bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of key genes and pathways associated with topotecan treatment using multiple bioinformatics tools
Authors: Kang Yu-Mei , Lan Alexander , Huang Yen-Hua , Hsu Kai-Mei , Chao Yee , Lan Keng-Li 
Published: April 2020

Background:
The goal of this study is to determine critical genes and pathways associated with topotecan using publicly accessible bioinformatics tools.

Methods:
Topotecan signatures were downloaded from the Library of Integrated Network-Based Cellular Signatures (LINCS) database (http://www.ilincs.org/ilincs/). Differentially expressed genes (DEGs) were defined as genes that appeared at least three times with p values <0.05 and a fold change of ≥50% (|log2FC| ≥ 0.58). Hub genes were identified by evaluating the following parameters using a protein-protein interaction network: node degrees, betweenness, and eigenfactor scores. Hub genes and the top-40 DEGs by |log2FC| were used to generate a Venn diagram, and key genes were identified. Functional and pathway enrichment analysis was performed using the Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Information on ovarian cancer patients derived from The Cancer Genome Atlas (TCGA) database was analyzed, and the effect of topotecan on the protein expression was examined by Western blotting.

Results:
Eleven topotecan signatures were downloaded, and 65 upregulated and 87 downregulated DEGs were identified. Twenty-one hub genes were identified. We identified eight key genes as upregulated genes, including NFKBIA, IKBKB, GADD45A, CDKN1A, and HIST2H2BE, while EZH2, CDC20, and CDK7 were identified as downregulated genes, which play critical roles in the cell cycle and carcinogenesis in KEGG analysis. In the TCGA analysis, the CDKN1A+/EZH2− group had the longest median survival, while the CDKN1A−/EZH2+ group had the shortest median survival. Topotecan-treated murine ovarian (MOSEC), colorectal (CT26), and lung (LLC) cancer cell lines displayed upregulated CDKN1A encoding p21 and downregulated Ezh2.

Conclusion:
Using publicly accessible bioinformatics tools, we evaluated key genes and pathways related to topotecan and examined the key genes using the TCGA database and in vitro studies.
Loop Electrosurgical Excision Procedure or Cervical Conization to Exclude Cervical Cancer Before Simple Hysterectomy
Authors: Pretorius Robert G. , Belinson Jerome L. , Peterson Patricia 
Published: April 2020

Objective
The aim of the study was to determine which women require loop electrosurgical excision procedure (LEEP) or cervical conization (cone) to exclude cervical cancer after colposcopy for evaluation of abnormal cervical cancer screening tests yet before simple hysterectomy.

Materials and Methods
Review of electronic medical records from colposcopy clinics followed by chart review of women with cervical cancer was conducted.

Results
Of 18,537 cervical colposcopies for evaluation of abnormal cervical cancer screening tests, 0.6% (103/18,537) had cervical cancer; of 103 women with cervical cancer, 57 had neither cervical biopsy nor endocervical curettage (ECC) showing cancer or rule-out cancer (occult cancers) and were diagnosed by subsequent LEEP (n = 22), cone (n = 31), failed cone (n = 1), or hysterectomy (n = 3). The relative risk of occult cervical cancer at colposcopy for ECC of cervical intraepithelial neoplasia (CIN) 2 or CIN 3 versus ECC not CIN 2 or CIN 3 was 51.5 (5.0% vs 0.1%), for cervical biopsy of CIN 3 versus not CIN 3, was 34.5 (3.9% vs 0.1%), and for colposcopic impression of CIN 2, CIN 3, or cancer (CIN 2+) versus impression not CIN 2+, was 8.5 (1.9% vs 0.2%). If the 10.9% (2,018/18,537) of colposcopies with ECC of CIN 2 or CIN 3, cervical biopsy of CIN 3, or colposcopic impression of CIN 2+ had subsequent LEEP or cone, 96.5% (55/57) of occult cervical cancers would be detected before hysterectomy.

Conclusions
After colposcopy, women with ECC of CIN 2 or CIN 3, cervical biopsy of CIN 3, or colposcopic impression of CIN 2+ require LEEP or cone before simple hysterectomy.
Smoking in nursing students
Authors: Fernández-García Daniel , Ordás Beatriz , Fernández-Peña Rosario , Bárcena-Calvo Carmen , Ordoñez César , Amo-Setién Francisco José , Gómez-Salgado Juan , Martínez-Isasi Santiago 
Published: April 2020

Abstract
The role of nursing students as future health promoters of healthy behaviors is influenced by their attitude towards smoking. A cross-sectional study using a self-administered survey was performed to analyze smoking prevalence among undergraduate the nursing students who attend nursing faculties in 2 European countries (Spain and Portugal) during academic period 2015 to 2016. A total of 1469 subjects were surveyed (response rate of 79.8%). An 80% of the students were female with a mean age of 21.9 (4.8) years. The overall prevalence of tobacco use was 18.9%, with an average percentage of 16.2% in Portugal and 18.3% in Spain. Statistical significance was observed in relation to smoke and previous studies (16.4% vs 27.1%; P < .001). Only 1.1% of the students reported using electronic cigarette. 15.8% of smokers started smoking while at university with statistical gender and previous studies differences (P < .001). Fagerström and Richmond test showed low nicotine dependence (2.8 ± 2) and moderate motivation to stop smoking (4.9 ± 3), respectively. Smoking prevalence among nursing students was slightly higher than the general European population. For that reason, measures to reduce tobacco use have to be focused on students and university policies on tobacco control should be a challenge in the future.
Efficacy of photodynamic therapy and periodontal treatment in patients with gingivitis and fixed orthodontic appliances
Authors: Rosa Ellen Perim , Murakami-Malaquias-Silva Felipe , Schalch Tânia Oppido , Teixeira Daniela Bezerra , Horliana Ricardo Fidos , Tortamano Andre , Tortamano Isabel Peixoto , Buscariolo Inês Aparecida , Longo Priscila Larcher , Negreiros Renata Matalon , Bussadori Sandra Kalil , Motta Lara Jansiski , Horliana Anna Carolina Ratto Tempestini 
Published: April 2020

Abstract
It is known that the presence of orthodontic brackets predisposes for a change in the biofilm, facilitating the development of gingivits. The sites are difficult to access with a toothbrush and periodontal curette, worsening inflammation, in addition, a gingival hyperplasia is associated with poor hygiene. The objective of this study is to evaluate the impact of photodinamyc therapy (PDT) as an adjuvant treatment, considering clinical immunoregulatory and microbiological parameters. This randomized, controlled, double-blind clinical study will include 34 patients, both genders, having used fixed appliance for more than 12 months, with gingivitis. Participants will be divided into two groups: G1 (n = 17)- Scaling and Root Planing + PDT placebo and G2 (n = 17)- Scaling and Root Planing + PDT. In G2 the following dosimetric parameters will be used: methylene blue 0.005%, λ= 660 nanometers (nm), 9 Joules (J) per site, irradiance= 3.5Watts (W)/ centimeters (cm), radiant exposure= 318J/cm2. All participants will receive oral hygiene guidance prior the curetes scaling. The clinical periodontal data to be analyzed are plaque index, gingival index and probing depth. Crevicular fluid, from 4 pre-determined sites and saliva, will be collected and analysed for IL-6, IL-1β, IL-8, TNF-α and IL-10 cytokines using ELISA (Enzyme immunoabsorption assay) method. Total Bacteria count will also be performed, by qPCR and Universal16SrRNA gene. All analysis will be realized using in the baseline (T0), 7 (T1) and 21 (T2) days after treatment. Oral health-related quality of life will be assessed using the OHIP-14 questionnaire at times T0 and T2. If sample distribution is normal, the Student T-test will be applied if it is not normal, the Mann-Whitney test will be used. The data will be presented in terms of ± PD and The significance level will be set at p < 0.05. Our results may improve quality of life and add data to establish a therapeutic alternative for gingivitis during the orthodontic treatment. Registration: clinicaltrials.gov NCT04037709. https://clinicaltrials.gov/ct2/show/NCT04037709 - Registered in July 2019.
Diagnostic value of pentraxin 3 in respiratory tract infections
Authors: Ye Wu , Huang Qing-Dong , Tang Ting-Yu , Qin Guang-Yue 
Published: April 2020

Abstract

Background:
Pentraxin 3 is an acute inflammatory protein of the long pentraxin subfamily. A meta-analysis was performed to assess diagnostic accuracy of pentraxin 3 for respiratory tract infections.

Methods:
We identify studies examining diagnostic value of pentraxin 3 for respiratory tract infections by searching Pubmed, Web of Knowledge, and Cochrane Library. The sensitivity, specificity, negative likelihood ratio (LR), positive LR, and diagnostic odds ratio were pooled. The area under the summary receiver operator characteristic (SROC) curve and Q point value (Q∗) were calculated.

Results:
A total of 8 studies with 961 individuals were eligible for this meta-analysis. The pooled sensitivity of pentraxin 3 in diagnosis of respiratory tract infections was 0.78, the pooled specificity was 0.73, the area under the SROC curve was 0.84, and the Q∗ was 0.77. The area under the SROC curve of serum and bronchoalveolar lavage fluid (BALF) pentraxin 3 was 0.85 and 0.89, respectively. Meta-regression analysis revealed that cutoff value was the source of heterogeneity among the included studies. The Deek funnel plot test suggested no evidence of publication bias. Subgroup analyses showed that the area under the SROC curve of pentraxin 3 in diagnosis of ventilator-associated pneumonia (VAP) was 0.89.

Conclusion:
Pentraxin 3 has a moderate accuracy for diagnosing respiratory tract infections and VAP. The overall diagnostic value of BALF level of pentraxin 3 is superior to its serum concentration.
Exploring immune-related genes with prognostic value in microenvironment of breast cancer from TCGA database
Authors: Yang Hao , Zhao Kankan , Kang Houlong , Wang Mengchuan , Wu Aiguo 
Published: April 2020

Abstract
Breast cancer is one of the most common malignancies in women worldwide. Many studies have shown that tumor microenvironment cells, immune cells, and stromal cell infiltration have an important impact on prognosis, so it is important to identify biomarkers for achieving better treatment and prognosis.
To better understand the relationship between immune and stromal cell-related genes and prognosis, we screened patients with breast cancer in The Cancer Genome Atlas (TCGA) database and divided them into high and low groups based on immune/stromal scores. We next identified differentially expressed immune-related genes that are significantly associated with the prognosis of patients with breast cancer for functional enrichment analysis and protein–protein interaction networks, respectively. Finally, we selected a separate breast cancer cohort in gene expression synthesis (GEO) for validation.
Both immune scores and stromal scores are meaningful in the correlation of subtype classification. Disease-free survival of cases with the high score group of immune scores is statistically longer than the cases in the low score group. Differentially expressed immune-related genes extracted from the comparison can effectively evaluate the prognosis of patients with breast cancer and these genes are primarily involved in immune responses, extracellular matrix, and chemokine activity. At last, we obtained a series of verified tumor immune-related genes that predict the prognosis of patients with breast cancer.
Combining the Estimation of Stromal and Immune Cells in Malignant Tumor Tissues using Expression database and the TCGA database to extract the list of tumor microenvironment related genes which may help to outline the prognosis of patients with breast cancer. Some previously overlooked genes have the potential to become additional biomarkers for breast cancer. Further research on these genes can reveal a new understanding of the potential relationship between tumor microenvironment and breast cancer prognosis.
Cotton dust exposure and risk of lung cancer
Authors: Huang Xinru 
Published: April 2020

Abstract
Findings on the association between cotton dust exposure and lung cancer risk in epidemiologic studies have been inconsistent. Therefore, we conducted a meta-analysis of data from observational studies to quantify this association.
PubMed, EMBASE, and the Cochrane library databases were searched for observational studies with data on cotton dust exposure and lung cancer risk. Studies that reported adjusted relative risks (RRs) with 95% confidence intervals (CIs) of lung cancer associated with cotton dust exposure were included. Subgroup analyses were conducted according to key characteristics.
Fifteen studies involving a total of 73,812 individuals were included in the meta-analysis. Combining estimates from all the 15 observational studies, cotton dust exposure was associated with a decreased risk of lung cancer (combined RR, 0.78; 95% CI, 0.66–0.91; P = .002). Pooled estimates of multivariate RRs by gender were 0.71 (95% CI, 0.58–0.88; P = .001) among males, based on 7 studies, and 0.77 (95% CI, 0.67–0.89; P
< .001) among females, based on 9 studies. Further analyses examining the influence of a single study on the results by omitting a study at each turn yielded a range of RR from 0.74 to 0.82.
Our meta-analysis indicates that cotton dust exposure is associated with a decreased risk of lung cancer.
Xiaoqinglong decoction (a traditional Chinese medicine) combined conventional treatment for acute exacerbation of chronic obstructive pulmonary disease
Authors: Gao Zhen , Jing Jing , Liu Yingying 
Published: April 2020

AbstractBackground:A traditional Chinese medicine classic herbal formula named Xiaoqinglong decoction (XQLD) is widely used in China for acute exacerbation of chronic obstructive pulmonary disease (AECOPD). The efficacy and safety of XQLD for AECOPD was evaluated in this systematic review.Methods:Five databases, including the Cochrane Library, PubMed, China National Knowledge Infrastructure, Wanfang database, and Chinese Science and Technology Periodical Database were searched up to October 5, 2018 for randomized control trials in treating AECOPD with XQLD.Result:Thirty-eight trials were identified. Compared with conventional therapy (CT), XQLD plus CT significantly improve the total clinical efficacy rate (Risk Ratio [RR] = 1.22, 95% confidence interval [CI] = 1.18–1.26,P < .00001). Forced expiratory volume in the first second (FEV1) (mean difference [MD] = 0.37, 95% CI = 0.27–0.46;P < .00001), FEV1%pre (MD = 4.52, 95% CI = 2.42–6.62;P < .00001), FEV1/forced vital capacity (MD = 5.11, 95% CI = 4.21–6.00;P < .00001), PaO2(MD = 7.17, 95% CI = 4.80–9.54;P < .00001); lowered cough symptom score (MD = −0.65; 95% CI = −0.70 to −0.59;P < .00001), sputum symptom score (MD = −0.41; 95% CI = −0.45 to −0.37;P < .00001), wheezing symptom score (MD = −0.49; 95% CI = −0.60 to −0.38;P < .00001); reduce cough relief time (MD = −1.28; 95% CI = −1.53 to −1.02;P < .00001), sputum relief time (MD = −1.19; 95% CI = −1.42 to −0.96;P < .00001), wheezing relief time (MD = −1.65; 95% CI = −2.63 to −0.68;P = .0009), lassitude relief time (MD = −2.16; 95% CI = −3.44 to −0.89;P = .0009), and PaCO2(MD = −7.63, 95% CI = −9.62 to −5.63;P < .00001). Benefit for interleukin (IL)-4 (MD = −9.20, 95% CI = −13.59 to −4.81;P < .00001), IL-6 (MD = −5.07, 95% CI = −8.14 to −2.01;P = .001), IL-8 (MD = −5.59, 95% CI = −6.09 to −5.08;P < .00001), tumor necrosis factor (TNF)-α (MD = −5.93, 95% CI = −6.97 to −4.89;P < .00001), Interferon (INF)-γ (MD = 18.03, 95% CI = 13.22–22.84;P < .00001), and C-reactive protein (MD = −3.93, 95% CI = −5.97 to −1.89;P = .0002). For adverse events, there were no difference between XILD plus CT and CT.Conclusion:XQLD plus CT was more effective than CT alone for treating chronic obstructive pulmonary disease. Further higher quality trials are needed. The safety of XQLD remained uncertain.
Efficacy and tolerability of paroxetine in adults with social anxiety disorder
Authors: Li Xinyuan , Hou Yanbo , Su Yingying , Liu Hongping , Zhang Beilin , Fang Shaokuan 
Published: April 2020

Abstract

Objective:
The present study aimed to estimate the comprehensive efficacy and tolerability of paroxetine in adult patients with social anxiety disorder (SAD).

Methods:
We conducted a comprehensive literature review of the PubMed, Embase, Cochrane Central Register of Controlled Trials, Web of Science, and ClinicalTrials databases for eligible randomized controlled trials (RCTs). The efficacy outcome was the mean change of different kinds of scale scores as well as response and remission rates. The secondary outcome was tolerability, defined as the discontinuation rate and the incidence of adverse events (AEs).

Results:
Our meta-analysis included 13 RCTs. Mean changes in the Liebowitz Social Anxiety Scale (LSAS) total score, fear and avoidance subscale of LSAS scores were all significantly greater in patients with SAD that received paroxetine compared to those received placebo (total: MD = 13.46, 95%CI 10.59–16.32, P < .00001; fear: MD = 6.76, 95%CI 4.89–8.62, P < .00001; avoidance: MD = 6.54, 95%CI 4.63–8.45, P < .00001). Response and remission rates were both significantly greater in patients with SAD that received paroxetine compared to those received placebo (response: OR = 3.02, 95%CI 2.30–3.97, P < .00001; remission: OR = 3.14, 95%CI 2.25–4.39, P < .00001). There was no significant difference in discontinuation rate due to any reason between two groups (OR = 1.06, 95%CI 0.81–1.39, P = .65). Discontinuation rate due to AEs was higher in paroxetine than placebo group (OR = 3.41, 95%CI 2.45–4.72, P < .00001) whereas the rate due to lack of efficacy was higher in placebo as compared with paroxetine group (OR = 0.14, 95%CI 0.09–0.22, P < .00001). The incidence of any AE was significantly increased in patients that received paroxetine (OR = 1.83, 95%CI 1.43–2.35, P < .00001).

Conclusion:
Paroxetine was an effective and well-tolerated treatment option for adult patients with SAD.
Impact of statin use on cancer-specific mortality and recurrence
Authors: Yang Jing , Li Chunyu , Shen Ying , Zhou Hong , Shao Yueqin , Zhu Wei , Chen Yan 
Published: April 2020

AbstractThis meta-analysis mainly summarized the studies reporting an association between statin use and cancer-specific mortality and recurrence or progression of cancer patients.We systematically searched for studies about the statin used in cancer patients in electronic databases, including PubMed, Web of Science, Cochrane, Clinical Trials, from inception through the November 2019. A total of 60 studies which included 953,177 participants were eligible with 233,322 cancer patients used statin. Our analysis selected studies presented with outcome based on hazard ratios (HRs) and 95% confidence intervals (CIs) of cancer-specific mortality and cancer recurrence-free survival or progression-free survival. Heterogeneity between the studies was examined usingI2statistics, and sensitivity analyses were conducted to assess the robustness of the findings. All statistical analyses were performed using RevMan software (version 5.3).The use of statin was potentially associated with a decline in cancer-specific mortality in cancer patients (HR = 0.78; 95% CI: 0.74, 0.84; n = 39;I2 = 85%). Furthermore, statin use was associated with improved recurrence-free survival (HR = 0.87; 95% CI: 0.78,0.97; n = 23;I2 = 64%), but not with improvement in progression-free survival (HR = 1.05; 95% CI: 0.95,1.16; n = 14; I2 = 38%).The meta-analysis demonstrated that statin use could exhibit potential survival benefit in the prognosis of cancer patients. But our results are conservative for statins to improve disease recurrence and progression. These findings should be assessed in a prospective randomized cohort.
Cell-Block cytology in diagnosis of primary central nervous system lymphoma
Authors: Huang Kaiyuan , Zhou Lei , Tong Ying 
Published: April 2020

Abstract

Introduction:
Primary Central Nervous System Lymphoma (PCNSL) remains a diagnostic challenge due to the variable clinical manifestations. Liquid biopsies, particularly those involving cell-free DNA (cfDNA) from plasma, are rapidly emerging as important and minimally invasive adjuncts to traditional biopsies. However, conventional pathology may be still essential to obtain a diagnosis.

Patient concerns:
A 56-year-old woman presented with a progressive headache, dizziness, blurred vision, and lower limbs weakness with dysesthesia. Atypical clinical and radiological presentations, previous empirical treatment in another hospital, together with the patient's refusal to stereotactic brain biopsy made it challenging to diagnose. Her status deteriorated continuously during hospitalization.

Diagnosis:
Lumber punctual was performed, and CSF cytological analysis revealed malignancy cells with a high nuclear-cytoplasmic ratio. However, these cells were too loose to perform immunohistochemical stains. Genetic aberrations detections with CSF and peripheral blood sample were also inconclusive. We made a “cell-block” using the sedimentary cells collected from CSF collected through multiple aspirations via an Omaya reservoir. We further performed cytopathological and immunohistochemical analysis using this “cell-block,” which finally confirmed the diagnosis of diffuse large-B cell PCNSL.

Interventions:
Intracranial chemotherapy began afterwards (MTX 15 mg and dexamethasone 5 mg, twice per weeks).

Outcomes:
Unfortunately, this patient was dead 2 weeks later due to severe myelosuppression and secondary septic shock.

Conclusion:
We provided “cell-block” method, which collects cell components from large amount of CSF for cytology and immunohistochemical analysis. “Cell-block” cytology can be an alternative diagnostic method in diagnosis of PCNSL.
Physical activity is associated with lower health care costs among Taiwanese individuals with diabetes mellitus
Authors: Su Chun-Lang , Wang Lee , Ho Chien-Chang , Nfor Oswald Ndi , Hsu Shu-Yi , Lee Chun-Te , Ko Pei-Chieh , Lin Yi-Tien , Liaw Yung-Po 
Published: April 2020

Abstract
The economic burden of diabetes has increased over time with disease severity. Previous publications investigating the effects of physical activity (PA) on medical costs have made use of small sample sizes. We assessed the relationship between PA and 1-year medical expenditure among Taiwanese patients with type-2 diabetes mellitus (T2DM).
Data were recruited from three governmental databases, including the 2012 adult preventive health service database. Participants were grouped as inactive (no exercise), insufficiently active (exercise < 150 minutes/week), and sufficiently active (exercise >150 minutes/week) individuals. Patients were stratified according to age and Charlson score. Multivariate linear regression models were used to determine β-coefficients and their P values.
Overall, 218,960 individuals were identified with diabetes. The prevalence of the disease was 13.1% among sufficiently active, 35% among insufficiently active, and 51.9% among physically inactive adults. In general, patients who had exercise >150 minutes/week had lower health care spending (i.e., US$ 755.83) followed by those who had less than 150 minutes/week (US$ 880.08) when compared with inactive patients (P < .0001). Moreover, health care costs derived from outpatient or inpatient care were lower for sufficiently active than inactive participants (P < .0001).
Compared with being sedentary, PA was associated with lower health care costs of Taiwanese adults with diabetes mellitus.