Characterizing the pathogenicity and mycotoxin production capacity of Fusarium spp. causing root rot of Angelica sinensis in China.

Root rot is a very destructive soil-borne disease, which severely affects the quality and yield of Angelica sinensis in major planting areas of Gansu Province, China. Twelve Fusarium strains were identified from root rot tissue and infected soil in the field, by comparing each isolate strain internal transcriptional spacer, translation elongation factor 1-α sequence and RNA polymerase second largest subunit gene (RPB2) with the sequences of known fungal species in the NCBI database. Of these isolates, four were F. acuminatum, followed by three F. solani, two F. oxysporum, and one each of F. equiseti, F. redolens, and F. avenaceum. Under greenhouse conditions, pathogenicity testing experiment was carried out using five strains: two F. acuminatum, one F. solani, one F. oxysporum, and one F. equiseti. Among them, the incidence of F. acuminatum-induced root rot on A. sinensis was 100%; hence, it was the most aggressive. Liquid chromatography was used to show that F. acuminatum was capable of producing neosolaniol (NEO), deoxynivalenol (DON), and T-2 toxins. Of these, the level of NEO produced by F. acuminatum was high, compared with the other two toxins. By isolating Fusarium spp. and characterizing their toxin-producing capacity, this work provides a new information for effectively preventing and controlling A. sinensis root rot in the field, as well as improving the quality of its medicinal materials. Keywords: Angelica sinensis, Fusarium spp., mycotoxins, pathogenicity tests, root rot disease.

Ln3+ Induced Thermally Activated Delayed Fluorescence of Chiral Heterometallic Clusters Ln2Ag28.

A series of TADF-active compounds: 0D chiral Ln-Ag(I) clusters L-/D-Ln2Ag28-0D (Ln = Eu/Gd) and 2D chiral Ln-Ag(I) cluster-based frameworks L-/D-Ln2Ag28-2D (Ln = Gd) has been synthesized. Atomic-level structural analysis showed that the chiral Ag(I) cluster units {Ag14S12} in L-/D-Ln2Ag28-0D and L-/D-Ln2Ag28-2D exhibited similar configurations, linked by varying numbers of [Ln(H2O)x]3+ (x = 6 for 0D, x = 3 for 2D) to form the final target compounds. Temperature-dependent emission spectra and decay lifetimes measurement demonstrated the presence of TADF in L-Ln2Ag28-0D (Ln = Eu/Gd) and L-Gd2Ag28-2D. Experimentally, the remarkable TADF properties primarily originated from {Ag14S12} moieties in these compounds. Notably, {Ag14S12} in L-Eu2Ag28-0D and L-Gd2Ag28-2D displayed higher promote fluorescence rate and shorter TADF decay times than L-Gd2Ag28-0D. Combined with theoretical calculations, it was determined that the TADF behaviors of {Ag14S12} cluster units were induced by 4f perturbation of Ln3+ ions. Specially, while maintaining ΔE(S1-T1) small enough, it can significantly increase k(S1→S0) and reduce TADF decay time by adjusting the type or number of Ln3+ ions, thus achieving the purpose of improving TADF for cluster-based luminescent materials.

Theoretical Kinetic Study on Hydrogen Abstraction Reactions from n-Pentane by NO2.

The interaction of fuel with NOx chemistry is important for the construction of the reaction mechanism and engine application. In this work, the reaction pathways of nC5H12 + NO2 were studied by high-level electronic structure calculations (DLPNO-CCSD(T)-F12/cc-pVTZ-F12//B2PLYPD3/cc-pVTZ). The rate constants were calculated by using the multistructural canonical transition-state theory with the Eckart tunneling method (TST/MS-T/ET). The studied condition is in a wide temperature range of 298-2400 K. The influence of MS-T anharmonicity and tunneling effect will be clarified for these site-specific H-abstraction pathways. The result reflects the large deviation introduced by the treatment of MS-T anharmonicity, especially at a high temperature. For the same type of reactions, the rate constants of H-abstraction both occurring at the secondary carbon are not almost identical. The branching ratios show that abstraction from the secondary site forming cis-HONO (R2c) contributes 36-78% to nC5H12 consumption in the temperature range of 298-2400 K. The current results show that the multistructural torsional anharmonicity has a crucial influence on the accurate estimation of branching ratios.

Functional Characterization of a Novel SLC4A4 Variant and Uniparental Isodisomy in Proximal Renal Tubular Acidosis Patient.

SLC4A4 variants are the etiologies of inherited proximal renal tubular acidosis (pRTA), which results in metabolic acidosis, hypokalemia, glaucoma, band keratopathy, and cataract. This study aims to characterize SLC4A4 variant and uniparental isodisomy of chromosome 4 in a patient, and analyse the functional characterization of SLC4A4 variants. This study analyzed renal tubular acidosis disease genes by whole exome sequencing (WES). H3M2 algorithm was used to analyze the run of homozygosity region in chromosomal regions in trio-WES data. The pathogenicity analysis of variants was performed using bioinformatics tools. Additionally, protein stability was analyzed by cycloheximide chase assay. Whole-cell patch clamping was used to examine the electrophysiological properties of NBCe1-A. A novel homozygous SLC4A4 variant was identified in the patient: a missense variant c.496C > T, p. Arg166Trp (NM_003759.4). But the father was heterozygous variant carrier, and the mother did not detect the variant. The H3M2 and UPDio algorithm revealed paternal uniparental isodisomy on chromosome 4 in the patient. SIFT, Poly Phen-2, FATHMM and Mutant Taster showed that the variant might be pathogenic. The tertiary structure analysis showed that the variant could cause structural damage to NBCe1 protein. Foldx results showed that the protein stability of the variant was slightly reduced. Cycloheximide chase assay demonstrated that the variant affects protein stability. The result of electrophysiological studies showed that the variant altered Na+/HCO3- cotransport activity of protein. In conclusion, the study is the first to report a pRTA patient with Arg166Trp variant with UPiD (4) pat and analyze the function of Arg166Trp variant.

First Report of Powdery Mildew Caused by Erysiphe cruciferarum on Orychophragmus violaceus in China.

Orychophragmus violaceus is an annual or perennial herb in the Brassicaceae family. It is widely planted in China and used as an ornamental and green manure plant (Luo et al. 2022). In September 2022, a survey conducted in a 600 m2 garden in Lanzhou (36°06'N, 103°43'E) found that over 70% of O. violaceus plants were infected with powdery mildew, with 80% of the leaf area on the upper surface of infected leaves was infected. The white colonies on the upper surface of the leaves gradually expanded, thickened, and spread to cover the stem surface. In severe cases, entire foliage withered and the plants died. Fungal structures were taken from the leaves with adhesive tape and placed in sterile water for microscopic observation. The conidiophores were upright, cylindrical, composed of 3 to 4 cells, and measured 92.3 ± 12.9 × 9.2 ± 0.6 µm (n=30). Conidial pedicels had 21.6 ± 3.4 µm (n=50) long cylindrical podocytes. Monoconidia were cylindrical or oval in shape, 32.9 ± 6.1 µm long and 15.1 ± 2.1 µm wide (n=80). Conidia lacked an obvious cellulose body. The bud tubes formed from the end of conidia, and papillary appressoria developed on the epiphytic mycelia. Based on these morphological characteristics, the pathogen was initially identified as Erysiphe cruciferarum (Braun et al. 2012). To validate the identity, the internal transcribed spacer (ITS) region of an isolate EYL was amplified by PCR and sequenced using both ITS1/ITS4 and ITS5/PM6 primers (Takamatsu et al. 2001). The resulting sequences were deposited at GenBank (accession nos: OR437967 and OR437969). The ITS sequence of the isolate EYL (OR437967) is 99% (451/453) identical to E. cruciferarum (KP730001) on Brassica napus in China and that of the isolate EYL (OR437969) is 100% (509/509) identical to E. cruciferarum (KM260718) on B. juncea in Vietnam. Pathogenicity experiments were performed on six-week-old plants with an average of 10 ± 0.8 leaves. In the inoculated group, five healthy plants were inoculated by gently pressing the upper surface of diseased leaves against the upper surface of leaves of healthy plants for about 5 to 10 seconds. In the control group, the leaves of five healthy plants were treated with asymptomatic using the same method as described above. The plants were maintained in a greenhouse set at 25℃, 14-h photoperiod, and ≥ 70% humidity. After 13 days, all inoculated plants showed symptoms of powdery mildew, while the plants in the control group had no symptoms. The fungus on the inoculated plant was re-isolated and identified as E. cruciferarum based on its morphological characteristics and ITS sequence. Powdery mildew caused by E. cruciferarum has been reported on Cleome hassleriana in Italy and B. juncea in Australia (Garibaldi et al. 2009; Kaur et al. 2008). To our knowledge, this is the first time that powdery mildew caused by E. cruciferarum have been reported on O. violaceus in China. This disease poses a potential threat to the quality and yield of O. violaceus plants, which may warrant the development of preventative and management strategies in the future.

First Report of Powdery Mildew Caused by Erysiphe cruciferarum on Centella asiatica in China.

Centella asiatica belongs to the Umbelliferae family of perennial herbaceous plants, which are grown worldwide for use as health supplements, edible vegetables and traditional herbs, and are of vital medicinal and edible value in China. (Biswas et al. 2021). In October 2022, the investigation in the 800 m2 garden of Lanzhou (36°06' N,103°43' E) found that more than 80% of C. asiatica plants were infected by powdery mildew, and the leaf infection rate was 90%. The disease severely affects the actual value of C. asiatica. At the beginning of the disease, thin, radial, irregular white colonies appear on the leaves and gradually spread to the stems. The white colony then expands and thickens, covering the upper surface of the whole leaf, and gradually spreading to the lower parts of the stem and leaf. In severe cases, the leaves wither and die. A small portion of fungal spores was glued from the leaf surface with adhesive tape and placed in sterile water for microscopic examination (Zhang et al. 2022). The conidiophore is upright, cylindrical, composed of 3-4 cells, and its size is 72 to 110 × 8 to 10 µm. Conidial pedicels have 16 to 26 µm long cylindrical podocytes. Monoconidia are cylindrical or oval in shape, 16 to 37 µm long, width 11 to 18 µm (n=80). Conidia lack an obvious cellulose body. The bud tube is formed from the end of conidia, and papillary appressorium develops on the epiphytic mycelia. Based on these morphological characteristics, the pathogen was initially identified as Erysiphe cruciferarum (Braun et al. 2012). To validate the identity, the internal transcribed spacer (ITS) of the pathogen (JXC) rDNA was amplified by PCR and sequenced with PM6/ITS5 and PM5/ITS4 primers (Takamatsu et al. 2001). The resulting sequences were registered to GenBank (GenBank Accession OP935627 and OQ253404). At the same time, the ITS sequence size was 535 bp and 521 bp respectively. The ITS sequence of the JXC was 99% (527/534) identical to E.cruciferarum (KT588635) on Eschscholzia californica in Slovakia and 99% (527/534) identical to E.cruciferarum (KC878683) on Chinese Cabbage in China. The ITS sequences from GenBank were subjected to conduct maximum likelihood phylogenetic analysis by MEGA 7.0. The data indicate that strain JXC and E. cruciferarum are clustered on the same branch. The pathogenicity test was performed according to Koch's postulate. By gently pressing the infected leaves on five healthy potted C. asiatica. Meanwhile, five uninoculated plants were used as controls (Zhang et al. 2022). The plants were put into a greenhouse culture (25℃, 14 h light, 10 h dark, humidity ≥ 70%). After 12 days, the inoculated plants showed symptoms of powdery mildew, while the control group had no symptoms. The fungus on the inoculated plant was re-isolated, and identified as E. cruciferarum based on morphological observations and molecular identification. The powdery mildew caused by E.cruciferarum has been reported on Indian mustard in Korea and Chinese cabbage in China, respectively (Kim et al. 2009; Zhao et al. 2014). To our knowledge, this is the first report of C. asiatica powdery mildew caused by E.cruciferarum in China. This finding poses a potential threat to the quality and yield of C. asiatica plants, while providing a preventive basis for the cultivation of C. asiatica.

Preliminary study on dosimetry characteristics of a novel cylindrical dose verification system.

OBJECTIVE: To develop a novel ionization chamber array dosimetry system, study its dosimetry characteristics, and perform preliminary tests for plan dose verification. METHODS: The dosimetry characteristics of this new array were tested, including short-term and long-term reproducibility, dose linearity, dose rate dependence, field size dependence, and angular dependence. The open field and MLC field plans were designed for dose testing. Randomly select 30 patient treatment plans (10 intensity-modulated radiation therapy [IMRT] plans and 20 volumetric modulated arc therapy [VMAT] plans) that have undergone dose verification using Portal Dosimetry to perform verification measurement and evaluate dose verification test results. RESULTS: The dosimetry characteristics of the arrays all performed well. The gamma passing rates (3%/2 mm) were more than 96% for the combined open field and MLC field plans. The average gamma pass rates were (99.54 ± 0.58)% and (96.70 ± 3.41)% for the 10 IMRT plans and (99.32 ± 0.89)% and (94.91 ± 6.01)% for the 20 VMAT plans at the 3%/2 mm and 2%/2 mm criteria, respectively, which is similar to the Portal Dosimetry's measurement results. CONCLUSIONS: This novel ionization chamber array demonstrates good dosimetry characteristics and is suitable for clinical IMRT and VMAT plan verifications.

An Unsupervised Learning-Based Regional Deformable Model for Automated Multi-Organ Contour Propagation.

The aim of this study is to evaluate a regional deformable model based on a deep unsupervised learning model for automatic contour propagation in breast cone-beam computed tomography-guided adaptive radiation therapy. A deep unsupervised learning model was introduced to map breast's tumor bed, clinical target volume, heart, left lung, right lung, and spinal cord from planning computed tomography to cone-beam CT. To improve the traditional image registration method's performance, we used a regional deformable framework based on the narrow-band mapping, which can mitigate the effect of the image artifacts on the cone-beam CT. We retrospectively selected 373 anonymized cone-beam CT volumes from 111 patients with breast cancer. The cone-beam CTs are divided into three sets. 311 / 20 / 42 cone-beam CT images were used for training, validating, and testing. The manual contour was used as reference for the testing set. We compared the results between the reference and the model prediction for evaluating the performance. The mean Dice between manual reference segmentations and the model predicted segmentations for breast tumor bed, clinical target volume, heart, left lung, right lung, and spinal cord were 0.78 ± 0.09, 0.90 ± 0.03, 0.88 ± 0.04, 0.94 ± 0.03, 0.95 ± 0.02, and 0.77 ± 0.07, respectively. The results demonstrated a good agreement between the reference and the proposed contours. The proposed deep learning-based regional deformable model technique can automatically propagate contours for breast cancer adaptive radiotherapy. Deep learning in contour propagation was promising, but further investigation was warranted.

Applications of artificial intelligence (AI) in researches on non-alcoholic fatty liver disease(NAFLD) : A systematic review.

Non-alcoholic fatty liver disease (NAFLD) is one of the most important causes of chronic liver disease in the world, it has been found that cardiovascular and renal risks and diseases are also highly prevalent in adults with NAFLD. Diagnosis and treatment of NAFLD face many challenges, although the medical science has been very developed. Efficiency, accuracy and individualization are the main goals to be solved. Evaluation of the severity of NAFLD involves a variety of clinical parameters, how to optimize non-invasive evaluation methods is a necessary issue that needs to be discussed in this field. Artificial intelligence (AI) has become increasingly widespread in healthcare applications, and it has been also brought many new insights into better analyzing chronic liver disease, including NAFLD. This paper reviewed AI related researches in NAFLD field published recently, summarized diagnostic models based on electronic health record and lab test, ultrasound and radio imaging, and liver histopathological data, described the application of therapeutic models in personalized lifestyle guidance and the development of drugs for NAFLD. In addition, we also analyzed present AI models in distinguishing healthy VS NAFLD/NASH, and fibrosis VS non-fibrosis in the evaluation of NAFLD progression. We hope to provide alternative directions for the future research.

Atom-Precise Chiral Lanthanide-Silver(I) Heterometallic Clusters Ln3Ag5.

Three pairs of chiral Ln-Ag(I) clusters d/l-Ln3Ag5 with C3 symmetry were prepared by d/l-penicillamine as multidentate ligand bridged Ln3+ and Ag(I) ions. The chiral ligand induced the molecular cluster to be chiral, and the CD spectra of the chiral compounds d/l-Ln3Ag5 were slightly blue-shifted due to the lanthanide contraction. The studies of optical properties indicated that tunable photoluminescence from {AgS}-to-Ln3+ was achieved by introducing Ln3+ ions with different emission bands or regulating various excitation light.

Family of Nanoclusters, Ln33 (Ln = Sm/Eu) and Gd32, Exhibiting Magnetocaloric Effects and Fluorescence Sensing for MnO4.

A family of nanoclusters, [Ln33(EDTA)12(OAc)2(CO3)4(µ3-OH)36(µ5-OH)4(H2O)38]·OAc·xH2O (x ≈ 50, Ln = Sm for 1; x ≈ 70, Ln = Eu for 2) and [Gd32(EDTA)12(OAc)2(C2O4)(CO3)2(µ3-OH)36(µ5-OH)4(H2O)36]·x(H2O) (x ≈ 70 for 3; H4EDTA = ethylene diamine tetraacetic acid), was prepared through the assembly of repeating subunits under the action of an anion template. The analysis of the structures showed that compounds 1 and 2 containing 33 Ln3+ ions were isostructural, which were constructed by three kinds of subunits in the presence of CO32- as an anion template, while compound 3 had a slightly different structure. Compound 3 containing 32 Gd3+ ions was formed by three types of subunits in the presence of CO32- and C2O42- as a mixed anion template. The CO32- anions came from the slow fixation of CO2 in the air. Meanwhile, one kind of high-nuclearity lanthanide clusters showed high chemical stability. The quantum Monte Carlo (QMC) calculation suggested that weak antiferromagnetic interactions were dominant between Gd3+ ions in 3. Magnetocaloric studies showed that compound 3 had a large entropy change of 43.0 J kg-1 K-1 at 2 K and 7 T. Surprisingly, compound 2 showed excellent recognition and detection effects for permanganate in aqueous solvents based on the fluorescence quenching phenomenon.

[Analysis of a child with severe combined immunodeficiency due to variants of DCLRE1C gene].

OBJECTIVE: To explore the genetic etiology of a child with severe combined immunodeficiency (SCID). METHODS: Whole exome sequencing (WES) and copy number variation (CNV) analysis were carried out to screen potential variants in the proband. Suspected variants were validated by Sanger sequencing and qPCR. RESULTS: WES showed that the proband harbored compound heterozygous variants of the DCLRE1C gene, namely deletion of exons 1-3 and c.322G>A (p.Val108Met) in exon 5. The exon 1-3 deletion was derived from his father and was known to be pathogenic, while the c.322G>A was derived from his mother and was unreported previously. CONCLUSION: The compound heterozygous variants of the DCLRE1C gene probably underlay the SCID in this child.

[Analysis of gene variant in an infant with succinic semialdehyde dehydrogenase deficiency].

OBJECTIVE: To explore the genetic basis for a child with succinate semialdehyde dehydrogenase deficiency. METHODS: Peripheral blood samples of the proband and his parents were collected and subjected to Sanger sequencing. High-throughput sequencing was used to verify the gene variants. Bioinformatic software was used to analyze the pathogenicity of the variant sites. RESULTS: Sanger sequencing showed that the proband carried a homozygous c.1529C>T (p.S510F) variant of the ALDH5A1 gene, for which his mother was a carrier. The same variant was not detected in his father. However, high-throughput sequencing revealed that the child and his father both had a deletion of ALDH5A1 gene fragment (chr6: 24 403 265-24 566 986). CONCLUSION: The c.1529C>T variant of the ALDH5A1 gene and deletion of ALDH5A1 gene fragment probably underlay the disease in the child. High-throughput sequencing can detect site variation as well as deletion of gene fragment, which has enabled genetic diagnosis and counseling for the family.

[Genetic analysis of 46,XY disorders of sex development in children caused by a new NR5A1 gene variant].

OBJECTIVE: To explore the genetic basis for a child with 46,XY disorders of sex development (DSD) and explore its genotype-phenotype correlation. METHODS: The child was subjected to whole exome sequencing (WES), and exons 1 to 7 of NR5A1 were subjected to multiplex ligation-dependent probe amplification (MLPA) analysis. RESULTS: The patient presented with rudimentary vulva of a female with Tanner stage 1. B-mode ultrasonography has detected ovary and uterus. The child was found to have a chromosome karyotype of 46,XY. WES revealed that the patient has harbored heterozygous deletion of exon 5 of the NR5A1 gene, which was a novel pathogenic variant inherited from the mother. No abnormality was found in the father. CONCLUSION: The main symptoms of 46,XY DSD children are insufficient external genitalia masculinization, for which variants of the NR5A1 gene are an important cause. WES has improved the detection rate of genetic variants and provided a solid basis for genetic counseling of the affected families.

[Analysis of gene variant in a Chinese child affected with dihydropyrimidinase deficiency].

OBJECTIVE: To analyze the molecular etiology of a Chinese child affected with dihydropyrimidinase deficiency. METHODS: Genomic DNA was extracted from peripheral blood samples of the family members. Pathogenic variant was determined by whole exome sequencing and verified by Sanger sequencing. RESULTS: The child was found to harbor homozygous c.905G>A (p.Arg302Gln) variants in exon 5 of the DPYS gene, for which her parents were both heterozygous carriers. CONCLUSION: The homozygous c.905G>A (p.Arg302Gln) variants of the DPYS gene probably underlies the dihydropyrimidinase deficiency in the child. Above result has enabled genetic counseling and prenatal diagnosis for this family.

LncRNA HULC promotes lung squamous cell carcinoma by regulating PTPRO via NF-κB.

Accumulating studies have implicated that long noncoding RNA (lncRNA) plays a vital role in lung cancer. However, little is known of the role of lncRNA highly upregulated in liver cancer (HULC) in the pathogenesis of lung squamous cell carcinoma (LSCC). In this study, we investigated the modifying effects and underlying mechanisms of lncRNA HULC in LSCC. Significantly decreased level of lncRNA HULC was observed in LSCC samples compared with adjacent tissues. Besides, the expression of lncRNA HULC was negatively associated with protein tyrosine phosphatase receptor type O (PTPRO) in LSCC. Moreover, lncRNA HULC could promote the proliferation of LSCC cells by downregulating the expression PTPRO dependent on the phosphorylation and activation of nuclear factor-κB (NF-κB). The present study firstly shows strong evidence supporting a critical role of lncRNA HULC in promoting LSCC by regulating PTPRO/NF-κB signaling pathway, which provides new promising biomarkers for LSCC.

Relative Rates of Hydrogen Shift Isomerizations Depend Strongly on Multiple-Structure Anharmonicity.

Hydroperoxyalkylperoxy species (OOQOOH) are important intermediates that are generated during the autoignition of transport fuels. A key reaction of hydroperoxyalkylperoxy radicals is a [1,5] hydrogen shift, for which kinetics data are experimentally unavailable. Here we study two typical OOQOOH reactions and compare their kinetics to one another and to a previous study to learn the effect of structural variations of the alkyl group on the competition between alternative [1,5] hydrogen shifts of hydroperoxyalkylperoxy species. We use electronic structure calculations to determine previously missing thermochemical data, and we use variational transition state theory with multidimensional tunneling, multiple structures, torsional potential anharmonicity, and high-frequency anharmonicity to obtain more accurate rate constants than the ones that can be computed by conventional single-structure harmonic transition state theory and than the empirically estimated rate constants that are currently used in combustion modeling. The calculated temperature range is 298-1500 K. The roles of various factors in determining the rates are elucidated, and we find an especially strong effect of multiple structure anharmonicity due to torsions. Thus, even though there is some cancellation between the anharmonicity of the reactant and the anharmonicity of the transition state, and even though the reactants are very similar in structure, differing only by a methyl group, the effect of multiple structure anharmonicity has a large effect on the relative rates, as large as a factor of 17 at room temperature and as large as a factor of 7 at 1500 K. This has broad implications for the estimation of reaction rates in many subfields of chemistry, including combustion chemistry and atmospheric chemistry, where rates of reaction of complex molecules are usually estimated without explicit consideration of this fundamental entropic effect. In addition, the pressure-dependence of the rate constants is modeled by system-specific quantum Rice-Ramsperger-Kassel theory for a reversible isomerization.

Baicalin promotes apoptosis and inhibits proliferation and migration of hypoxia-induced pulmonary artery smooth muscle cells by up-regulating A2a receptor via the SDF-1/CXCR4 signaling pathway.

BACKGROUND: Baicalin is a flavonoid compound that exerts specific pharmacological effect in attenuating the proliferation, migration, and apoptotic resistance of hypoxia-induced pulmonary artery smooth muscle cells (PASMCs). However, the underlying mechanism has not been fully elucidated yet. Although our previous studies had indicated that activation of A2aR attenuates CXCR expression, little is known about the relationship between A2aR and SDF-1/CXCR4 axis in hypoxic PASMCs. In this study, we aimed to investigate the effect of A2aR on the SDF-1/CXCR4 axis in hypoxic PASMCs, the mechanism underlying this effect, and whether baicalin exerts its protective functions though A2aR. METHODS: Rat PASMCs were cultured under normoxia/hypoxia and divided into nine groups: normoxia, hypoxia, hypoxia + AMD3100 (a CXCR4 antagonist), hypoxia + baicalin, hypoxia + negative virus, normoxia + A2aR knockdown, hypoxia + A2aR knockdown, hypoxia + CGS21680 (an A2aR agonist), and hypoxia + A2aR knockdown + baicalin. Lentiviral transfection methods were used to establish the A2aR knockdown model in PASMCs. Cells were incubated under hypoxic conditions for 24 h. Expression levels of A2aR, SDF-1, and CXCR4 were detected using RT-qPCR and western blot. The proliferation and migration rate were observed via CCK-8 and Transwell methods. Cell cycle distribution and cell apoptosis were measured by flow cytometry (FCM) and the In-Situ Cell Death Detection kit (Fluorescein). RESULTS: Under hypoxic conditions, levels of A2aR, SDF-1, and CXCR4 were significantly increased compared to those under normoxia. The trend of SDF-1 and CXCR4 being inhibited when A2aR is up-regulated was more obvious in the baicalin intervention group. Baicalin directly enhanced A2aR expression, and A2aR knockdown weakened the function of baicalin. SDF-1 and CXCR4 expression levels were increased in the hypoxia + A2aR knockdown group, as were the proliferation and migration rates of PASMCs, while the apoptotic rate was decreased. Baicalin and CGS21680 showed opposite effects. CONCLUSIONS: Our data indicate that baicalin efficiently attenuates hypoxia-induced PASMC proliferation, migration, and apoptotic resistance, as well as SDF-1 secretion, by up-regulating A2aR and down-regulating the SDF-1/CXCR4 axis.

Condensing Raman spectrum for single-cell phenotype analysis.

BACKGROUND: In recent years, high throughput and non-invasive Raman spectrometry technique has matured as an effective approach to identification of individual cells by species, even in complex, mixed populations. Raman profiling is an appealing optical microscopic method to achieve this. To fully utilize Raman proling for single-cell analysis, an extensive understanding of Raman spectra is necessary to answer questions such as which filtering methodologies are effective for pre-processing of Raman spectra, what strains can be distinguished by Raman spectra, and what features serve best as Raman-based biomarkers for single-cells, etc. RESULTS: In this work, we have proposed an approach called rDisc to discretize the original Raman spectrum into only a few (usually less than 20) representative peaks (Raman shifts). The approach has advantages in removing noises, and condensing the original spectrum. In particular, effective signal processing procedures were designed to eliminate noise, utilising wavelet transform denoising, baseline correction, and signal normalization. In the discretizing process, representative peaks were selected to signicantly decrease the Raman data size. More importantly, the selected peaks are chosen as suitable to serve as key biological markers to differentiate species and other cellular features. Additionally, the classication performance of discretized spectra was found to be comparable to full spectrum having more than 1000 Raman shifts. Overall, the discretized spectrum needs about 5storage space of a full spectrum and the processing speed is considerably faster. This makes rDisc clearly superior to other methods for single-cell classication.

GPU-Meta-Storms: computing the structure similarities among massive amount of microbial community samples using GPU.

MOTIVATION: The number of microbial community samples is increasing with exponential speed. Data-mining among microbial community samples could facilitate the discovery of valuable biological information that is still hidden in the massive data. However, current methods for the comparison among microbial communities are limited by their ability to process large amount of samples each with complex community structure. SUMMARY: We have developed an optimized GPU-based software, GPU-Meta-Storms, to efficiently measure the quantitative phylogenetic similarity among massive amount of microbial community samples. Our results have shown that GPU-Meta-Storms would be able to compute the pair-wise similarity scores for 10 240 samples within 20 min, which gained a speed-up of >17 000 times compared with single-core CPU, and >2600 times compared with 16-core CPU. Therefore, the high-performance of GPU-Meta-Storms could facilitate in-depth data mining among massive microbial community samples, and make the real-time analysis and monitoring of temporal or conditional changes for microbial communities possible. AVAILABILITY AND IMPLEMENTATION: GPU-Meta-Storms is implemented by CUDA (Compute Unified Device Architecture) and C++. Source code is available at http://www.computationalbioenergy.org/meta-storms.html.