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.

New evidence suggests that the clinical success of chemotherapy is not merely due to tumor cell toxicity but also arises from the restoration of immunosurveillance, which has been immensely neglected in previous preclinical and clinical researches. There is an urgent need for novel insights into molecular mechanisms and regimens that uplift the efficacy of immunotherapy since only a minority of cancer patients are responsive to immune checkpoint inhibitors (ICIs). Recent findings on combination therapy of chemotherapy and ICIs have shown promising results. This strategy increases tumor recognition and elimination by the host immune system while reducing immunosuppression by the tumor microenvironment. Currently, several preclinical studies are investigating molecular mechanisms that give rise to the immunomodulation by chemotherapeutic agents and exploit them in combination therapy with ICIs in order to achieve a synergistic clinical activity. In this review, we summarize studies that exhibit the capacity of conventional chemotherapeutics to elicit anti-tumor immune responses, thereby facilitating anti-tumor activities of the ICIs. In conclusion, combining chemotherapeutics with ICIs appears to be a promising approach for improving cancer treatment outcomes.

https://www.frontiersin.org/articles/10.3389/fonc.2022.939249/pdf

Chemotherapy reinforces anti-tumor immune response and enhances clinical efficacy of immune checkpoint inhibitors

In order to explore the detection of gamma radiation via intramolecular photoinduced electron transfer (PET) and the interaction between molecular structures and fluorescence enhancement, we conducted an in-depth study of the perylene tetracarboxylic diimide (PDI) series of fluorescent probes capable of detecting HCl in the non-polar CHCl3 solutions. To simulate the interaction between ionizing radiation and fluorescent molecules, we used HCl titration method to predict the ability of PDI-n to detect gamma rays. The results show that the combination of PDI-n and HCl can enhance the fluorescence through retro-PET process. In addition, the fluorescence enhancement multiple gradually decreased with the enlargement of alkylamine side chains. In the direct irradiation experiment of ionizing radiation, PDI-n can also show a good fluoresence enhancement to gamma rays. Similar to the above HCl titration tests, the fluorescence increament stronthly depends on the alkylamine side chains lengths. The maximum fluorescence increament of PDI-1 is 22.24, and the fluorescence enhancement multiple of PDI-1–PDI-4 decreases when increasing the alkyl chain length. Besides, combining density functional theory (DFT), time-dependent density functional theory (TDDFT) calculations and electrochemical tests, the relative positions of each energy level obtained from the experiment indicate that the PDI-n molecule is beneficial to the occurrence of the intramolecular PET effect. Using femtosecond transient absorption spectroscopy (fs-TAS) and transient fluorescence spectroscopy (TFS) tests, the lifetime of charge separation was obtained, and the efficiency of the PET process was characterized by the rate constant. We found that fluorescent molecules with shorter side chains can realize PET more efficiently. Therefore, this work exploits the intramolecular PET mechanism for efficiently detecting gamma rays using a series of fluorescent probes, and reveals the law of the influence of molecular chain length on the PET effect. Which provides theoretical support for the development of new materials for effective and sensitive detection of ionizing radiation. 

Effective Fluorescent Turn-on Detection of Ionizing Radiations Through Controllable Intramolecular Photoinduced Electron Transfer

Structures, Scaling Relations, and Selectivities of the Copper-Based Binary Catalysts for CO2 Reduction Reactions

Cloud computing has demonstrated tremendous capability in a wide spectrum of online services. Virtualization provides an efficient solution to the utilization of modern multicore processor systems while affording significant flexibility. The growing popularity of virtualized datacenters motivates deeper understanding of the interactions between virtual machine management and the micro-architecture behaviors of the privileged domain. We argue that these behaviors must be factored into the design of processor microarchitecture in virtualized datacenters. In this work, we use performance counters on modern servers to study the micro-architectural execution characteristics of the privileged domain while performing various VM management operations. Our study shows that today's state-of-the-art processor still has room for further optimizations when executing virtualized cloud workloads, particularly in the organization of last level caches and on-chip cache coherence protocol. Specifically, our analysis shows that: shared caches could be partitioned to eliminate interference between the privileged domain and guest domains; the cache coherence protocol could support a high degree of data sharing of the privileged domain; and cache capacity or CPU utilization occupied by the privileged domain could be effectively managed when performing management workflows to achieve high system throughput.

Lixin Zhang

Papers

Chemotherapy reinforces anti-tumor immune response and enhances clinical efficacy of immune checkpoint inhibitors

Effective Fluorescent Turn-on Detection of Ionizing Radiations Through Controllable Intramolecular Photoinduced Electron Transfer

Structures, Scaling Relations, and Selectivities of the Copper-Based Binary Catalysts for CO2 Reduction Reactions

Understanding the implications of virtual machine management on processor microarchitecture design

N, S, P Tri-Doped Carbon as Highly Efficient Catalyst for Oxygen Reduction Reaction