The present and future of QCD Al-bataineh, A.; Avakian, H.; Barnea, N. ...
Nuclear physics. A,
07/2024, Volume:
1047, Issue:
C
Journal Article
Peer reviewed
Open access
This White Paper presents an overview of the current status and future perspective of QCD research, based on the community inputs and scientific conclusions from the 2022 Hot and Cold QCD Town ...Meeting. We present the progress made in the last decade toward a deep understanding of both the fundamental structure of the sub-atomic matter of nucleon and nucleus in cold QCD, and the hot QCD matter in heavy ion collisions. We identify key questions of QCD research and plausible paths to obtaining answers to those questions in the near future, hence defining priorities of our research over the coming decades.
Six stable C84 isomers satisfying isolated pentagon rule (IPR) have been theoretically identified by infrared (IR), X-ray photoelectron (XPS) and near-edge X-ray absorption fine structure (NEXAFS) ...spectra. The XPS and NEXAFS spectra at the K-edge for all nonequivalent carbon atoms were simulated by the density functional theory method. NEXAFS spectra show stronger dependence than IR and XPS spectra on the six C84 isomers, which can be properly used for isomer identification. Furthermore, spectral components of total spectra for carbon atoms in different local environment have been explored.
Although returning crop residue to fields is a recommended measure for improving soil carbon (C) stocks in agroecosystems, the response of newly formed soil C (NFC) to the integrated supply of ...residue and nutrients and the microbial mechanisms involved in NFC are not fully understood. Therefore, an 84-day incubation experiment was conducted to ascertain the microbial mechanisms that underpin the NFC response to inputs of residue and nitrogen (N), phosphorus (P), and sulfur (S) in two black (Phaeozem) soils from experimental plots at Gongzhuling, Jilin Province and Hailun, Heilongjiang Province, China. The results showed that adding residue alone accelerated microbial nutrient mining, which was supported by decreases of 8–16％ in the ratios of C:N and C:P enzyme activities, relative to soils with nutrient inputs. The NFC amounts increased from 1156 to 1722 mg kg?1 in Gongzhuling soil and from 725 to 1067 mg kg?1 in Hailun soil as the levels of nutrient supplementation increased. Boosted regression tree analysis suggested that β-glucosidase (BG), acid phosphatase (AP), microbial biomass C (MBC), and Acidobacteria accounted for 27.8, 18.5, 14.7, and 8.1％, respectively, of the NFC in Gongzhuling soil and for 25.9, 29.5, 10.1, and 13.9％, respectively, of the NFC in Hailun soil. Path analysis determined that Acidobacteria positively influenced NFC both directly and indirectly by regulating BG, AP, and MBC, in which MBC acquisition was regulated more by AP. The amount of NFC was lower in Hailun soil than in Gongzhuling soil and was directly affected by AP, indicating the importance of soil properties such as SOC and pH in determining NFC. Overall, our results reveal the response of NFC to supplementation by N, P, and S, which depends on Acidobacteria and Proteobacteria, and their investment in BG and AP in residue-amended soil.
Neuropathic pain (NP) takes a heavy toll on individual life quality, yet gaps in its molecular characterization persist and effective therapy is lacking. This study aimed to provide comprehensive ...knowledge by combining transcriptomic and proteomic data of molecular correlates of NP in the anterior cingulate cortex (ACC), a cortical hub responsible for affective pain processing.
The NP model was established by spared nerve injury (SNI) in Sprague-Dawley rats. RNA sequencing and proteomic data from the ACC tissue isolated from sham and SNI rats 2 weeks after surgery were integrated to compare their gene and protein expression profiles. Bioinformatic analyses were performed to figure out the functions and signaling pathways of the differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) enriched in.
Transcriptomic analysis identified a total of 788 DEGs (with 49 genes upregulated) after SNI surgery, while proteomic analysis found 222 DEPs (with 89 proteins upregulated). While Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses of the DEGs suggested that most of the altered genes were involved in synaptic transmission and plasticity, bioinformatics analysis of the DEPs revealed novel critical pathways associated with autophagy, mitophagy, and peroxisome. Notably, we noticed functionally important NP-related changes in the protein that occurred in the absence of corresponding changes at the level of transcription. Venn diagram analysis of the transcriptomic and proteomic data identified 10 overlapping targets, among which only three genes (XK-related protein 4, NIPA-like domain-containing 3, and homeodomain-interacting protein kinase 3) showed concordance in the directions of change and strong correlations between mRNA and protein levels.
The present study identified novel pathways in the ACC in addition to confirming previously reported mechanisms for NP etiology, and provided novel mechanistic insights for future research on NP treatment. These findings also imply that mRNA profiling alone fails to provide a complete landscape of molecular pain in the ACC. Therefore, explorations of changes at the level of protein are necessary to understand NP processes that are not transcriptionally modulated.
Metastasis remains one of the major challenges before hepatocellular carcinoma (HCC) is finally conquered. This paper summarized a decade's studies on HCC metastasis at the Liver Cancer Institute of ...Fudan University. We have established a stepwise metastatic human HCC model system, which included a metastatic HCC model in nude mice (LCI-D20), a HCC cell line with high metastatic potential (MHCC97), a relatively low metastatic potential cell clone (MHCC97L) and several stepwise high metastatic potential cell clones (MHCC97H, HCCLM3, and HCCLM6) from their parent MHCC97 cell. Endeavors have been made for searching human HCC metastasis-related chromosomes/proteins/genes. Monogene-based studies revealed that HCC invasion/metastasis was similar to that of other solid tumors, and the biological characteristics of small HCC were only slightly better than that of large HCC. Using comparative genomic hybridization (CGH), fluorescence in situ hybridization (FISH), genotyping, cDNA microarray, and 2-dimensional gel electrophoresis, we obtained some interesting results. In particular, in collaboration with the National Institute of Health (NIH) in the United States, we generated a molecular signature that can classify metastatic HCC patients, identified osteopontin as a lead gene in the signature, and found that genes favoring metastasis progression were initiated in the primary tumors. We also found that chromosome 8p deletion, particularly in the region of 8p23, was associated with HCC metastasis. Cytokeratin 19 was identified as one of the proteins, which was found in MHCC97H, but not in MHCC97L cells. Experimental interventions using the high metastatic nude mice model have provided clues for the prevention of HCC metastasis. Translation from workbench to bedside demonstrated that serum VEGF, microvessel density, and p53 scoring may be of value for the prediction of postoperative metastatic recurrence. Interferon alpha proved effective for the prevention of recurrence both experimentally and clinically. In conclusion, HCC metastasis that probably initiated in the primary tumor is a multigene-involved, multistep, and changing process. The further elucidation of the mechanism underlying HCC metastasis will provide a more solid basis for the prediction and prevention of the metastatic recurrence of HCC.
Sixty-one SARS coronavirus genomic sequences derived from the early, middle, and late phases of the severe acute respiratory syndrome (SARS) epidemic were analyzed together with two viral sequences ...from palm civets. Genotypes characteristic of each phase were discovered, and the earliest genotypes were similar to the animal SARS-like coronaviruses. Major deletions were observed in the Orf8 region of the genome, both at the start and the end of the epidemic. The neutral mutation rate of the viral genome was constant but the amino acid substitution rate of the coding sequences slowed during the course of the epidemic. The spike protein showed the strongest initial responses to positive selection pressures, followed by subsequent purifying selection and eventual stabilization.
Schistosoma japonicum causes schistosomiasis in humans and livestock in the Asia-Pacific region. Knowledge of the genome of this parasite should improve understanding of schistosome-host ...interactions, biomedical aspects of schistosomiasis and invertebrate evolution. We assigned 43,707 expressed sequence tags (ESTs) derived from adult S. japonicum and their eggs to 13,131 gene clusters. Of these, 35% shared no similarity with known genes and 75% had not been reported previously in schistosomes. Notably, S. japonicum encoded mammalian-like receptors for insulin, progesterone, cytokines and neuropeptides, suggesting that host hormones, or endogenous parasite homologs, could orchestrate schistosome development and maturation and that schistosomes modulate anti-parasite immune responses through inhibitors, molecular mimicry and other evasion strategies.
Abstract
The LHAASO-WFCTA experiment, which aims to observe cosmic rays in the sub-EeV range using the fluorescence technique, uses a new generation of high-performance telescopes. To ensure that the ...experiment has excellent detection capability associated with the measurement of the energy spectrum, the primary composition of cosmic rays, and so on, an accurate geometrical reconstruction of air-shower events is fundamental. This paper describes the development and testing of geometrical reconstruction for stereo viewed events using the WFCTA (Wide Field of view Cherenkov/Fluorescence Telescope Array) detectors. Two approaches, which take full advantage of the WFCTA detectors, are investigated. One is the stereo-angular method, which uses the pointing of triggered SiPMs in the shower trajectory, and the other is the stereo-timing method, which uses the triggering time of the fired SiPMs. The results show that both methods have good geometrical resolution; the resolution of the stereo-timing method is slightly better than the stereo-angular method because the resolution of the latter is slightly limited by the shower track length.
Summary
The Arabidopsis NPR1/NIM1 gene is a key regulator of systemic acquired resistance (SAR). Over‐expression of NPR1 leads to enhanced resistance in Arabidopsis. To investigate the role of NPR1 ...in monocots, we over‐expressed the Arabidopsis NPR1 in rice and challenged the transgenic plants with Xanthomonas oryzae pv. oryzae (Xoo), the rice bacterial blight pathogen. The transgenic plants displayed enhanced resistance to Xoo. RNA blot hybridization indicates that enhanced resistance requires expression of NPR1 mRNA above a threshold level in rice. To identify components mediating the resistance controlled by NPR1, we used NPR1 as bait in a yeast two‐hybrid screen. We isolated four cDNA clones encoding rice NPR1 interactors (named rTGA2.1, rTGA2.2, rTGA2.3 and rLG2) belonging to the bZIP family. rTGA2.1, rTGA2.2 and rTGA2.3 share 75, 76 and 78% identity with Arabidopsis TGA2, respectively. In contrast, rLG2 shares highest identity (81%) to the maize liguleless (LG2) gene product, which is involved in establishing the leaf blade–sheath boundary. The interaction of NPR1 with the rice bZIP proteins in yeast was impaired by the npr1‐1 and npr1‐2 mutations, but not by the nim1‐4 mutation. The NPR1–rTGA2.1 interaction was confirmed by an in vitro pull‐down experiment. In gel mobility shift assays, rTGA2.1 binds to the rice RCH10 promoter and to a cis‐element required sequence‐specifically for salicylic acid responsiveness. This is the first demonstration that the Arabidopsis NPR1 gene can enhance disease resistance in a monocot plant. These results also suggest that monocot and dicot plants share a conserved signal transduction pathway controlling NPR1‐mediated resistance.
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