bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimating Unreported COVID-19 Cases in the United States Based on the tvSIRu Model
Authors: Liu Lingbo , Hu Tao , Bao Shuming , Wu Hao , Peng Zhenghong , Wang Ru 
Published: October 2020

Abstract
BackgroundThe potential unreported infection may impair and mislead policymaking for COVID-19，and the contemporary spread of COVID-19 varies in different counties of the United States. It is necessary to estimate the cases that may be underestimated based on county-level data to take better countermeasures against COVID-19. We suggested taking time-varying SIR models with unreported infection rates (UIR)to estimate the factual COVID-19 cases in the United States.MethodsSIR integrated with unreported infection rates (SIRu) of fixed time effect and SIR with time-varying parameters (tvSIRu)were applied to estimate and compare the value of transmission rate(TR), UIR, and infection fatality rate (IFR) based on US county-level COVID-19 data. ResultsBased on US county-level COVID-19 data from January 22 (T1) to August 20 (T212) in 2020, SIRu was first tested and verified by a general OLS regression. The further regression of SIRu at the country-level showed that the average values of TR, UIR, and IFR were 0.034,19.5, 0.51% respectively. The range of TR, UIR, IFR of all states ranged were 0.007-0.157 (mean=0.048) ,7.31-185.6 (mean=38.89), and 0.04%-2.22% (mean=0.22%). Among time-varying transmission rate equations, the power function showed better fitness, which indicated a decline in TR decreasing from 227.58 (T1) to 0.022 (T212). The general equation of tvSIRu showed that both the UIR and IFR were gradually increasing, wherein, the UIR has an estimate of 9.1(95%CI = 5.7-14.0), and IFR was 0.70% (0.52%-0.95%) at T212.InterpretationDespite the decline in TR and IFR, the UIR of the United States is still on the rise, which had been supposed to decrease with sufficient tests or improved countersues. The US medical system may be largely affected by severe cases in the rapid spread of COVDI-19.
WITHDRAWN: Elementary Quadrature for the Riccati equation
Authors: Zhao Ji-Xiang 
Published: October 2020

Abstract
Using suitable transformation in combination with a specific Riccati-type equation solvable, the problem of solving Riccati equation can be transformed into that of a quasi-Abel equation of the second kind. By the extended Julia’s integrability condition, the general solutions of Riccati equation in the form of elementary quadrature are obtained, which contains numerous. This method opens up a new prospect for the study of nonlinear differential equations by analytical method.
Floristics and Structure of Arboreal Components in a Restored Atlantic Forest Area
Authors: Silva Wiane Meloni , Martins Sebastião Venâncio , Cruz Ricardo Alcántara de la , Torres Carlos Moreira Miquelino Eleto , Cosimo Luiz Henrique Elias , Zanuncio José Cola 
Published: October 2020

Abstract
Background: Coffee and livestock degrade Seasonal Semideciduous Forests in the Zona da Mata region of the Atlantic Forest biome in Brazil. The floristic composition must be studied to preserve and conserve forest remnants. The objective was to evaluate the arboreal structure, characterize the seed dispersal syndrome and the ecological group of forest species of a 45-year-old restored area in Viçosa, Minas Gerais state, Brazil. The phytosociological parameters density, frequency, dominance and importance value, Shannon's diversity and Pielou's equability were evaluated considering individuals with DBH (diameter at breast height) ≥ 5 cm in sixteen contiguous plots (25 x 25 m). Results: A total of 1,323 individuals from 109 species and 35 botanical families were registered, of which 90 were native and 15 exotic species. The importance value (VI= 11.9%) was highest for Guarea guidonia (Fabaceae). The Shannon's diversity (H') was 3.46 and the equability (J') was 0.74. The number of species (33%) was largest for the initial secondary successional class and the number of individuals with zoochoric dispersion syndrome for the late secondary class (38.3%). The basal area was 44.1 m² ha-1 and the average height was 13 m (ranging from 2 to 32 m). Conclusion: The restored Semideciduous Seasonal Forest is in an advanced successional stage with zoochoric species and a great number of late secondary species.
High concordance between next generation sequencing and single-nucleotide polymorphism array in preimplantation genetic testing for aneuploid
Authors: Ou Zhanhui , Chen Zhiheng , Deng Yu , Yin Minna , Sun Ling 
Published: October 2020

Abstract
Background: Single-nucleotide polymorphism array (SNP array) and next generation sequencing (NGS) in detecting chromosome aneuploidy are widely used in clinical work. Aims: To compare the concordance between NGS and SNP array in 67 embryos (from 23 couples). Methods: In the first part of the study, 28 blastocysts with unknown ploidy were both analyzed with NGS and SNP array. While in the second part, 39 with normal ploidy detected by NGS were re-analyzed with SNP array. Results: In the first part of the study, the concordance rate between NGS and SNP array was 92.9% (26/28). Among the 28 blastocysts, 18 were abnormal and 10 blastocysts were with normal ploidy status when analyzed by NGS. Among the 18 abnormal blastocysts, two blastocysts were with low level of mosaicism as analyzed by NGS, but euploid with SNP array. In the second part, concordance rate between NGS and SNP array was 100% (39/39). At last, one couple had no blastocyst to transfer. The other 22 couples were transferred with single blastocyst. Among them, two couples suffered abortions before 12 weeks, and the karyotype of villus was normal. One couple with only 1 normal blastocyst failed to conceive after the transfer. In total nineteen couples had healthy babies born. Conclusions: There was a high concordance rate between NGS and SNP array. But NGS was also able to detect mosaicism sensitively. Hence, using NGS for PGT-A may increase the chances of having a healthy and live newborn child.
Factors Related to ICU-Acquired Infections Incidence in Iran: Analysis of National Nosocomial Infections Registry Data
Authors: Izadi Neda , Eshrati Babak , Mehrabi Yadollah , Etemad Korosh , Hashemi-Nazari Seyed-Saeed 
Published: October 2020

Abstract
Background: Patients admitted to intensive care units (ICUs) are particularly susceptible to hospital-acquired infections (HAIs) and the HAIs are higher in the ICUs than other wards of the hospital. This study aimed at investigating factors associated with ICU-acquired infections incidence in Iran. Methods: In this multi-center study, Iranian nosocomial infections surveillance (INIS) and hospital statistics and information system (AVAB) were used to collect data on patients with HAIs in 2018. The data was expanded based on 12 months of the year (13,632 records in terms of "hospital-ward-month") and then, the last observation carried forward method was used to replace the missing data. The generalized negative binomial regression with “patient-days” as an offset variable was used to identify the factors affecting ICU-acquired infections incidence.Results: The median age of patients was 57.5 (IQR=55.09) years. Of the 22.92%, 5.76%, 13.62%, 43.41%, and 14.29% of patients were in NICU, PICU, internal ICU, general ICU, and surgical ICU, respectively. Only 13.73% of hospitals were in efficient zone (zone III). Based on multivariable regression, the number of death (IRR=1.02), the number of infections due to the device (catheters and ventilators) (IRR=1.1), ward type (PICU (IRR=1.58), internal ICU (IRR=1.63), general ICU (IRR=1.53) and surgical ICU (IRR=1.47)), hospital's expertise, hospital's accreditation, bed occupancy rate indicator (IRR=1.17 for moderate conditions) were associated with an increase of ICU-acquired infections incidence. Infection due to ventilator, infection due to catheter, and the number of surgery in hospitals reduced 5%, 7%, and 1% incidence of infections, respectively. Conclusions: Based on the results, the most common ICU-acquired infections were VAE and UTI. Therefore due to the high sensitivity of intensive care units, full hygiene should be taught to the medical staff, especially the ICU wards. Ventilators and catheters should be used in special circumstances and minimum duration.
Crocetin suppresses angiogenesis through inhibiting Sonic hedgehog signaling pathway in gastric cancer
Authors: Zhou Ye , Zang Mingde , Hou Junyi , Wang Jiangli , Huang Yakai , Ding Xusheng , Wang Yanong 
Published: October 2020

Abstract
BackgroundCrocetin is an active component of saffron stigma, which has important therapeutic effects on various diseases including tumors, arthritis, hemorrhages, etc. However, the effects of crocetin on gastric cancer (GC) cells and their underlying mechanisms remain unclear.MethodsCell counting kit‑8 (CCK‑8), transwell assays, F-actin staining, tube formation and vasculogenic mimicry (VM) assays were used to examine the effects of crocetin on cell proliferation, migration and angiogenesis in GC. Enzyme linked immunosorbent assay (ELISA) and Western blot assay were performed to evaluate expression level of Sonic hedgehog (Shh) signaling and activation of epithelial‑mesenchymal transition (EMT) in GC cells treated with or without crocetin. Proliferation of xenograft tumors was detected by immunohistochemistry. ResultsCrocetin significantly inhibited tube formation of human umbilical vein endothelial (HUVEC) cells and VM formation of GC cells, as well as its proliferation, invasion and migration. Crocetin destroyed cytoskeleton and mosaic vessels formed by HUVEC and GC cells. Furthermore, we found that crocetin suppressed cell proliferation, migration, EMT, tube and VM formation through inhibiting Shh signaling pathway. Utilization of recombinant Shh reversed the suppressing effects of crocetin on cell proliferation, migration, angiogenesis and EMT. In addition, anti-tumor effect of crocetin was confirmed in xenograft tumors.ConclusionsCrocetin suppressed GC progression by inhibiting cell proliferation, migration and angiogenesis including tubes formed by HUVEC cells and VM vessels formed by GC cells, which were mediated by suppressing Shh signaling pathway. These results indicated that crocetin may function as an effective therapeutic drug against GC.
RDH10 and ATRA sensitize triple-negative breast cancer to taxane-based chemotherapy through regulation of PIN1
Authors: Grainger Jordan , Zhang Lingxin , Yu Jia , Vedell Peter T , Thompson Kevin , Kalari Krishna R , Suman Vera J , Boughey Judy C , Goetz Matthew P , Wang Liewei 
Published: October 2020

Abstract
Background: With few targeted therapies available for triple-negative breast cancer (TNBC), there is a critical need to identify biomarkers that can predict chemotherapy-response. Copy number amplifications (CNAmps) have been implicated in tumorigenesis, progression, and treatment response. Previously, we performed a prospective neoadjuvant chemotherapy study (BEAUTY) and identified a 5 Mb CNAmp in TNBC patients associated with pathological complete response rates to taxane- and anthracycline-based chemotherapy. Here we further interrogated this amplicon and its role in chemotherapy response. Methods: Using siRNA screening of genes identified in the 5 Mb CNAmp, followed by cytotoxicity assays, we identified RDH10 significantly associated with chemo-sensitivity in TNBC cell lines. Functional studies were performed using RDH10 knockdown or overexpression followed by cytotoxicity, cell proliferation, luciferase reporter assays, HPLC or western blot.Results: RDH10 is a rate-limiting step involved in the synthesis of all-trans retinoic acid (ATRA) - the active metabolite of retinoid metabolism that is frequently aberrant in cancer. Previous studies demonstrated ATRA to be a potent inhibitor of PIN1, a key regulator of several oncogenic signaling pathways often amplified in TNBC. We discovered that genetic manipulation of RDH10 affected ATRA intracellular concentrations, contributing to PIN1 degradation and taxane-response. Furthermore, co-treatment of TNBC cells with ATRA significantly increased taxane-sensitivity.Conclusion: RDH10 amplification increases endogenous levels of ATRA and degrades PIN1 in TNBC. ATRA-mediated degradation of PIN1 sensitizes TNBC to chemotherapy, suggesting that RDH10 may be a novel biomarker of taxane response and the addition of ATRA to standard chemotherapy may improve chemo-sensitivity.
Ice XIX: The second hydrogen-ordered polymorph related to ice VI
Authors: Gasser Tobias , Thoeny Alexander , Fortes Andrew , Loerting Thomas 
Published: October 2020

Abstract
We here report ex situ calorimetry and high-resolution neutron powder diffraction data of a novel ice polymorph produced at 1.8 GPa and recovered to ambient pressure at 80 K. Ice XIX, previously called ice β-XV by us, is shown to be partially hydrogen-ordered and crystallising in a √2 x √2 × 1 supercell with respect to the parent ice VI phase. Our powder data match two nearly degenerate structural models in space-groups \(P\stackrel{-}{4}\) and Pcc2, in which the water molecules are partially antiferroelectrically ordered. Key to the synthesis of deuterated ice XIX is the use of DCl as dopant and the use of a D2O/H2O mixture, where the small H2O fraction nucleates ice XIX. This provides the basis to study the first order-order transition known in ice physics, from ice XIX to its sibling ice XV at ambient pressure. It proceeds via a transition state, ice VI‡, which contains a disordered H-sublattice, whereas both ice XIX and ice XV are fully crystalline.
Prognostic nomogram for patients with invasive endocervical adenocarcinoma incorporating HPV E6/E7 mRNA in situ hybridization and clinical characteristics
Authors: Liu Li-Li , Chen Shu-Lin , Yan Shu-Mei , Li Yue , Yang Xia , Zhang Shi-Wen , Yang Hai-Xia , Wan Ting , Luo Rong-Zhen 
Published: October 2020

Abstract
Background: Human papillomavirus (HPV) E6/E7 mRNA in situ hybridization (HPV E6/E7 RNAscope) appears to be a sensitive and specific method. We aimed to examine the diagnostic and prognostic utility of this technique in endocervical adenocarcinoma (ECA) and build a useful prognostic nomogram model using this approach. Methods: The model was constructed from a retrospective study of 200 patients with ECA who had undergone surgery at Sun Yat-sen University Cancer Center between 2010 and 2014. The model's predictive efficiency and discriminative capability were defined by a concordance index (C-index) and calibration curve. Results: The overall sensitivity and specificity of HPV E6/E7 RNAscope for distinguishing HPV-associated adenocarcinoma (HPVA) from non HPV-associated adenocarcinoma (NHPVA) in the whole cohort were 75.8% and 80%, respectively, compared to 60.2% and 90.0% for p16 immunohistochemistry, 80.5% and 80.0% for HPV DNA, and 63.3% and 50% for HPV genotype. The independent factors derived from multivariable analysis of the whole cohort to predict overall survival (OS) were age, lymphovascular invasion (LVI), lymph node involvement (LNI), and HPV E6/E7 RNAscope, which were all incorporated into the nomogram with (nomogram B) or without (nomogram A) FIGO stage and treatment. The C-index of nomogram A for predicting OS was 0.825 (p = 0.002 and p < 0.001), which was significantly higher than the C-index for FIGO stage (0.653) and treatment (0.578). No significant difference occurred between nomograms A (0.825) and B (0.836). Furthermore, a risk stratification system was established to accurately stratify patients with ECA into two subgroups with significantly different prognosis. Conclusions: HPV E6/E7 RNAscope is highly specific for ECA, and the proposed nomogram using HPV E6/E7 RNAscope showed more accurate outcome in terms of prognosis in patients with ECA.
Integrated weighted gene co-expression network analysis identified that TLR2 and CD40 are related to coronary artery disease
Authors: Qi Bin , Chen Jian-Hong , Tao Lin , Zhu Chuan-Meng , Wang Yong , Deng Guo-Xiong , Miao Liu 
Published: October 2020

Abstract
Background: The current research attempted to identify possible hub genes and pathways of coronary artery disease (CAD) and to detect the possible mechanisms.Methods: Array data from GSE90074 were downloaded from the Gene Expression Omnibus (GEO) database. Integrated weighted gene co-expression network analysis (WGCNA) was performed to analyze the gene module and clinical characteristics. Gene Ontology annotation, Disease Ontology and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed by clusterProfiler and the DOSE package in R. A protein-protein interaction (PPI) network was established using Cytoscape software, and significant modules were analyzed using Molecular Complex Detection to identify hub genes. Then, further functional validation of hub genes in other microarrays and population samples was performed, and survival analysis was performed to investigate the prognosis.Results: A total of 660 genes were located in three modules and associated with CAD. GO functions identified 484 biological processes, 39 cellular components, and 22 molecular functions with an adjusted P < 0.05. Approximately 38 pathways were enriched in KEGG pathway analysis, and 147 DO items were identified with an adjusted P < 0.05 (false discovery rate, FDR set at < 0.05). There were a total of four modules with a score > 10 after PPI network analysis using the MCODE app, and two hub genes (TLR2 and CD14) were identified. Then, we validated the information from the GSE60993 dataset using the GSE59867 dataset and population samples, and we found that these two genes were associated with plaque vulnerability. These two genes varied at different time points after myocardial infarction, and both of them had the lowest prognosis of heart failure when they were expressed at low levels.Conclusion: We performed an integrated WGCNA and validated that TLR2 and CD14 were closely associated with the severity of coronary artery disease, plaque instability and the prognosis of heart failure after myocardial infarction.
Transposable Element Subfamily Annotation is Unreliable in Biological Replicates
Authors: Carey Kaitlin , Patterson Gilia , Wheeler Travis J 
Published: October 2020

Abstract
Background: Transposable element (TE) sequences are classified into families based on the reconstructed history of replication, and into subfamilies based on more fine-grained features that in some cases capture family history, and in other cases are simply intended to improve annotation sensitivity. We evaluate the reliability of annotation with common subfamilies by assessing the extent to which subfamily annotation is reproducible in replicate copies created by segmental duplications in the human genome, and in homologous copies shared by human and chimpanzee.Results: We find that standard methods annotate over 10% of replicates as belonging to different subfamilies, despite the fact that they are expected to be annotated as belonging to the same subfamily. Point mutations and homologous recombiniation appear to be responsible for some of this discordant annotation (particularly in the young Alu family), but are unlikely to fully explain the annotation unreliability.Conclusions: The surprisingly high level of disagreement in subfamily annotation of homologous sequence highlights a need for further research into definition of TE subfamilies, methods for representing subfamily annotation confidence of TE instances, and approaches to better utilizing such nuanced annotation data in downstream analysis.
Identification of novel inhibitors of Angiotensin-converting enzyme 2 (ACE-2) receptor from Urtica dioica to combat coronavirus disease 2019 (COVID-19)
Authors: Upreti Shobha , Prusty Jyoti Sankar , Pandey Satish Chandra , Kumar Awanish , Samant Mukesh 
Published: October 2020

Abstract
The pandemic outbreak of coronavirus (SARS-CoV-2) is rapidly spreading across the globe, so the development of anti-SARS-CoV-2 agents is urgently needed. Angiotensin-converting enzyme 2 (ACE-2), a human receptor that facilitates entry of SARS-CoV-2, serves as a prominent target for drug discovery. In the present study, we have applied the bioinformatics approach for screening of a series of bioactive chemical compounds from Himalayan stinging nettle (Urtica dioica) as potent inhibitors of ACE-2 receptor (PDB ID: 1R4L). The molecular docking was applied to dock a set of representative compounds within the active site region of target receptor protein using 0.8 version of the PyRx virtual screen tool and analyzed by using discovery studio visualizer. Based on the highest binding affinity, 16 compounds were shortlisted as a lead molecule using molecular docking analysis. Among them, β-sitosterol was found with the highest binding affinity -12.2 Kcal/mol and stable interactions with the amino acid residues present on the active site of the ACE-2 receptor. Similarly, Luteoxanthin and Violaxanthin followed by rutin also displayed stronger binding efficiency. We propose these compounds as potential lead candidates for the development of target specific therapeutic drugs against COVID-19.
Rapid Electrochemical Detection of Coronavirus SARS-CoV-2.
Authors: Chaibun Thanyarat , Puenpa Jiratchaya , Ngamdee Tatchanun , Boonapatcharoen Nimaradee , Athamanolap Pornpat , O’Mullane Anthony Peter , Vongpunsawad Sompong , Poovorawan Yong , Yin Lee Su , Lertanantawong Benchaporn 
Published: October 2020

Abstract
COVID-19 is a highly contagious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Diagnosis of COVID-19 depends on quantitative reverse transcription PCR (qRT-PCR), which is time-consuming and requires expensive instrumentation. Here, we report an ultrasensitive electrochemical biosensor based on isothermal rolling circle amplification (RCA) for rapid detection of SARS-CoV-2. The assay involves the hybridization of the RCA amplicons with probes that were functionalized with redox active labels that are detectable by an electrochemical biosensor. The one-step sandwich hybridization assay could detect as low as 1 copy/mL of N and S genes, in less than 2 hours. Sensor evaluation with 105 clinical samples, including 40 SARS-CoV-2 positive and 9 samples positive for other respiratory viruses, gave a 100% concordance result with qRT-PCR, with complete correlation between the biosensor current signals and quantitation cycle (Cq) values. In summary, this biosensor could be used as an on-site, real-time diagnostic test for COVID-19.