bluuebunny/crossref_metadata_2025_split huggingface dataset:
Elemental Testing Using Inductively Coupled Plasma Mass Spectrometry in Clinical Laboratories
Authors: Yang He S , LaFrance Delecia R , Hao Ying 
Published: January 2021

Abstract

Objectives
This review aims to describe the principles underlying different types of inductively coupled plasma mass spectrometry (ICP-MS), and major technical advancements that reduce spectral interferences, as well as their suitability and wide applications in clinical laboratories.

Methods
A literature survey was performed to review the technical aspects of ICP-MS, ICP-MS/MS, high-resolution ICP-MS, and their applications in disease diagnosis and monitoring.

Results
Compared to the atomic absorption spectrometry and ICP-optical emission spectrometry, ICP-MS has advantages including improved precision, sensitivity and accuracy, wide linear dynamic range, multielement measurement capability, and ability to perform isotopic analysis. Technical advancements, such as collision/reaction cells, triple quadrupole ICP-MS, and sector-field ICP-MS, have been introduced to improve resolving power and reduce interferences. Cases are discussed that highlight the clinical applications of ICP-MS including determination of toxic elements, quantification of nutritional elements, monitoring elemental deficiency in metabolic disease, and multielement analysis.

Conclusions
This review provides insight on the strategies of elemental analysis in clinical laboratories and demonstrates current and emerging clinical applications of ICP-MS.
Does Size Affect the Rate of Perforation? A Cross-sectional Study of Medical Gloves
Authors: Zare Asma , Choobineh Alireza , Jahangiri Mehdi , Seif Mozhgan , Dehghani Fatemeh 
Published: January 2021

Abstract

Objectives
Healthcare workers often have unnoticed minor abrasions on their hands, putting them at risk of contracting infectious diseases from patients, if the integrity of the medical gloves is compromised. This study aimed to compare the rate and location of glove perforation between well-fitted and ill-fitted gloves.

Methods
The participants of this cross-sectional study were 45 midwives in the maternity ward of a hospital in Shiraz city, Iran. A total of nine pairs of medical gloves including three pairs of fit size, three pairs of gloves with one size smaller (tight), and three pairs of gloves with one size larger (loose) were given to subjects, and asked them to use the gloves during episiotomy repair operations. After completing the task, all gloves were collected safely and gloves perforation was investigated based on water test (NF EN 455-1).

Results
The perforation rate of the fit, tight, and loose medical gloves was 20, 37.78, and 34.81%, respectively. The results showed a significant difference between glove perforation of different glove sizes (P &lt; 0.05). In general, there was a significant difference between the perforation rate of the fit glove and ill-fitted gloves (P = 0.013).

Conclusions
Wearing the wrong size gloves may increase the glove perforation rate. Providing a wide range of glove sizes by the hospital management, and choosing the best glove size can be very effective in reducing the glove perforation and increasing safety for healthcare workers and patients.
A semisupervised model to predict regulatory effects of genetic variants at single nucleotide resolution using massively parallel reporter assays
Authors: Yang Zikun , Wang Chen , Erjavec Stephanie , Petukhova Lynn , Christiano Angela , Ionita-Laza Iuliana 
Published: January 2021

AbstractMotivationPredicting regulatory effects of genetic variants is a challenging but important problem in functional genomics. Given the relatively low sensitivity of functional assays, and the pervasiveness of class imbalance in functional genomic data, popular statistical prediction models can sharply underestimate the probability of a regulatory effect. We describe here the presence-only model (PO-EN), a type of semisupervised model, to predict regulatory effects of genetic variants at sequence-level resolution in a context of interest by integrating a large number of epigenetic features and massively parallel reporter assays (MPRAs).ResultsUsing experimental data from a variety of MPRAs we show that the presence-only model produces better calibrated predicted probabilities and has increased accuracy relative to state-of-the-art prediction models. Furthermore, we show that the predictions based on pretrained PO-EN models are useful for prioritizing functional variants among candidate eQTLs and significant SNPs at GWAS loci. In particular, for the costimulatory locus, associated with multiple autoimmune diseases, we show evidence of a regulatory variant residing in an enhancer 24.4 kb downstream of CTLA4, with evidence from capture Hi-C of interaction with CTLA4. Furthermore, the risk allele of the regulatory variant is on the same risk increasing haplotype as a functional coding variant in exon 1 of CTLA4, suggesting that the regulatory variant acts jointly with the coding variant leading to increased risk to disease.Availability and implementationThe presence-only model is implemented in the R package ‘PO.EN’, freely available on CRAN. A vignette describing a detailed demonstration of using the proposed PO-EN model can be found on github at https://github.com/Iuliana-Ionita-Laza/PO.EN/Supplementary informationSupplementary data are available at Bioinformatics online.
Comparison of observation-based and model-based identification of alert concentrations from concentration–expression data
Authors: Kappenberg Franziska , Grinberg Marianna , Jiang Xiaoqi , Kopp-Schneider Annette , Hengstler Jan G , Rahnenführer Jörg 
Published: January 2021

Abstract

Motivation
An important goal of concentration–response studies in toxicology is to determine an ‘alert’ concentration where a critical level of the response variable is exceeded. In a classical observation-based approach, only measured concentrations are considered as potential alert concentrations. Alternatively, a parametric curve is fitted to the data that describes the relationship between concentration and response. For a prespecified effect level, both an absolute estimate of the alert concentration and an estimate of the lowest concentration where the effect level is exceeded significantly are of interest.

Results
In a simulation study for gene expression data, we compared the observation-based and the model-based approach for both absolute and significant exceedance of the prespecified effect level. Results show that, compared to the observation-based approach, the model-based approach overestimates the true alert concentration less often and more frequently leads to a valid estimate, especially for genes with large variance.

Availability and implementation
The code used for the simulation studies is available via the GitHub repository: https://github.com/FKappenberg/Paper-IdentificationAlertConcentrations.

Supplementary information
Supplementary data are available at Bioinformatics online.
Cost-effectiveness of bilateral vs. single internal thoracic artery grafts at 10 years
Authors: Little Matthew , Gray Alastair M , Altman Douglas G , Benedetto Umberto , Flather Marcus , Gerry Stephen , Lees Belinda , Murphy Jacqueline , Gaudino Mario , Taggart David P ,   for the Arterial Revascularization Trial Investigators
Published: January 2021

Abstract

Aims
Using bilateral internal thoracic arteries (BITAs) for coronary artery bypass grafting (CABG) has been suggested to improve survival compared to CABG using single internal thoracic arteries (SITAs) for patients with advanced coronary artery disease. We used data from the Arterial Revascularization Trial (ART) to assess long-term cost-effectiveness of BITA grafting compared to SITA grafting from an English health system perspective.

Methods and results
Resource use, healthcare costs, and quality-adjusted life years (QALYs) were assessed across 10 years of follow-up from an intention-to-treat perspective. Missing data were addressed using multiple imputation. Incremental cost-effectiveness ratios were calculated with uncertainty characterized using non-parametric bootstrapping. Results were extrapolated beyond 10 years using Gompertz functions for survival and linear models for total cost and utility. Total mean costs at 10 years of follow-up were £17 594 in the BITA arm and £16 462 in the SITA arm [mean difference £1133 95% confidence interval (CI) £239 to £2026, P = 0.015]. Total mean QALYs at 10 years were 6.54 in the BITA arm and 6.57 in the SITA arm (adjusted mean difference −0.01 95% CI −0.2 to 0.1, P = 0.883). At 10 years, BITA grafting had a 33% probability of being cost-effective compared to SITA, assuming a cost-effectiveness threshold of £20 000. Lifetime extrapolation increased the probability of BITA being cost-effective to 51%.

Conclusions
BITA grafting has significantly higher costs but similar quality-adjusted survival at 10 years compared to SITA grafting. Extrapolation suggests this could change over lifetime.
Exome-Wide Association Study Identifies FN3KRP and PGP as New Candidate Longevity Genes
Authors: Torres Guillermo G , Nygaard Marianne , Caliebe Amke , Blanché Hélène , Chantalat Sophie , Galan Pilar , Lieb Wolfgang , Christiansen Lene , Deleuze Jean-François , Christensen Kaare , Strauch Konstantin , Müller-Nurasyid Martina , Peters Annette , Nöthen Markus M , Hoffmann Per , Flachsbart Friederike , Schreiber Stefan , Ellinghaus David , Franke Andre , Dose Janina , Nebel Almut 
Published: January 2021

Abstract
Despite enormous research efforts, the genetic component of longevity has remained largely elusive. The investigation of common variants, mainly located in intronic or regulatory regions, has yielded only little new information on the heritability of the phenotype. Here, we performed a chip-based exome-wide association study investigating 62 488 common and rare coding variants in 1248 German long-lived individuals, including 599 centenarians and 6941 younger controls (age &lt; 60 years). In a single-variant analysis, we observed an exome-wide significant association between rs1046896 in the gene fructosamine-3-kinase-related-protein (FN3KRP) and longevity. Noteworthy, we found the longevity allele C of rs1046896 to be associated with an increased FN3KRP expression in whole blood; a database look-up confirmed this effect for various other human tissues. A gene-based analysis, in which potential cumulative effects of common and rare variants were considered, yielded the gene phosphoglycolate phosphatase (PGP) as another potential longevity gene, though no single variant in PGP reached the discovery p-value (1 × 10E−04). Furthermore, we validated the previously reported longevity locus cyclin-dependent kinase inhibitor 2B antisense RNA 1 (CDKN2B-AS1). Replication of our results in a French longevity cohort was only successful for rs1063192 in CDKN2B-AS1. In conclusion, we identified 2 new potential candidate longevity genes, FN3KRP and PGP which may influence the phenotype through their role in metabolic processes, that is, the reverse glycation of proteins (FN3KRP) and the control of glycerol-3-phosphate levels (PGP).
One year later: The effect of changing azole-treated bulbs for organic tulips bulbs in hospital environment on the azole-resistant Aspergillus fumigatus rate
Authors: Rocchi Steffi , Godeau Chloé , Scherer Emeline , Reboux Gabriel , Millon Laurence 
Published: January 2021

Abstract

Azole-treated plant bulbs have already been evoked as a potential explanation of the worldwide spread of azole-resistant Aspergillus fumigatus (ARAf). We previously pointed out the presence of a high rate of ARAf (71% of A. fumigatus detected on azole-supplemented media) in flower beds containing azole-treated bulbs at the hospital's surroundings. We show here that planting organic bulbs can be a solution to reduce ARAf burden (from 71% rate to below 3%). The results suggest that replacing treated bulbs with organic bulbs may be sufficient to regain a population that is predominantly susceptible in just 1 year.

Lay Summary
Antifungal resistance is increasingly observed in fungal pathogens. This study argues that planting organic bulbs in hospitals’ outdoor surroundings could be a good alternative to continue to beautify green spaces, without the risk of dissipating antifungal-resistant fungal pathogens.
A new determination of the primordial helium abundance using the analyses of H ii region spectra from SDSS
Authors: Kurichin O A , Kislitsyn P A , Klimenko V V , Balashev S A , Ivanchik A V 
Published: January 2021

ABSTRACTThe precision measurement of the primordial helium abundance Yp is a powerful probe of the early Universe. The most common way to determine Yp is the analyses of observations of metal-poor H ii regions found in blue compact dwarf galaxies. We present the spectroscopic sample of 100 H ii regions collected from the Sloan Digital Sky Survey. The final analysed sample consists of our sample and HeBCD data base from Izotov et al. (2007). We use a self-consistent procedure to determine physical conditions, current helium abundances, and metallicities of the H ii regions. From a regression to zero metallicity, we have obtained Yp = 0.2462 ± 0.0022, which is one of the most stringent constraints obtained with such methods up to date and is in a good agreement with the Planck result $Y_{\rm p}^{\it {\mathrm{ Planck}}} = 0.2471 \pm 0.0003$. Using the determined value of Yp and the primordial deuterium abundance taken from Particle Data Group (Zyla et al. 2020) we put a constraint on the effective number of neutrino species Neff = 2.95 ± 0.16, which is consistent with the Planck one Neff = 2.99 ± 0.17. Further increase of statistics potentially allows us to achieve Planck accuracy, which in turn will become a powerful tool for studying the self-consistency of the standard cosmological model and/or physics beyond.
A critical role for linker DNA in higher-order folding of chromatin fibers
Authors: Brouwer Thomas , Pham Chi , Kaczmarczyk Artur , de Voogd Willem-Jan , Botto Margherita , Vizjak Petra , Mueller-Planitz Felix , van Noort John 
Published: January 2021

Abstract
Nucleosome-nucleosome interactions drive the folding of nucleosomal arrays into dense chromatin fibers. A better physical account of the folding of chromatin fibers is necessary to understand the role of chromatin in regulating DNA transactions. Here, we studied the unfolding pathway of regular chromatin fibers as a function of single base pair increments in linker length, using both rigid base-pair Monte Carlo simulations and single-molecule force spectroscopy. Both computational and experimental results reveal a periodic variation of the folding energies due to the limited flexibility of the linker DNA. We show that twist is more restrictive for nucleosome stacking than bend, and find the most stable stacking interactions for linker lengths of multiples of 10 bp. We analyzed nucleosomes stacking in both 1- and 2-start topologies and show that stacking preferences are determined by the length of the linker DNA. Moreover, we present evidence that the sequence of the linker DNA also modulates nucleosome stacking and that the effect of the deletion of the H4 tail depends on the linker length. Importantly, these results imply that nucleosome positioning in vivo not only affects the phasing of nucleosomes relative to DNA but also directs the higher-order structure of chromatin.
Prediction of Pathological and Radiological Nature of Glioma by Mass Spectrometry Combined With Machine Learning
Authors: Suzuki Keiko , Yoshimura Kentaro , Kawataki Tomoyuki , Hanihara Mitsuto , Takeda Sen , Kinouchi Hiroyuki 
Published: January 2021

ABSTRACT

BACKGROUND
We have previously developed a medical diagnostic pipeline that employs mass spectrometry and machine learning. It does not annotate molecular markers that are specific to cancer but uses entire mass spectra for predicting the properties of glioma.

OBJECTIVE
To validate the power of our diagnostic method in predicting the pathological and radiological properties of glioma with a simple sample preparation procedure.

METHODS
A total of 10 patients with glioma and 4 nonglioma patients who went through surgical resection were enrolled in our hospital. A total of 1020 mass spectra were acquired from 88 specimens. In order to examine the prediction power of the diagnostic pipeline that we have developed, we performed 10-fold cross-validation for pathological and radiological findings and calculated agreement rates with the conventional methods such as pathological diagnosis (World Health Organization [WHO] grading, MIB-1 labeling index [LI], mutations in the isocitrate dehydrogenase [IDH]-1 gene, and positive 5-aminolevulinic acid [5-ALA] fluorescence) and radiological information (gadolinium [Gd]-enhanced area and high-intensity area on fluid-attenuated inversion recovery [FLAIR] imaging).

RESULTS
Prediction accuracy for WHO malignant grade was 91.37%. Those for MIB-1 LI ≥ 10% and IDH-1 mutation-positive were 82.84% and 87.75%, respectively. Our method achieved an accurate prediction of 95.00% for the 5-ALA-positive lesion. The present method displayed an accuracy of 82.36% in predicting the area of FLAIR hyperintensity and 81.27% for the Gd-enhanced area.

CONCLUSION
Our methodology achieved a higher rate of prediction of glioma in terms of pathology and radiology. Research is ongoing to develop a validation cohort to verify the biological profiles of glioma specimens.
Standardization of imaging methods for machine learning in neuro-oncology
Authors: Li Xiao Tian , Huang Raymond Y 
Published: January 2021

Abstract
Radiomics is a novel technique in which quantitative phenotypes or features are extracted from medical images. Machine learning enables analysis of large quantities of medical imaging data generated by radiomic feature extraction. A growing number of studies based on these methods have developed tools for neuro-oncology applications. Despite the initial promises, many of these imaging tools remain far from clinical implementation. One major limitation hindering the use of these models is their lack of reproducibility when applied across different institutions and clinical settings. In this article, we discuss the importance of standardization of methodology and reporting in our effort to improve reproducibility. Ongoing efforts of standardization for neuro-oncological imaging are reviewed. Challenges related to standardization and potential disadvantages in over-standardization are also described. Ultimately, greater multi-institutional collaborative effort is needed to provide and implement standards for data acquisition and analysis methods to facilitate research results to be interoperable and reliable for integration into different practice environments.
The origins and impact of outflow from super-Eddington flow
Authors: Kitaki Takaaki , Mineshige Shin , Ohsuga Ken , Kawashima Tomohisa 
Published: January 2021

Abstract
It is widely believed that super-Eddington accretion flow can produce powerful outflow, but where does this originate and how much mass and energy are carried away in which directions? To answer these questions, we perform a new large-box, two-dimensional radiation hydrodynamic simulation, paying special attention lest the results should depend on the adopted initial and boundary conditions. We achieve a quasi-steady state at an unprecedentedly large range, r = 2–600rS (with rS being the Schwarzschild radius), from the black hole. The accretion rate onto the central 10 M⊙ black hole is $\dot{M}_{\rm BH} \sim 180 L_{\rm Edd}/c^{2}$, whereas the mass outflow rate is ${\dot{M}}_{\rm outflow} \sim 24 L_{\rm Edd}/c^2$ (where LEdd and c are the Eddington luminosity and the speed of light, respectively). The ratio ${\dot{M}}_{\rm outflow}/{\dot{M}}_{\rm BH} \sim 0.14$ is much less than previously reported. By careful inspection we find that most of the outflowing gas reaching the outer boundary originates from the region at R ≲ 140rS, while gas at 140–230rS forms failed outflow. Therefore, significant outflow occurs inside the trapping radius ∼450rS. The mechanical energy flux (or mass flux) reaches its maximum in the direction of ∼15° (∼80°) from the rotation axis. The total mechanical luminosity is Lmec ∼ 0.16LEdd, while the isotropic X-ray luminosity varies from $L_{\rm X}^{\rm ISO}\sim 2.9 L_{\rm Edd}$ (for a face-on observer) to ∼2.1LEdd (for a nearly edge-on observer). The power ratio is $L_{\rm mec}/L_{\rm X}^{\rm ISO}\sim 0.05$–0.08, in good agreement with observations of ultra-luminous X-ray sources surrounded by optical nebulae.
Mental wellbeing in a pandemic: the role of solidarity and care
Authors: Chan Hui Yun 
Published: January 2021

Abstract
COVID-19 deeply affects many spheres of life. Lockdown measures implemented worldwide have accentuated mental wellbeing changes in the population from the perspectives of space and social relations. These changes leave lasting imprints on individuals and communities. This article draws upon solidarity and care ethics in exploring their role in rebuilding mental wellbeing in the light of constraints arising from lockdown. The diversity of responses to physical and social isolation during the pandemic illuminates the distinctly relational nature of human beings, offering the opportunity for care and solidarity to respond to mental wellbeing challenges in an inclusive and context-sensitive way.
Benefits, Motivations, and Challenges of International Collaborative Research: A Sociology of Science Case Study
Authors: Dusdal Jennifer , Powell Justin J W 
Published: January 2021

AbstractContemporary science is marked by expanding and diverse forms of teamwork. Collaboration across organizational and cultural boundaries extends the possibilities of discovery. International collaborative research projects often provide findings beyond what one team could achieve alone. Motivated to maintain existing relationships and grow their scientific network, researchers increasingly collaborate, despite often unrecognized or underappreciated costs, since such projects are challenging to manage and carry out. Rarely studied in-depth and longitudinally, the perspectives of scientific team members are crucial to better understand the dynamics of durable collaboration networks. Thus, this retrospective case study of a sociology of science project applies the novel method of autoethnography to examine teamwork benefits, motivations, and challenges. Key challenges found include spatial distance and differences of culture, language, and career stage. This study, spanning North America, Europe, the Middle East, and East Asia, focused on collaborators’ characteristics and evolving perceptions of team dynamics over a decade.