bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluating the Effect of a Modified Sample Preparation on SARS-CoV-2 Detection in a Cartridge-Based Platform
Authors: Zhen Wei , Whitfield Natalie N , Smith Elizabeth , Shaw Christine , Ivy Cristina , Douglas Caylee , Bickford Stephanie , Berry Gregory J 
Published: March 2021

Abstract

Introduction
The ePlex® SARS-CoV-2 emergency use authorization (EUA) test is a cartridge-based assay for the detection of SARS-CoV-2 in nasopharyngeal specimens. Since performance data has been previously published on this platform, the manufacturer has modified the workflow design in order to improve assay performance. Evaluation of the new workflow, which eliminated the sample delivery device (SDD), led to a dramatic improvement of assay performance while saving time and making cartridge loading more convenient.

Methods
145 confirmed positive nasopharyngeal swab specimens were used to evaluate the assay analytical sensitivity, accuracy, and overall time-saving for the 2 workflows that is with and without the use of SDD on the ePlex SARS-CoV-2 test.

Results
Elimination of the SDD step led to a dramatic increase in accuracy and the overall limit of detection when using 145 previously defined and valid SARS-CoV-2 positive specimens with relatively low, medium, and high cycle thresholds (CT). This simple workflow change led to an overall detection from 94/145 (64.8%) to 131/145 (90.3%), with an additional 37 specimens being detected. CT value ranges revealed that 90% of the specimens in the 33 ≤ CT &lt; 35.3 CT range were detected, whereas with the SDD workflow, only 30% of positive specimens were detected in this same range. Hands-on time for each specimen also improved and showed overall time savings.

Conclusion
The simple workflow modification eliminating the SDD led to an overall improvement in the detection of positive specimens and also simplified workflow and reduced hands-on time.
Adaptations of Breast Imaging Centers to the COVID-19 Pandemic: A Survey of California and Texas
Authors: Chalfant James S , Cohen Ethan O , Leung Jessica W T , Pittman Sarah M , Kothari Pranay D , Downey John R , Sohlich Rita E , Chong Alice , Grimm Lars J , Hoyt Anne C , Ojeda-Fournier Haydee , Joe Bonnie N , Trinh Long , Rosen Eric L , Feig Stephen A , Aminololama-Shakeri Shadi , Ikeda Debra M 
Published: March 2021

Abstract

Objective
To determine the early impact of the COVID-19 pandemic on breast imaging centers in California and Texas and compare regional differences.

Methods
An 11-item survey was emailed to American College of Radiology accredited breast imaging facilities in California and Texas in August 2020. A question subset addressed March–April government restrictions on elective services (“during the shutdown” and “after reopening”). Comparisons were made between states with chi-square and Fisher’s tests, and timeframes with McNemar’s and paired t-tests.

Results
There were 54 respondents (54/240, 23%, 26 California, 28 Texas). Imaging volumes fell during the shutdown and remained below pre-pandemic levels after reopening, with reduction in screening greatest (ultrasound 12% of baseline, mammography 13%, MRI 23%), followed by diagnostic MRI (43%), procedures (44%), and diagnostics (45%). California reported higher volumes during the shutdown (procedures, MRI) and after reopening (diagnostics, procedures, MRI) versus Texas (P = 0.001–0.02). Most screened patients (52/54, 96% symptoms and 42/54, 78% temperatures), and 100% (53/53) modified check-in and check-out. Reading rooms or physician work were altered for social distancing (31/54, 57%). Physician mask (45/48, 94%), gown (15/48, 31%), eyewear (22/48, 46%), and face shield (22/48, 46%) use during procedures increased after reopening versus pre-pandemic (P &lt; 0.001–0.03). Physician (47/54, 87%) and staff (45/53, 85%) financial impacts were common, but none reported terminations.

Conclusion
Breast imaging volumes during the early pandemic fell more severely in Texas than in California. Safety measures and financial impacts on physicians and staff were similar in both states.
NEM6, KBTBD13-Related Congenital Myopathy: Myopathological Analysis in 18 Dutch Patients Reveals Ring Rods Fibers, Cores, Nuclear Clumps, and Granulo-Filamentous Protein Material
Authors: Bouman Karlijn , Küsters Benno , De Winter Josine M , Gillet Cynthia , Van Kleef Esmee S B , Eshuis Lilian , Brochier Guy , Madelaine Angeline , Labasse Clémence , Boulogne Claire , Van Engelen Baziel G M , Ottenheijm Coen A C , Romero Norma B , Voermans Nicol C , Malfatti Edoardo 
Published: March 2021

Abstract
Nemaline myopathy type 6 (NEM6), KBTBD13-related congenital myopathy is caused by mutated KBTBD13 protein that interacts improperly with thin filaments/actin, provoking impaired muscle-relaxation kinetics. We describe muscle morphology in 18 Dutch NEM6 patients and correlate it with clinical phenotype and pathophysiological mechanisms. Rods were found in in 85% of biopsies by light microscopy, and 89% by electron microscopy. A peculiar ring disposition of rods resulting in ring-rods fiber was observed. Cores were found in 79% of NEM6 biopsies by light microscopy, and 83% by electron microscopy. Electron microscopy also disclosed granulofilamentous protein material in 9 biopsies. Fiber type 1 predominance and prominent nuclear internalization were found. Rods were immunoreactive for α-actinin and myotilin. Areas surrounding the rods showed titin overexpression suggesting derangement of the surrounding sarcomeres. NEM6 myopathology hallmarks are prominent cores, rods including ring-rods fibers, nuclear clumps, and granulofilamentous protein material. This material might represent the histopathologic epiphenomenon of altered interaction between mutated KBTBD13 protein and thin filaments. We claim to classify KBTBD13-related congenital myopathy as rod-core myopathy.
Poplar MYB117 promotes anthocyanin synthesis and enhances flavonoid B-ring hydroxylation by up-regulating the flavonoid 3′,5′-hydroxylase gene
Authors: Ma Dawei , Tang Hao , Reichelt Michael , Piirtola Eerik-Mikael , Salminen Juha-Pekka , Gershenzon Jonathan , Constabel C Peter 
Published: March 2021

Abstract
Flavonoids, such as anthocyanins, proanthocyanidins, and flavonols, are widespread plant secondary metabolites and important for plant adaptation to diverse abiotic and biotic stresses. Flavonoids can be variously hydroxylated and decorated; their biological activity is partly dependent on the degree of hydroxylation of the B-ring. Flavonoid biosynthesis is regulated by MYB transcription factors, which have been identified and characterized in a diversity of plants. Here we characterize a new MYB activator, MYB117, in hybrid poplar (Populus tremula×tremuloides). When overexpressed in transgenic poplar plants, MYB117 enhanced anthocyanin accumulation in all tissues. Transcriptome analysis of MYB117-overexpressing poplars confirmed the up-regulation of flavonoid and anthocyanin biosynthesis genes, as well as two flavonoid 3′,5′-hydroxylase (F3′5′H) genes. We also identified up-regulated cytochrome b5 genes, required for full activity of F3′5′H . Phytochemical analysis demonstrated a corresponding increase in B-ring hydroxylation of anthocyanins, proanthocyanidins, and flavonols in these transgenics. Similarly, overexpression of F3′5′H1 directly in hybrid poplar also resulted in increased B-ring hydroxylation, but without affecting overall flavonoid content. However, the overexpression of the cytochrome b5 gene in F3′5′H1-overexpressing plants did not further increase B-ring hydroxylation. Our data indicate that MYB117 regulates the biosynthesis of anthocyanins in poplar, but also enhances B-ring hydroxylation by up-regulating F3′5′H1.
Seasonal and long-term consequences of esca grapevine disease on stem xylem integrity
Authors: Bortolami Giovanni , Farolfi Elena , Badel Eric , Burlett Regis , Cochard Herve , Ferrer Nathalie , King Andrew , Lamarque Laurent J , Lecomte Pascal , Marchesseau-Marchal Marie , Pouzoulet Jerome , Torres-Ruiz Jose M , Trueba Santiago , Delzon Sylvain , Gambetta Gregory A , Delmas Chloe E L 
Published: March 2021

AbstractHydraulic failure has been extensively studied during drought-induced plant dieback, but its role in plant-pathogen interactions is under debate. During esca, a grapevine (Vitis vinifera) disease, symptomatic leaves are prone to irreversible hydraulic dysfunctions but little is known about the hydraulic integrity of perennial organs over the short- and long-term. We investigated the effects of esca on stem hydraulic integrity in naturally infected plants within a single season and across season(s). We coupled direct (ks) and indirect (kth) hydraulic conductivity measurements, and tylose and vascular pathogen detection with in vivo X-ray microtomography visualizations. Xylem occlusions (tyloses) and subsequent loss of stem hydraulic conductivity (ks) occurred in all shoots with severe symptoms (apoplexy) and in more than 60% of shoots with moderate symptoms (tiger-stripe), with no tyloses in asymptomatic shoots. In vivo stem observations demonstrated that tyloses occurred only when leaf symptoms appeared, and resulted in more than 50% loss of hydraulic conductance in 40% of symptomatic stems, unrelated to symptom age. The impact of esca on xylem integrity was only seasonal, with no long-term impact of disease history. Our study demonstrated how and to what extent a vascular disease such as esca, affecting xylem integrity, could amplify plant mortality through hydraulic failure.
A Galactic survey of radio jets from massive protostars
Authors: Purser S J D , Lumsden S L , Hoare M G , Kurtz S 
Published: March 2021

ABSTRACT
In conjunction with a previous southern-hemisphere work, we present the largest radio survey of jets from massive protostars to date with high-resolution (∼0.04 arcsec) Jansky Very Large Array observations towards two subsamples of massive star-forming regions of different evolutionary statuses: 48 infrared-bright, massive, young, stellar objects (MYSOs) and 8 infrared dark clouds (IRDCs) containing 16 luminous ($\hbox{$\, L_{\rm {bol}}$}\gt 10^3\hbox{${\rm \, L_{\odot }}$}$) cores. For 94 per cent of the MYSO sample, we detect thermal radio (α ≥ −0.1 whereby Sν ∝ να) sources coincident with the protostar, of which 84 per cent (13 jets and 25 candidates) are jet like. Radio luminosity is found to scale with $\hbox{$\, L_{\rm {bol}}$}$ similarly to the low-mass case supporting a common mechanism for jet production across all masses. Associated radio lobes tracing shocks are seen towards 52 per cent of jet-like objects and are preferentially detected towards jets of higher radio and bolometric luminosities, resulting from our sensitivity limitations. We find jet mass-loss rate scales with bolometric luminosity as $\hbox{$\dot{m}_{\rm jet}$}\propto \hbox{$\, L_{\rm {bol}}$}^{0.9\pm 0.2}$, thereby discarding radiative, line-driving mechanisms as the dominant jet-launching process. Calculated momenta show that the majority of jets are mechanically capable of driving the massive, molecular outflow phenomena since pjet &gt; poutflow. Finally, from their physical extent we show that the radio emission cannot originate from small, optically thick H ii regions. Towards the IRDC cores, we observe increasing incidence rates/radio fluxes with age using the proxy of increasing luminosity-to-mass (L/M) and decreasing infrared flux ratios $({S_{70{\rm \, \mu m}}}/{S_{24{\rm \, \mu m}}})$. Cores with $({L}/{M})\,\lt \,40\, \hbox{${\rm \, L_{\odot }}$}\hbox{${\rm \, M_{\odot }}$}^{-1}$ are not detected above ($5.8{\rm \, GHz}$) radio luminosities of ${\sim}1{\rm \, mJy}{\rm \, kpc}^2$.
Particle-in-cell simulations of the Cassini spacecraft’s interaction with Saturn’s ionosphere during the Grand Finale
Authors: Zhang Zeqi , Desai Ravindra T , Miyake Yohei , Usui Hideyuki , Shebanits Oleg 
Published: March 2021

ABSTRACT
A surprising and unexpected phenomenon observed during Cassini’s Grand Finale was the spacecraft charging to positive potentials in Saturn’s ionosphere. Here, the ionospheric plasma was depleted of free electrons with negatively charged ions and dust accumulating up to over 95 per cent of the negative charge density. To further understand the spacecraft–plasma interaction, we perform a three-dimensional Particle-In-Cell study of a model Cassini spacecraft immersed in plasma representative of Saturn’s ionosphere. The simulations reveal complex interaction features such as electron wings and a highly structured wake containing spacecraft-scale vortices. The results show how a large negative ion concentration combined with a large negative to positive ion mass ratio is able to drive the spacecraft to the observed positive potentials. Despite the high electron depletions, the electron properties are found as a significant controlling factor for the spacecraft potential together with the magnetic field orientation which induces a potential gradient directed across Cassini’s asymmetric body. This study reveals the global spacecraft interaction experienced by Cassini during the Grand Finale and how this is influenced by the unexpected negative ion and dust populations.
Towards a volumetric census of close white dwarf binaries – I. Reference samples
Authors: Inight K , Gänsicke Boris T , Breedt E , Marsh T R , Pala A F , Raddi R 
Published: March 2021

ABSTRACT
Close white dwarf binaries play an important role across a range of astrophysics, including thermonuclear supernovae, the Galactic low-frequency gravitational wave signal, and the chemical evolution of the Galaxy. Progress in developing a detailed understanding of the complex, multithreaded evolutionary pathways of these systems is limited by the lack of statistically sound observational constraints on the relative fractions of various sub-populations and their physical properties. The available samples are small, heterogeneous, and subject to a multitude of observational biases. Our overarching goal is to establish a volume-limited sample of all types of white dwarf binaries that is representative of the underlying population as well as sufficiently large to serve as a benchmark for future binary population models. In this first paper, we provide an overview of the project, and assemble reference samples within a distance limit of 300 pc of known white dwarf binaries spanning the most common sub-classes: post-common envelope binaries containing a white dwarf plus a main-sequence star, cataclysmic variables, and double-degenerate binaries. We carefully vet the members of these “Gold” samples, which span most of the evolutionary parameter space of close white dwarf binary evolution. We also explore the differences between magnitude and volume limited close white dwarf binary samples, and discuss how these systems evolve in their observational properties across the Gaia Hertzsprung–Russell diagram.
The EDGE-CALIFA survey: self-regulation of star formation at kpc scales
Authors: Barrera-Ballesteros J K , Sánchez S F , Heckman T , Wong T , Bolatto A , Ostriker E , Rosolowsky E , Carigi L , Vogel S , Levy R C , Colombo D , Luo Yufeng , Cao Yixian 
Published: March 2021

ABSTRACT
The processes that regulate star formation are essential to understand how galaxies evolve. We present the relation between star formation rate density, ΣSFR , and hydrostatic mid-plane pressure,Ph, for 4260 star-forming regions of kpc size located in 96 galaxies included in the EDGE-CALIFA survey covering a wide range of stellar masses and morphologies. We find that these two parameters are tightly correlated, showing a smaller scatter in comparison to other star-forming relations. A power law, with a slightly sublinear index, is a good representation of this relation. Its residuals show a significant anticorrelation with both stellar age and metallicity whereas the total stellar mass may also play a secondary role in shaping the ΣSFR–Ph relation. For actively star-forming regions, we find that the effective feedback momentum per unit stellar mass (p*/m*), measured from thePh/ΣSFR  ratio increases withPh. The median value of this ratio for all the sampled regions is larger than the expected momentum just from supernovae explosions. Morphology of the galaxies, including bars, does not seem to have a significant impact in the ΣSFR–Ph relation. Our analysis indicates that local ΣSFR self-regulation comes mainly from momentum injection to the interstellar medium from supernovae explosions. However, other mechanisms in disc galaxies may also play a significant role in shaping the ΣSFR at kpc scales. Our results also suggest thatPh is the main parameter that modulates star formation at kpc scales, rather than individual components of the baryonic mass.
On the impact of batch effect correction in TCGA isomiR expression data
Authors: Ibing Susanne , Michels Birgitta E , Mosdzien Moritz , Meyer Helen R , Feuerbach Lars , Körner Cindy 
Published: March 2021

Abstract
MicroRNAs (miRNAs) are small non-coding RNAs with diverse functions in post-transcriptional regulation of gene expression. Sequence and length variants of miRNAs are called isomiRs and can exert different functions compared to their canonical counterparts. The Cancer Genome Atlas (TCGA) provides isomiR-level expression data for patients of various cancer entities collected in a multi-center approach over several years. However, the impact of batch effects within individual cohorts has not been systematically investigated and corrected for before. Therefore, the aim of this study was to identify relevant cohort-specific batch variables and generate batch-corrected isomiR expression data for 16 TCGA cohorts. The main batch variables included sequencing platform, plate, sample purity and sequencing depth. Platform bias was related to certain length and sequence features of individual recurrently affected isomiRs. Furthermore, significant downregulation of reported tumor suppressive isomiRs in lung tumor tissue compared to normal samples was only observed after batch correction, highlighting the importance of working with corrected data. Batch-corrected datasets for all cohorts including quality control are provided as supplement. In summary, this study reveals that batch effects present in the TCGA dataset might mask biologically relevant effects and provides a valuable resource for research on isomiRs in cancer (accessible through GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE164767).
A Novel Framework for Network-Targeted Neuropsychiatric Deep Brain Stimulation
Authors: Allawala Anusha , Bijanki Kelly R , Goodman Wayne , Cohn Jeffrey F , Viswanathan Ashwin , Yoshor Daniel , Borton David A , Pouratian Nader , Sheth Sameer A 
Published: March 2021

Abstract
Deep brain stimulation (DBS) has emerged as a promising therapy for neuropsychiatric illnesses, including depression and obsessive-compulsive disorder, but has shown inconsistent results in prior clinical trials. We propose a shift away from the empirical paradigm for developing new DBS applications, traditionally based on testing brain targets with conventional stimulation paradigms. Instead, we propose a multimodal approach centered on an individualized intracranial investigation adapted from the epilepsy monitoring experience, which integrates comprehensive behavioral assessment, such as the Research Domain Criteria proposed by the National Institutes of Mental Health. In this paradigm-shifting approach, we combine readouts obtained from neurophysiology, behavioral assessments, and self-report during broad exploration of stimulation parameters and behavioral tasks to inform the selection of ideal DBS parameters. Such an approach not only provides a foundational understanding of dysfunctional circuits underlying symptom domains in neuropsychiatric conditions but also aims to identify generalizable principles that can ultimately enable individualization and optimization of therapy without intracranial monitoring.
Impact of race on care, readmissions, and survival for patients with glioblastoma: an analysis of the National Cancer Database
Authors: Hodges Tiffany R , Labak Collin M , Mahajan Uma V , Wright Christina Huang , Wright James , Cioffi Gino , Gittleman Haley , Herring Eric Z , Zhou Xiaofei , Duncan Kelsey , Kruchko Carol , Sloan Andrew E , Barnholtz-Sloan Jill S 
Published: March 2021

Abstract

Background
The objective of this study was to explore racial/ethnic factors that may be associated with survival in patients with glioblastoma by querying the National Cancer Database (NCDB).

Methods
The NCDB was queried for patients diagnosed with glioblastoma between 2004 and 2014. Patient demographic variables included age at diagnosis, sex, race, ethnicity, Charlson–Deyo score, insurance status, and rural/urban/metropolitan location of zip code. Treatment variables included surgical treatment, extent of resection, chemotherapy, radiation therapy, type of radiation, and treatment facility type. Outcomes included 30-day readmission, 30- and 90-day mortality, and overall survival. Multivariable Cox regression analyses were performed to evaluate variables associated with race and overall survival.

Results
A total of 103 652 glioblastoma patients were identified. There was a difference in the proportion of patients for whom surgery was performed, as well as the proportion receiving radiation, when stratified by race (P &lt; .001). Black non-Hispanics had the highest rates of unplanned readmission (7.6%) within 30 days (odds ratio [OR]: 1.39 compared to White non-Hispanics, P &lt; .001). Asian non-Hispanics had the lowest 30- (3.2%) and 90-day mortality (9.8%) when compared to other races (OR: 0.52 compared to White non-Hispanics, P = .031). Compared to White non-Hispanics, we found Black non-Hispanics (hazard ratio [HR]: 0.88, P &lt; .001), Asian non-Hispanics (HR: 0.72, P &lt; .001), and Hispanics (HR: 0.69, P &lt; .001) had longer overall survival.

Conclusions
Differences in treatment and outcomes exist between races. Further studies are needed to elucidate the etiology of these race-related disparities and to improve outcomes for all patients.
Clinical Value Evaluation of microRNA-324-3p and Other Available Biomarkers in Patients With HBV Infection–Related Hepatocellular Carcinoma
Authors: Zhao Li , Yang Qian , Liu Jianbo 
Published: March 2021

Abstract

Background
Patients with hepatitis B virus (HBV) infection are at high risk of hepatocellular carcinoma (HCC). This study aimed to evaluate the expression of microRNA-324-3p (miR-324-3p) in HBV-related HCC and explore the clinical significance of serum miR-324-3p and other available biomarkers in the diagnosis and prognosis of HBV-related HCC.

Methods
Expression of miR-324-3p in HBV infection–related cells and patients was estimated using quantitative real-time polymerase chain reaction (PCR). Receiver operating characteristic (ROC) curves were constructed to evaluate the diagnostic performance of serum miR-324-3p, alpha-fetoprotein (AFP), and protein induced by vitamin K absence/antagonist II (PIVKA-II) in the differentiation of HBV-related HCC from healthy controls and chronic hepatitis B patients (CHB). The relationship between serum miR-324-3p and patients’ clinical features was assessed using the chi-square test, and the value of miR-324-3p to predict overall survival prognosis was evaluated using Kaplan-Meier methods and Cox regression assay in patients with HBV-related HCC.

Results
HBV-related HCC cells had significantly increased miR-324-3p compared with normal and HBV-unrelated HCC cells, and serum miR-324-3p in HCC patients with HBV infection was also higher than that in healthy controls and CHB. Serum miR-324-3p had relatively high diagnostic accuracy for the screening of HCC cases with HBV infection, and the combination of miR-324-3p, AFP, and PIVKA-II showed improved diagnostic performance. Additionally, high-serum miR-324-2p in HBV-related HCC patients was associated with cirrhosis, tumor size, clinical stage, and poor overall survival prognosis.

Conclusions
High-serum miR-324-3p may be involved in the progression of HBV-related hepatitis to HCC and may serve as a candidate biomarker for the diagnosis and prognosis of HBV-related HCC.