bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization and genetic diversity of Helicobacter pylori type IV secretion system components, CagI and CagN and its association with clinical outcomes among Iranian patients
Authors: Azizimoghaddam Yasaman , Kermanpour Sadaf , Mirzaei Nasrin , Houri Hamidreza , Yadegar Abbas , Kumar Navin , Aghdaei Hamid Asadzadeh , Zali Mohammad Reza 
Published: September 2020

Abstract
Background

A number of cagPAI genes in H. pylori genome was proposed to be the most probably evolved under a diversifying selection and evolutionary pressure. Among them, CagI and CagN are described as a part of the two different-operon of cagPAI that are involved in the T4SS, but the definite association of these factors with clinical manifestations is unclear.
Methods

A total of 70 H. pylori isolates were obtained from different gastroduodenal pateints. All isolates were examined for the presence of primary H. pylori virulence genes by PCR analysis. Direct DNA sequence analysis was performed for the cagI and cagN genes. The results were compared with reference strain.
Results

The cagI, cagN, cagA, cagL, vacA s1m1, vacA s1m2, vacA s2m2, babA2, sabA and dupA genotypes were detected in 80%, 91.4%, 84%, 91.4%, 32.8%, 42.8%, 24.4%, 97.1%, 84.3%, and 84.3% of the total isolates, respectively. The most variable codon usage in cagI was observed at residues 20 to 25, 55 to 60, 94, 181 to 199, 213 to 221, 241 to 268, and 319 to 320, while the most variable codon usage in CagN hypervariable motif (CagNHM) was observed at residues 53 to 63. This CagNHM region is postulated to contain GDEEITEEEKK sequence in the P12 reference strain. Sequencing data analysis of cagN revealed a conserved hypothetical hexapeptide repeat (EAKDEN/K) in residues of 278–283 among six H. pylori isolates, which needs further studies to evaluate its putative function.
Conclusion

The present study demonstrated a high prevalence of cagI and cagN genes among Iranian H. pylori isolates with gastroduodenal diseases. Furthermore, no significant correlation between cagI and cagN variants and clinical outcomes was observed. However, all patients had high prevalence of cagPAI genes including cagI, cagN, cagA and cagL that indicates more potential role of these genes in disease outcome.
The role of intermittent negative pressure wound therapy combined with a mesh incision in the salvage of perforator flap with venous congestion, a case report
Authors: Li Zhaoyue , Xie Kun , He Rui , Li Qiang , Zhou Changqing , Qi Xin , Jiang Shan , Shen Yimeng , Wen Bing 
Published: September 2020

Abstract
Background: The application of perforator flap is becoming wide. The most common postoperative complication is venous congestion but traditional treatments’ effect is limited. A new method called negative pressure wound therapy(NPWT) was introduced to improve wound healing. Many scholars have tried this method with continuous mode and achieved good outcomes. In this paper, we tried a different mode(intermittent) of negative pressure wound therapy on congested perforator flaps after a mesh incision, and we expected this paper could provide information for follow-up clinical research.Case presentation: A retrospective research of 6 patients (6 perforator flaps) who had been suffered from venous congestion from June, 2016 to June, 2019 was performed. All flaps were treated by intermittent negative pressure wound therapy after a mesh incision. Among 6 flaps, 4 of them were totally survived while the other 2 of them were mostly survived.Conclusions: Intermittent negative pressure wound therapy combined with a mesh incision can be a safe option to rescue perforator flaps with venous congestion. This technique has a certain success rate and clinical application value.
Impact of Diabetes Mellitus on the Early-Phase Arterial Healing After Drug-Eluting Stent Implantation
Authors: Ishihara Takayuki , Sotomi Yohei , Tsujimura Takuya , Iida Osamu , Kobayashi Tomoaki , Hamanaka Yuma , Omatsu Takashi , Sakata Yasushi , Higuchi Yoshiharu , Mano Toshiaki 
Published: September 2020

Abstract
Background: Early arterial healing after drug-eluting stent (DES) implantation may enable short dual-antiplatelet therapy (DAPT) strategy. The impact of diabetes mellitus (DM) on this healing has not been elucidated. We used coronary angioscopy (CAS) to compare intravascular status of DM and non-DM patients in the early phase after DES implantation.Methods: This study was a multicenter retrospective observational study. We analyzed CAS findings of 337 lesions from 270 patients evaluated 3-5 months after DES implantation. We divided the lesion into two groups: DM (n=149) and non-DM (n=188). We assessed neointimal coverage (NIC) grades (dominant, maximum and minimum), thrombus adhesion and maximum yellow color grade. NIC was graded as follows: grade 0, stent struts were not covered; grade 1, stent struts were covered by thin layer; grade 2, stent struts were buried under neointima. Yellow color was graded as grade 0, white; grade 1, light yellow; grade 2, yellow; grade 3, intensive yellow.Results: Minimum NIC grade was significantly lower in DM than in non-DM groups (p=0.002), whereas dominant and maximum NIC grades were similar between them (p=0.59 and p=0.94, respectively), as were thrombus adhesion (44.3% vs. 38.8%, p=0.32) and maximum yellow color grade (p=0.78). A multivariate analysis demonstrated that DM was an independent predictor of minimum NIC of grade 0 (odds ratio: 2.14, 95% confidence interval: 1.19-3.86, p=0.011).Conclusion: DM patients showed more uncovered struts than non-DM patients 3-5 months after DES implantation, suggesting that the recent ultra-short DAPT strategy might not be easily applied to DM patients.
Use of a novel Screen–Enrich–Combine(-biomaterials) Circulating System for filling of a 3D-printed open Ti6Al4V frame with mesenchymal stem cells/β-tricalcium phosphate to repair complex anatomical bone defects in load-bearing areas
Authors: Chu Wenxiang , Liu Zhiqing , Gan Yaokai , Chang Yongyun , Jiao Xin , Jiang Wenbo , Dai Kerong 
Published: September 2020

Abstract
Background: Repairing complex anatomical load-bearing bone defects is difficult because it requires restoration of load-bearing function, reconstruction of anatomical shape and repair by regenerated bone. We previously developed a Screen–Enrich–Combine(-biomaterials) Circulating System (SECCS) for rapid intraoperative enrichment of autologous bone marrow mesenchymal stem cells (MSCs) to enhance the osteogenic ability of porous bone substitutes. In this study, we prepared a 3D-printed Ti6A14V macroporous frame matching the defect shape to provide early load-bearing support and evaluated the efficacy of filling the frame with SECCS-processed MSCs/beta tricalcium phosphate (β-TCP) for long-term bone growth. Method: Mechanical testing of the cylindrical Ti6Al4V frame identified optimal 3D printing parameters. The lateral part of a goat distal femur was used as the defect model, and a matching electron beam melting technology-prepared (EBM) Ti6Al4V frame was fitted. Three frames filled with nothing, pure porous β-TCP or SECCS-processed MSCs/β-TCP were fixed onto the defect site. Repair efficacy was evaluated by X-ray radiography, computed tomography, histology and histomorphology. Results: In the basic regular hexagon printing unit, the combined side width (w) and inscribed circle diameter (d) determines the printing frame’s mechanical strength. The compressive load was significantly higher for w = 1.9 mm, d = 4.4 mm than for w = 1.7 mm, d = 4.0 mm or w = 2.0 mm, d = 5.0 mm (P < 0.05). The EBM-prepared Ti6Al4V defect-matched frame was well maintained 9 months after implantation. The MSCs successfully adhered to the wall of the porous β-TCP in the SECCS-processed group and had spread fully in the test samples. Each goat in the MSCs/β-TCP–filling group had approximately 31,321.7 ± 22,554.7 MSCs and a larger area of new bone growth inside the frame than the areas in the control and blank groups.Conclusion: Filling the 3D-printed Ti6Al4V large-aperture frame with osteogenic materials achieved biological reconstruction over a larger area of regenerated bone for repair of complex anatomical weight-bearing bone defects under the condition of early frame-supported load bearing. MSCs/β-TCP prepared by SECCS can be used as a filling material for this type of bone defect to obtain more efficacious bone repair.
Prognostic Significance of SQSTM1 in Breast Cancer: A Comprehensive Analysis
Authors: Liu Yang , Du Qian , Sun Dan , Han Ruiying , Teng Mengmeng , Zhang Ying , Dong Yuzhu , Chen Siying , You Haisheng , Dong Yalin 
Published: September 2020

Abstract
Background: SQSTM1 (Sequestosome 1, p62) is degraded by activated autophagy and involved in the progression of in various types of cancers. However, the prognostic role and underlying regulation mechanism of SQSTM1 in the progression and development of breast cancer remain unclear.Methods: In this study, 1336 samples with available mRNA data from Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) database and 27 formalin fixation and paraffin embedding (FFPE) tissue samples from the First Affiliated Hospital of Xi’an Jiaotong University were collected to evaluate SQSTM1 expression in mRNA and protein levels. Kaplan–Meier and Cox regression were used for revealing prognostic value in three independent breast cancer independent datasets. Tumor Immune Estimation Resource (TIMER) database and Gene Set Variation Analysis (GSVA) was used to explore the relationship of SQSTM1 mRNA expression and immune infiltration level in breast cancer. Dysregulation mechanisms of SQSTM1 were also explored including copy number variation (CNV), somatic mutation, epigenetic alterations and other transcription and post-transcription level using multiple datasets. Finally, Gene Set Enrichment Analysis (GSEA) was constructed to elucidate functional regulating performance of SQSTM1 in breast cancer.Results: The results showed that mRNA and protein level of SQSTM1 were significantly elevated in breast cancer and receiver operating characteristic (ROC) curve showed that p62 may act as diagnostic biomarker. Lower expression of SQSTM1 predicted better outcome through multiple datasets. It was also found that SQSTM1 correlated with immune infiltrates in breast cancer. Moreover, CNV and methylation of SQSTM1 DNA was correlated with SQSTM1 dysregulation and act as prognostic factors for breast cancer patients. Yet, somatic mutation status of SQSTM1 didn’t show any prognostic relevance. We also identified diverse transcription factors that directly bound to SQSTM1 DNA and the miRNAs which may regulate SQSTM1 mRNA. Finally, functional enrichment analysis revealed that SQSTM1 is related to cell signal transduction, oxidative stress and autophagy in breast cancer.Conclusion: Our findings revealed that SQSTM1 plays a key role in the progression of breast cancer and might be a promising biomarker for the diagnosis and personalized treatment of breast cancer patients.
Differential Metabolites in Chinese Autistic Children: A Multi-Centre Study Based on Urinary 1H-NMR Metabolomics Analysis
Authors: Ma Yu , Zhou Hao , Li Chunpei , Zou Xiaobing , Luo Xuerong , Wu Lijie , Li Tingyu , Chen Xiang , Mao Meng , Huang Yi , Li Erzhen , An Yanpeng , Zhang Lili , Wang Tianqi , Xu Xiu , Yan Weili , Jiang Yonghui , Wang Yi 
Published: September 2020

Abstract
Background: Autism spectrum disorder (ASD) is a group of early-onset neurodevelopmental disorders. However, there is no valuable biomarker for the early diagnosis of ASD. Our large-scale and multi-centre study aims to identify metabolic variations between ASD and healthy children and to investigate differential metabolites and associated pathogenic mechanisms.Methods: 117 autistic children and 119 healthy children were recruited from research centres of 7 cities. Urine samples were assayed by 1H-NMR metabolomics analysis to detect metabolic variations. Multivariate statistical analysis, including principal component analysis (PCA) and orthogonal projection to latent structure discriminant analysis (OPLS-DA), as well as univariate analysis were used to assess differential metabolites between the ASD and control groups. The differential metabolites were further analysed by receiver operating characteristics (ROC) curve analysis and metabolic pathways analysis.Results: Compared with the control group, the ASD group showed higher levels of glycine, guanidinoacetic acid, creatine, hydroxyphenylacetylglycine, phenylacetylglycine and formate and lower levels of 3-aminoisobutanoic acid, alanine, taurine, creatinine, hypoxanthine and N-methylnicotinamide. ROC curve showed relatively significant diagnostic values for hypoxanthine (area under the curve (AUC) = 0.657, 95% CI 0.588 to 0.726), creatinine (AUC = 0.639, 95% CI 0.569 to 0.709), creatine (AUC = 0.623, 95% CI 0.552 to 0.694), N-methylnicotinamide (AUC = 0.595, 95% CI 0.523 to 0.668) and guanidinoacetic acid (AUC = 0.574, 95% CI 0.501 to 0.647) in the ASD group. Combining the metabolites creatine, creatinine and hypoxanthine, the AUC of the ROC curve reached 0.720 (95% CI 0.659 to 0.777). Significantly altered metabolite pathways associated with differential metabolites were glycine, serine and threonine metabolism, arginine and proline metabolism, and taurine and hypotaurine metabolism.Limitations: Due to the restriction of research centres, inconsistent urine collection times may have affected the quality of metabolic analyses. Moreover, it is necessary to compare metabolite levels that vary with ASD severity to better clarify the pathogenesis of ASD.Conclusions: Urinary amino acid metabolites significantly altered in children with ASD. Amino acid metabolic pathways might play important roles in the pathogenic mechanisms of ASD.Clinical Trial registration: National Study on Autism Spectrum Disorder in China (NCT02200679). Registered July 24, 2014. https://www.clinicaltrials.gov/ct2/show/NCT02200679
Acute Miliary Tuberculosis in Pregnancy After in Vitro Fertilization and Embryo Transfer: Report of Seven Cases and Systemic Review
Authors: Gai Xiaoyan , Chi Hongbin , Cao Wenli , Zeng Lin , Chen Lixue , Zhang Weixia , Song Donghong , Wang Ying , Liu Ping , Li Rong , Sun Yongchang 
Published: September 2020

Abstract
BackgroundWhile miliary tuberculosis (TB) in pregnancy is rare after in vitro fertilization and embryo transfer (IVF-ET), it poses a serious threat to the health of pregnant women and their fetuses. The present study aimed to describe the clinical features of miliary TB and pregnancy outcomes of patients after IVF-ET.MethodsData of infertile patients who received IVF-ET at Peking University Third Hospital between January 2012 to December 2017 were retrospectively analyzed. Patients who developed miliary TB during pregnancy were identified, and clinical characteristics of miliary TB were described. The keywords “infertility,” “in vitro fertilization and embryo transfer,” and “tuberculosis” were used to search for articles published from 1980 to 2019 in PubMed, Medline, and EMBASE databases.ResultsOf 62,755 enrolled women, 7137 (11.4%) showed signs of prior pulmonary TB on chest X-ray (CXR). Seven patients aged 28–35 years had miliary TB during pregnancy, with two patients complicated by TB meningitis. All of these patients presented with fever. Notably, old TB lesions were detected on CXR in six patients before IVF-ET; nevertheless, no anti-TB therapy was administered. Furthermore, salpingography revealed oviduct obstruction in all patients (7/7). Patients received anti-TB therapy following a diagnosis of miliary TB and were clinically cured. However, pregnancy was terminated due to spontaneous (4/7) and induced (3/7) abortion. Previous literature indicates that signs of prior TB on CXR and oviduct obstruction on laparoscopy are risk factors for TB reactivation during pregnancy, which displayed a trend for hematogenous dissemination.ConclusionsTB reactivation, mostly as miliary TB and TB meningitis, is severe in pregnant women after IVF-ET and deleterious to pregnancy outcomes. The coexistence of primary infertility, untreated prior pulmonary TB, and fallopian tube obstruction is a risk factor for TB dissemination.
Modification of N-Terminal α-Amine of Proteins via Biomimetic ortho-quinone-mediated Oxidation
Authors: Wang Ping , Wang Siyao , Zhou Qingqing , Li Yunxue , Chen Xiaoping , Luo Rong-Hua , Yang Liu-Meng , Zheng Yong-Tang 
Published: September 2020

Abstract
Naturally abundant quinones are important molecules, which play essential roles in various biological processes due to their reduction potential. In contrast to their universality, the reactions between quinones and proteins remain sparse. Herein, we report the development of unprecedented strategy to protein modification via a biomimetic quinone-mediated oxidation at the N-terminus. By exploiting unique reactivity of an ortho-quinone reagent, the α-amine of protein N-terminus was oxidized to generate aldo or keto handle for orthogonal conjugation. Its applications have been demonstrated using a range of proteins, including myoglobin and ubiquitin. The effect of this method was further highlighted via the preparation of a series of 17 MIP-1β analogs, followed by preliminary anti-HIV activity and cell viability assays, respectively. This method offers a fast, efficient and complementary approach to existing strategies for protein N-terminus modification.
Putative Risk Factors of Prostate Cancer in Unscreened Ghanaian Men
Authors: Gyamfi Michael Adu , Anto Enoch Odame , Acheampong Emmanuel , Obirikorang Christian , Obirikorang Yaa 
Published: September 2020

Abstract
African countries with weak health systems and infrastructure are at risk of high incidence and mortality of prostate cancer. The absence of specific causative agents for prostate cancer calls for early detection strategies and the identification of susceptible factors. We undertook a community-based prostate-specific antigen screening of Ghanaian men to ascertain the association between putative risk factors and prostate cancer. Using an adjusted PSA cut-off we found a prostate cancer prevalence of 12.5% with most men diagnosed between 62–77 years (Mean; 69.50 ± 8.46). We found no statitsically significant association between putative risk factors such as obesity, hypertension, intake of alcohol, and smoking with prostate cancer. However, we observed a significant association between age and occupation, and prostate cancer. Prostate cancer is a growing challenge in Ghanaian men. Detection with PSA offers diagnostic significance and may help in reducing the burden in men. Differences in genetic and environmental differences between populations call for a population-specific assessment of risk factors.
Metagenomic analyses and genetic diversity of Tomato leaf curl virus complex affecting tomato plants in Kenya
Authors: Avedi Edith Khamonya , Adediji Adedapo Olutola , Kilalo Dora Chao , Olubayo Florence Mmogi , Macharia Isaac , Ateka Elijah Miinda , Machuka Eunice Magoma , Mutuku Josiah Musembi 
Published: September 2020

Abstract
Background
Tomato production is threatened worldwide by the occurrence of begomoviruses which are associated with tomato leaf curl diseases. There is little information on the molecular properties of tomato begomoviruses in Kenya, hence we investigated the population and genetic diversity of begomoviruses associated with tomato leaf curl in Kenya.
Methods
In 2018, we obtained tomato leaf samples with virus-like symptoms from farmers’ fields across Kenya and used Illumina sequencing to identify associated begomoviruses. Using the sequences, we determined the genetic diversity of begomoviruses. Additionally, selection pressure and recombinant isolates within the population were evaluated.
Results
Twelve complete begomovirus genomes were obtained from our samples with an average coverage of 99.9%. The sequences showed 95.7–99.7% identity among each other and 95.9–98.9% similarities with a Tomato leaf curl virus Arusha virus (ToLCArV) isolate from Tanzania. When we analyzed the amino acid sequences, we detected the highest identities in the regions coding for the coat protein gene (98.5–100%) within the isolates, and with the C4 gene of ToLCArV (97.1–100%). Phylogenetic algorithms clustered all Kenyan isolates in the same clades with ToLCArV, thus confirming the isolates to be a variant of the virus. Recombination analyses identified four putative events (P ≤ 0.05) among the isolates. Estimation of selection pressure within the virus population revealed the occurrence of negative or purifying selection in 5 out of the 6 coding regions.
Conclusions
The begomovirus associated with tomato leaf curl diseases in Kenya is a variant of ToLCArV possibly originating from Tanzania. Recombinant virus strains were detected within the population and there are divergence evolutionary events within the coding regions of the virus in Kenya. This information is useful in the development of appropriate management strategies for the disease.
Excretion of urine extracellular vesicles bearing markers of activated immune cells and calcium/phosphorus physiology differ between calcium kidney stone formers and non-stone formers
Authors: Zhang Jiqing , Kumar Sanjay , Jayachandran Muthuvel , Wang Stanley , Wilson Elena M. , Lieske John C. 
Published: September 2020

Abstract
Backgrounds:
Previous studies have demonstrated that excretion of urinary extracellular vesicles (EVs) from different nephron segments differs between kidney stone formers and non-stone formers (NSFs), and could reflect pathogenic mechanisms of urinary stone disease. In this study we quantified selected populations of specific urinary EVs carrying protein markers of immune cells and calcium/phosphorus physiology in calcium stone formers (CSFs) compared to non-stone formers (NSFs).
Methods
Incident CSFs (n = 24) and age- and sex- matched NSFs (n = 21) were studied. Clinical data were abstracted and biobanked cell-free urine samples were used to quantify specific urinary EV populations. EVs carrying proteins related to renal calcium/phosphorus physiology (phosphorus transporters (PiT1 and PiT2), Klotho, and fibroblast growth factor 23 (FGF23)); markers associated with EV generation (anoctamin-4 (ANO4) and Huntington interacting protein 1 (HIP1)), and markers shed from activated immune cells were quantified by standardized and published method of digital flow cytometry.
Results
The urine pH of CSFs was lower than NSFs (P < 0.05), whereas urine excretion of calcium, phosphorus, and calcium oxalate and uric acid supersaturation (SS) were significantly higher in CSFs compared to NSFs (P < 0.05). Urinary excretion of EVs with markers of total leukocytes (CD45), neutrophils (CD15), macrophages (CD68), Klotho, FGF23, PiT1, PiT2, and ANO4 were each markedly lower in CSFs than NSFs (P < 0.05) whereas excretion of those with markers of monocytes (CD14), T-Lymphocytes (CD3), B-Lymphocytes (CD19), plasma cells (CD138 plus CD319 positive ) were not different between the groups. Urinary excretion of EVs expressing PiT1 and PiT2 negatively (P < 0.05) correlated with urinary phosphorus excretion whereas excretion of EVs expressing FGF23 correlated negatively (P < 0.05) with both urinary calcium and phosphorus excretion.
Conclusions
Urinary excretion of EVs derived from specific types of activated immune cells and EVs with proteins related to calcium/phosphorus regulation were different between CSFs and NSFs. Thus, further validation of these and other populations of urinary EVs could identify biomarkers that elucidate novel pathogenic mechanisms of calcium stone formation in specific subsets of patients.