can also analyze the opinions of entities, evaluate whether they are positive or negative, and provide insight into many aspects of consumer sentiment toward product brands. This type of information can enable enterprises to manage the reputation of their brands and to respond more quickly to changes in the marketplace. We present the key technologies--such as entity-name grouping, entity-relation extraction, and entity-oriented opinion mining--that were developed to support these functions. EagleEye has been successfully deployed to a number of clients across a variety of industries in China. Several case studies are presented to demonstrate in practice the capability and business value of EagleEye.

EagleEye: entity-centric business intelligence for smarter decisions

Embodiments of the present invention provide a computer, control equipment and a data processing method The computer comprises a processing unit and the control equipment; the processing unit is used for adding a tag to an application request and sending the application request added with the tag to the control equipment; the control equipment is used for receiving the application request added with the tag and determining an amount of resources allocated to the application request according to the tag and a pre-stored resource allocation strategy, wherein the resource allocation strategy comprises a corresponding relationship between the tag and the amount of the resources allocated to the application request; and the control equipment is further used for indicating component parts of the computer to process the application request according to the amount of the resources allocated to the application request The computer, the control equipment and the data processing method are used for improving service quality of the application request

Computer, control equipment and data processing method

Osteocytes function as the master orchestrator of bone remodeling activity in the telophase of osseointegration. However, most contemporary studies focus on the manipulation of osteoblast and/or osteoclast functionality via implant surface engineering, which neglects the pivotal role of osteocytes in de novo bone formation. It is confirmative that osteocyte processes extend directly to the implant surface, but whether the surface physicochemical properties can affect the functionality of osteocytes and determine the fate of the osseointegration in the final remodeling stage remains to be determined. Titania nanotube arrays (NTAs) with distinct diameters were fabricated to investigate the relationship between the nanoscale topography and the functionality of osteocytes. In vitro results pinpointed that NTA with a diameter of 15 nm (NTA-15) significantly promote osteogenesis of osteocytes via the enhancement of spreading, proliferation, and mineralization. The osteocyte transcriptome of each group further revealed that the TGF-β signaling pathway plays a pivotal role in osteocyte-mediated osteogenesis. The in vivo study definitely mirrored the aforementioned results, that NTA-15 significantly promotes bone formation around the implant. Consequently, nanoscaled topography-induced osteocyte functionality is important in late osseointegration. This suggests that surface designs targeting osteocytes may, therefore, be a potential approach to solving the aseptic loosening of the implant, and thus strengthen osseointegration.

/pdf/differential-nanoscale-topography-dedicates-osteocyte-1dvgpd66.pdf

Differential Nanoscale Topography Dedicates Osteocyte-Manipulated Osteogenesis via Regulation of the TGF-β Signaling Pathway

The speed gap between processors and memory continues to widen. This problem has led to an increased reliance on complex cache hierarchies. Caches are very effective for programs with near 100% cache hit rates, but they fail on many important applications that do not exhibit sufficient data locality. In the same vein, TLBs fail in their role of hiding the latency of virtual-to-physical address translation. A TLB typically contains between 64 and 512 entries, which leads to low TLB hit rates for applications with poor data locality and large working sets. 
We propose to attack these problems by using an extra level of address translation at the main memory controller—an idea first introduced by Swanson, Stoller, and Carter [93]. Remapping physical addresses at the memory controller allows data structures with poor locality to be reorganized into data structures with high locality without copying, which can significantly increase TLB and cache hit rates. 
This dissertation investigates the effectiveness of physical address remapping at the memory controller by exploring five efficient remapping mechanisms that can be categorized into three families: remapping strided accesses, remapping through an indirection vector, and remapping-based page coloring. 
Remapping strided accesses reorganizes sparse data items distributed along fixed strides into dense regions. We consider two different strided remapping algorithms: stride remapping creates dense cache lines from data items whose virtual addresses are distributed along a nonunit stride; and transpose remapping creates the transpose of a two-dimensional matrix. Remapping through an indirection vector packs dense cache lines from disjoint memory locations according to addresses stored in an indirection vector. It enables application programs to access arbitrarily distributed data items as if they were stored sequentially. We consider both static and dynamic forms of this remapping. The static form requires that the indirection vector exists naturally in the program. The dynamic form dynamically creates a small indirection vector. Remapping-based page coloring performs coarse-grained remapping at the memory controller. It recolors physical pages without copying. 
This dissertation explores different ways to implement these remapping mechanisms and compares them with conventional data reorganization methods that employ copying or a relocation buffer. We evaluate the performance of these remapping mechanisms on a suite of benchmarks that do not perform well on conventional memory systems. This evaluation includes both execution-driven simulation and analytical modeling. The results show that address remapping at the memory controller improves the performance of these benchmarks by an average of 124%. Remapping outperforms data reorganization via copying by an average of 66% and reorganization via a relocation buffer by an average of 61%.

Efficient remapping mechanisms for an adaptable memory system

: This document describes ISIM, the simulator for the Impulse Adaptable Memory System. Impulse adds two new features to a conventional memory system. First, it supports a configurable, extra level of address remapping at the memory controller. Second, it supports prefetching at the memory controller. Consequently, two new units, a remapping controller and a memory controller cache, are added to a traditional memory system to support the new Impulse features. ISIM is based on Paint, a PA-RISC instruction set interpreter. ISIM extends Paint with a detailed Impulse memory system model which includes a primary data cache, a secondary data cache, a system bus, an Impulse memory controller, and a renovated DRAM backend. Note that this document focuses on the Impulse extensions only. The reader should consult the Paint technical report 2 for an overview of the Paint simulation environment and terminology.

https://apps.dtic.mil/sti/pdfs/ADA438175.pdf

Lixin Zhang

Papers

EagleEye: entity-centric business intelligence for smarter decisions

Computer, control equipment and data processing method

Differential Nanoscale Topography Dedicates Osteocyte-Manipulated Osteogenesis via Regulation of the TGF-β Signaling Pathway

Efficient remapping mechanisms for an adaptable memory system

ISIM: The Simulator for The Impulse Adaptable Memory System