bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quality of Otology and Neurotology Research in Otolaryngology Journals
Authors: Socolovsky Leandro D. , Krishnan Pavan , Ramraj Rahul , Retnam Reuben , Sima Adam , Bauschard Michael J. , Coelho Daniel H. 
Published: June 2020

Objective:
To identify trends in the quality of otology studies published in general otolaryngology journals over a 20-year period.

Study Design:
Retrospective analysis.

Methods:
Otologic and neurotologic papers from 1997, 2007, and 2017 were identified in the three general otolaryngology journals with the highest Eigenfactor scores: the Laryngoscope, European Archives of Otorhinolaryngology, and Otolaryngology–Head and Neck Surgery. The studies were reviewed and assigned level of evidence (LoE) based on standards set by the Centres for Evidence Based Medicine (CEBM). One-way analysis of variance were calculated with a 95% bootstrap sensitivity analysis performed.

Results:
A total of 786 otology articles were reviewed for level of evidence, of which 557 (70.8%) were original, clinical research, eligible for LoE assignation. Total publications increased for each year in all three journals. Both the absolute number and proportion of high evidence studies (level of evidence 1 and 2) increased with respect to time in all three journals. Lower evidence studies (level of evidence 3, 4, or 5) made up 66.8% of total publications in 2017. There was a reduction in average level of evidence (towards higher quality evidence) by 0.431 units from 1997 to 2017 (Diff = –0.431 between 1997 and 2017, p < 0.001). There was no significant difference in rate of change of level of evidence between 1997 and 2007 and 2007 and 2017 (0.033, p = 0.864).

Conclusion:
Over a 20-year period the number of total publications increased with time. The majority of otology publications in 2017 were lower evidence studies, though significant increases in the number and proportion of high evidence studies in general otolaryngology journals were observed throughout the study period.
Cerebrospinal Fluid Norepinephrine and Neurocognition in HIV and Methamphetamine Dependence
Authors: Saloner Rowan , Cherner Mariana , Iudicello Jennifer E. , Heaton Robert K. , Letendre Scott L. , Ellis Ronald J. 
Published: June 2020

Objective:HIV disease and methamphetamine (METH) dependence share overlapping mechanisms of neurotoxicity that preferentially compromise monoamine-rich frontostriatal circuitry. However, norepinephrine (NE) function is poorly understood in HIV and METH dependence. We evaluated associations between cerebrospinal fluid (CSF) NE and HIV, METH dependence, and neurocognition.Methods:Participants included 125 adults, stratified by HIV serostatus (HIV+/HIV−) and recent METH dependence (METH+/METH−), who underwent comprehensive neurocognitive testing and lumbar puncture. CSF NE was assayed using high-performance liquid chromatography. Multivariable regression modelled NE as a function of HIV, METH, and their interaction, adjusting for demographic and clinical factors. Pearson correlations examined relationships between NE and demographically-adjusted neurocognitive domain scores.Results:HIV significantly interacted with METH (P< 0.001) such that compared with HIV−/METH−, CSF NE was markedly elevated in the single risk-groups (HIV+/METH−:d= 0.96; HIV−/METH+:d= 0.79) and modestly elevated in the dual-risk group (HIV+/METH+:d= 0.48). This interaction remained significant after adjustment for lifetime depression, antidepressant use, and race/ethnicity. In the full sample, higher NE levels significantly correlated with worse global function (r= −0.19), learning (r= −0.23), and delayed recall (r= −0.18). Similar relationships between higher NE and worse neurocognition were detected in the METH− groups (ie, HIV−/METH− and HIV+/METH−) and in the virally-suppressed persons HIV+ subgroup, but not in the METH+ groups (ie, HIV−/METH+, HIV+/METH+).Discussion:HIV and METH independently, but not additively, relate to noradrenergic excess in the central nervous system, and perturbations to noradrenergic function may represent a pathophysiological mechanism of HIV-related neurocognitive dysfunction. Consistent with prior reports that noradrenergic excess compromises hippocampal and prefrontal function, higher NE related to worse neurocognition, even among successfully treated persons with HIV. Pharmacological and psychosocial interventions that stabilize NE function may improve neurocognition in persons with HIV.
On Identifying and Mitigating Bias in the Estimation of the COVID-19 Case Fatality Rate
Authors: Angelopoulos Anastasios Nikolas , Pathak Reese , Varma Rohit , Jordan Michael I. 
Published: June 2020

AbstractThe relative case fatality rates (CFRs) between groups and countries are key measures of relative risk that guide policy decisions regarding scarce medical resource allocation during the ongoing COVID-19 pandemic. In the middle of an active outbreak when surveillance data is the primary source of information, estimating these quantities involves compensating for competing biases in time series of deaths, cases, and recoveries. These include time- and severity-dependent reporting of cases as well as time lags in observed patient outcomes. In the context of COVID-19 CFR estimation, we survey such biases and their potential significance. Further, we analyze theoretically the effect of certain biases, like preferential reporting of fatal cases, on naive estimators of CFR. We provide a partially corrected estimator of these naive estimates that accounts for time lag and imperfect reporting of deaths and recoveries. We show that collection of randomized data by testing the contacts of infectious individuals regardless of the presence of symptoms would mitigate bias by limiting the covariance between diagnosis and death. Our analysis is supplemented by theoretical and numerical results and a simple and fast open-source codebase.1
Identification of immunodominant linear epitopes from SARS-CoV-2 patient plasma
Authors: Farrera-Soler Lluc , Daguer Jean-Pierre , Barluenga Sofia , Cohen Patrick , Pagano Sabrina , Yerly Sabine , Kaiser Laurent , Vuilleumier Nicolas , Winssinger Nicolas 
Published: June 2020

AbstractA novel severe acute respiratory syndrome coronavirus (SARS-CoV-2) is the source of a current pandemic (COVID-19) with devastating consequences in public health and economic stability. Using a peptide array to map the antibody response of plasma from healing patients, we identified immunodominant linear epitopes corresponding to key proteolytic sites on the spike protein.
Discovery and biosynthesis of gladiochelins: unusual lipodepsipeptide siderophores fromBurkholderia gladioli
Authors: Dashti Yousef , Nakou Ioanna T. , Mullins Alex J. , Webster Gordon , Jian Xinyun , Mahenthiralingam Eshwar , Challis Gregory L. 
Published: June 2020

AbstractBurkholderiais a genus of diverse Gram-negative bacteria that includes several opportunistic pathogens. Siderophores, which transport iron from the environment into microbial cells, are important virulence factors in most pathogenicBurkholderiaspecies. However, it is widely believed thatBurkholderia gladioli, which can infect the lungs of cystic fibrosis (CF) sufferers, does not produce siderophores.B. gladioliBCC0238, isolated from the lung of a CF patient, produces two novel metabolites in a minimal medium containing glycerol and ribose as carbon sources. HPLC purification, followed by detailed spectroscopic analyses, identified these metabolites as unusual lipodepsipeptides containing a unique citrate-derived fatty acid and a rare dehydro-β-alanine residue. The absolute configurations of the amino acid residues in the two metabolites was elucidated using Marfey’s method and the gene cluster responsible for their biosynthesis was identified by bioinformatics and insertional mutagenesis. In-frame deletions and enzyme activity assays were used to investigate the functions of several proteins encoded by the biosynthetic gene cluster, which was found in the genomes of mostB. gladioliisolates, suggesting that its metabolic products play an important role in the growth and/or survival of the species. The Chrome Azurol S (CAS) assay showed the metabolites bind ferric iron and that this supresses their production when added to the growth medium. Moreover, a gene encoding a TonB-dependent ferric-siderophore receptor is adjacent to the biosynthetic genes. Together, these observations suggest that these metabolites likely function as siderophores inB. gladioli.
scRNA-Sequencing uncovers a TCF-4-dependent transcription factor network regulating commissure development
Authors: Wittmann Marie-Theres , Kirchner Philipp , Ekici Arif B. , Sock Elisabeth , Lie D. Chichung , Reis André 
Published: June 2020

AbstractIntercortical connectivity is important for higher cognitive brain functions by providing the basis for integrating information from both hemispheres. We show that ablation of the neurodevelopmental disorder associated bHLH factorTcf4results in complete loss of forebrain commissural systems in mice. Applying a new bioinformatic strategy integrating transcription factor expression levels and regulon activities from single cell RNA-sequencing data predicted a TCF-4 interacting transcription factor network in intercortical projection neurons regulating commissure formation. This network comprises a number of regulators previously linked to the pathogenesis of intellectual disability, autism-spectrum disorders and schizophrenia, e.g.Foxg1, Sox11andBrg1. Furthermore, we demonstrate that TCF-4 and SOX11 biochemically interact and cooperatively control commissure formationin vivo, and regulate the transcription of genes implied in this process. Our study provides a regulatory transcriptional network for the development of interhemispheric connectivity with potential pathophysiological relevance in neurodevelopmental disorders.
Research on the Trend of the Height of Han Students Aged 7-18 in China
Authors: Hong Chenlu , Rui Zhang , Wu Fei 
Published: June 2020

AbstractAimsTo make time series analysis on the 29-year (1985−2014) trends in height among Han Students Aged 7-18 in China and predict their future height from the perspective of interdisciplinary studies of demography and physical education.MethodsThe data were from the findings of seven cross-sectional surveys from the Chinese National Survey on Students’ Constitution and Health (CNSSCH). The mean, standard error, variance analysis, trend test, F test, T test, development growth and growth rate were used to make a descriptive analysis of height trends. The ARIMA model in the time series analysis was applied to predict the height development of Han students in 2024.ResultsThe height of students aged 7-18 substantially increased from 1985 to2014. The mean of the height of boys increased by 3.99 cm, 8.01 cm, 8.31 cm, 8.63 cm, 9.81 cm, 11.62 cm, 10.38 cm, 9.22 cm, 7.50 cm, 5.59 cm, 4.51 cm, and 3.79 cm, respectively. The mean of the height of girls increased by 6.66 cm, 7.36 cm, 8.00 cm, 8.84 cm, 9.60 cm, 8.66 cm, 5.57 cm, 4.65 cm, 3.95 cm, 3.32 cm, 2.87 cm and 3.32 cm, respectively. The increasing disparity of the sex differential in the mean height was also observed. From 1985 to 2014, the mean of height difference between boys and girls aged 7-18 had been increased constantly. Their mean height differences were 3.27 cm, 4.03 cm, 4.64 cm, and 5.13 cm, respectively in 1985, 1995, 2005, and 2014. A narrowing of the urban−rural differential in the mean height was observed. In 1985, on average, urban boys aged 7-18 were 4.18cm higher than rural boys in the same age group. And the height differences between urban and rural boys in the same age group were 3.58 cm, 3.18 cm and 2.41 cm, respectively in 1995, 2005 and 2014. According to comparison results, the mean height of urban girls was greater than that of rural girls, and the height difference between urban and rural girls had been constantly narrowed as well. The results of 4 comparisons showed that the height differences between urban and rural girls were 3.68 cm, 3.12 cm, 2.62 cm, and 1.98 cm, respectively.ConclusionsThere was a general increase in the height of Chinese Han students aged 7-18 in the past 29 years and difference between sex, rural-urban and age have been observed. In 2024, the height of students will continue to grow.
Progression / remission of Coronavirus disease 2019: Data driven recommendations for repeating SARS-CoV-2 nucleic acid amplification tests
Authors: Williams Kaitlyn , Idriss Reed , Dodge Jessica , Barasch Samuel 
Published: June 2020

ABSTRACTAimsThis short study was performed to better understand the time frame associated with changes in SARS-CoV-2 nucleic acid testing and provide recommendations for repeat testing. Recommendations were useful as little guidance is available for repeat testing in patients being followed expectantly for changes in disease.MethodsA review of laboratory data of tests for SARS-CoV-2 nucleic acid was performed selecting patients who had changing results. Time between changes in test results was determined to provide guidance for repeat testing.ResultsThe interquartile range of data for patients who had a negative to positive change in lab testing (“progression”) was 6-16 days (Median 9). The interquartile range of data for patients who had a positive to negative change in test results (“remission”) was 9-21 days (Median 14).ConclusionBecause sampling of the nares or nasopharynx can be variable, repeat testing should be performed swiftly when symptomatic patients are negative. The data in this short study varies widely, so authors recommend repeat testing during a period of time associated with the interquartile range or median (see results above).
HYFI: Hybrid filling of the dead-time gap for faster zero echo time imaging
Authors: Froidevaux Romain , Weiger Markus , Rösler Manuela B. , Brunner David O. , Pruessmann Klaas P. 
Published: June 2020

AbstractPurposeTo improve the SNR efficiency of zero echo time (ZTE) MRI pulse sequences for faster imaging of short-T2 components at large dead-time gaps.MethodsHYFI is s strategy of retrieving inner k-space data missed during the dead-time gap arising from radio-frequency excitation and switching in ZTE imaging. It performs hybrid filling of the inner k-space with a small single-point-imaging core surrounded by a stack of shells acquired on radial readouts in an onion-like fashion. The exposition of this concept is followed by translation into guidelines for parameter choice and implementation details. The imaging properties and performance of HYFI are studied in simulations as well as phantom, in-vitro and in-vivo imaging, with an emphasis on comparison with the PETRA technique (pointwise encoding time reduction with radial acquisition).ResultsSimulations predict higher SNR efficiency of HYFI compared to PETRA at preserved image quality with the advantage increasing with the size of the k-space gap. These results are confirmed by imaging experiments with gap sizes of 25 to 50 Nyquist dwells, in which scan times for similar SNR could be reduced by 25 to 60%.ConclusionThe HYFI technique provides both high SNR efficiency and image quality, thus outperforming previously known ZTE-based pulse sequences in particular for large k-space gaps. Promising applications include direct imaging of ultra-short T2 components, such as the myelin bilayer or collagen, T2 mapping of ultra-fast relaxing signals, and ZTE imaging with reduced chemical shift artifacts.
Effect of hydroxychloroquine on SARS-CoV-2 viral load in patients with COVID-19
Authors: Faíco-Filho Klinger Soares , Conte Danielle Dias , de Souza Luna Luciano Kleber , Almeida Carvalho Joseane Mayara , Sitta Perosa Ana Helena , Bellei Nancy 
Published: June 2020

ABSTRACTBackgroundSome studies have shown that hydroxychloroquine (HCQ) is an effective drug in reducing the in vitro replication of SARS-CoV-2. However, the in vivo effect of HCQ still unclear. This study aims to evaluate viral load clearance in patients with COVID-19 who underwent HCQ treatment in comparison with a control group that did not receive the drug.MethodsThis prospective study comprised consecutive viral load measurements in patients with COVID-19 hospitalized with a moderate illness. Patients received 400 mg of HCQ every 12 hours for 10 days according to the medical decision. Nasal swab samples were collected at the 1st, 7th, and 14th days of the admission.Results155 samples were collected from 66 patients with COVID-19 (60% female), with a median age of 58 years. The viral load between studied groups, assumed as a semiquantitative measure of cycle threshold (Ct) values, presented no significant difference within the three consecutive measures (ΔCt) (p>0.05). We also analyzed the ΔCt viral load at different intervals of sample collection (Δt <7; 7-12 and >12 days) without significant differences at any ΔCt (p>0.05).ConclusionIn this study, we did not observe any change in viral load in vivo with the use of HCQ.SummaryWe evaluate viral load clearance in patients with COVID-19 who took hydroxychloroquine (HCQ) for treatment and those who not. Prospective viral load measurements have shown any change in viral load in vivo with the use of HCQ.
Evidence of Increased Hemangioblastic and Early Hematopoietic Potential in Chronic Myeloid Leukemia (CML)-derived Induced Pluripotent Stem Cells (iPSC)
Authors: Telliam G. , Féraud O. , Baykal-Köse S. , Griscelli F. , Imeri J. , Latsis T. , Bennaceur-Griscelli A. , Turhan A.G. 
Published: June 2020

ABSTRACTHemangioblasts derived from mesodermal lineage are the earliest precursors of hematopoietic stem cells and endothelial cells. Embryonic stem cells (ESC) and induced pluripotent stem cells (iPSC) are the only experimental systems in which these cells can be assayed and quantified. We show here using CML-derived iPSC and blast-cell colony forming (Bl-CFC) assays that hemangioblasts are highly expanded in CML derived iPSC as compared to human H1-ESC-derived hemangioblasts. BCR-ABL signaling pathway is intact in these cells with evidence of CRK-L phosphorylation which is reduced by the use of Imatinib. Hematopoietic progenitor assays generated using blast-CFC demonstrates also a highly increased hematopoietic progenitor potential of these cells as compared to H1-ESC. The same results were also obtained using hematopoietic progenitor assays via embryoid body formation. In CML iPSC, we have also found a significant reduction of Aryl Hydrocarbon Receptor (AHR) expression which is involved in hematopoietic quiescence. Further inhibition of AHR using StemRegenin (SR1), an AHR antagonist, led to an increase of blast-cell colonies in CML iPSC whereas the use of an AHR agonist inhibited blast cell colonies. Thus, our results show for the first time, the possibility of establishment of a myeloproliferative phenotype using patient-derived iPSC and the presence of a major expansion hemangioblast compartment and derived hematopoietic progenitors in this context. They also suggest that the AHR signaling pathway could represent a novel druggable target in CML.
Reading frame restoration at the EYS locus, and allele-specific chromosome removal after Cas9 cleavage in human embryos
Authors: Zuccaro Michael V. , Xu Jia , Mitchell Carl , Marin Diego , Zimmerman Raymond , Rana Bhavini , Weinstein Everett , King Rebeca T. , Smith Morgan , Tsang Stephen H. , Goland Robin , Jasin Maria , Lobo Rogerio , Treff Nathan , Egli Dieter 
Published: June 2020

SummaryThe correction of disease-causing mutations in human embryos could reduce the burden of inherited genetic disorders in the fetus and newborn, and improve the efficiency of fertility treatments for couples with disease-causing mutations in lieu of embryo selection. Here we evaluate the repair outcomes of a Cas9-induced double-strand break (DSB) introduced on the paternal chromosome at the EYS locus, which carries a frame-shift mutation causing blindness. We show that the most common repair outcome is microhomology-mediated end joining, which occurs during the first cell cycle in the zygote, leading to embryos with non-mosaic restoration of the reading frame. However, about half of the breaks remain unrepaired, resulting in an undetectable paternal allele and, upon entry into mitosis, loss of one or both chromosomal arms. Thus, Cas9 allows for the modification of chromosomal content in human embryos in a targeted manner, which may be useful for the prevention of trisomies.HighlightsCas9-mediated DSB induction and repair by end joining occurs within hoursEnd joining provides an efficient way to restore reading frames without mosaicismUnrepaired DSBs persist through mitosis and result in frequent chromosome loss
Exportin Crm1 is important for Swi6 nucleocytoplasmic shuttling and MBF transcription activation inSaccharomyces cerevisiae
Authors: Belanger Kenneth D. , Yewdell William T. , Barber Matthew F. , Russo Amy N. , Pettit Mark A. , Damuth Emily K. , Hussain Naveen , Geier Susan J. , Belanger Karyn G. 
Published: June 2020

AbstractThe Swi6 protein acts as a transcription factor in budding yeast, functioning in two different heterodimeric complexes, SBF and MBF, that activate the expression of distinct but overlapping sets of genes. Swi6 undergoes regulated changes in nucleocytoplasmic localization throughout the cell cycle that correlate with changes in gene expression. While the process of Swi6 nuclear import is well understood, mechanisms underlying its nuclear export remain unclear. Here we investigate Swi6 nuclear export and its impact on Swi6 function. We show that the exportin Crm1, in addition to three other karyopherins previously shown to affect Swi6 localization, is important for Swi6 nuclear export and activity. A truncation of Swi6 that removes a putative Crm1 nuclear export signal results in the loss of changes in nucleocytoplasmic Swi6 localization that normally occur during progression through the cell cycle. Mutagenesis of the NES-like sequence or removal of Crm1 activity using leptomycin B results in a similar decrease in nuclear export as cells enter S-phase. Using two-hybrid analysis, we also show that Swi6 associates with Crm1in vivo. Alteration of the Crm1 NES in Swi6 results in a decrease in MBF-mediated gene expression, but does not affect expression of an SBF reporter, suggesting that export of Swi6 by Crm1 regulates a subset of Swi6 transcription activation activity. Finally, alteration of the Crm1 NES in Swi6 results in cells that are larger than wild type, but not to the extent of those with a complete Swi6 deletion. Expressing a Swi6 NES mutant in combination with a deletion of Msn5, an exportin involved in Swi6 nuclear export and specifically affecting SBF activation, further increases the large cell phenotype, but still not to the extent observed in a Swi6 deletion mutant. These data suggest that Swi6 has at least two different exportins, Crm1 and Msn5, each of which interacts with a distinct nuclear export signal and influences expression of a different subset of Swi6-controlled genes.Summary StatementPrecise intracellular localization is important for the proper activity of proteins. Here we provide evidence that the Swi6 transcription factor important for cell cycle progression shuttles between the cell nucleus and cytoplasm, its nuclear export is important for its activity, and that it contains a nuclear export signal (NES) recognized by the Crm1 nuclear transport factor.