Machine learning algorithm as a prognostic tool for Epstein-Barr virus reactivation after haploidentical hematopoietic stem cell transplantation.

Epstein-Barr virus (EBV) reactivation is one of the most important infections after hematopoietic stem cell transplantation (HSCT) using haplo-identical related donors (HID). We aimed to establish a comprehensive model with machine learning, which could predict EBV reactivation after HID HSCT with anti-thymocyte globulin (ATG) for graft-versus-host disease (GVHD) prophylaxis. We enrolled 470 consecutive acute leukemia patients, 60% of them (n = 282) randomly selected as a training cohort, the remaining 40% (n = 188) as a validation cohort. The equation was as follows: Probability (EBV reactivation) =   1 1       +       e x p ( - Y ) , where Y = 0.0250 × (age) - 0.3614 × (gender) + 0.0668 × (underlying disease) - 0.6297 × (disease status before HSCT) - 0.0726 × (disease risk index) - 0.0118 × (hematopoietic cell transplantation-specific comorbidity index [HCT-CI] score) + 1.2037 × (human leukocyte antigen disparity) + 0.5347 × (EBV serostatus) + 0.1605 × (conditioning regimen) - 0.2270 × (donor/recipient gender matched) + 0.2304 × (donor/recipient relation) - 0.0170 × (mononuclear cell counts in graft) + 0.0395 × (CD34+ cell count in graft) - 2.4510. The threshold of probability was 0.4623, which separated patients into low- and high-risk groups. The 1-year cumulative incidence of EBV reactivation in the low- and high-risk groups was 11.0% versus 24.5% (P < .001), 10.7% versus 19.3% (P = .046), and 11.4% versus 31.6% (P = .001), respectively, in total, training and validation cohorts. The model could also predict relapse and survival after HID HSCT. We established a comprehensive model that could predict EBV reactivation in HID HSCT recipients using ATG for GVHD prophylaxis.

Traceability of Geographic Origin Using Human Skin and Oral Microbiota.

OBJECTIVES: To explore the possibility of using human skin and oral microorganisms to estimate the geographic origin of an individual through the sequencing analysis of bacterial 16S rRNA gene. METHODS: Microbial DNA was extracted from the palm and oral microorganisms of the Han population in Shanghai and Chifeng, Inner Mongolia, and the composition and diversity of the microbiota were analyzed by full-length 16S rRNA gene sequencing. Then, differential species were screened and a geographic location prediction model was constructed. RESULTS: The compositions of palm and oral microorganisms between Shanghai and Chifeng samples were both different. The abundance and uniformity of palm side skin microorganisms were higher in Chifeng samples than in Shanghai samples, while there was no significant difference in oral microorganisms. Permutational multivariate analysis of variance (PERMANOVA) confirmed that the ß-diversity between the samples from the two places were statistically significant, and the coefficients of determination (R2) for skin and oral samples were 0.129 and 0.102, respectively. Through principal co-ordinates analysis (PCoA), the samples from the two places could be preliminarily distinguished. The predictive model had the accuracies of 0.90 and 0.83 for the geographic origin using the skin and oral samples, respectively. CONCLUSIONS: There are differences in the compositions of palm and oral microbiota between Han populations in Shanghai and Chifeng. The prediction model constructed by the random forest algorithm can trace the unknown individuals from the above two places.

Genetic Polymorphism of 16 X-STR Loci in Xinjiang Uygur Population.

OBJECTIVES: To study the genetic polymorphism and population genetic parameters of 16 X-STR loci in Xinjiang Uygur population. METHODS: The Goldeneye® DNA identification system 17X was used to amplify 16 X-STR loci in 502 unrelated individuals (251 females and 251 males). The amplified products were detected by 3130xl genetic analyzer. Allele frequencies and population genetic parameters were analyzed statistically. The genetic distances between Uygur and other 8 populations were calculated. Multidimensional scaling and phylogenetic tree were constructed based on genetic distance. RESULTS: In the 16 X-STR loci, a total of 67 alleles were detected in 502 Xinjiang Uygur unrelated individuals. The allele frequencies ranged from 0.001 3 to 0.572 4. PIC ranged from 0.568 8 to 0.855 3. The cumulative discrimination power in females and males were 0.999 999 999 999 999 and 0.999 999 999 743 071, respectively. The cumulative mean paternity exclusion chance in trios and in duos were 0.999 999 997 791 859 and 0.999 998 989 000 730, respectively. The genetic distance between Uygur population and Kazakh population was closer, and the genetic distance between Uygur and Han population was farther. CONCLUSIONS: The 16 X-STR loci are highly polymorphic and suitable for identification in Uygur population, which can provide a powerful supplement for the study of individual identification, paternity identification and population genetics.

Application Progress of Massively Parallel Sequencing Technology in STR Genetic Marker Detection.

In recent years, more and more forensic genetics laboratories have begun to apply massively parallel sequencing (MPS) technology, that is, next-generation sequencing (NGS) technology, to detect common forensic genetic markers, including short tandem repeat (STR), single nucleotide polymorphism (SNP), the control region or whole genome of mitochondrial DNA (mtDNA), as well as messenger RNA (mRNA), etc., for forensic practice, such as individual identification, kinship analysis, ancestry inference and body fluid identification. As the most widely used genetic marker in forensic genetics, STR is currently mainly detected by capillary electrophoresis (CE) platform. Compared with CE platform, MPS technology has the advantages of simultaneous detection of a large number of genetic markers, massively parallel detection of samples, the polymorphism of sequence detected by NGS makes STR have the advantages of higher resolution and system efficiency. However, MPS technology is expensive, there is no uniform standard so far, and there are problems such as how to integrate MPS-STR data with the existing CE-STR database. This review summarizes the current status of the application of MPS technology in the detection of STR genetic markers in forensic genetics, puts forward the main problems that need to be solved urgently, and prospects the application prospect of this technology in forensic genetics.

An improved whole-cell biotransformation system for (S)-equol production.

(S)-equol, the most active metabolite of the soybean isoflavones in vivo, has exhibited various biological activities and clinical benefits. Existing studies on the heterologous biosynthesis of (S)-equol via the engineered E. coli constructed have been significantly progressed. In the present study, the engineered E. coli was further improved to be more suitable for (S)-equol production. The four enzymes involved in the biosynthesis of (S)-equol and another GDH for NADPH regeneration were combined to construct the recombinant E. coli BL21(DE3). The optimal conditions for (S)-equol production were explored, respectively. The yield of equol reached 98.05% with 1 mM substrate daidzein and 4% (wt/vol) glucose. Even when the substrate concentration increased to 1.5 mM, (S)-equol could maintain a high yield of 90.25%. Based on the 100 ml one-pot reaction system, (S)-equol was produced with 223.6 mg/L in 1.5 h. The study presented a more suitable engineered E. coli for the production of (S)-equol.

Comprehensive analysis of CXCR family members in lung adenocarcinoma with prognostic values.

BACKGROUND: The expression profiles and molecular mechanisms of CXC chemokine receptors (CXCRs) in Lung adenocarcinoma (LUAD) have been extensively explored. However, the comprehensive prognostic values of CXCR members in LUAD have not yet been clearly identified. METHODS: Multiple available datasets, including Oncomine datasets, the cancer genome atlas (TCGA), HPA platform, GeneMANIA platform, DAVID platform and the tumor immune estimation resource (TIMER) were used to detect the expression of CXCRs in LUAD, as well as elucidate the significance and value of novel CXCRs-associated genes and signaling pathways in LUAD. RESULTS: The mRNA and/or protein expression of CXCR1, CXCR2, CXCR3, CXCR4, CXCR5 and CXCR6 displayed predominantly decreased in LUAD tissues as compared to normal tissues. On the contrary, compared with the normal tissues, the expression of CXCR7 was significantly increased in LUAD tissues. Subsequently, we constructed a network including CXCR family members and their 20 related genes, and the related GO functions assay showed that CXCRs connected with these genes participated in the process of LUAD through several signal pathways including Chemokine signaling pathway, Cytokine-cytokine receptor interaction and Neuroactive ligand-receptor interaction. TCGA and Timer platform revealed that the mRNA expression of CXCR family members was significantly related to individual cancer stages, cancer subtypes, patient's gender and the immune infiltration level. Finally, survival analysis showed that low mRNA expression levels of CXCR2 (HR = 0.661, and Log-rank P = 1.90e-02), CXCR3 (HR = 0.674, and Log-rank P = 1.00e-02), CXCR4 (HR = 0.65, and Log-rank P = 5.01e-03), CXCR5 (HR = 0.608, and Log-rank P = 4.80e-03) and CXCR6 (HR = 0.622, and Log-rank P = 1.85e-03) were significantly associated with shorter overall survival (OS), whereas high CXCR7 mRNA expression (HR = 1.604, and Log-rank P = 4.27e-03) was extremely related with shorter OS in patients. CONCLUSION: Our findings from public databases provided a unique insight into expression characteristics and prognostic values of CXCR members in LUAD, which would be benefit for the understanding of pathogenesis, diagnosis, prognosis prediction and targeted treatment in LUAD.

Application of SifaInDel 45plex System in the Han and Mongolian Populations.

OBJECTIVES: To investigate the genetic polymorphism of InDel loci in SifalnDel 45plex system in the Han population in Jiangsu Province and the Mongolian population in Inner Mongolia, and to evaluate the effectiveness of the system in forensic medicine. METHODS: SifaInDel 45plex system was used for genotyping in blood samples of 398 unrelated individuals from the above two populations, and allele frequencies and population genetic parameters of the two populations were calculated respectively. Eight intercontinental populations in the gnomAD database were used as reference populations. The genetic distances between the two studied populations and eight reference populations were calculated based on the allele frequencies of 27 autosomal-InDels (A-InDels). The phylogenetic trees and multidimensional scaling (MDS) analysis diagrams were constructed accordingly. RESULTS: Among two studied populations, the 27 A-InDels and 16 X-InDels showed no linkage disequilibrium between each other and the allele frequency distributions were in Hardy-Weinberg equilibrium. The CDP of the 27 A-InDels in two studied populations were all higher than 0.999 999 999 9, and the CPEtrio were all less than 0.999 9. The CDP of the 16 X-InDels in Han in Jiangsu and Mongolian in Inner Mongolia female and male samples were 0.999 997 962, 0.999 998 389, and 0.999 818 940, 0.999 856 063, respectively. The CMECtrio were all less than 0.999 9. The results of population genetics showed that the Jiangsu Han nationality, Inner Mongolia Mongolian nationality and East Asian population clustered into one branch, showing closer genetic relationship. The other 7 intercontinental populations clustered into another group. And the above 3 populations displayed distant genetic relationships with the other 7 intercontinental populations. CONCLUSIONS: The InDels in the SifaInDel 45plex system have good genetic polymorphism in the two studied populations, which can be used for forensic individual identification or as an effective complement for paternity identification, and to distinguish different intercontinental populations.

[Isolation, identification, and degradation characteristics of three effective PAHs degradation strains]. / 3æ ªå¤šçŽ¯èŠ³çƒƒé«˜æ•ˆé™è§£èŒæ ªçš„åˆ†ç¦»é‰´å®šåŠé™è§£ç‰¹æ€§.

Isolating dominant strains for the degradation of polycyclic aromatic hydrocarbons (PAHs) is of great practical significance for the restoration of ecosystem polluted by PAHs. A total of 11 strains with capacity of degrading PAHs were obtained from soil polluted by PAHs around a coking plant, by enrichment culture, acclimation, and plate isolation. Three of them with effective PAH-degrading capability were identified and screened out by morphological observation, physiobiochemical characterization, and 16S rRNA gene sequencing, and respectively, named as DJ-3, DJ-8 and DJ-10. Based on the results of 16S rRNA gene sequencing, DJ-3, DJ-8, and DJ-10 were identified as Pseudomonas sp. Klebsiella sp., and Bacillus sp. The degradation rate of phenanthrene (200 mg·L-1), pyrene (200 mg·L-1), and naphthol (160 mg·L-1) by three strains (DJ-3, DJ-8 and DJ-10) after seven-day incubation were 48.9%-65.9%, 38.9%-43.1%, and 57.6%-64.9%, respectively. The degradation rates of mixed PAHs sample (1200 mg·L-1) by three strains were 49.1%, 44.5%, and 53.9%, which were significantly higher than other eight strains, indicating that they were highly effective in PAHs degradation. There was no antagonistic relationship among the three strains. This study would lay a foundation for building efficient PAHs degrading strains and improve the in situ bioremediation of PAHs contaminated soil.

Corrigendum to "Inhibition of Uncoupling Protein 2 Enhances the Radiosensitivity of Cervical Cancer Cells by Promoting the Production of Reactive Oxygen Species".

[This corrects the article DOI: 10.1155/2020/5135893.].

High-phosphorus diet controlled for sodium elevates blood pressure in healthy adults via volume expansion.

Whether increasing exposure to dietary phosphorus can lead to adverse clinical outcomes in healthy people is not clear. In this open-label prospective cross-over study, we are to explore the impact of various dietary phosphorus intake on mineral, sodium metabolisms and blood pressure in young healthy adults. There were 3 separate study periods of 5 days, each with a 5 days washout period between different diets interventions. Six young healthy male volunteers with normal nutrition status were recruited in Phase I Clinical Research Center and sequentially exposed to the following diets: (a) normal-phosphorus diet (NPD): 1500 mg/d, (b) low-phosphorus diet (LPD): 500 mg/d, (c) high-phosphorus diet (HPD): 2300 mg/d. HPD induced a significant rise in daily average serum phosphate (1.47 ± 0.02 mmol/L [4.56 ± 0.06 mg/dl]) compared to NPD (1.34 ± 0.02 mmol/L [4.15 ± 0.06 mg/dL]) and LPD (1.17 ± 0.02 mmol/L [3.63 ± 0.06 mg/dL]) (p < .05). Daily average levels of serum parathyroid hormone and fibroblast growth factor 23 in HPD were significantly higher, and serum 1,25(OH)2 D3 was remarkably lower than those in LPD. HPD induced a significant decrease in daily average serum aldosterone and an increase in daily average atrial natriuretic peptide level compared to LPD. The 24-hour urine volume in HPD subjects was less than that in LPD subjects. HPD significantly increased daily average systolic blood pressure by 6.02 ± 1.24 mm Hg compared to NPD and by 8.58 ± 1.24mm Hg compared to LPD (p < .05). Our study provides the first evidence that 5-day high-phosphorus diet can induce elevation in SBP in young healthy adults, which may due to volume expansion.

Inhibition of Uncoupling Protein 2 Enhances the Radiosensitivity of Cervical Cancer Cells by Promoting the Production of Reactive Oxygen Species.

OBJECTIVE: The mechanism of enhanced radiosensitivity induced by mitochondrial uncoupling protein UCP2 was investigated in HeLa cells to provide a theoretical basis as a novel target for cervical cancer treatment. METHODS: HeLa cells were irradiated with 4 Gy X-radiation at 1.0 Gy/min. The expression of UCP2 mRNA and protein was assayed by real-time quantitative polymerase chain reaction and western blotting. UCP2 siRNA and negative control siRNA fragments were constructed and transfected into HeLa cells 24 h after irradiation. The effect of UCP2 silencing and irradiation on HeLa cells was determined by colony formation, CCK-8 cell viability, γH2AX immunofluorescence assay of DNA damage, Annexin V-FITC/PI apoptosis assay, and propidium iodide cell cycle assay. The effects on mitochondrial structure and function were investigated with fluorescent probes including dichlorodihydrofluorescein diacetate (DCFH-DA) assay of reactive oxygen species (ROS), rhodamine 123, and MitoTracker Green assay of mitochondrial structure and function. RESULTS: Irradiation upregulated UCP2 expression, and UCP2 knockdown decreased the survival of irradiated HeLa cells. UCP2 silencing sensitized HeLa cells to irradiation-induced DNA damage and led to increased apoptosis, cell cycle arrest in G2/M, and increased mitochondrial ROS. Increased radiosensitivity was associated with an activation of P53, decreased Bcl-2, Bcl-xl, cyclin B, CDC2, Ku70, and Rad51 expression, and increased Apaf-1, cytochrome c, caspase-3, and caspase-9 expression. CONCLUSIONS: UCP2 inhibition augmented the radiosensitivity of cervical cancer cells, and it may be a potential target of radiotherapy of advanced cervical cancer.

Seven new species of the Stenus cirrus group (Coleoptera, Staphylinidae) from Sichuan, Southwest China.

Seven new species of the Stenus cirrus group collected from Sichuan, Southwest China are described: S. cariniventris Tang, Liu Dong, sp. n., S. jiangrixini Tang, Liu Dong, sp. n., S. lineatus Tang, Liu Dong, sp. n., S. emeishanus Tang, Liu Dong, sp. n., S. jiudingshanus Tang, Liu Dong, sp. n., S. xichangensis Tang, Liu Dong, sp. n., S. brevilineatus Tang, Liu Dong, sp. n. The diagnostic characters of the new species are illustrated, and a key to species of the group from Sichuan Province is provided.

[Preparation and Characterization of a Calcium Alginate/Biochar Microsphere and Its Adsorption Characteristics and Mechanisms for Pb(â ¡)].

A microsphere (CA/BC) was prepared using biochar (BC) encapsulated with calcium alginate (CA) as a green adsorbent for Pb(Ⅱ) removal from aqueous solution. The effects of the initial Pb(Ⅱ) concentration, initial pH value of the Pb(Ⅱ) solution, and equilibrium contact time were investigated. The isothermal thermodynamic data of the BC and CA/BC conformed to the Langmuir model. The maximum adsorption capacities of the BC and CA/BC from the Langmuir equation were 93.20 mg·g-1 and 155.04 mg·g-1 respectively, at pH=5. The adsorption of Pb(Ⅱ) by the BC was in good agreement with the pseudo-second-order equation, indicating that chemisorption was the rate-controlling step. The adsorption of Pb(Ⅱ) by the CA/BC was in good agreement with the pseudo-first-order model, which suggested that the rate-limiting step was governed by diffusion. Mechanism studies for Pb(Ⅱ) removal by the CA/BC showed that the nature of Pb(Ⅱ) abstraction took place through ion exchange between Ca(Ⅱ) and Pb(Ⅱ) as well as via the formation of a coordination complex.

Blastic plasmacytoid dendritic cell neoplasm: A case report.

Blastic plasmacytoid dendritic cell neoplasm (BPDCN), formerly known as agranular cluster of differentiation (CD)4+/CD56+ hematodermic neoplasm, is a rare and aggressive type of lymphoma, with only ~100 cases reported worldwide. BPDCN is a hematological malignancy derived from precursors of plasmacytoid dendritic cells and is clinically characterized by cutaneous manifestations involving the lymph nodes and peripheral blood, a leukemia-like dissemination and a poor prognosis. The present study reports the case of a 54-year-old male who presented with symptoms characteristic of BPDCN. Pathological and immunohistochemical analysis of abdominal skin lesion biopsies were used to determine a diagnosis of stage IIIE BPDCN. Although cyclophosphamide, doxorubicin, vincristine and prednisolone chemotherapy was administered, the patient succumbed to BPDCN nine days after the discontinuation of chemotherapy. Thus, the period from BPDCN presentation to mortality was ≤3 months. The case reported in the present study was characterized by rapid development and poor prognosis, and displayed additional features of BPDCN, including systemic dissemination and a short survival period.