bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characteristics of Human Papillomavirus Infection Among Women With Cervical Cytological Abnormalities in the Zhoupu District, Shanghai City, China, 2014–2019
Authors: Li Ping , Liu Qing , Li Wei , Liu Zhou , Xing Baoling , Wu Suqin , Zhou Zhaoli , Sun Liping , Ren He , Li Hengfeng , Li Huaping 
Published: August 2020

Abstract
Background: Human papillomavirus (HPV) infection is the main cause of precancerous lesions and cervical cancer in women. To determine the epidemiological characteristics as well as the relationship between the HPV genotype and cytology test results among women, we retrospectively collected and analyzed the data from Zhoupu District hospital in Shanghai, China.Methods: We made a retrospective analysis of human papillomavirus prevalence rate of 23,724 women between 2014 and 2019 in the District Zhoupu of Shanghai City in China. Their cervical exfoliations were collected. HPV genotype testing was performed using a commercial kit designed to detect 21 HPV subtypes including 15 high-risk HPV subtypes(16, 18, 31, 33, 35, 39, 45, 51, 52, 53, 56, 58, 59, 66 ,68) and 6 low-risk HPV subtypes(6, 11, 42, 43, 44 and 81). And the thinPrep cytological test (TCT) was also performed at the same time.Results: Among all 23,724 cases, 3,816 (16.08%) women were infected with HPV. HPV52 (3.19%), HPV58 (2.47%) and HPV16 (2.34%) had higher prevalence. 3,480(91.20%) single-type infections were more common than 336(8.8%) multiple-type infections. Single-type infection was more frequently seen in women aged 50–60 years (16.63%) and <30 years (15.37%), and multiple-type infection was more common in those aged >= 60 (2.67%). Significant differences in secular trends from 2014 to 2019 were observed for subtypes HPV52, 58 and 16.HPV positive rates of women changed significantly along with the time period from 2014 to 2019.Among 4,502 TCT positive women, 15 (4.04%), 125 (2.64%) ,159 (1.54%), 4,202(17.71%) and 1(0.004%) had atypical squamous cells (ASC), high-grade squamous intraepithelial lesions (HSIL), low-grade squamous intraepithelial lesions (LSIL), atypical glandular cells (AGC) and cervical adenocarcinoma respectively. The HPV infection rates were 66.08%, 63.99%, 115.20%, 119.50%, and 31.72% for NILM, AGCs, HSILs LSILs and ASCs, respectively.Conclusions: HPV and TCT screening were a key step in the secondary prevention of cervical cancer. Further tracking the results of HPV and TCT was an important clinical strategy for the treatment of cervical precancerous lesions. The widespread use of preventive HPV vaccines can significantly reduce the incidence of pre-neoplastic and neoplastic cervical lesions.
Predicting in-silico electron ionization mass spectra using quantum chemistry
Authors: Wang Shunyang , Kind Tobias , Tantillo Dean J. , Fiehn Oliver 
Published: August 2020

Abstract
Compound identification by mass spectrometry needs reference mass spectra. While there are over 102 million compounds in PubChem, less than 300,000 curated electron ionization (EI) mass spectra are available from NIST or MoNA mass spectral databases. Here, we test quantum chemistry methods (QCEIMS) to generate in-silico EI mass spectra (MS) by combining molecular dynamics (MD) with statistical methods. To test the accuracy of predictions, in-silico mass spectra of 451 small molecules were generated and compared to experimental spectra from the NIST 17 mass spectral library. The compounds covered 43 chemical classes, ranging up to 358 Da. Organic oxygen compounds had a lower matching accuracy, while computation time exponentially increased with molecular size. The parameter space was probed to increase prediction accuracy including initial temperatures, the number of MD trajectories and impact excess energy (IEE). Conformational flexibility was not correlated to the accuracy of predictions. Overall, QCEIMS can predict 70 eV electron ionization spectra of chemicals from first principles. Improved methods to calculate potential energy surfaces (PES) are still needed before QCEIMS mass spectra of novel molecules can be generated at large scale.
Impact of Corticosteroids and Immunosuppressive Therapies on Symptomatic SARS-CoV-2 Infection in a Large Cohort of Patients with Chronic Inflammatory Arthritis
Authors: Favalli Ennio Giulio , Bugatti Serena , Klersy Catherine , Biggioggero Martina , Rossi Silvia , De Lucia Orazio , Bobbio-Pallavicini Francesca , Murgo Antonella , Balduzzi Silvia , Caporali Roberto , Montecucco Carlomaurizio 
Published: August 2020

Abstract
Background: Prevalence and outcomes of Coronavirus Disease (COVID)-19 in relation to immunomodulatory medications are still unknown. The aim of the study is to investigate the impact of glucocorticoids and immunosuppressive agents on COVID-19 in a large cohort of patients with chronic immune-mediated inflammatory arthritis.Methods: The study was conducted in the arthritis outpatient clinic at two large Academic Hospitals in the COVID-19 most endemic area of Northern Italy (Lombardy). We circulated a cross-sectional survey exploring the prevalence of Severe Acute Respiratory Syndrome-Coronavirus-2 nasopharyngeal swab positivity and the occurrence of acute respiratory illness (fever and/or cough and/or dyspnea), administered face-to-face or by phone to consecutive patients from 25th February to 20th April 2020. COVID-19 cases were defined as confirmed or highly suspicious according to the World Health Organization criteria. The impact of medications on COVID-19 incidence was evaluated. Results: The study population included 2050 adults with chronic inflammatory arthritis receiving glucocorticoids, conventional-synthetic (cs), or targeted-synthetic/biological (ts/b) disease-modifying drugs (DMARDs). Laboratory-confirmed COVID-19 and highly suspicious infection were recorded in 1.1% and 1.4% of the population, respectively. Treatment with glucocorticoids was independently associated with increased risk of COVID-19 (adjusted OR [95% CI] ranging from 1.23 [1.04-1.44] to 3.20 [1.97-5.18] depending on the definition used). Conversely, patients treated with ts/bDMARDs were at reduced risk (adjusted OR ranging from 0.46 [0.18-1.21] to 0.47 [0.46-0.48]). No independent effects of csDMARDs were observed.Conclusions: During the COVID-19 outbreak, treatment with immunomodulatory medications appears safe. Conversely, glucocorticoids, even at low-dose, may confer increased risk of infection.Trial registration: retrospectively registered
Mining and Reuse on Design Knowledge of Non-standard Special Tool Based on Deep Learning
Authors: Wang Mingwei , Zhou Jingtao , Chen Xiaoying , Li Zeyu 
Published: August 2020

Abstract
Aiming at the problems of design difficulty, low efficiency and unstable quality of non-standard special tools, facing the strong correlation between part machining features and tools, this article takes the two-dimensional engineering drawings of tools and parts as research objects, proposes the research on mining and reuse on design knowledge of non-standard special tool based on deep learning. Firstly, a dual-channel deep belief network is established to complete the feature modeling of machining features and tool features; secondly, the deep belief network is used to realize the association relationship mining between the machining features and tool features; thirdly, both the key local features of the tool and the overall similar design case of the tool are reused through association rule reasoning; finally, the non-standard special turning tool is used as an example to verify the effectiveness of the proposed method.
Magnetic resonance imaging and ultrasound for prediction of residual tumor size in early breast cancer within the ADAPT subtrials
Authors: Graeser Monika , Schrading Simone , Gluz Oleg , Strobel Kevin , Herzog Christopher , Umutlu Lale , Frydrychowicz Alex , Rjosk-Dendorfer Dorothea , Würstlein Rachel , Culemann Ralph , Adams Jascha , Nitzsche Henrik , Prange Anna , Kümmel Sherko , Grischke Eva-Maria , Forstbauer Helmut , Braun Michael , Potenberg Jochem , Schumann Raquel von , Aktas Bahriye , Kolberg-Liedtke Cornelia , Harbeck Nadia , Kuhl Christiane , Nitz Ulrike 
Published: August 2020

Abstract
Background: Prediction of histological tumor size by post-neoadjuvant therapy (NAT) ultrasound and magnetic resonance imaging (MRI) was evaluated in different breast cancer subtypes.Methods: Imaging was performed after 12-week NAT in patients enrolled into three neoadjuvant WSG ADAPT subtrials. Imaging performance for prediction of tumor size was analyzed across increasing size ranges (≤10, ≤20 and ≤30 mm) and summarized using positive (PPV) and negative predictive values (NPV).Results: 248 and 588 patients had MRI and ultrasound, respectively. Tumor size was over- or underestimated by <10 mm in 4.4% and 21.8% of patients by MRI and in 10.2% and 15.8% by ultrasound. Overall, PPV (correctly predicted tumor size ≤10, ≤20 or ≤30 mm) of MRI and ultrasound increased from 0.61 and 0.72 for ≤10 mm tumors to 0.88 and 0.96 for ≤30 mm tumors; NPV (correctly predicted tumor size >10, >20 or >30 mm) decreased from 0.89 and 0.74 to 0.69 and 0.22. Across all tumor size ranges, ultrasound demonstrated higher PPV than MRI in HR+/HER2+ tumors while both methods had a similarly low PPV in HR-/HER2- and HR-/HER2+ tumors. MRI had a higher NPV than ultrasound with the exception of HR-/HER2- tumors measuring ≤10 and ≤20 mm where both methods had similar NPV. Conclusions: Ultrasound is less likely than MRI to underestimate the size of HR+/HER2+ tumors while MRI is associated with a lower risk to overestimate the size of HR+/HER2+ and HR-/HER2+ tumors. These findings may help to select the most optimal imaging approach for planning surgery after NAT. Trial registration: Clinicaltrials.gov, NCT01815242 (registration March 21, 2013, NCT01817452 (registration March 25, 2013), NCT01779206 (registration January 30, 2013).
A large-scale database of T-cell receptor beta (TCRβ) sequences and binding associations from natural and synthetic exposure to SARS-CoV-2.
Authors: Nolan Sean , Vignali Marissa , Klinger Mark , Dines Jennifer N. , Kaplan Ian M. , Svejnoha Emily , Craft Tracy , Boland Katie , Pesesky Mitch , Gittelman Rachel M. , Snyder Thomas M. , Gooley Christopher J. , Semprini Simona , Cerchione Claudio , Mazza Massimiliano , Delmonte Ottavia M. , Dobbs Kerry , Carreño-Tarragona Gonzalo , Barrio Santiago , Sambri Vittorio , Martinelli Giovanni , Goldman Jason D. , Heath James R. , Notarangelo Luigi D. , Carlson Jonathan M. , Martinez-Lopez Joaquin , Robins Harlan S. 
Published: August 2020

Abstract
We describe the establishment and current content of the ImmuneCODE™ database, which includes hundreds of millions of T-cell Receptor (TCR) sequences from over 1,400 subjects exposed to or infected with the SARS-CoV-2 virus, as well as over 135,000 high-confidence SARS-CoV-2-specific TCRs. This database is made freely available, and the data contained in it can be downloaded and analyzed online or offline to assist with the global efforts to understand the immune response to the SARS-CoV-2 virus and develop new interventions.
Repositioning of ligands that target spike glycoprotein as potential drugs against SARS-CoV-2
Authors: Ramírez-Salinas Gema Lizbeth , Martínez-Archundia Marlet , Correa-Basurto José , García-Machorro Jazmín 
Published: August 2020

Abstract
The worldwide health emergency of the SARS-CoV-2 pandemic and the absence of a specific treatment for this new coronavirus have led to the use of computational strategies (drug repositioning) to search for treatments. The aim of this work is to identify FDA-approved drugs with the potential for binding to the spike structural glycoprotein at the hinge site, receptor binding motif (RBM), and fusion peptide (FP) using molecular docking simulations. It was identified drugs that binding to amino acids crucial for down to up conformational change, receptor recognition, and fusion of the viral membrane with the cell membrane. Results show some drugs that bind to hinge site amino acids (Varenicline, or even steroids as Betamethasone) while other drugs bind to crucial amino acids for RBM (Naldemedine, Atovaquone, Cefotetan) or FP (Edarbi, Maraviroc, Difluprednate); and highlights the Saquinavir that binds both the RBM and the FP. Therefore, these drugs could inhibit spike glycoprotein and prevent viral entry (possible anti-COVID-19 drugs). Several drugs are in clinical studies; focused on another pharmacological target (candesartan, Atovaquone, Losartan, Maviroc and Ritonavir) in this work we propose an additional target, the spike glycoprotein. These results can impact in the proposal of treatments that can inhibit the first steps virus replication cycle.
Decreased T Cell Levels in Critically Ill Coronavirus Patients: single-center, prospective and observational study
Authors: Wang Changsong , Liu Zhiyu , Xu Jingjing , Liu Haitao , Luo Yunpeng , Kang Kai , Li Xueting , Yang Wei , Fei Dongsheng , Zhao Mingyan , Yu Kaijiang 
Published: August 2020

Abstract
Background: Since Dec. 2019, COVID-19 pandemic has been outbreak. T cells play an important role in dealing with various disease-causing pathogens. However, the role of T cells played in COVID-19 patients is still unknown. Our study aimed to describe immunologic state of the critical ill COVID-19 patients. Methods: 63 patients with confirmed COVID-19 pneumonia admitted Department of Intensive Care Unit of the First Affiliated Hospital of Harbin Medical University. The immunologic characteristics（lymphocyte apoptosis, the expression of PD-1 and HLA-DR in T cells, T cell subset levels, redistribution and the production of inflammatory factors）as well as their laboratory parameters were compared between severe group and critical group.Results: The level of T cells in peripheral blood was decreased in critical patients compared with that in severe patients, but the expression levels of PD-1 (CD4+: 24.71% VS 30.56%; CD8+: 33.05% VS 32.38%) and HLA-DR (T cells: 36.28% VS 27.44%; monocytes: 20.58% VS 23.83%) in T cells were not significantly changed, and apoptosis and necrosis were not different in lymphocytes (apoptosis: 1.04% VS 1.27%; necrosis: 0.67% VS 1.11%), granulocytes, or monocytes between those two groups.Conclusions: There is severe immunosuppression in critical ill COVID-19 patients. Redistribution of T cells might be the main reason for lymphocytic decline. Decreasing the infiltration of T lymphocytes in the lung may be beneficial for the treatment of COVID-19. Trial registration: The study was approved by the Ethics Committee of the First Affiliated Hospital of Harbin Medical University. Code number: kyk2020003.
Low Diaphragm Muscle Mass Predicts Adverse Outcome in Patients Hospitalized for Covid-19 Pneumonia
Authors: Corradi Francesco , Isirdi Alessandro , Brusasco Claudia , Santori Gregorio , Falcone Marco , Gargani Luna , Romei Chiara , Barbieri Greta , Guarracino Fabio , Vetrugno Luigi , Landoni Giovanni , Forfori Francesco 
Published: August 2020

Abstract
Purpose: The aim of this study was to evaluate whether measurement of diaphragm thickness by ultrasonography may be a clinically useful noninvasive method for identifying patients at risk of adverse outcomes defined as need of invasive mechanical ventilation or death. Methods: We retrospectively reviewed the records of consecutive of 77 patients with laboratory-confirmed Covid-19 infection admitted to our intermediate care unit in Pisa between March 5 and March 30, 2020, with follow up until hospital discharge or death. Logistic regression was used identify variables potentially associated with adverse outcomes and those P<0.10 were entered into a multivariate logistic regression model. Cumulative probability for lack of adverse outcomes in patients with or without low baseline diaphragm muscle mass was calculated with the Kaplan–Meier product-limit estimator.Results: The main findings of this study are that 1) patients who developed adverse outcomes had thinner diaphragm than those who did not (2.0 vs 2.2 mm, p:0.001), 2) DT and lymphocyte count were independent significant predictors of adverse outcomes, with end-expiratory DT being the strongest (-708, OR: 0.492, p: 0.018).Conclusion: Diaphragmatic ultrasound may be a valid tool to evaluate the risk of respiratory failure. Evaluating the need of mechanical ventilation treatment should be based not only on PaO2/FiO2, but on a more comprehensive assessment including DT because if the lungs become less compliant a thinner diaphragm, albeit free of intrinsic abnormality, may become exhausted, thus contributing to severe respiratory failure.
Is Quarantine for COVID-19 Pandemic Associated with Psychological Burden in Primary Ciliary Dyskinesia? A Prospective Study.
Authors: Riccio Maria Pia , Borrelli Melissa , Fioretti Maria Teresa , Bene Margherita Del , Bravaccio Carmela , Poeta Marco , Santamaria Francesca 
Published: August 2020

Abstract
Background: Primary ciliary dyskinesia (PCD) is a rare disorder with variable disease progression. Information on the psychological impact of the Coronavirus Disease 2019 (COVID-19) quarantine in PCD, a condition with characteristics of personal and familiar increased stress due to frequent pulmonary exacerbations and high risk of lung function deterioration, is lacking. We designed a prospective study to assess the psychological burden and parental stress during the COVID-19 lockdown in Italy in a PCD population.Methods: Questionnaires assessing psychological well-being were administered to 10 PCD patients <15 years-old’s mothers (Group A: Parenting Stress Index-Short Form), to 17 PCD patients >=15 years-old (Group B: Psychological General Well-Being Index) and to 27 controls. We compared the PCD pulmonary exacerbations from the beginning of the outbreak and the frequency of weekly chest physiotherapy sessions during quarantine to the same period in 2019. Results: Seventy percent of Group A cases did not present parental stress levels. Ninety percent of Group B subjects did not show scores indicating distress. Groups A and B showed no significant difference versus controls in parental stress and psychological well-being, respectively. In the whole PCD population pulmonary exacerbations from the beginning of outbreak were less than in the same period of 2019 (p<0.05), and weekly chest physiotherapy sessions significantly increased during the quarantine compared to the same period of 2019 (p<0.05).Conclusions: We found that during COVID-19 quarantine, a PCD population in Italy neither developed psychological distress nor had a psychological burden significantly different than controls. We speculate that the low pulmonary exacerbation rate, explained by lower exposure to infectious triggers or by improved compliance to weekly chest physiotherapy, likely contributes to the psychological well-being of PCD patients and their families. The evaluation of the psychological burden and parental stress is a valuable tool for measuring the emotional impact of PCD and ultimately improving the medical care to PCD patients and their families, especially when exceptional events such as a pandemic occur.
Electrochemical performance of La2NiO4+δ-Ce0.55La0.45O2-δ as a promising bifunctional oxygen electrode for reversible solid oxide cells
Authors: Li Pengzhang , Yang Wei , Tian Chuanjin , Zhao Wenyan , Lü Zhe , Xie Zhipeng , Wang Chang-An 
Published: August 2020

Abstract
In this work, La2NiO4+δ-xCe0.55La0.45O2-δ (denoted as LNO-xLDC) with various LDC contents (x = 0, 10, 20, 30 and 40, wt %) were prepared and evaluated as bifunctional oxygen electrodes for reversible solid oxide cells (RSOCs). Compared with the pure LNO, the optimum composition of LNO-30LDC exhibited the lowest polarization resistance (Rp) of 0.53 and 0.12 Ω·cm2 in air at 650 and 750 oC, respectively. The enhanced electrochemical performance of LNO-30LDC oxygen electrode was mainly attributed to the extended triple phase boundary and more oxygen ionic transfer channels. The hydrogen electrode supported single cell with LNO-30LDC oxygen electrode displayed peak power densities of 276, 401 and 521 mW·cm-2 at 700, 750 and 800 oC, respectively. Moreover, the electrolysis current density of the single cell demonstrated 526.39 mA·cm-2 under 1.5 V at 800 oC, and the corresponding hydrogen production rate was 220.03 ml·cm-2·h-1. The encouraging results indicated that LNO-30LDC was a promising bifunctional oxygen electrode material for RSOCs.
Development a quantitative segmentation model to assess the effect of comorbidity on patients with COVID-19
Authors: Zhang Cui , Yang Guangzhao , Cai Chunxian , Xu Zhihua , Wu Hai , Guo Youmin , Xie Zongyu , Shi Hengfeng , Cheng Guohua , Wang Jian 
Published: August 2020

Abstract
Background: The coronavirus disease 2019 (COVID-19) has brought a global disaster. Quantitative lesions may provide the radiological evidence of the severity of pneumonia and further to assess the effect of comorbidity on patients with COVID-19.Methods: 294 patients with COVID-19 were enrolled from February, 24, 2020 to June, 1, 2020 from six centers. Multi-task Unet network was used to segment the whole lung and lesions from chest CT images. This deep learning method was pre-trained in 650 CT images (550 in primary dataset and 100 in test dataset) with COVID-19 or community acquired pneumonia and Dice coefficients in test dataset were calculated. 50 CT scans of 50 patients (15 with comorbidity and 35 without comorbidity) were random selected to mark lesions manually. The results will be compared with the automatic segmentation model. Eight quantitative parameters were calculated based on the segmentation results to evaluate the effect of comorbidity on patients with COVID-19.Results: Quantitative segmentation model was proved to be effective and accurate with all Dice coefficients more than 0.85 and all accuracies more than 0.95. Of the 294 patients, 52 (17.7%) patients were reported having at least one comorbidity, 14 (4.8%) having more than one comorbidity. Patients with any comorbidity were older (P<0.001), had longer incubation period (P<0.001), were more likely to have abnormal laboratory findings (P<0.05) and be in severity status (P<0.001). More lesions (including larger volume of lesion, consolidation and ground-glass opacity) were shown in patients with any comorbidity than patients without comorbidity (all P<0.001). The more comorbidities patients have, the poorer CT manifestation is. The median volume of lesion, consolidation and ground-glass opacity in diabetes mellitus group was largest among the three prevalently single comorbidity groups.Conclusions: Multi-task Unet network can make quantitative CT analysis of lesions to assess the effect of comorbidity on patients with COVID-19, further to provide the radiological evidence of the severity of pneumonia. More lesions were found in CT images of cases with comorbidity. The more comorbidities patients have, the poorer CT manifestation is.