bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human papillomavirus infection and cervical intraepithelial neoplasia progression are associated with increased vaginal microbiome diversity in a Chinese cohort
Authors: Chen Yulian , Qiu Xingdi , Wang Wenjing , Li Dong , Wu Anyue , Hong Zubei , Di Wen , Qiu Lihua 
Published: August 2020

Abstract
Background
In this study, the association between human papillomavirus (HPV) infection and related cervical intraepithelial neoplasia (CIN) or cervical cancer and vaginal microbiome was evaluated in Chinese cohorts.

Methods
The vaginal bacterial composition of five groups, HPV-infected women without CINs (HPV, n = 78), women with low-grade squamous intraepithelial lesions (LSIL, n = 51), women with high-grade squamous intraepithelial lesions (HSIL, n = 23), women with invasive cervical cancer (Cancer, n = 9) and healthy women without HPV infection (Normal, n = 68), was characterized by deep sequencing of barcoded 16S rRNA gene fragments (V3–4) using Illumina MiSeq.

Results
HPV infection increased vaginal bacterial richness and diversity regardless of the status of CINs. The vaginal bacterial richness and diversity were further augmented in women with cervical cancer. Lactobacillus was the most abundant genus in all groups. HPV infection had a negative influence on the abundances of Lactobacillus, Gardnerella and Atopobium. Accordingly, HPV infection increased the relative abundance of Prevotella, Bacillus, Anaerococcus, Sneathia, Megasphaera, Streptococcus and Anaerococcus. The increased proportions of Bacillus, Anaerococcus and the reduced abundance of Gradnerella vaginalis were probably related with the progression of CINs severity. HPV infection without CINs or cancerous lesions was strongly associated with Megasphaera. The most abundant bacterium in the LSIL group was Prevotella amnii. However, Prevotella timonensis, Shuttleworthia and Streptococcaceae at the family level were three taxa related to HSIL. Furthermore, more taxa were associated with the Cancer group including Bacillus, Sneathia, Acidovorax, Oceanobacillus profundus, Fusobacterium, Veillonellaceae at the family level, Anaerococcus and Porphyromonas uenonis. Samples in the Normal group were mostly assigned to CST III. HPV infection converted the vaginal bacterial community structure from CST III to CST IV. Furthermore, the proportions of CST IV were gradually augmented with the progression of the severity of CINs.

Conclusions
This work interpreted the differential vaginal bacteria under HPV infection and various precancerous or cancerous lesions in a Chinese cohort. We distinguished the specific microbes and the vaginal bacterial structure that were related with the progression of CINs severity in Chinese women.
Genome-wide capture sequencing to detect hepatitis C virus at the end of antiviral therapy
Authors: Peng Peng , Xu Yanjuan , Fried Michael W. , Di Bisceglie Adrian M. , Fan Xiaofeng 
Published: August 2020

Abstract
Background
Viral relapse is a major concern in hepatitis C virus (HCV) antiviral therapy. Currently, there are no satisfactory methods to predict viral relapse, especially in the era of direct acting antivirals in which the virus often quickly becomes undetectable using PCR-based approaches that focus on a small viral region. Next-generation sequencing (NGS) provides an alternative option for viral detection in a genome-wide manner. However, owing to the overwhelming dominance of human genetic content in clinical specimens, direct detection of HCV by NGS has a low sensitivity and hence viral enrichment is required.

Methods
Based on template-dependent multiple displacement amplification (tdMDA), an improved method for whole genome amplification (Wang et al., 2017. Biotechniques 63, 21–27), we evaluated two strategies to enhance the sensitivity of NGS-based HCV detection: duplex-specific nuclease (DSN)-mediated depletion of human sequences and HCV probe-based capture sequencing.

Results
In DSN-mediated depletion, human sequences were significantly reduced in the two HCV serum samples tested, 65.3% → 55.6% → 33.7% (#4727) and 68.6% → 56% → 21% (#4970), respectively for no normalization, self- and driver-applied normalization. However, this approach was associated with a loss of HCV sequences perhaps due to its micro-homology with the human genome. In capture sequencing, HCV-mapped sequencing reads occupied 96.8% (#4727) and 22.14% (#4970) in NGS data, equivalent to 1936x and 7380x enrichment, respectively. Capture sequencing was then applied to ten serum samples collected at the end of HCV antiviral therapy. Interestingly, the number of HCV-mapped reads was significantly higher in relapsed patients (n = 5) than those from patients with sustained virological response (SVR) (n = 5), 102.4 ± 72.3 vs. 2.6 ± 0.55, p = 0.014.

Conclusions
Our data provides concept evidence for a highly sensitive HCV detection by capture sequencing. The abundance difference of HCV sequencing reads at the end of HCV antiviral therapy could be applied to predict treatment outcomes.
Prevalence and recurrence of bacteraemia in hospitalised people who inject drugs – a single Centre retrospective cohort study in Denmark
Authors: Thønnings Sara , Jansåker Filip , Sundqvist Christoffer , Thudium Rebekka Faber , Nielsen Susanne Dam , Knudsen Jenny Dahl 
Published: August 2020

Abstract
Background
People who inject drugs (PWID) have increased risk of acquiring blood-transmitted chronic viral infections such as Hepatitis B (HBV), Hepatitis C (HCV) and Human Immunodeficiency Virus (HIV) as well as increased risk of acquiring bacterial infections. We aimed to identify and describe bacteraemic episodes, their recurrence rates, predictive and prognostic factors amongst hospitalised PWID.

Methods
In this retrospective cohort study, we included 257 hospitalised PWID during 2000–2006 with follow up at the Department of Infectious Diseases, Hvidovre Hospital, Denmark. Data collection included comorbidity (HBV-, HCV-, HIV-, and psychiatric comorbidities), social information (contact to an addiction treatment centre, homelessness), opioid substitution treatment (OST), treatment completion and microbiology findings. There was a 10-years follow-up regarding mortality.

Results
The study identified 257 patients classified as PWID. Of these, 58 (22.6%) had at least one episode of bacteraemia during their first hospital admission. Recurrence was found in 29 (50.0%) of the bacteraemia cases. Staphylococcus aureus was the dominant microorganism of both first and recurrent episodes with 24 (41.4%) and nine (31.4%) of cases, respectively. A psychiatric diagnose was significantly associated with a lower risk of bacteraemia in the multivariate analysis (OR: 0.29, [95%CI: 0.11–0.77], P = 0.01). Mortality was significantly higher in patients with bacteraemia (17.2% vs. 3.0%, P < 0.01, OR: 6.67 [95%CI: 2.33–20], P < 0.01).

Conclusions
In hospitalised PWID, bacteraemia was found in 22.6% and was associated with at higher mortality. The most common microorganism of bacteraemia was S. aureus. Psychiatric comorbidity was significantly associated with a lower risk of bacteraemia.
Patients with mild traumatic brain injury and acute neck pain at the emergency department are a distinct category within the mTBI spectrum: a prospective multicentre cohort study
Authors: Coffeng Sophie M. , Jacobs Bram , de Koning Myrthe E. , Hageman Gerard , Roks Gerwin , van der Naalt Joukje 
Published: August 2020

Abstract
Background
Acute neck pain (ANP) has recently been demonstrated to be a predictor of persistent posttraumatic complaints after mild traumatic brain injury (mTBI). The aim of this study was to determine specific characteristics of patients with ANP following mTBI, their posttraumatic complaints and relationship with functional outcome.

Methods
Data from a prospective follow-up study of 922 mTBI patients admitted to the emergency department (ED) in three level-one trauma centres were analysed. Patients were divided into two groups: 156 ANP patients and 766 no acute neck pain (nANP) patients. Posttraumatic complaints were evaluated 2 weeks and 6 months post-injury using standardized questionnaires and functional outcome was evaluated at 6 months with the Glasgow Outcome Scale Extended (GOSE).

Results
ANP patients were more often female (p < 0.01), younger (38 vs. 47 years, p < 0.01) with more associated acute symptoms at the ED (p < 0.05) compared to nANP patients. More motor vehicle accidents (12% vs. 6%, p = 0.01) and less head wounds (58% vs. 73%, p < 0.01) in ANP patients indicated ‘high-energy low-impact’ trauma mechanisms. ANP patients showed more posttraumatic complaints 2 weeks and 6 months post-injury (p < 0.05) and more often incomplete recovery (GOSE < 8) was present after 6 months (56% vs. 40%, p = 0.01).

Conclusions
MTBI patients with acute neck pain at the ED constitute a distinct group within the mTBI spectrum with specific injury and demographic characteristics. Early identification of this at risk group already at the ED might allow specific and timely treatment to avoid development of incomplete recovery.
Co-occurrence of Moyamoya syndrome and Kartagener syndrome caused by the mutation of DNAH5 and DNAH11: a case report
Authors: Zhang Lili , Feng Xungang , Zhang Junhu , Hao Yanlei , Wang Yuzhong 
Published: August 2020

Abstract
Background
Kartagener syndrome is an autosomal recessive inherited disorder of primary ciliary dyskinesia. Moyamoya syndrome refers to a moyamoya angiopathy associated with other neurological and/or extra-neurological symptoms, or due to a well identified acquired or inherited cause. We herein reported a case of a 48-year-old woman who was favored the diagnosis of Kartagener syndrome and moyamoya syndrome. The whole genome sequencing and bioinformatics analysis showed a homozygotic nonsense mutation in the dynein, axonemal, heavy chain (DNAH) 5 gene, and heterozygotic missense mutation in the DNAH11 gene. This is the first report of the co-occurrence of the two rare diseases.

Case presentation
A case of a 48-year-old woman was presented with hemiplegia and slurred speech. The magnetic resonance imaging of the brain confirmed acute cerebral infarction in the right basal ganglia region, semi-oval center, insular lobe, and frontal parietal lobe. The electrocardiogram showed inverted “P” waves in L1 and AVL on left-sided chest leads and computed tomography scan of the chest showed bronchiectasis changes, cardiac shadow and apex on the right side, and situs inversus of aortic arch position. The digital subtraction angiography showed inversion of the aortic arch, and bilateral internal carotid arteries are occluded from the ophthalmic segment. The clinical, radiological, and laboratory findings made the diagnosis of Kartagener syndrome and moyamoya syndrome. The whole genome sequencing and bioinformatics analysis showed a homozygotic nonsense mutation in DNAH5 gene, and heterozygotic missense mutation in the DNAH11 gene.

Conclusion
The combined mutation of DNAH5 and DNAH11 may lead to the overlapping dysfunction of motile and nonmotile cilia, which contribute to the co-occurrence of Kartagener syndrome and moyamoya syndrome. Our report deserves further confirm by more case reports.
Is opium use associated with an increased risk of lung cancer? A case-control study
Authors: Naghibzadeh-Tahami Ahmad , Marzban Maryam , Yazdi-Feyzabadi Vahid , Dabiri Shahryar , Mohseni Shokrollah , Abbasi Rayeni Reza , Samareh Fekri Mitra , Larizadeh Mohammad Hasan , Karimpour Behnaz , Khanjani Narges 
Published: August 2020

AbstractBackgroundIn recent years, lung cancer (LC) incidence has increased in Iran. The use of opium and its derivatives (O&D) has increased as well. This study aimed to investigate the association between the use of O&D and LC incidence.MethodsIn this case-control study conducted in Kerman, Iran; 140 patients with lung cancer and 280 healthy controls matched by age, sex, and place of residence were included. Data, including O&D use, cigarette smoking, alcohol use, and diet, were collected using a structured questionnaire. The relation between the use of O&D and LC was evaluated using conditional logistic regression adjusted for tobacco smoking, education, daily intake of fruit, vegetables, red meat, and hydrogenated fats.ResultsOpium ever-use was associated with an increased risk of LC (Adjusted Odds Ratio (AOR) =5.95, 95% CI: 1.87–18.92). Participants were divided into low and high use groups based on the median of opium use in the control group. A significant dose-response relation was observed between the amount of daily O&D use and LC; and the relation was stronger in high users (AORlow users = 3.81% CI: 1.13–12.77 and ORhigh users = 9.36, 95% CI: 2.05–42.72). Also, LC was higher among participants starting the use of O&D at younger ages (≤ 41 years old vs never users AOR = 8.64, 95% CI: 1.90–39.18) compared to those who started at an older age (> 41 years old vs never users, AOR = 4.71, 95% CI: 1.38–16.08). The association between opium, and lung cancer among non-smokers was OR: 6.50 (95% CI: 2.89 to 14.64).ConclusionThe results of this study show that opium use is probably a dose related risk factor for lung cancer.
Epidemiological features and survival outcomes in patients with malignant pulmonary blastoma: a US population-based analysis
Authors: Bu Xiang , Liu Jing , Wei Linyan , Wang Xiqiang , Chen Mingwei 
Published: August 2020

Abstract
Background
Pulmonary blastoma (PB) is a rare lung primary malignancy with poorly understood risk factors and prognosis. We sought to investigate the epidemiologic features and long-term outcomes of PB.

Methods
A population-based cohort study was conducted to quantify the death risk of PB patients. All subjects diagnosed with malignant PB from 1988 to 2016 were screened from the Surveillance, Epidemiology and End Results database. Cox regression model of all-cause death and competing risk analysis of cause-specific death were performed.

Results
We identified 177 PB patients with a median survival of 108 months. The 5 and 10-year survival rate in all PB patients were 58.2 and 48.5%, as well as the 5 and 10-year disease-specific mortality were 33.5 and 38.6%. No sex or race disparities in incidence and prognosis was observed. The death risk of PB was significantly associated with age at diagnosis, clinical stage, histologic subtype and surgery treatment (p<0.01). On multivariable regression analyses, older age, regional stage and no surgery predicted higher risk of both all-cause and disease-specific death in PB patients.

Conclusion
We described the epidemiological characteristics of PB and identified its prognostic factors that were independently associated with worse clinical outcome.
Effect of microwave ablation treatment of hepatic malignancies on serum cytokine levels
Authors: Zhao Jing , Li Qiang , Muktiali Merlin , Ren Bingjie , Hu Yingxi , Li Dapeng , Li Zhi , Li Daoming , Xie Yufeng , Tao Min , Liang Rongrui 
Published: August 2020

Abstract
Background
Microwave ablation (MWA) is widely used to treat unresectable primary and secondary malignancies of the liver, and a limited number of studies indicate that ablation can cause not only necrosis at the in situ site but also an immunoreaction of the whole body. This study aimed to investigate the effects of MWA on cytokines in patients who underwent MWA for a hepatic malignancy.

Methods
Patients admitted to the Oncology Department in the First Affiliated Hospital of Soochow University between June 2015 and February 2019 were selected. Peripheral blood was collected from patients with a hepatic malignancy treated with MWA. The levels of cytokines (IL-2, IFN-γ, TNF-α, IL-12 p40, IL-12 p70, IL-4, IL-6, IL-8, IL-10, and vascular endothelial growth factor (VEGF)) were detected with a Milliplex® MAP Kit. The comparison times were as follows: before ablation, 24 h after ablation, 15 days after ablation, and 30 days after ablation. Data were analyzed using a paired sample t-tests and Spearman’s correlation analysis.

Results
A total of 43 patients with hepatic malignancies were assessed. There were significant differences in IL-2, IL-12 p40, IL-12 p70, IL-1β, IL-8, and TNF-α at 24 h after MWA. Significant increases (> 2-fold vs. before ablation) were observed in IL-2, IL-1β, IL-6, IL-8, IL-10, and TNF-α after MWA. Elevated IL-2 and IL-6 levels after ablation were positively correlated with energy output during the MWA procedure.

Conclusions
WA treatment for hepatic malignancies can alter the serum levels of several cytokines such as IL-2 and IL-6.
Author response to “lack of benefit from low dose computed tomography in screening for lung cancer”
Authors: Huang Kai-Lin , Wang Shih-Yuan , Lu Wan-Chen , Chang Ya-Hui , Su Jian , Lu Yen-Ta 
Published: August 2020

AbstractWe explain to Dr. Benjamin (corresponding author) about why low-dose computed tomography reduce lung cancer mortality without significantly reducing all-cause mortality. We also conduct an up-to-date meta-analysis to evaluate low-dose computed tomography clinical effectiveness compared with usual care of lung cancer screening.
A translation and preliminary validation of the Dutch Wound-QoL questionnaire
Authors: Amesz Stella F. , Klein Toni M. , Meulendijks Audrey M. , Nguyen Tuong-Vi , Blome Christine , Roodbol Petrie F. , van Montfrans Catherine 
Published: August 2020

Abstract
Background
Chronic wounds have a major impact on patients’ health-related quality of life (HRQoL). Therefore, measuring HRQoL is an indispensable part of the treatment of patients with chronic wounds. The aim of this study was to translate and validate the Wound-QoL, a wound-specific HRQoL questionnaire, in a Dutch population.

Methods
The Wound-QoL was translated into Dutch according to the international standards. Patients with chronic wounds were asked to complete questionnaires at baseline (T0) and after six weeks (T1), including Wound-QoL, EQ-5D-3L (a generic questionnaire to measure HRQoL) and a visual analogue scale (VAS) measuring wound pain. If patients were not able to complete the questionnaire by themselves, it was read out to them by a nurse. Further data were obtained from medical records.

Results
Of the 120 patients included, 64 (53.3%) completed the questionnaire by themselves. To 55 patients (45.8%), the questionnaire was read out. The internal consistency of the Wound-QoL global score was high at both time points (T0: Cronbach’s α = 0.89, T1: Cronbach’s α = 0.92). The item selectivity for global score ranged from r = 0.25 to r = 0.77 at T0 and from r = 0.40 to r = 0.79 at T1. Overall, the self-completion and read-out subgroups showed similar internal consistency and item selectivity scores. With regard to convergent validity, significant correlations were found between Wound-QoL and EQ-5D-3L (T0: r = − 0.45, p < 0.001, T1: r = − 0.50, p < 0.001) as well as between Wound-QoL and pain VAS (T0: r = 0.23, p = 0.012, T1: r = 0.37, p = 0.001) at both time points. Responsiveness analyses showed significant correlations between changes in Wound-QoL and changes in EQ-5D-3L (r = − 0.37, p < 0.001), pain VAS (r = 0.24, p = 0.044) and wound size (r = 0.24, p = 0.013). The self-completion and read-out subgroups showed differences in convergent validity and responsiveness.

Conclusions
The results indicate that the Dutch version of the Wound-QoL has positive psychometric properties. However, more research is needed to further explore the differences between self-completed and read-out questionnaires.
Patterns, trends, and factors associated with contraceptive use among adolescent girls in Zambia (1996 to 2014): a multilevel analysis
Authors: Chola Mumbi , Hlongwana Khumbulani , Ginindza Themba G. 
Published: August 2020

AbstractBackgroundDespite high levels of pregnancy and childbearing among adolescents in Africa, contraceptive use remains low. Examining variations in contraceptive use among adolescent girls is vital for informing programs to improve contraceptive utilisation among this segment of the population. This study aimed to examine the patterns, trends, and factors associated with contraceptive use among adolescents in Zambia over the period 1996–2014.MethodsThe study involved an analysis of data from 1996, 2001/2, 2007 and 2013/14 Zambia Demographic and Health Surveys focusing on adolescent girls aged 15–19 years. Analysis entailed descriptive statistics and estimation of multilevel logistic regression models examining variations in contraceptive use among adolescent girls over time. Estimates withp-values less than 0.05 were considered statistically significant.ResultsResults showed that contraceptive use remains low and ranged from 7.6% in 1996 to 10.9% in 2013/14, reflecting a change of 3.3 percentage points over 18 years. Over the 18 years, contraceptive use was significantly associated with age, level of education, and marital status. Older adolescent girls and those with higher levels of education were significantly more likely to use contraception compared to younger ones and those with lower levels of education. Although initially significant (AOR 0.556, 95% CI 0.317, 0.974 in 1996), rural-urban differences disappeared between 2001/2 and 2007 but re-emerged in 2013/14 (AOR 0.654, 95% CI 0.499, 0.859). Across all survey years, adolescents who were married or living with a partner were significantly more likely to use contraceptives compared to those who were not married.ConclusionsThe findings suggest the need for targeted interventions to improve contraceptive use among sexually active adolescent girls in the country in general, and those who are disadvantaged in particular.
Cell metabolomics to study the function mechanism of Cyperus rotundus L. on triple-negative breast cancer cells
Authors: Ma Shuangshuang , Wang Fukai , Zhang Caijuan , Wang Xinzhao , Wang Xueyong , Yu Zhiyong 
Published: August 2020

Abstract
Background
Triple-negative breast cancer (TNBC) is a kind of malignant tumor with higher recurrence and metastasis rate. According to historical records, the dry rhizomes Cyperus rotundus L. could be ground into powder and mixed with ginger juice and wine for external application for breast cancer. We studied the effect of the ethanol extract of Cyperus rotundus L. (EECR) on TNBC cells and found its’ apoptosis-inducing effect with a dose-relationship. But the function mechanism of EECR on TNBC is still mysterious. Hence, the present research aimed to detect its function mechanism at the small molecule level through ultra-high performance liquid chromatography coupled with quadrupole-time-of-flight mass spectrometry (UPLC-Q-TOF-MS/MS) metabolomics.

Methods
The CCK-8 assay and the Annexin V-FITC/PI assay were applied to test the effect of EECR on MDA-MB-231 cells and MDA-MB 468 cells at various concentrations of 0, 200, 400, and 600 μg/ml. UPLC-Q-TOF-MS/MS based metabolomics was used between the control group and the EECR treatment groups. Multivariate statistical analysis was used to visualize the apoptosis-inducing action of EECR and filtrate significantly changed metabolites.

Results
The apoptosis-inducing action was confirmed and forty-nine significantly changed metabolites (VIP > 1, p < 0.05, and FC > 1.2 or FC < 0.8) were identified after the interference of EECR. The level of significant differential metabolites between control group, middle dose group, and high dose group were compared and found that which supported the apoptosis-inducing action with dose-dependence.

Conclusion
By means of metabolism, we have detected the mechanism of EECR inducing apoptosis of TNBC cells at the level of small molecule metabolites and found that EECR impacted the energy metabolism of TNBC cells. In addition, we concluded that EECR induced apoptosis by breaking the balance between ATP-production and ATP-consumption: arresting the pathways of Carbohydrate metabolism such as Central carbon metabolism in cancer, aerobic glycolysis, and Amino sugar and nucleotide sugar metabolism, whereas accelerating the pathways of ATP-consumption including Amino Acids metabolism, Fatty acid metabolism, Riboflavin metabolism and Purine metabolism. Although further study is still needed, EECR has great potential in the clinical treatment of TNBC with fewer toxic and side effects.