bluuebunny/crossref_metadata_2025_split huggingface dataset:
Olfactory Dysfunction and Sinonasal Symptomatology in COVID‐19: Prevalence, Severity, Timing, and Associated Characteristics
Authors: Speth Marlene M. , Singer‐Cornelius Thirza , Oberle Michael , Gengler Isabelle , Brockmeier Steffi J. , Sedaghat Ahmad R. 
Published: May 2020

ObjectiveOlfactory dysfunction (OD)—hyposmia or anosmia—is a symptom of coronavirus disease 2019 (COVID‐19), caused by the novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). We sought to better determine prevalence, severity, and timing of OD in COVID‐19 relative to other sinonasal and pulmonary symptoms.Study DesignProspective, cross‐sectional.SettingRegional/cantonal hospital.SubjectsIn total, 103 patients diagnosed with COVID‐19 with reverse transcription polymerase chain reaction (RT‐PCR)–based testing.MethodsAll patients testing positive for COVID‐19 at Kantonsspital Aarau over a 6‐week period were approached. Timing and severity (at its worst, on scale of 0 [none], 1 [mild], 2 [moderate], and 3 [severe]) of OD, loss of taste, nasal obstruction, rhinorrhea/mucus production, fever, cough and shortness of breath (SOB) were assessed for each patient.ResultsPrevalence of OD was 61.2%, and severity of OD was strongly correlated with severity of loss of taste experienced (ρ = 0.87, P <. 001). OD was experienced on the first day of COVID‐19 by 8.7% and overall occurred at median infection day 3 (mean, 3.4; range, 0‐12). Most experiencing OD reported anosmia, and mean severity of all with OD was moderate to severe (mean [SD], 2.7 [0.6]). Nasal obstruction (49.5%) and rhinorrhea (35.0%) were frequently reported but not correlated with OD. SOB was more severe in patients with OD. OD was associated negatively with older age (OR, 0.96; 95% CI, 0.93‐0.99; P =. 007) and positively with female sex (OR, 2.46; 95% CI, 0.98‐6.19; P =. 056).ConclusionsOD is highly prevalent during COVID‐19, occurring early and severely, often in conjunction with loss of taste. OD is associated negatively with older age and positively with female sex. Patients with OD may also experience more severe SOB.
Cadaveric Simulation of Endoscopic Endonasal Procedures: Analysis of Droplet Splatter Patterns During the COVID‐19 Pandemic
Authors: Sharma Dhruv , Rubel Kolin E. , Ye Michael J. , Shipchandler Taha Z. , Wu Arthur W. , Higgins Thomas S. , Burgin Sarah J. , Ting Jonathan Y. , Illing Elisa A. 
Published: May 2020

ObjectiveThe primary mode of viral transmission of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) is thought to occur through the spread of respiratory droplets. The objective of this study was to investigate droplet and splatter patterns resulting from common endoscopic endonasal procedures.Study DesignCadaver simulation series.SettingDedicated surgical laboratory.Subjects and MethodsAfter instilling cadaver head specimens (n = 2) with fluorescein solution, endoscopic endonasal procedures were systematically performed to evaluate the quantity, size, and distance of droplets and splatter following each experimental condition.ResultsThere were no observable fluorescein droplets or splatter noted in the measured surgical field in any direction after nasal endoscopy, septoplasty with microdebrider‐assisted turbinoplasty, cold‐steel functional endoscopic sinus surgery (FESS), and all experimental conditions using an ultrasonic aspirator. Limited droplet spread was noted with microdebrider FESS (2 droplets, <1 mm in size, within 10 cm), drilling of the sphenoid rostrum with a diamond burr (8, <1 mm, 12 cm), and drilling of the frontal beak with a cutting burr (5, <1 mm, 9 cm); however, the use of concurrent suction while drilling resulted in no droplets or splatter. The control condition of external activation of the drill resulted in gross contamination (11, 2 cm, 13 cm).ConclusionOur results indicate that there is very little droplet generation from routine rhinologic procedures. The droplet generation from drilling was mitigated with the use of concurrent suction. Extreme caution should be used to avoid activating powered instrumentation outside of the nasal cavity, which was found to cause droplet contamination.
Management of the Clinical and Academic Mission in an Urban Otolaryngology Department During the COVID‐19 Global Crisis
Authors: Batra Pete S. , LoSavio Phillip S. , Michaelides Elias , Revenaugh Peter C. , Tajudeen Bobby A. , Al‐khudari Samer , Husain Inna , Papagiannopoulos Peter , Smith Ryan , Stenson Kerstin M. , Wiet R. Mark 
Published: May 2020

ObjectiveThe objective of this study was to assess the strategic changes implemented in the departmental mission to continue safe delivery of otolaryngology care and to support the broader institutional mission during the COVID‐19 pandemic response.Study DesignRetrospective assessment was performed to the response and management strategy developed to transform the clinical and academic enterprise.SettingLarge urban tertiary care referral center.ResultsThe departmental structure was reorganized along new clinical teams to effectively meet the system directives for provision of otolaryngology care and support for inpatient cases of COVID‐19. A surge deployment schedule was developed to assist frontline colleagues with clinical support as needed. Outpatient otolaryngology was consolidated across the system with conversion of the majority of visits to telehealth. Operative procedures were prioritized to ensure throughput for emergent and time‐critical urgent procedures. A tracheostomy protocol was developed to guide management of emergent and elective airways. Educational and research efforts were redirected to focus on otolaryngology care in the clinical context of the COVID‐19 crisis.ConclusionEmergence of the COVID‐19 global health crisis has challenged delivery of otolaryngology care in an unparalleled manner. The concerns for preserving health of the workforce while ethically addressing patient career needs in a timely manner has created significant dilemmas. A proactive, thoughtful approach that reorganizes the overall departmental effort through provider and staff engagement can facilitate the ability to meet the needs of otolaryngology patients and to support the greater institutional mission to combat the pandemic.
Factors Associated With Intubation and Prolonged Intubation in Hospitalized Patients With COVID‐19
Authors: Hur Kevin , Price Caroline P. E. , Gray Elizabeth L. , Gulati Reeti K. , Maksimoski Matthew , Racette Samuel D. , Schneider Alexander L. , Khanwalkar Ashoke R. 
Published: May 2020

ObjectiveTo identify risk factors associated with intubation and time to extubation in hospitalized patients with coronavirus disease 2019 (COVID‐19).Study DesignRetrospective observational study.SettingTen hospitals in the Chicago metropolitan area.Subjects and MethodsPatients with laboratory‐confirmed COVID‐19 admitted between March 1 and April 8, 2020, were included. We evaluated sociodemographic and clinical characteristics associated with intubation and prolonged intubation for acute respiratory failure secondary to COVID‐19 infection.ResultsOf the 486 hospitalized patients included in the study, the median age was 59 years (interquartile range, 47‐69); 271 (55.8%) were male; and the median body mass index was 30.6 (interquartile range, 26.5‐35.6). During the hospitalization, 138 (28.4%) patients were intubated; 78 (56.5%) were eventually extubated; 21 (15.2%) died; and 39 (28.3%) remained intubated at a mean ± SD follow‐up of 19.6 ± 6.7 days. Intubated patients had a significantly higher median age (65 vs 57 years, P <. 001) and rate of diabetes (56 [40.6%] vs 104 [29.9%], P =. 031) as compared with nonintubated patients. Multivariable logistic regression analysis identified age, sex, respiratory rate, oxygen saturation, history of diabetes, and shortness of breath as factors predictive of intubation. Age and body mass index were the only factors independently associated with time to extubation.ConclusionIn addition to clinical signs of respiratory distress, patients with COVID‐19 who are older, male, or diabetic are at higher risk of requiring intubation. Among intubated patients, older and more obese patients are at higher risk for prolonged intubation. Otolaryngologists consulted for airway management should consider these factors in their decision making.
Identification of patients with embolic stroke of undetermined source and low risk of new incident atrial fibrillation: The AF-ESUS score
Authors: Ntaios George , Perlepe Kalliopi , Lambrou Dimitris , Sirimarco Gaia , Strambo Davide , Eskandari Ashraf , Karagkiozi Efstathia , Vemmou Anastasia , Korompoki Eleni , Manios Efstathios , Makaritsis Konstantinos , Vemmos Konstantinos , Michel Patrik 
Published: May 2020

Background and aims Only a minority of patients with Embolic Stroke of Undetermined Source (ESUS) receive prolonged cardiac monitoring despite current recommendations. The identification of ESUS patients who have low probability of new diagnosis of atrial fibrillation (AF) could potentially support a strategy of more individualized allocation of available resources and hence, increase their diagnostic yield. We aimed to develop a tool that can identify ESUS patients who have low probability of new incident AF. Methods We performed multivariate stepwise regression in a pooled dataset of consecutive ESUS patients from three prospective stroke registries to identify predictors of new incident AF. The coefficient of each independent covariate of the fitted multivariable model was used to generate an integer-based point scoring system. Results Among 839 patients (43.1% women, median age 67.0 years) followed-up for a median of 24.3 months (2999 patient-years), 125 (14.9%) had new incident AF. The proposed score assigns 3 points for age ≥ 60 years; 2 points for hypertension; −1 point for left ventricular hypertrophy reported at echocardiography; 2 points for left atrial diameter >40 mm; −3 points for left ventricular ejection fraction <35%; 1 point for the presence of any supraventricular extrasystole recorded during all available 12-lead standard electrocardiograms performed during hospitalization for the ESUS; −2 points for subcortical infarct; −3 points for the presence of non-stenotic carotid plaques. The rate of new incident AF during follow-up was 1.97% among the 42.3% of the cohort who had a score of ≤0, compared to 26.9% in patients with > 0 (relative risk: 13.7, 95%CI: 5.9--31.5). The area under the curve of the score was 84.8% (95%CI: 79.9--86.9%). The sensitivity and negative predictive value of a score of ≤0 for new incident AF during follow-up were 94.9% (95%CI: 89.3--98.1%) and 98.0% (95%CI: 95.8--99.3%), respectively. Conclusions The proposed AF-ESUS score has high sensitivity and high negative predictive value to identify ESUS patients who have low probability of new incident AF. Patients with a score of 1 or more may be better candidates for prolonged automated cardiac monitoring. Clinical trial registration URL: https://www.clinicaltrials.gov / Unique identifier: NCT02766205.
Surgical Treatment of Ossifications of the Cervical Anterior Longitudinal Ligament: A Retrospective Cohort Study
Authors: Glinski Alexander von , Takayanagi Ariel , Elia Christopher , Ishak Basem , Listmann Mishan , Pierre Clifford A. , Blecher Ronen , Hayman Erik , Chapman Jens R. , Oskouian Rod J. 
Published: May 2020

Study Design: Retrospective cohort study Objectives: The study aims to evaluate anterior cervical discectomy and fusion (ACDF) in the treatment of patients with ossification of the anterior longitudinal ligament (OALL). Methods: We retrospectively reviewed cases performed at our institution between January 2015 and December 2018; adult (age ≥18 years) patients who underwent anterior cervical decompression and fusion in the presence of dysphagia and OALL. Ten patients (9 male, 1 female, mean age 64.4 years) with OALL who underwent ACDF were included. Charts were reviewed for demographics and comorbidities. Primary outcomes assessed were intra- and postoperative complications. Secondary outcomes were fusion rates, instrumentation failure, postsurgical instability/deformity, and readmission rates. Results: The average duration of symptoms prior to surgery was 12.3 months. All patients presented with dysphagia (mean Bazaz score 2.0). The average number of levels with OALL was 4.7 (±1.67). All patients underwent ACDF and 3 patients underwent additional posterior cervical fusion for kyphotic deformity correction or when extensive laminectomy was required. We did not encounter any intraoperative complications. Eight patients (72%) had solid fusion demonstrated on the lateral x-rays and no evidence of progressive kyphotic deformity. We did not encounter any instrumentation failure or loosening. Two patients developed recurrence of dysphagia (Bazaz scores 2 and 3 respectively). Conclusion: ACDF for OALL with dysphagia and concomitant myelopathy in our small series of 10 patients demonstrate good fusion and clinical outcomes. Larger studies will be necessary to determine the optimal treatment for patients with dysphagia due to OALL.
Dissent with modification: how postcreationism’s claim of hyperrapid speciation opposes yet embraces evolutionary theory
Authors: Duff R. Joel , Beatman Thomas R. , MacMillan David S. 
Published: May 2020

AbstractThe development of creationism to its multiple modern forms has been made possible in part by its appropriation and misuse of mainstream scientific terms. Here we illustrate how anti-evolutionary advocates have redefined the terms macroevolution and microevolution to advance their view of the origins of biological diversity. We identify and describe an ideological movement within modern young-earth creationism we call postcreationism, those that have embraced a hyperrapid speciation model of the origin of biological diversity. Postcreationism is demonstrated with specific examples from young-earth creationist publications and Ark Encounter creationist theme park, with takeaways for addressing these ideas in evolutionary biology education.
Enhancing SVM for survival data using local invariances and weighting
Authors: Sanz Hector , Reverter Ferran , Valim Clarissa 
Published: May 2020

AbstractBackgroundThe necessity to analyze medium-throughput data in epidemiological studies with small sample size, particularly when studying biomedical data may hinder the use of classical statistical methods. Support vector machines (SVM) models can be successfully applied in this setting because they are a powerful tool to analyze data with large number of predictors and limited sample size, especially when handling binary outcomes. However, biomedical research often involves analysis of time-to-event outcomes and has to account for censoring. Methods to handle censored data in the SVM framework can be divided into two classes: those based on support vector regression (SVR) and those based on binary classification. Methods based on SVR seem to be suboptimal to handle sparse data and yield results comparable to Cox proportional hazards model and kernel Cox regression. The limited work dedicated to assess methods based on of SVM for binary classification has been based on SVM learning using privileged information and SVM with uncertain classes.ResultsThis paper proposes alternative methods and extensions within the binary classification framework, specifically, a conditional survival approach for weighting censored observations and a semi-supervised SVM with local invariances. Using simulation studies and some real datasets, we evaluate those two methods and compare them with a weighted SVM model, SVM extensions found in the literature, kernel Cox regression and Cox model.ConclusionsOur proposed methods perform generally better under a wide variety of realistic scenarios about the structure of biomedical data. Specifically, the local invariances method using the conditional survival approach is the most robust method under different scenarios and is a good approach to consider as an alternative to other time-to-event methods. When analysing real data is a method to be considered and recommended since outperforms other methods in proportional and non-proportional scenarios and sparse data, which is something usual in biomedical data and biomarkers analysis.
fcScan: a versatile tool to cluster combinations of sites using genomic coordinates
Authors: El-Kurdi Abdullah , Khalil Ghiwa Ali , Khazen Georges , Khoueiry Pierre 
Published: May 2020

Abstract
Background
Finding combinations of homotypic or heterotypic genomic sites obeying a specific grammar in DNA sequences is a frequent task in bioinformatics. A typical case corresponds to the identification of cis-regulatory modules characterized by a combination of transcription factor binding sites in a defined window size. Although previous studies identified clusters of genomic sites in species with varying genome sizes, the availability of a dedicated and versatile tool to search for such clusters is lacking.

Results
We present fcScan, an R/Bioconductor package to search for clusters of genomic sites based on user defined criteria including cluster size, inter-cluster distances and sites order and orientation allowing users to adapt their search criteria to specific biological questions. It supports GRanges, data frame and VCF/BED files as input and returns data in GRanges format. By performing clustering on vectorized data, fcScan is adapted to search for genomic clusters in millions of sites as input in short time and is thus ideal to scan data generated by high throughput methods including next generation sequencing.

Conclusions
fcScan is ideal for detecting cis-regulatory modules of transcription factor binding sites with a specific grammar as well as genomic loci enriched for mutations. The flexibility in input parameters allows users to perform searches targeting specific research questions. It is released under Artistic-2.0 License. The source code is freely available through Bioconductor (https://bioconductor.org/packages/fcScan) and GitHub (https://github.com/pkhoueiry/fcScan).
Knock-out of TERMINAL FLOWER 1 genes altered flowering time and plant architecture in Brassica napus
Authors: Sriboon Sukarkarn , Li Haitao , Guo Chaocheng , Senkhamwong Thaveep , Dai Cheng , Liu Kede 
Published: May 2020

Abstract
Background
TERMINAL FLOWER 1 (TFL1) is a member of phosphatidylethanolamine-binding protein (PEBP) family, which plays an important role in the determination of floral meristem identity and regulates flowering time in higher plants.

Results
Five BnaTFL1 gene copies were identified in the genome of Brassica napus. The phylogenetic analysis indicated that all five BnaTFL1 gene copies were clustered with their corresponding homologous copies in the ancestral species, B. rapa and B. oleracea. The expression of the BnaTFL1s were confined to flower buds, flowers, seeds, siliques and stem tissues and displayed distinct expression profiles. Knockout mutants of BnaC03.TFL1 generated by CRISPR/Cas9 exhibited early flowering phenotype, while the knockout mutants of the other gene copies had similar flowering time as the wild type. Furthermore, knock-out mutants of individual BnaTFL1 gene copy displayed altered plant architecture. The plant height, branch initiation height, branch number, silique number, number of seeds per silique and number of siliques on the main inflorescence were significantly reduced in the BnaTFL1 mutants.

Conclusions
Our results indicated that BnaC03.TFL1 negatively regulates flowering time in B. napus. BnaC03.TFL1 together with the other BnaTFL1 paralogues are essential for controlling the plant architecture.
Anti-inflammatory activity of berberine in non-alcoholic fatty liver disease via the Angptl2 pathway
Authors: Lu Zengsheng , He Beihui , Chen Zhiyun , Yan Maoxiang , Wu Liyan 
Published: May 2020

Abstract
Background
Nonalcoholic fatty liver disease (NAFLD) has become the most common liver disease worldwide. Recent studies have shown that the Angptl2 pathway mediated hepatic inflammatory response plays an important role in the progression of nonalcoholic fatty liver disease. Our study investigated the possible molecular mechanisms of berberine (BBR) in the treatment of the liver inflammatory response in the livers of rats with high-fat diet-induced NAFLD via the Angptl2 pathway.

Results
At the end of 12 weeks, compared with the control group rats, the high-fat- diet group rats showed obvious pathological and biochemical changes. The levels of pro-infalmmatory cytokines (CCL2, TNF-α) were increased, the infiltration of inflammatory cells (CCR2) was elevated, and the hepatic mRNA and protein levels of Angptl2, NF-κB and Foxo1 were increased to different degrees. Nevertheless, following treatment with BBR, liver tissue pathology, biochemical data, and Angptl2 pathway-related genes expression were significantly ameliorated.

Conclusions
Our findings demonstrate that BBR might attenuate the liver inflammatory response in the livers of rats with high-fat diet-induced NAFLD through the regulation of the Angptl2 pathway.
Allele mining unlocks the identification of RYMV resistance genes and alleles in African cultivated rice
Authors: Pidon Hélène , Chéron Sophie , Ghesquière Alain , Albar Laurence 
Published: May 2020

Abstract
Background
Rice yellow mottle virus (RYMV) is a major rice pathogen in Africa. Three resistance genes, i.e. RYMV1, RYMV2 and RYMV3, have been previously described. RYMV1 encodes the translation initiation factor eIF(iso)4G1 and the best candidate genes for RYMV2 and RYMV3 encode a homolog of an Arabidopsis nucleoporin (CPR5) and a nucleotide-binding domain and leucine-rich repeat containing domain (NLR) protein, respectively. High resistance is very uncommon in Asian cultivated rice (Oryza sativa), with only two highly resistant accessions identified so far, but it is more frequent in African cultivated rice (Oryza glaberrima).

Results
Here we report the findings of a resistance survey in a reference collection of 268 O. glaberrima accessions. A total of 40 resistant accessions were found, thus confirming the high frequency of resistance to RYMV in this species. We analysed the variability of resistance genes or candidate genes in this collection based on high-depth Illumina data or Sanger sequencing. Alleles previously shown to be associated with resistance were observed in 31 resistant accessions but not in any susceptible ones. Five original alleles with a frameshift or untimely stop codon in the candidate gene for RYMV2 were also identified in resistant accessions. A genetic analysis revealed that these alleles, as well as T-DNA insertions in the candidate gene, were responsible of RYMV resistance. All 40 resistant accessions were ultimately linked to a validated or candidate resistance allele at one of the three resistance genes to RYMV.

Conclusion
This study demonstrated that the RYMV2 resistance gene is homologous to the Arabidopsis CPR5 gene and revealed five new resistance alleles at this locus. It also confirmed the close association between resistance and an amino-acid substitution in the leucine-rich repeat of the NLR candidate for RYMV3. We also provide an extensive overview of the genetic diversity of resistance to RYMV in the O. glaberrima species, while underlining the contrasted pattern of diversity between O. glaberrima and O. sativa for this trait. The different resistance genes and alleles will be instrumental in breeding varieties with sustainable field resistance to RYMV.