SCAN+rVV10: A promising van der Waals density functional

The newly developed "strongly constrained and appropriately normed" (SCAN) meta-generalized-gradient approximation (meta-GGA) can generally improve over the non-empirical Perdew-Burke-Ernzerhof (PBE) GGA not only for strong chemical bonding, but also for the intermediate-range van der Waals (vdW) interaction. However, the long-range vdW interaction is still missing. To remedy this, we propose here pairing SCAN with the non-local correlation part from the rVV10 vdW density functional, with only two empirical parameters. The resulting SCAN+rVV10 yields excellent geometric and energetic results not only for molecular systems, but also for solids and layered-structure materials, as well as the adsorption of benzene on coinage metal surfaces. Especially, SCAN+rVV10 outperforms all current methods with comparable computational efficiencies, accurately reproducing the three most fundamental parameters---the inter-layer binding energies, inter-, and intra-layer lattice constants---for 28 layered-structure materials. Hence, we have achieved with SCAN+rVV10 a promising vdW density functional for general geometries, with minimal empiricism

Life fingerprints of nuclear reactions in the body of animals

Nuclear reactions are a very important natural phenomenon in the universe. On the earth, cosmic rays constantly cause nuclear reactions. High energy beams created by medical devices also induce nuclear reactions in the human body. The biological role of these nuclear reactions is unknown. Here we show that the in vivo biological systems are exquisite and sophisticated by nature in influence on nuclear reactions and in resistance to radical damage in the body of live animals. In this study, photonuclear reactions in the body of live or dead animals were induced with 50-MeV irradiation. Tissue nuclear reactions were detected by positron emission tomography (PET) imaging of the induced beta+ activity. We found the unique tissue "fingerprints" of beta+ (the tremendous difference in beta+ activities and tissue distribution patterns among the individuals) are imprinted in all live animals. Within any individual, the tissue "fingerprints" of 15O and 11C are also very different. When the animal dies, the tissue "fingerprints" are lost. The biochemical, rather than physical, mechanisms could play a critical role in the phenomenon of tissue "fingerprints". Radiolytic radical attack caused millions-fold increases in 15O and 11C activities via different biochemical mechanisms, i.e. radical-mediated hydroxylation and peroxidation respectively, and more importantly the bio-molecular functions (such as the chemical reactivity and the solvent accessibility to radicals). In practice biologically for example, radical attack can therefore be imaged in vivo in live animals and humans using PET for life science research, disease prevention, and personalized radiation therapy based on an individual's bio-molecular response to ionizing radiation

Synchronicity of Stress Wave Propagation in Bolt Body and Anchorage Medium

Accurate assessment of anchoring quality depends on the accuracy of assessing stress wave velocity in the anchor system. Stress wave velocity is closely related to collaborative vibration and depends on the degree of bonding between anchor body and anchorage medium. Bonding differences can be large at different ages. Based on stress wave reflection methods, non-destructive testing of anchors was performed using sensors arranged at the same cross-section of the anchor body and anchorage medium, which showed stress wave synchronization. In the early stage of filling, stress wave synchronicity was poorer between the anchor body and mortar. Therefore, the anchor should not be treated as a composite material when determining its wave velocity. Once the mortar hardens, the stress waves become more synchronous and the anchor can be regarded as a composite material. Stress wave synchronicity between the anchor body and mortar is related to mortar age and anchorage length. The anchor length required to provide stress wave synchronization between the anchor body and mortar decreases with increasing mortar age. Stress wave velocity rules were derived for different ages to provide the basis for accurately determining the stress wave velocity in the anchor

Age-related modulation of the nitrogen resorption efficiency response to growth requirements and soil nitrogen availability in a temperate pine plantation

Nitrogen (N) resorption is a key strategy for conserving N in forests, and is often affected by soil nutrient condition and N sink strength within the plant. However, our understanding of the age-related pattern of N resorption and how increasing N deposition will affect this pattern is limited. Here, we investigated N resorption along a chronosequence of stands ranging in age from 2 to 100 years old, and conducted a 4-year exogenous N input experiment in stands at age class 11, 20, and 45 in a Larix Principis-rupprechtii plantation in north China. We found a logarithmic increase in leaf N resorption efficiency (NRE) and green leaf N concentration, and a logarithmic decrease in senesced-leaf N concentration along the stand-age chronosequence. Leaf NRE was negatively correlated with plant-available N concentration. Stand-level N resorption was positively correlated with the annual N requirement for tree growth. N resorption contributed to 45, 62, and 68% of the annual N supply in the 11-, 20-, and 45-year-old stands, respectively. Our exogenous N input experiment showed that leaf NRE in the 11- and 20-year-old stands decreased 17 and 12% following a 50-kg N ha¯¹ y¯¹ input. However, leaf NRE was not affected in the 45-year-old stand. The increases in leaf NRE and the contribution of N resorption to annual N supply along stand ages suggested that, with stand development, tree growth depends more on N resorption to supply its N need. Furthermore, the leaf NRE of mature stand was not decreased under exogenous N input, suggesting that mature stands can be stronger sinks for N deposition than young stands due to their higher capacity to retain the deposited N within plants via internal cycle. Ignoring age-related N use strategies can lead to a bias in N cycle models when evaluating forest net primary production under increasing global N deposition

Titanium-capped carbon chains as promising new hydrogen storage media

The capacity of Ti-capped sp carbon atomic chains for use as hydrogen storage media is studied using first-principles density functional theory. The Ti atom is strongly attached at one end of the carbon chains via d-p hybridization, forming stable TiCn complexes. We demonstrate that the number of adsorbed H2 on Ti through Kubas interaction depends upon the chain types. For polyyne (n even) or cumulene (n odd) structures, each Ti atom can hold up to five or six H2 molecules, respectively. Furthermore, the TiC5 chain effectively terminated on a C20 fullerene can store hydrogen with optimal binding of 0.52 eV/H2. Our results reveal a possible way to explore high-capacity hydrogen storage materials in truly one-dimensional carbon structures.Comment: accepted for publication in Physical Chemistry Chemical Physic

Immunosuppression Induced by Chronic Inflammation and the Progression to Oral Squamous Cell Carcinoma

Oral squamous cell carcinoma (OSCC) is an aggressive, invasive malignancy of epithelial origin. The progression from premalignant lesions—oral leukoplakia (OLK) and oral lichen planus (OLP)—to OSCC involves complex inflammatory processes that have not been elucidated. We investigated the roles of inflammatory mediators and infiltrating immunocytes in the pathogenic progression of OLK and OLP to OSCC. The occurrence of regulatory T-cells (Tregs) and tumor-associated macrophages (TAMs) and the expression of anti-inflammatory cytokines and proinflammatory cytokines were investigated in OLK, OLP, and OSCC tissues. Immunohistochemical staining of CD4, FOXP3, CD68, TGF-β1, IL-10, IL-4, IFN-γ, and MCP-1 showed that the occurrence of Tregs and TAMs increased in parallel with disease progression in OLK and OSCC. IL-10 gradually increased during the early stages of OLK and in OSCC. Infiltrating IL-4+ macrophages were seen with increasing frequency in OLK tissue during the progression of oral dysplasia. Fewer TGF-β1+ macrophages were seen in OSCC than in OLK and OLP. The expression of IFN-γ decreased gradually with the OLK development and had the lowest expression in OSCC. MCP-1 expression did not change significantly during the development of OSCC. The results suggested that the immunosuppression induced by chronic inflammation promotes tumorigenesis in OSCC, rather than initiating it

Intraspecific comparative genomics of isolates of the Norway spruce pathogen (Heterobasidion parviporum) and identification of its potential virulence factors

Background: Heterobasidion parviporum is an economically most important fungal forest pathogen in northern Europe, causing root and butt rot disease of Norway spruce (Picea abies (L.) Karst.). The mechanisms underlying the pathogenesis and virulence of this species remain elusive. No reference genome to facilitate functional analysis is available for this species. Results: To better understand the virulence factor at both phenotypic and genomic level, we characterized 15 H. parviporum isolates originating from different locations across Finland for virulence, vegetative growth, sporulation and saprotrophic wood decay. Wood decay capability and latitude of fungal origins exerted interactive effects on their virulence and appeared important for H. parviporum virulence. We sequenced the most virulent isolate, the first full genome sequences of H. parviporum as a reference genome, and re-sequenced the remaining 14 H. parviporum isolates. Genome-wide alignments and intrinsic polymorphism analysis showed that these isolates exhibited overall high genomic similarity with an average of at least 96% nucleotide identity when compared to the reference, yet had remarkable intra-specific level of polymorphism with a bias for CpG to TpG mutations. Reads mapping coverage analysis enabled the classification of all predicted genes into five groups and uncovered two genomic regions exclusively present in the reference with putative contribution to its higher virulence. Genes enriched for copy number variations (deletions and duplications) and nucleotide polymorphism were involved in oxidation-reduction processes and encoding domains relevant to transcription factors. Some secreted protein coding genes based on the genome-wide selection pressure, or the presence of variants were proposed as potential virulence candidates. Conclusion: Our study reported on the first reference genome sequence for this Norway spruce pathogen (H. parviporum). Comparative genomics analysis gave insight into the overall genomic variation among this fungal species and also facilitated the identification of several secreted protein coding genes as putative virulence factors for the further functional analysis. We also analyzed and identified phenotypic traits potentially linked to its virulence.Peer reviewe

Structural Basis for dsRNA Recognition, Filament Formation, and Antiviral Signal Activation by MDA5

SummaryMDA5, a viral double-stranded RNA (dsRNA) receptor, shares sequence similarity and signaling pathways with RIG-I yet plays essential functions in antiviral immunity through distinct specificity for viral RNA. Revealing the molecular basis for the functional divergence, we report here the crystal structure of MDA5 bound to dsRNA, which shows how, using the same domain architecture, MDA5 recognizes the internal duplex structure, whereas RIG-I recognizes the terminus of dsRNA. We further show that MDA5 uses direct protein-protein contacts to stack along dsRNA in a head-to-tail arrangement, and that the signaling domain (tandem CARD), which decorates the outside of the core MDA5 filament, also has an intrinsic propensity to oligomerize into an elongated structure that activates the signaling adaptor, MAVS. These data support a model in which MDA5 uses long dsRNA as a signaling platform to cooperatively assemble the core filament, which in turn promotes stochastic assembly of the tandem CARD oligomers for signaling