bluuebunny/crossref_metadata_2025_split huggingface dataset:
Harmonization of technical image quality in computed tomography: comparison between different reconstruction algorithms and kernels from six scanners
Authors: Juntunen Mikael A K , Rautiainen Jari , Hänninen Nina E , Kotiaho Antti O 
Published: March 2022

Abstract

Purpose. The radiology department faces a large number of reconstruction algorithms and kernels during their computed tomography (CT) optimization process. These reconstruction methods are proprietary and ensuring consistent image quality between scanners is becoming increasingly difficult. This study contributes to solving this challenge in CT image quality harmonization by modifying and evaluating a reconstruction algorithm and kernel matching scheme. Methods. The Catphan 600 phantom was scanned with six different CT scanners from four vendors. The phantom was scanned with volumetric CT dose indices (CTDIvols) of 10 mGy and 40 mGy, and the data were reconstructed using 1 mm and 5 mm slices with each combination of reconstruction algorithm, body region kernel, and iterative and deep learning reconstruction strength. A matching scheme developed in previous research, which utilizes the noise power spectrum (NPS) and modulation transfer function (MTF), was modified based on our organization’s needs and used to identify the matching reconstruction algorithms and kernels between different scanners. Results. The matching paradigm produced good matching results, and the mean ± standard deviation (median) matching function values for the different acquisition settings were (a value of 1 indicates a perfect match): CTDIvol 10 mGy, 1 mm slice: 0.78 ± 0.31 (0.94); CTDIvol 10 mGy, 5 mm slice: 0.75 ± 0.33 (0.93); CTDIvol 40 mGy, 1 mm slice: 0.81 ± 0.28 (0.95); CTDIvol 40 mGy, 5 mm slice: 0.75 ± 0.33 (0.93). In general, soft reconstruction kernels, i.e., noise-reducing kernels that reduce sharpness, of one vendor were matched with the soft kernels of another vendor, and vice versa for sharper kernels. Conclusions. Combined quantitative assessment of NPS and MTF allows effective strategy for harmonization of technical image quality between different CT scanners. A software was also shared to support CT image quality harmonization in other institutions.
Reentry in cardiac ventricular epicardial tissue due to SCN5A L812Q gene mutation: a computational study
Authors: Satish Helan , Reddy M Ramasubba 
Published: March 2022

Abstract
Cardiovascular diseases are the major cause of sudden death. Brugada syndrome is an inherited rare disease, that leads to death due to ventricular fibrillation (VF). Brugada Syndrome is related to mutations in the genes that encode SCN5A, a subunit of sodium ion channel (NaV). This computational study investigates the mechanism of loss of function gene mutation (SCN5A L812Q) in sodium ion channel that leads to spiral wave and further develops into VF in an epicardial tissue with homozygous condition. Study was made on wild type, L812Q heterozygous mutated and homozygous mutated ventricular tissues. Ten Tusscher human ventricular cell model (TP06) was used for the simulation study. VF is developed when a spiral wave that causes ventricular arrhythmia breaks. This leads to the formation of multiple spiral waves that are activated on different regions of the ventricles called wave break. This is observed in the epicardial tissue with homozygous condition as the effect of SCN5A L812Q gene mutation. This indicates that VF occurs in the SCN5A L812Q gene mutated homozygous ventricular epicardial tissue that may further lead to Brugada syndrome.
Simulation studies of tungsten impurity behaviors during neon impurity seeding with tungsten bundled charge state model using SOLPS-ITER on EAST
Authors: GAO Shanlu , LIU Xiaoju , DENG Guozhong , MING Tingfeng , LI Guoqiang , ZHANG Xuexi , WU Xiaodong , WU Xiaohe , LI Bang , FAN Haochen , GAO Xiang 
Published: March 2022

Abstract
An investigation into tungsten (W) impurity behaviors with the update of the EAST lower W divertor for H-mode has been carried out using SOLPS-ITER. This work aims to study the effect of external neon (Ne) impurity seeding on W impurity sputtering with the bundled charge state model. As the Ne seeding rate increases, plasma parameters, W concentration (

C

W

), and eroded W flux (

Γ

W

Ero

) at both targets are compared and analyzed between the highly resolved bundled model ‘jett’ and the full W charge state model. The results indicate that ‘jett’ can produce divertor behaviors essentially in agreement with the full W charge state model. The bundled scheme with high resolution in low W charge states (<W20+) has no obvious effect on the Ne impurity distribution and thus little effect on W sputtering by Ne. Meanwhile, parametric scans of radial particle and thermal transport diffusivities (

D

⊥

and

χ

e
,
i

) in the SOL are simulated using the ‘jett’ bundled model. The results indicate that the transport diffusivity variations have significant influences on the divertor parameters, especially for W impurity sputtering.
Thermal release tape-assisted semiconductor membrane transfer process for hybrid photonic devices embedding quantum emitters
Authors: Haws Cori , Guha Biswarup , Perez Edgar , Davanco Marcelo , Song Jin Dong , Srinivasan Kartik , Sapienza Luca 
Published: March 2022

Abstract
The ability to combine different materials enables a combination of complementary properties and device engineering that cannot be found or exploited within a single material system. In the realm of quantum nanophotonics, one might want to increase device functionality by, for instance, combining efficient classical and quantum light emission available in III–V semiconductors, low-loss light propagation accessible in silicon-based materials, fast electro-optical properties of lithium niobate, and broadband reflectors and/or buried metallic contacts for local electric field application or electrical injection of emitters. However, combining different materials on a single wafer is challenging and may result in low reproducibility and/or low yield. For instance, direct epitaxial growth requires crystal lattice matching for producing of defect-free films, and wafer bonding requires considerable and costly process development for high bond strength and yield. We propose a transfer printing technique based on the removal of arrays of free-standing membranes and their deposition onto a host material using a thermal release adhesive tape-assisted process. This approach is versatile, in that it poses limited restrictions on the transferred and host materials. In particular, we transfer 190 nm-thick GaAs membranes that contain InAs quantum dots and which have dimensions up to about 260 μm × 80 μm onto a gold-coated silicon substrate. We show that the presence of a back reflector combined with the etching of micropillars significantly increases the extraction efficiency of quantum light from a single quantum dot line, reaching photon fluxes exceeding 8 × 105 photons per second. This flux is four times higher than the highest count rates measured from emitters outside the pillars on the same chip. Given its versatility and ease of processing, this technique provides a path to realising hybrid quantum nanophotonic devices that combine virtually any material in which free-standing membranes can be made onto any host substrate, without specific compatibility issues and/or requirements.
The value of qualitative data in Quality Improvement Projects in the care of older adults: the case of frailty scores in the emergency department
Authors: Pascall Jones Paul , Tomkow Louise 
Published: March 2022

Abstract
This commentary discusses the role and value of qualitative data when undertaking quality improvement (QI) focussing on the care of older adults. To illustrate this, we reflect on our own experiences of planning a QI project to improve the documentation of Clinical Frailty Scale (CFS) scores in the emergency department (ED) during the coronavirus disease of 2019 (COVID-19) pandemic. National clinical guidance for COVID-19 states that all adults over the age of 65 should be given a CFS at the first point of contact during hospital admission. Therefore, there is a need to improve CFS documentation, specifically in acute care settings.
We describe how qualitative methods facilitated an understanding of the barriers to CFS documentation in ED. Staff see the CFS as a useful tool for inter-professional communication, though there are tensions between clinical guidance and their beliefs. Staff had moral concerns about how an ED-allocated CFS might limit available treatment options for older adults. Our findings demonstrate how qualitative methods can illuminate the important social and moral dimensions of why improvement does or does not occur.
Primary Central Nervous System Anaplastic Large Cell Lymphoma, ALK Positive
Authors: Ahrendsen Jared T , Ta Robert , Li Jingwei , Weinberg Olga K , Ferry Judith A , Hasserjian Robert P , Meredith David M , Varma Hemant , Sadigh Sam , Michaels Phillip D 
Published: March 2022

Abstract

Objectives
Primary central nervous system anaplastic large cell lymphoma, anaplastic lymphoma kinase positive (primary CNS ALCL, ALK+) is a rare CNS lymphoma whose description is limited to case reports. These tumors have a variable clinical course, and prognosis is primarily determined by age. We present the largest case series to date of primary CNS ALCL, ALK+, with observational data.

Methods
A retrospective search of multiple academic centers was performed to identify cases of primary CNS ALCL, ALK+. We also performed a review of published cases of primary CNS ALCL, ALK+. Clinical history, radiography, pathology, and genetic testing data were obtained to determine the prognostic implications in the context of clinical course.

Results
We identified three cases of primary CNS ALCL, ALK+ from our databases. A literature review identified 30 published reports of 31 individual cases. Clinical features for the combined 34 cases included a median age of 18.5 years, with a male to female ratio of 4.7:1, and the most common symptom was headache. Genetic studies demonstrated an ALK rearrangement by fluorescence in situ hybridization, and a gene fusion assay confirmed an NPM1-ALK gene fusion in one case.

Conclusions
We present the largest case series to date of a rare primary CNS lymphoma with additional diagnostic and clinical information.
Leaf surface traits contributing to wettability, water interception and uptake of above-ground water sources in shrubs of Patagonian arid ecosystems
Authors: Cavallaro Agustín , Carbonell-Silletta Luisina , Burek Antonella , Goldstein Guillermo , Scholz Fabián G , Bucci Sandra J 
Published: March 2022

Abstract

Background and Aims
The ecohydrological significance of leaf wetting due to atmospheric water in arid and semiarid ecosystems is not well understood. In these environments, the inputs of precipitation or dew formation resulting in leaf wetting have positive effects on plant functioning. However, its impact on plant water relations may depend on the degree of leaf surface wettability. In this study we evaluated leaf wettability and other leaf traits and its effects on foliar water uptake and canopy interception in plant species of a Patagonian steppe. We also studied how leaf traits affecting wettability vary seasonally from growing to dry season.

Methods
Contact angle of a water droplet with the leaf surface, water adhesion, droplet retention angle, stomatal density, cuticular conductance, canopy interception and maximum foliar water uptake were determined in six dominant shrub species.

Key results
All species increased leaf wettability during the dry season and most species were considered highly wettable. The leaf surface had very high capacity to store and retain water. We found a negative correlation between foliar water uptake and leaf hydrophilia.

Conclusions
Despite the diversity of life forms, including cushion shrubs and tall shrubs, as well as phenological variability, all species converged in similar seasonal changes in leaf traits that favour wettability. Intercepted water by crowns and the extremely high capacity of retention of droplets on leaf surfaces can have a significant impact on eco-hydrological process in water limited ecosystems where most of water sources during the growing and the dry season may be small rainfall events or dew, which do not always increase soil water availability.
Annotating regulatory elements by heterogeneous network embedding
Authors: Lu Yurun , Feng Zhanying , Zhang Songmao , Wang Yong 
Published: March 2022

Abstract

Motivation
Regulatory elements (REs), such as enhancers and promoters, are known as regulatory sequences functional in a heterogeneous regulatory network to control gene expression by recruiting transcription regulators and carrying genetic variants in a context specific way. Annotating those REs relies on costly and labor-intensive next-generation sequencing and RNA-guided editing technologies in many cellular contexts.

Results
We propose a systematic Gene Ontology Annotation method for Regulatory Elements (RE-GOA) by leveraging the powerful word embedding in natural language processing. We first assemble a heterogeneous network by integrating context specific regulations, protein–protein interactions and gene ontology (GO) terms. Then we perform network embedding and associate regulatory elements with GO terms by assessing their similarity in a low dimensional vector space. With three applications, we show that RE-GOA outperforms existing methods in annotating TFs’ binding sites from ChIP-seq data, in functional enrichment analysis of differentially accessible peaks from ATAC-seq data, and in revealing genetic correlation among phenotypes from their GWAS summary statistics data.

Availability and implementation
The source code and the systematic RE annotation for human and mouse are available at https://github.com/AMSSwanglab/RE-GOA.

Supplementary information
Supplementary data are available at Bioinformatics online.
Effects of Confounding Bias in Coronavirus Disease 2019 (COVID-19) and Influenza Vaccine Effectiveness Test-Negative Designs Due to Correlated Influenza and COVID-19 Vaccination Behaviors
Authors: Doll Margaret K , Pettigrew Stacy M , Ma Julia , Verma Aman 
Published: March 2022

Abstract

Background
The test-negative design is commonly used to estimate influenza and coronavirus disease 2019 (COVID-19) vaccine effectiveness (VE). In these studies, correlated COVID-19 and influenza vaccine behaviors may introduce a confounding bias where controls are included with the other vaccine-preventable acute respiratory illness (ARI). We quantified the impact of this bias on VE estimates in studies where this bias is not addressed.

Methods
We simulated study populations under varying vaccination probabilities, COVID-19 VE, influenza VE, and proportions of controls included with the other vaccine-preventable ARI. Mean bias was calculated as the difference between estimated and true VE. Absolute mean bias in VE estimates was classified as low (&lt;10%), moderate (10% to &lt;20%), and high (≥20%).

Results
Where vaccination probabilities are positively correlated, COVID-19 and influenza VE test-negative studies with influenza and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ARI controls, respectively, underestimate VE. For COVID-19 VE studies, mean bias was low for all scenarios where influenza represented ≤25% of controls. For influenza VE studies, mean bias was low for all scenarios where SARS-CoV-2 represented ≤10% of controls. Although bias was driven by the conditional probability of vaccination, low VE of the vaccine of interest and high VE of the confounding vaccine increase its magnitude.

Conclusions
Where a low percentage of controls is included with the other vaccine-preventable ARI, bias in COVID-19 and influenza VE estimates is low. However, influenza VE estimates are likely more susceptible to bias. Researchers should consider potential bias and its implications in their respective study settings to make informed methodological decisions in test-negative VE studies.
Menopause modulates the circulating metabolome: evidence from a prospective cohort study
Authors: Karppinen Jari E , Törmäkangas Timo , Kujala Urho M , Sipilä Sarianna , Laukkanen Jari , Aukee Pauliina , Kovanen Vuokko , Laakkonen Eija K 
Published: March 2022

Abstract

Aims
We studied the changes in the circulating metabolome and their relation to the menopausal hormonal shift in 17β-oestradiol and follicle-stimulating hormone levels among women transitioning from perimenopause to early postmenopause.

Methods and results
We analysed longitudinal data from 218 Finnish women, 35 of whom started menopausal hormone therapy during the study. The menopausal transition was monitored with menstrual diaries and serum hormone measurements. The median follow-up was 14 months (interquartile range: 8–20). Serum metabolites were quantified with targeted nuclear magnetic resonance metabolomics. The model results were adjusted for age, follow-up duration, education, lifestyle, and multiple comparisons. Menopause was associated with 85 metabolite measures. The concentration of apoB (0.17 standard deviation [SD], 99.5% confidence interval [CI] 0.03–0.31), very-low-density lipoprotein triglycerides (0.25 SD, CI 0.05–0.45) and particles (0.21 SD, CI 0.05–0.36), low-density lipoprotein (LDL) cholesterol (0.17 SD, CI 0.01–0.34) and particles (0.17 SD, CI 0.03–0.31), high-density lipoprotein (HDL) triglycerides (0.24 SD, CI 0.02–0.46), glycerol (0.32 SD, CI 0.07–0.58) and leucine increased (0.25 SD, CI 0.02–0.49). Citrate (−0.36 SD, CI −0.57 to −0.14) and 3-hydroxybutyrate concentrations decreased (−0.46 SD, CI −0.75 to −0.17). Most metabolite changes were associated with the menopausal hormonal shift. This explained 11% and 9% of the LDL cholesterol and particle concentration increase, respectively. Menopausal hormone therapy was associated with increased medium-to-large HDL particle count and decreased small-to-medium LDL particle and glycine concentration.

Conclusions
Menopause is associated with proatherogenic circulating metabolome alterations. Female sex hormones levels are connected to the alterations, highlighting their impact on women’s cardiovascular health.
Colletotrichum falcatum modulates the olfactory behavior of the sugarcane borer, favoring pathogen infection
Authors: Franco Flávia P , Túler Amanda C , Gallan Diego Z , Gonçalves Felipe G , Favaris Arodí P , Peñaflor Maria Fernanda G V , Leal Walter S , Moura Daniel S , Bento José Maurício S , Silva-Filho Marcio C 
Published: March 2022

Abstract
Some pathogens can manipulate their host plants and insects to optimize their fitness, increasing the attraction of insects to the infected plant in ways that facilitate pathogen acquisition. In tropical American sugarcane crops, the fungus Colletotrichum falcatum, the red rot causal agent, usually occurs in association with the sugarcane borer Diatraea saccharalis, resulting in large losses of this crop. Considering this association, we aimed to identify the effects of C. falcatum on D. saccharalis host preference and performance as well as the effect of this insect on C. falcatum sugarcane infection. Here, we show that the fungus C. falcatum modulates D. saccharalis behavior to its own benefit. More specifically, C. falcatum-infected sugarcane plants showed a dramatic increase in VOCs, luring D. saccharalis females to lay eggs on these plants. Therefore, sugarcane infection by the fungus C. falcatum increased in cooccurrence with insect herbivory, benefiting the pathogen when associated with D. saccharalis.
Using a theatre-based programme to prevent gender-based violence: evidence from Australia
Authors: Crisp Beth R , Taket Ann 
Published: March 2022

Summary
Bystander interventions play an important contribution to efforts to prevent violence against women and arts-based interventions have been effective as part of a range of health promotion programmes. You the Man is a theatre-based programme, which contributes to violence prevention efforts in community settings. Requiring a single actor and minimal props, the programme consists of a 30–35 min play about intimate partner violence and sexual assault followed by a moderated post-performance panel discussion including staff from local support agencies. Although it has received positive feedback in a range of settings, the only previously published evaluation involved establishing short and long-term impacts on American high school students. This article examines the short-term impacts from attending You the Man events on a different audience, i.e. Australian adults. Anonymous online surveys conducted prior and 4 weeks after events were completed by 41 participants of whom 29 were female and 12 were male, three-quarters of whom were aged between 18 and 49, and who attended events at university campuses (46.3%), in workplaces (34.1%), at sporting clubs (12.2%) and community centres (7.3%). At follow up, participants regarded the severity of abusive and coercive behaviours as being higher than at baseline, their capacity to intervene as a bystander had increased, as had the number of sources of support they would recommend to someone experiencing gender-based violence. Hence, theatre-based programmes can positively affect attitudes in relation to gender-based violence, increase bystander knowledge about safe ways to intervene and positively affect intended bystander intervention.
Undertaking graphic facilitation to enable participation in health promotion interventions in disadvantaged neighbourhoods in Denmark
Authors: Sandholdt Catharina Thiel , Srivarathan Abirami , Kristiansen Maria , Malling Gritt Marie Hviid , Olesen Kathrine Vingum Møller , Jeppesen Mette , Lund Rikke 
Published: March 2022

SummaryThis study reports on a health promotion intervention (HPI), where graphic facilitation (GF) was used as an innovative method to enable participation in a co-design process in a multi-ethnic and disadvantaged neighbourhood in Denmark. The aim was to enable middle-aged and older residents to participate in the research process of planning and evaluating the HPI, as well as in the activities it constituted. GF was used to document statements and inputs from residents through visual meeting minutes and resident experiences with coronavirus disease 2019 (COVID-19) lockdown were drawn by a graphic facilitator. We use the ladder of participation as a framework to unfold the participation enabled by GF. During the HPI, data were produced through ethnographic field studies in and outside the neighbourhood and in design workshops with residents. The study finds that GF helped in reaching a target group difficult to engage in research and that the engagement of a graphic facilitator shifted the power-balance between the researchers and the residents, redistributing expertise. Carrying out GF in a HPI is a collaborative endeavour and in addition to research competences, it requires the artistic and relational skills of a graphic facilitator. The co-created process of the visual minutes and COVID-19 experiences created a sense of ownership and encouraged the residents to reflect on their interaction with the researchers. The redistribution of expertise was conditioned by the power dynamics present and GF helped unfold these dynamics. This is especially important in an HPI engaging socio-economically vulnerable populations.