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

Gold nanoparticles have been used in biomedical applications since their first colloidal syntheses more than three centuries ago. However, over the past two decades, their beautiful colors and unique electronic properties have also attracted tremendous attention due to their historical applications in art and ancient medicine and current applications in enhanced optoelectronics and photovoltaics. In spite of their modest alchemical beginnings, gold nanoparticles exhibit physical properties that are truly different from both small molecules and bulk materials, as well as from other nanoscale particles. Their unique combination of properties is just beginning to be fully realized in range of medical diagnostic and therapeutic applications. This critical review will provide insights into the design, synthesis, functionalization, and applications of these artificial molecules in biomedicine and discuss their tailored interactions with biological systems to achieve improved patient health. Further, we provide a survey of the rapidly expanding body of literature on this topic and argue that gold nanotechnology-enabled biomedicine is not simply an act of ‘gilding the (nanomedicinal) lily’, but that a new ‘Golden Age’ of biomedical nanotechnology is truly upon us. Moving forward, the most challenging nanoscience ahead of us will be to find new chemical and physical methods of functionalizing gold nanoparticles with compounds that can promote efficient binding, clearance, and biocompatibility and to assess their safety to other biological systems and their long-term term effects on human health and reproduction (472 references).

The golden age: gold nanoparticles for biomedicine

Molecular self-assembly is the spontaneous association of molecules under equilibrium conditions into stable, structurally well-defined aggregates joined by noncovalent bonds. Molecular self-assembly is ubiquitous in biological systems and underlies the formation of a wide variety of complex biological structures. Understanding self-assembly and the associated noncovalent interactions that connect complementary interacting molecular surfaces in biological aggregates is a central concern in structural biochemistry. Self-assembly is also emerging as a new strategy in chemical synthesis, with the potential of generating nonbiological structures with dimensions of 1 to 10(2) nanometers (with molecular weights of 10(4) to 10(10) daltons). Structures in the upper part of this range of sizes are presently inaccessible through chemical synthesis, and the ability to prepare them would open a route to structures comparable in size (and perhaps complementary in function) to those that can be prepared by microlithography and other techniques of microfabrication.

Molecular self-assembly and nanochemistry: A chemical strategy for the synthesis of nanostructures

The discovery of the enhancement of Raman scattering by molecules adsorbed on nanostructured metal surfaces is a landmark in the history of spectroscopic and analytical techniques. Significant experimental and theoretical effort has been directed toward understanding the surface-enhanced Raman scattering (SERS) effect and demonstrating its potential in various types of ultrasensitive sensing applications in a wide variety of fields. In the 45 years since its discovery, SERS has blossomed into a rich area of research and technology, but additional efforts are still needed before it can be routinely used analytically and in commercial products. In this Review, prominent authors from around the world joined together to summarize the state of the art in understanding and using SERS and to predict what can be expected in the near future in terms of research, applications, and technological development. This Review is dedicated to SERS pioneer and our coauthor, the late Prof. Richard Van Duyne, whom we lost during the preparation of this article.

/pdf/present-and-future-of-surface-enhanced-raman-scattering-34aqgcm385.pdf

Present and Future of Surface-Enhanced Raman Scattering

Abstract Using a symmetry-preserving regularisation of a vector $$\times $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mo>×</mml:mo> </mml:math> vector contact interaction (SCI), we complete a systematic treatment of twelve semileptonic transitions with vector meson final states: $$D\rightarrow \rho $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:mi>D</mml:mi> <mml:mo>→</mml:mo> <mml:mi>ρ</mml:mi> </mml:mrow> </mml:math> , $$D_{(s)}\rightarrow K^*$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:msub> <mml:mi>D</mml:mi> <mml:mrow> <mml:mo>(</mml:mo> <mml:mi>s</mml:mi> <mml:mo>)</mml:mo> </mml:mrow> </mml:msub> <mml:mo>→</mml:mo> <mml:msup> <mml:mi>K</mml:mi> <mml:mo>∗</mml:mo> </mml:msup> </mml:mrow> </mml:math> , $$D_s\rightarrow \phi $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:msub> <mml:mi>D</mml:mi> <mml:mi>s</mml:mi> </mml:msub> <mml:mo>→</mml:mo> <mml:mi>ϕ</mml:mi> </mml:mrow> </mml:math> , $$B\rightarrow \rho $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:mi>B</mml:mi> <mml:mo>→</mml:mo> <mml:mi>ρ</mml:mi> </mml:mrow> </mml:math> , $$B_s\rightarrow K^*$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:msub> <mml:mi>B</mml:mi> <mml:mi>s</mml:mi> </mml:msub> <mml:mo>→</mml:mo> <mml:msup> <mml:mi>K</mml:mi> <mml:mo>∗</mml:mo> </mml:msup> </mml:mrow> </mml:math> , $$B_{(s)}\rightarrow D_{(s)}^*$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:msub> <mml:mi>B</mml:mi> <mml:mrow> <mml:mo>(</mml:mo> <mml:mi>s</mml:mi> <mml:mo>)</mml:mo> </mml:mrow> </mml:msub> <mml:mo>→</mml:mo> <mml:msubsup> <mml:mi>D</mml:mi> <mml:mrow> <mml:mo>(</mml:mo> <mml:mi>s</mml:mi> <mml:mo>)</mml:mo> </mml:mrow> <mml:mo>∗</mml:mo> </mml:msubsup> </mml:mrow> </mml:math> , $$B_c \rightarrow B_{(s)}^*, J/\psi , D^*$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:msub> <mml:mi>B</mml:mi> <mml:mi>c</mml:mi> </mml:msub> <mml:mo>→</mml:mo> <mml:msubsup> <mml:mi>B</mml:mi> <mml:mrow> <mml:mo>(</mml:mo> <mml:mi>s</mml:mi> <mml:mo>)</mml:mo> </mml:mrow> <mml:mo>∗</mml:mo> </mml:msubsup> <mml:mo>,</mml:mo> <mml:mi>J</mml:mi> <mml:mo>/</mml:mo> <mml:mi>ψ</mml:mi> <mml:mo>,</mml:mo> <mml:msup> <mml:mi>D</mml:mi> <mml:mo>∗</mml:mo> </mml:msup> </mml:mrow> </mml:math> ; and thereby finalise a unified analysis of semileptonic decays of heavy + heavy and heavy + light pseudoscalar mesons to both pseudoscalar and vector meson final states. The analysis is marked by algebraic simplicity, few parameters, and the ability to consistently describe systems from Nambu-Goldstone modes to heavy + heavy mesons. Regarding the behaviour of the transition form factors, the SCI results compare well wherever sound experimental or independent theory analyses are available; hence, the SCI branching fraction predictions should be a reasonable guide. Considering the ratios $$R(D_{(s)}^{(*)})$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:mi>R</mml:mi> <mml:mo>(</mml:mo> <mml:msubsup> <mml:mi>D</mml:mi> <mml:mrow> <mml:mo>(</mml:mo> <mml:mi>s</mml:mi> <mml:mo>)</mml:mo> </mml:mrow> <mml:mrow> <mml:mo>(</mml:mo> <mml:mrow /> <mml:mo>∗</mml:mo> <mml:mo>)</mml:mo> </mml:mrow> </mml:msubsup> <mml:mo>)</mml:mo> </mml:mrow> </mml:math> , $$R(J/\psi )$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:mi>R</mml:mi> <mml:mo>(</mml:mo> <mml:mi>J</mml:mi> <mml:mo>/</mml:mo> <mml:mi>ψ</mml:mi> <mml:mo>)</mml:mo> </mml:mrow> </mml:math> , $$R(\eta _c)$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:mi>R</mml:mi> <mml:mo>(</mml:mo> <mml:msub> <mml:mi>η</mml:mi> <mml:mi>c</mml:mi> </mml:msub> <mml:mo>)</mml:mo> </mml:mrow> </mml:math> , whose values are key tests of lepton universality in weak interactions, the SCI values agree with Standard Model predictions. The $$B_{(s)}\rightarrow D_{(s)}^*$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:msub> <mml:mi>B</mml:mi> <mml:mrow> <mml:mo>(</mml:mo> <mml:mi>s</mml:mi> <mml:mo>)</mml:mo> </mml:mrow> </mml:msub> <mml:mo>→</mml:mo> <mml:msubsup> <mml:mi>D</mml:mi> <mml:mrow> <mml:mo>(</mml:mo> <mml:mi>s</mml:mi> <mml:mo>)</mml:mo> </mml:mrow> <mml:mo>∗</mml:mo> </mml:msubsup> </mml:mrow> </mml:math> transitions are used to predict the precursor functions that evolve into the universal Isgur–Wise function in the heavy-quark limit, with results that conform with those from other sources where such are available. The study also exposes effects on the transition form factors that flow from interference between emergent hadron mass from the strong interaction and Higgs boson couplings via current-quark masses, including flavour symmetry violation. 

/pdf/heavy-heavy-and-heavy-light-pseudoscalar-to-vector-2xsa9mmt.pdf

Heavy + heavy and heavy + light pseudoscalar to vector semileptonic transitions

Dimethomorph (DMM) is a novel therapeutic fungicide, which is mainly used to control downy mildew, phytophthora, and other fungal diseases of grapes, leeks, and cucumbers. Its residue is harmful to...

Gold-based immunochromatographic strip assay for detecting dimethomorph in vegetables

Phospholipids have an important antioxidant effect on animals. The effects of different dietary phospholipid sources on the growth, antioxidant activity, immunity, and gut microbiota of female broodstock of Pacific white shrimp Litopenaeus vannamei were investigated. Four isoproteic and isolipid semi-purified diets containing 4% soybean lecithin (SL), egg yolk lecithin (EL), or krill oil (KO) and a control diet without phospholipid supplementation were fed to female broodstock of L. vannamei (34.7 ± 4.2 g) for 28 days. The growth performance, antioxidative capacity, and innate immunity of the female broodstock fed phospholipid supplemented diets were improved regardless of sources compared with the control shrimp. The effects on growth and antioxidant capacity in female shrimp fed the KO diet were highest. The innate immunity of female shrimp fed the EL and KO diets were significantly higher than shrimp fed the SL diet. Dietary phospholipid supplementation increased gut microbiota diversity and richness, and the Chao1 and ACE values in the KO group were significantly higher than in the control group. The richness of Proteobacteria, Photobacterium, and Vibrio decreased, whereas the richness of Firmicutes and Bacteroidetes increased in the shrimp fed the KO diet compared with the shrimp fed the SL and EL diets. The interactions of gut microbiota in shrimp fed the KO diet were the most complex, and the positive interaction was the largest among all the treatments. The functional genes of gut microbiota in shrimp fed the KO diet were significantly enriched in lipid metabolism and terpenoid/polyketide metabolism pathways. Spearman correlation analysis showed that Fusibacter had significantly positive correlations with antioxidant activity (total antioxidant capacity, superoxide dismutase, glutathione peroxidase), immune enzyme activity (phenoloxidase and lysozyme), and immune gene expression (C-type lectin 3, Caspase-1). All findings suggest that dietary phospholipids supplementation can improve the growth and health status of female L. vananmei broodstock. Krill oil is more beneficial in improving the antioxidant capacity and innate immunity than other dietary phospholipid sources. Furthermore, krill oil can help establish the intestinal immune barrier by increasing the richness of Fusibacter and promote the growth of female shrimp. Fusibacter may be involved in iron metabolism to improve the antioxidant capacity of female shrimp.

/pdf/growth-health-and-gut-microbiota-of-female-pacific-white-3q4l37nr.pdf

Growth, Health, and Gut Microbiota of Female Pacific White Shrimp, Litopenaeus vannamei Broodstock Fed Different Phospholipid Sources

Bloodstream infection (BSI) is associated with high mortality rates. Mycoplasma hominis, which rarely causes extragenital infections, has been shown to induce BSI and presents a clinical diagnostic and therapeutic challenge.In this study, we investigated the clinical characteristics, antibiotic resistance, and multilocus sequence typing (MLST) of eight BSI cases caused by M. hominis in South China from January 2018 to October 2021.Underlying immunosuppression and genitourinary tract surgery are important risk factors for M. hominis BSI. The most prevalent clinical symptoms and signs were fever. Additional findings included elevated neutrophil count and C-reactive protein level. Furthermore, in this study, all the patients had erythrocytopenia. M. hominis harbored the highest rate of resistance to levofloxacin (75.0%), followed by sparfloxacin (50.0%), and gatifloxacin (37.5%). gyrA S153L was the most frequent mutation in levofloxacin-resistant strains, followed by parC S91I. parC K144R may be related to resistance to gatifloxacin and sparfloxacin. Eight strains showed sensitivity to all the other antibiotics analyzed (doxycycline, minocycline, josamycin, and clindamycin). MLST was performed in seven isolates, and seven new sequence types were described. We compared our isolates with all M. hominis strains from the PubMLST database, and one major clonal complex and eight singletons were identified.Our study clarified and expanded the clinical features and antibiotic resistance of M. hominis BSI. These findings are useful for the clinical diagnosis and control of M. hominis BSI. 

/pdf/clinical-and-microbiological-characterization-of-bloodstream-1cm25a88.pdf

Clinical and Microbiological Characterization of Bloodstream Infections Caused by Mycoplasma hominis: An Overlooked Pathogen

CD96 was identified as a novel immune checkpoint. However, the role of CD96 in the gastric cancer (GC) microenvironment remains fragmentary. This study aimed to probe the clinical significance of CD96 to predict prognosis and therapeutic responsiveness, and to reveal the immune contexture and genomic features correlated to CD96 in GC patients. We enrolled 496 tumor microarray specimens of GC patients from Zhongshan Hospital (ZSHS) for immunohistochemical analyses. Four hundred and twelve GC patients from the Cancer Genome Atlas (TCGA) and 61 GC patients treated with pembrolizumab from ERP107734 published in the European Nucleotide Archive (ENA) were gathered for further analysis of the association between CD96+ cell infiltration and immune contexture, molecular characteristics, and genomic features by CIBERSORT and gene set enrichment analysis. Clinical outcomes were analyzed by Kaplan–Meier curves, the Cox model, interaction testing, and receiver operating characteristic analysis. High CD96+ cell infiltration predicted poor prognosis and inferior survival benefits from fluorouracil‐based adjuvant chemotherapy in the ZSHS cohort whereas superior therapeutic responsiveness to pembrolizumab was shown in the ENA cohort. CD96‐enriched tumors showed an immunosuppressive tumor microenvironment featured by exhausted CD8+ T‐cell infiltration in both the ZSHS and TCGA cohorts. Moreover, in silico analysis for the TCGA cohort revealed that several biomarker‐targeted pathways displayed significantly elevated enrichment levels in the CD96 high subgroup. This study elucidated that CD96 might drive an immunosuppressive contexture with CD8+ T‐cell exhaustion and represent an independent adverse prognosticator in GC. CD96 could potentially be a novel biomarker for precision medicine of adjuvant chemotherapy, immunotherapy, and targeted therapies in GC.

https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/cas.15537

Chuanlai Xu

Papers

Heavy + heavy and heavy + light pseudoscalar to vector semileptonic transitions

Gold-based immunochromatographic strip assay for detecting dimethomorph in vegetables

Growth, Health, and Gut Microbiota of Female Pacific White Shrimp, Litopenaeus vannamei Broodstock Fed Different Phospholipid Sources

Clinical and Microbiological Characterization of Bloodstream Infections Caused by Mycoplasma hominis: An Overlooked Pathogen

Impact of intratumoural CD96 expression on clinical outcome and therapeutic benefit in gastric cancer