bluuebunny/crossref_metadata_2025_split huggingface dataset:
Harmonization of Quantitative Parenchymal Enhancement in T1‐Weighted Breast MRI
Authors: van der Velden Bas H.M. , van Rijssel Michael J. , Lena Beatrice , Philippens Marielle E.P. , Loo Claudette E. , Ragusi Max A.A. , Elias Sjoerd G. , Sutton Elizabeth J. , Morris Elizabeth A. , Bartels Lambertus W. , Gilhuijs Kenneth G.A. 
Published: June 2020

BackgroundDifferences in imaging parameters influence computer‐extracted parenchymal enhancement measures from breast MRI.PurposeTo investigate the effect of differences in dynamic contrast‐enhanced MRI acquisition parameter settings on quantitative parenchymal enhancement of the breast, and to evaluate harmonization of contrast‐enhancement values with respect to flip angle and repetition time.Study TypeRetrospective.Phantom/PopulationsWe modeled parenchymal enhancement using simulations, a phantom, and two cohorts (N = 398 and N = 302) from independent cancer centers.Sequence Field/Strength1.5T dynamic contrast‐enhanced T1‐weighted spoiled gradient echo MRI. Vendors: Philips, Siemens, General Electric Medical Systems.AssessmentWe assessed harmonization of parenchymal enhancement in simulations and phantom by varying the MR parameters that influence the amount of T1‐weighting: flip angle (8°–25°) and repetition time (4–12 msec). We calculated the median and interquartile range (IQR) of the enhancement values before and after harmonization. In vivo, we assessed overlap of quantitative parenchymal enhancement in the cohorts before and after harmonization using kernel density estimations. Cohort 1 was scanned with flip angle 20° and repetition time 8 msec; cohort 2 with flip angle 10° and repetition time 6 msec.Statistical TestsPaired Wilcoxon signed‐rank‐test of bootstrapped kernel density estimations.ResultsBefore harmonization, simulated enhancement values had a median (IQR) of 0.46 (0.34–0.49). After harmonization, the IQR was reduced: median (IQR): 0.44 (0.44–0.45). In the phantom, the IQR also decreased, median (IQR): 0.96 (0.59–1.22) before harmonization, 0.96 (0.91–1.02) after harmonization. Harmonization yielded significantly (P < 0.001) better overlap in parenchymal enhancement between the cohorts: median (IQR) was 0.46 (0.37–0.58) for cohort 1 vs. 0.37 (0.30–0.44) for cohort 2 before harmonization (57% overlap); and 0.35 (0.28–0.43) vs. .0.37 (0.30–0.44) after harmonization (85% overlap).Data ConclusionThe proposed practical harmonization method enables an accurate comparison between patients scanned with differences in imaging parameters.Level of Evidence3Technical Efficacy Stage4
Evidence for mutations in SARS‐CoV‐2 Italian isolates potentially affecting virus transmission
Authors: Benvenuto Domenico , Demir Ayse Banu , Giovanetti Marta , Bianchi Martina , Angeletti Silvia , Pascarella Stefano , Cauda Roberto , Ciccozzi Massimo , Cassone Antonio 
Published: June 2020

AbstractItaly is the first western country suffering heavy severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) transmission and disease impact after coronavirus disease‐2019 pandemia started in China. Even though the presence of mutations on spike glycoprotein and nucleocapsid in Italian isolates has been reported, the potential impact of these mutations on viral transmission has not been evaluated. We have compared SARS‐CoV‐2 genome sequences from Italian patients with virus sequences from Chinese patients. We focussed upon three nonsynonymous mutations of genes coding for S(one) and N (two) viral proteins present in Italian isolates and absent in Chinese ones, using various bioinformatics tools. Amino acid analysis and changes in three‐dimensional protein structure suggests the mutations reduce protein stability and, particularly for S1 mutation, the enhanced torsional ability of the molecule could favor virus binding to cell receptor(s). This theoretical interpretation awaits experimental and clinical confirmation.
Potential neuroinvasive pathways of SARS‐CoV‐2: Deciphering the spectrum of neurological deficit seen in coronavirus disease‐2019 (COVID‐19)
Authors: Baig Abdul Mannan , Sanders Erin C. 
Published: June 2020

AbstractCoronavirus disease‐2019 (COVID‐19) was declared a global pandemic on 11 March 2020. Scientists and clinicians must acknowledge that severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has the potential to attack the human body in multiple ways simultaneously and exploit any weaknesses of its host. A multipronged attack could potentially explain the severity and extensive variety of signs and symptoms observed in patients with COVID‐19. Understanding the diverse tactics of this virus to infect the human body is both critical and incredibly complex. Although patients diagnosed with COVID‐19 have primarily presented with pulmonary involvement, viral invasion, and injury to diverse end organs is also prevalent and well documented in these patients, but has been largely unheeded. Human organs known for angiotensin‐converting enzyme 2 (ACE2) expression including the gastrointestinal tract, kidneys, heart, adrenals, brain, and testicles are examples of extra pulmonary tissues with confirmed invasion by SARS‐CoV‐2. Initial multiple organ involvement may present with vague signs and symptoms to alert health care professionals early in the course of COVID‐19. Another example of an ongoing, yet neglected element of the syndromic features of COVID‐19, are the reported findings of loss of smell, altered taste, ataxia, headache, dizziness, and loss of consciousness, which suggest a potential for neural involvement. In this review, we further deliberate on the neuroinvasive potential of SARS‐CoV‐2, the neurologic symptomology observed in COVID‐19, the host‐virus interaction, possible routes of SARS‐CoV‐2 to invade the central nervous system, other neurologic considerations for patients with COVID‐19, and a collective call to action.
Determining host factors contributing to disease severity in a family cluster of 29 hospitalized SARS‐CoV‐2 patients: Could genetic factors be relevant in the clinical course of COVID‐19?
Authors: Ikitimur Hande , Borku Uysal Betul , Cengiz Mahir , Ikitimur Barış , Uysal Harun , Ozcan Erkan , Islamoglu Mehmet Sami , Seyhan Serhat , Yavuzer Hakan , Yavuzer Serap 
Published: June 2020

AbstractIn this study, we report a large family cluster consisting of 29 genetically related patients hospitalized with coronavirus disease‐2019 (COVID‐19). We sought to determine the clinical characteristics relevant to the clinical course of COVID‐19 by comparing the family cluster to unrelated patients with SARS‐CoV‐2 infection so that the presence of potential determinants of disease severity, other than traditional risk factors previously reported, could be investigated. Twenty‐nine patient files were investigated in group 1 and group 2 was created with 52 consecutive patients with COVID‐19 having age and gender compatibility. The virus was detected for diagnosis. The clinical, laboratory and imaging features of all patients were retrospectively screened. Disease course was assessed using records regarding outcome from patient files retrospectively. Groups were compared with respect to baseline characteristics, disease severity on presentation, and disease course. There was no difference between the two groups in terms of comorbidity and smoking history. In terms of inhospital treatment, use differed not significantly between two groups. We found that all 29 patients in the group 1 had severe pneumonia, 18 patients had severe pneumonia. Hospitalization rates, length of hospital stay, and transferred to intensive care unit were found to be statistically significantly higher in the group 1. In the present study, COVID‐19 cases in the large family cluster were shown to have more severe disease and worse clinical course compared with consecutive patients with COVID‐19 presenting to the same time. We believe further studies into potential genetic mechanisms of host susceptibility to COVID‐19 should include such family clusters.
Detection of herpesviruses and enteroviruses in patients with suspected infectious meningoencephalitis in three referral hospitals in Yaounde, Cameroon
Authors: Tagnouokam‐Ngoupo Paul Alain , Toby Roselyne , Bomba Ebede Michelle Olivia , Kenmoe Sebastien , Ngo‐Malabo Elodie Teclaire , Sadeuh‐Mba Serge Alain , Biwole‐Sida Magloire , Njouom Richard 
Published: June 2020

AbstractIn Cameroon, routine diagnosis of central nervous system (CNS) infections is based on the detection of bacteria, fungi, parasites, and mycobacteria in cerebrospinal fluids. Therefore, there is no data on viral etiologies of meningoencephalitis (ME) in the country. We aim to identify viral etiologies (herpesviruses and enteroviruses) of ME in Cameroon, to provide useful information to physicians that will help improving management of ME. From February to May 2018, adult patients with clinical signs of ME in three referral hospitals in Yaounde were included. Detection of herpesviruses and enteroviruses was performed using reverse transcriptase polymerase chain reaction. P value of 5% was chosen as the threshold for statistical significance in statistical analyses. Eighty‐one patients were included and 15 (18.51%) were positive for herpesviruses. No enterovirus was detected. The most prevalent virus was Epstein‐Barr virus (8.6%) and most of herpesviruses were detected from human immunodefeciency virus (HIV)‐positive patients (86.7%). The overall mortality rate was high, 60.5% (49/81) and analysis of risk factors showed that HIV‐positive status and altered state of consciousness were associated with higher risk of death (odds ratio [OR], 5.41; confidence interval [CI]: 1.91‐16.88; P = .002 and OR, 3.24; CI: 1.11‐0.13; P = .036 respectively). We showed that herpesviruses are present in patients with ME symptoms in Yaounde and can be sometimes in coinfection with others common pathogens of CNS infections. There is therefore a need for increased clinician awareness and education regarding the diagnostic and management of CNS infections in Cameroon to limit unnecessary use of antibiotics.
Understanding the possible origin and genotyping of the first Bangladeshi SARS‐CoV‐2 strain
Authors: Alam A. S. M. Rubayet Ul , Islam M. Rafiul , Rahman M. Shaminur , Islam Ovinu Kibria , Hossain M. Anwar 
Published: June 2020

AbstractThe novel coronavirus, SARS‐CoV‐2, has caused the most unfathomable pandemic in the history of humankind. Bangladesh is also a victim of this critical situation. To investigate the genomic features of the pathogen from Bangladesh, the first complete genome of the virus has very recently been published. Therefore, long‐awaited questions regarding the possible origin and typing of the strain(s) can now be answered. Here, we endeavor to mainly discuss the published reports or online‐accessed data (results) regarding those issues and present a comprehensive picture of the typing of the virus alongside the probable origin of the subclade containing the Bangladeshi strain. Our observation suggested that this strain might have originated from the United Kingdom or the other European countries epidemiologically linked to the United Kingdom. According to different genotyping classification schemes, this strain belongs to the A2a clade under the G major clade, is of B and/or L type, and is a SARS‐CoV‐2a substrain. In the future, randomized genomic data will certainly increase in Bangladesh, however because of globalization and immigrant movement, we urgently need a mass regional sequencing approach targeting the partial or complete genome that can link the epidemiological data and may help in further clinical intervention.
High‐coverage SARS‐CoV‐2 genome sequences acquired by target capture sequencing
Authors: Wen Shaoqing , Sun Chang , Zheng Huanying , Wang Lingxiang , Zhang Huan , Zou Lirong , Liu Zhe , Du Panxin , Xu Xuding , Liang Lijun , Peng Xiaofang , Zhang Wei , Wu Jie , Yang Jiyuan , Lei Bo , Zeng Guangyi , Ke Changwen , Chen Fang , Zhang Xiao 
Published: June 2020

AbstractIn this study, we designed a set of SARS‐CoV‐2 enrichment probes to increase the capacity for sequence‐based virus detection and obtain the comprehensive genome sequence at the same time. This universal SARS‐CoV‐2 enrichment probe set contains 502 120 nt single‐stranded DNA biotin‐labeled probes designed based on all available SARS‐CoV‐2 viral sequences and it can be used to enrich for SARS‐CoV‐2 sequences without prior knowledge of type or subtype. Following the CDC health and safety guidelines, marked enrichment was demonstrated in a virus strain sample from cell culture, three nasopharyngeal swab samples (cycle threshold [Ct] values: 32.36, 36.72, and 38.44) from patients diagnosed with COVID‐19 (positive control) and four throat swab samples from patients without COVID‐19 (negative controls), respectively. Moreover, based on these high‐quality sequences, we discuss the heterozygosity and viral expression during coronavirus replication and its phylogenetic relationship with other selected high‐quality samples from the Genome Variation Map. Therefore, this universal SARS‐CoV‐2 enrichment probe system can capture and enrich SARS‐CoV‐2 viral sequences selectively and effectively in different samples, especially clinical swab samples with a relatively low concentration of viral particles.
SARS‐CoV‐2: A comprehensive review from pathogenicity of the virus to clinical consequences
Authors: Lotfi Melika , Rezaei Nima 
Published: June 2020

AbstractNowadays, severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), which caused novel coronavirus disease (COVID‐19) pandemic, is the worldwide challenge. The virus is highly contagious, and clinical consequences were very divers. It is estimated that if no effective action is taken, COVID‐19 could plague 90% of the world's population and kill over 40 million people. So, it is essential to understand the virus pathogenicity and follow the preventive methods to control the high morbidity and mortality rates. Meanwhile our current knowledge of COVID‐19 is still limited, despite hard efforts of scientists and clinicians during last few months. In this review article, we have collected the latest data about characteristics, pathogenesis, clinical manifestations, and diagnostic methods of SARS‐CoV‐2.
Validation of PATHFx 2.0: An open‐source tool for estimating survival in patients undergoing pathologic fracture fixation
Authors: Overmann Archie L. , Clark DesRaj M. , Tsagkozis Panagiotis , Wedin Rikard , Forsberg Jonathan A. 
Published: June 2020

AbstractTreatment decisions in patients with metastatic bone disease rely on accurate survival estimation. We developed the original PATHFx models using expensive, proprietary software and now seek to provide a more cost‐effective solution. Using open‐source machine learning software to create PATHFx version 2.0, we asked whether PATHFx 2.0 could be created using open‐source methods and externally validated in two unique patient populations. The training set of a well‐characterized, database records of 189 patients and the bnlearn package within R Version 3.5.1 (R Foundation for Statistical Computing), was used to establish a series of Bayesian belief network models designed to predict survival at 1, 3, 6, 12, 18, and 24 months. Each was externally validated in both a Scandinavian (n = 815 patients) and a Japanese (n = 261 patients) data set. Brier scores and receiver operating characteristic curves to assessed discriminatory ability. Decision curve analysis (DCA) evaluated whether models should be used clinically. DCA showed that the model should be used clinically at all time points in the Scandinavian data set. For the 1‐month time point, DCA of the Japanese data set suggested to expect better outcomes assuming all patients will survive greater than 1 month. Brier scores for each curve demonstrate that the models are accurate at each time point. Statement of Clinical Significance: we successfully transitioned to PATHFx 2.0 using open‐source software and externally validated it in two unique patient populations, which can be used as a cost‐effective option to guide surgical decisions in patients with metastatic bone disease.
Advances in cultivar choice, hazelnut orchard management, and nut storage to enhance product quality and safety: an overview
Authors: Silvestri Cristian , Bacchetta Loretta , Bellincontro Andrea , Cristofori Valerio 
Published: June 2020

AbstractEuropean hazelnut (Corylus avellana L.) is a major species of interest for nutritional use within the Betulaceae family and its nuts are widely used throughout the world in the chocolate, confectionery, and bakery industries. Recently its cultivation has been expanded in traditional producer countries and established in new places in the southern hemisphere, including Chile, South Africa, and Australia. Introducing hazelnut in new environments could reduce its productivity, lead the trees to experience eco‐physiological disorders, and expose the crop to high pressure from common and new pests and diseases. Thus, new approaches in cultivar choice guidance, in the sustainable orchard management and even in nut storage and kernel quality evaluation are urgently required to improve the hazelnut production and processing chain. The main objective of this study was to systematize the published information regarding recent findings about the cultural operations that directly influence nut and kernel quality, support varietal choice for new plantations, and list the recent advances in nut storage and in quality and safety evaluation. © 2020 Society of Chemical Industry
Use of Shear Wave Elastography for Quantitative Assessment of Muscle Stiffness After Botulinum Toxin Injection in Children With Cerebral Palsy
Authors: Bertan Huseyin , Oncu Julide , Vanli Ersin , Alptekin Kerem , Sahillioglu Ali , Kuran Banu , Yilmaz Figen 
Published: June 2020

ObjectivesThis study aimed to investigate the stiffness of the gastrocnemius (GC) muscle with acoustic radiation force impulse (ARFI) elastography after botulinum toxin‐A (BTX‐A) injection in children with spastic cerebral palsy (CP) and to examine the relationship between elastographic and clinical parameters.MethodsThis prospective randomized single‐blind controlled clinical study included 49 lower extremities of 33 children with spastic CP. They were randomized into 2 groups: group 1 (n = 25 extremities in 17 children) received BTX‐A injection and a home‐based exercise program; group 2 (n = 24 extremities in 16 children) received only a home‐based exercise program. Patients were evaluated in pretreatment and posttreatment periods in the first and third months with ARFI elastography, the Modified Ashworth Scale, Modified Tardieu Scale, Pediatric Functional Independence Measure, Gross Motor Function Classification System, and goniometric range of motion measurement of the ankle.ResultsA statistically significant difference was found in elastography of the GC muscle in group 1 only at the first month after treatment (P < .05). No statistical difference was found in elastography of the GC after treatment in group 2. According to the Modified Ashworth Scale, Modified Tardieu Scale, and ankle passive range of motion, group 1 showed significant improvements after treatment (P < .05). Also, there was a significant correlation between these clinical parameters and elastographic measurements (P < .05).ConclusionsAccording to the results of this study, the measurements from ARFI elastography combined with clinical parameters might be useful for evaluation of spasticity after BTX‐A treatment in children with CP. Also, they might be useful in distinguishing patients who will benefit clinically, especially in the early stages of treatment.
Two hits to the renin‐angiotensin system may play a key role in severe COVID‐19
Authors: Tseng Yu‐Hsin , Yang Rei‐Cheng , Lu Tzong‐Shi 
Published: June 2020

AbstractThe spike glycoprotein on the virion surface docking onto the angiotensin‐converting enzyme (ACE) 2 dimer is an essential step in the process of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection in human cells—involves downregulation of ACE2 expression with systemic renin‐angiotensin system (RAS) imbalance and promotion of multi‐organ damage. In general, the RAS induces vasoconstriction, hypertension, inflammation, fibrosis, and proliferation via the ACE/Ang II/Ang II type 1 receptor (AT1R) axis and induces the opposite effects via the ACE2/Ang (1‐7)/Mas axis. The RAS may be activated by chronic inflammation in hypertension, diabetes, obesity, and cancer. SARS‐CoV‐2 induces the ACE2 internalization and shedding, leading to the inactivation of the ACE2/Ang (1‐7)/Mas axis. Therefore, we hypothesize that two hits to the RAS drives COVID‐19 progression. In brief, the first hit originates from chronic inflammation activating the ACE/Ang II/AT1R axis, and the second originates from the COVID‐19 infection inactivating the ACE2/Ang (1‐7)/Mas axis. Moreover, the two hits to the RAS may be the primary reason for increased mortality in patients with COVID‐19 who have comorbidities and may serve as a therapeutic target for COVID‐19 treatment.
Down regulation of miR‐218, miR‐124, and miR‐144 relates to Parkinson's disease via activating NF‐κB signaling
Authors: Xing Rui‐Xian , Li Long‐Guang , Liu Xue‐Wen , Tian Bu‐Xian , Cheng Yan 
Published: June 2020

AbstractParkinson's disease (PD) is a neurological degenerative disorder that is partially induced by inflammation in the neural system. To explore the roles of disordered microRNAs in the development of PD, we screened 10 miRNAs in the brain samples of 15 postmortem PD patients and 10 postmortem healthy controls by qRT‐PCR. The direct targets of miRNAs were predicted by informatics tools and further confirmed by dual luciferase assay and immunoblotting. The function of miRNAs in regulating NF‐κB/p65 translocation was examined by immunoblotting, and the overactivation of NF‐κB signaling was examined by ELISA. The relationship between dysregulated miRNAs and cytokines was analyzed by correlation analysis. Three miRNAs were found to be reduced in the brains of patients with PD. KPNB1, KPNA3, and KPNA4 were identified as direct targets of miR‐218, miR‐124, and miR‐144. Additionally, KPNA3 was identified as a direct target of miR‐124, and KPNA4 was a direct target of both miR‐124 and miR‐218. The p65 translocation from the cytoplasm to the nucleus was repressed by miR‐124, miR‐218, and miR‐144 in the SH‐SY5Y cells. The NF‐κB signaling pathway was overactivated after miRNA inhibitor transfection. The upregulation of KPNB1, KPNA3, and KPNA4 in the brain samples of PD patients was confirmed by immunoblotting, and negative correlations were found between dysregulated miRNAs and cytokines. In conclusion, we identified that the downregulation of miR‐218, miR‐124, and miR‐144 in the brain was related to PD via activation of NF‐κB signaling, helping to unveil the role played by dysregulated miRNAs in the pathogenesis of PD and provide new potential targets for PD treatment.
Metabolism in tumor microenvironment: Implications for cancer immunotherapy
Authors: Shi Rongchen , Tang Yi‐Quan , Miao Hongming 
Published: June 2020

AbstractTumor microenvironment is a special environment for tumor survival, which is characterized by hypoxia, acidity, nutrient deficiency, and immunosuppression. The environment consists of the vasculature, immune cells, extracellular matrix, and proteins or metabolic molecules. A large number of recent studies have shown that not only tumor cells but also the immune cells in the tumor microenvironment have undergone metabolic reprogramming, which is closely related to tumor drug resistance and malignant progression. Tumor immunotherapy based on T cells gives patients new hope, but faces the dilemma of low response rate. New strategies sensitizing cancer immunotherapy are urgently needed. Metabolic reprogramming can directly affect the biological activity of tumor cells and also regulate the differentiation and activation of immune cells. The authors aim to review the characteristics of tumor microenvironment, the metabolic changes of tumor‐associated immune cells, and the regulatory role of metabolic reprogramming in cancer immunotherapy.