bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cancer subtype identification by consensus guided graph autoencoders
Authors: Liang Cheng , Shang Mingchao , Luo Jiawei 
Published: July 2021

Abstract

Motivation
Cancer subtype identification aims to divide cancer patients into subgroups with distinct clinical phenotypes and facilitate the development for subgroup specific therapies. The massive amount of multi-omics datasets accumulated in the public databases have provided unprecedented opportunities to fulfill this task. As a result, great computational efforts have been made to accurately identify cancer subtypes via integrative analysis of these multi-omics datasets.

Results
In this article, we propose a Consensus Guided Graph Autoencoder (CGGA) to effectively identify cancer subtypes. First, we learn for each omic a new feature matrix by using graph autoencoders, where both structure information and node features can be effectively incorporated during the learning process. Second, we learn a set of omic-specific similarity matrices together with a consensus matrix based on the features obtained in the first step. The learned omic-specific similarity matrices are then fed back to the graph autoencoders to guide the feature learning. By iterating the two steps above, our method obtains a final consensus similarity matrix for cancer subtyping. To comprehensively evaluate the prediction performance of our method, we compare CGGA with several approaches ranging from general-purpose multi-view clustering algorithms to multi-omics-specific integrative methods. The experimental results on both generic datasets and cancer datasets confirm the superiority of our method. Moreover, we validate the effectiveness of our method in leveraging multi-omics datasets to identify cancer subtypes. In addition, we investigate the clinical implications of the obtained clusters for glioblastoma and provide new insights into the treatment for patients with different subtypes.

Availabilityand implementation
The source code of our method is freely available at https://github.com/alcs417/CGGA.

Supplementary information
Supplementary data are available at Bioinformatics online.
Organism-specific training improves performance of linear B-cell epitope prediction
Authors: Ashford Jodie , Reis-Cunha João , Lobo Igor , Lobo Francisco , Campelo Felipe 
Published: July 2021

Abstract

Motivation
In silico identification of linear B-cell epitopes represents an important step in the development of diagnostic tests and vaccine candidates, by providing potential high-probability targets for experimental investigation. Current predictive tools were developed under a generalist approach, training models with heterogeneous datasets to develop predictors that can be deployed for a wide variety of pathogens. However, continuous advances in processing power and the increasing amount of epitope data for a broad range of pathogens indicate that training organism or taxon-specific models may become a feasible alternative, with unexplored potential gains in predictive performance.

Results
This article shows how organism-specific training of epitope prediction models can yield substantial performance gains across several quality metrics when compared to models trained with heterogeneous and hybrid data, and with a variety of widely used predictors from the literature. These results suggest a promising alternative for the development of custom-tailored predictive models with high predictive power, which can be easily implemented and deployed for the investigation of specific pathogens.

Availability and implementation
The data underlying this article, as well as the full reproducibility scripts, are available at https://github.com/fcampelo/OrgSpec-paper. The R package that implements the organism-specific pipeline functions is available at https://github.com/fcampelo/epitopes.

Supplementary information
Supplementary materials are available at Bioinformatics online.
Problematising Artificial Intelligence in Social Work Education: Challenges, Issues and Possibilities
Authors: Hodgson David , Goldingay Sophie , Boddy Jennifer , Nipperess Sharlene , Watts Lynelle 
Published: July 2021

Abstract
Artificial intelligence (AI) is the fourth industrial revolution, and in higher education it will fundamentally transform the work of academics and higher education administrators. AI will also have several implications for students, including a reconsideration of what sorts of skills and knowledge should be taught and developed in the academy to prepare students for digital working lives. As social work educators, we have begun to wonder what the implications of AI in the academy will have for social work education. For educators, there are implications for pedagogy that go well beyond the introduction of new digital tools that merely integrate into existing teaching models and practices. This is because AI will not simply add to existing teaching modes and practices, but will fundamentally transform teaching and learning. Drawing on recent literature and research into in AI and higher education, this article explores possible future implications for social work education. We identify the transformative and disruptive potential of AI in higher education, and consider how this intersects with the ethical and relational side of social work as a profession. Implications for social work education are canvassed
HPLC-UV and TLC-Densitometry Methods for Simultaneous Determination of Sofosbuvir and Daclatasvir: Application to Darvoni® Tablet
Authors: Fayed Ahmed S , Hegazy Maha A , Kamel Ebraam B , Eissa Maya S 
Published: July 2021

Abstract
Sofosbuvir and daclatasvir are co-formulated as directly acting antiviral agents used for treatment of hepatitis C virus. Two chromatographic methods were developed for their determination; the first one is an Reversed phase-high performance liquid chromatography (RP-HPLC) method, in which the separation was performed on C8 Zorbax® SB column (4.6 × 250 mm, 5 μm) using acetonitrile:water:0.05 M phosphate buffer, pH = 8 (50:45:5, v/v/v) as a mobile phase, and ultraviolet detection was performed at 280 nm. Good resolution was obtained, and linearity was confirmed in the range of 10–100 μg/mL for both drugs. The second method is Thin layer chromatography (TLC)-densitometric one, in which sofosbuvir and daclatasvir were separated on silica gel plates using ethyl acetate:hexane:methanol (9:0.5:0.5, v/v/v) as a developing system and the scanning wavelength was 280 nm. Linearity was confirmed over a concentration range of 0.4–25.4 μg/band for sofosbuvir, whereas for daclatasvir linearity scanning was in the range of 0.4–12.8 μg/band. Both antiviral agents can be quantified simultaneously in one analytical run, which is a great time- and cost-saving valor of the developed methods. This valor is even more important in the case of the combined dosage form (Darvoni® tablets) to the pharmaceutical market.
Acute coronary syndrome is associated with a substantial change in the platelet lipidome
Authors: Harm Tobias , Bild Alexander , Dittrich Kristina , Goldschmied Andreas , Nestele Jeremy , Chatterjee Madhumita , Fu Xiaoqing , Kolb Kyra , Castor Tatsiana , Borst Oliver , Geisler Tobias , Rath Dominik , LäMmerhofer Michael , Gawaz Meinrad 
Published: July 2021

Abstract

Aims
Platelets play a key role in the pathophysiology of coronary artery disease (CAD) and patients with enhanced platelet activation are at increased risk to develop adverse cardiovascular events. Beyond reliable cardiovascular risk factors such as dyslipoproteinaemia, significant changes of platelet lipids occur in patients with CAD. In this study, we investigate the platelet lipidome by untargeted liquid chromatography–mass spectrometry, highlighting significant changes between acute coronary syndrome (ACS) and chronic coronary syndrome (CCS) patients. Additionally, we classify the platelet lipidome, spotlighting specific glycerophospholipids as key players in ACS patients. Furthermore, we examine the impact of significantly altered lipids in ACS on platelet-dependent thrombus formation and aggregation.

Methods and results
In this consecutive study, we characterized the platelet lipidome in a CAD cohort (n = 139) and showed significant changes of lipids between patients with ACS and CCS. We found that among 928 lipids, 7 platelet glycerophospholipids were significantly up-regulated in ACS, whereas 25 lipids were down-regulated compared to CCS. The most prominent up-regulated lipid in ACS, PC18:0 (PC 10:0-8:0), promoted platelet activation and ex vivo platelet-dependent thrombus formation.

Conclusions
Our results reveal that the platelet lipidome is altered in ACS and up-regulated lipids embody primarily glycerophospholipids. Alterations of the platelet lipidome, especially of medium chain lipids, may play a role in the pathophysiology of ACS.
Who Sells During a Crash? Evidence from Tax Return Data on Daily Sales of Stock
Authors: Hoopes Jeffrey L , Langetieg Patrick , Nagel Stefan , Reck Daniel , Slemrod Joel , Stuart Bryan A 
Published: July 2021

Abstract
Using United States tax return data containing the universe of individual taxable stock sales from 2008 to 2009, we examine which individuals increased their sale of stocks following episodes of market tumult. We find that the increase was disproportionately concentrated among investors in the top 1% and top 0.1% of the overall income distribution, retired individuals and individuals at the very top of the dividend income distribution. Our estimates suggest that, following the day when Lehman Brothers collapsed, taxpayers in the top 0.1% sold $1.7 billion more in stocks than individuals in the bottom 75%. This difference is equal to 89% of average daily sales by taxpayers in the top 0.1%.
The role of cardiopulmonary exercise testing in predicting mortality and morbidity in people with congenital heart disease: a systematic review and meta-analysis
Authors: Wadey Curtis A , Weston Max E , Dorobantu Dan Mihai , Pieles Guido E , Stuart Graham , Barker Alan R , Taylor Rod S , Williams Craig A 
Published: July 2021

Abstract

Aims
The role of cardiopulmonary exercise testing (CPET) in predicting major adverse cardiovascular events (MACE) in people with congenital heart disease (ConHD) is unknown. A systematic review with meta-analysis was conducted to report the associations between CPET parameters and MACE in people with ConHD.

Methods and results
Electronic databases were systematically searched on 30 April 2020 for eligible publications. Two authors independently screened publications for inclusion, extracted study data, and performed risk of bias assessment. Primary meta-analysis pooled univariate hazard ratios across studies. A total of 34 studies (18 335 participants; 26.2 ± 10.1 years; 54% ± 16% male) were pooled into a meta-analysis. More than 20 different CPET prognostic factors were reported across 6 ConHD types. Of the 34 studies included in the meta-analysis, 10 (29%), 23 (68%), and 1 (3%) were judged as a low, medium, and high risk of bias, respectively. Primary univariate meta-analysis showed consistent evidence that improved peak and submaximal CPET measures are associated with a reduce risk of MACE. This association was supported by a secondary meta-analysis of multivariate estimates and individual studies that could not be numerically pooled.

Conclusion
Various maximal and submaximal CPET measures are prognostic of MACE across a variety of ConHD diagnoses. Further well-conducted prospective multicentre cohort studies are needed to confirm these findings.
Development of predictive models for egg freshness and shelf-life under different storage temperatures
Authors: Quan Chunli , Xi Qian , Shi Xueping , Han Rongwei , Du Qijing , Forghani Fereidoun , Xue Chuanyun , Zhang Jiacheng , Wang Jun 
Published: July 2021

Abstract
The objective of the present study was to develop models for egg freshness and shelf-life predictions for the selected evaluation indicators including egg weight, Haugh unit (HU), and albumen height. Experiments were carried out at different storage temperatures for a total period of 29–32 days. All data were collected and fitted in to Arrhenius equation for egg freshness, while the HU data were applied to a probability model for shelf-life prediction. The results showed that egg weight, albumen height, and HU decreased significantly, while albumen pH increased with the extension of storage time. The higher the storage temperature, the faster the egg quality decreased. In addition, the bias factor, accuracy factor, and the standard error of prediction were selected to verify the developed quality models. Maximum rescaled R-square statistic, the Hosmer–Lemeshow goodness-of-fit statistic, and the receiver operating characteristic curve were used to evaluate the goodness-of-fit of the developed probability model for the shelf-life of eggs, which indicated that the presented predictive models can be used to assess egg freshness and predict shelf-life during different storage temperatures.
Health promotion in secondary schools: participatory process for constructing a self-assessment tool
Authors: Serdà Bernat-Carles , Planas-Lladó Anna , delValle Arantza , Soler-Masó Pere 
Published: July 2021

Summary
This article presents the process of constructing an effective self-assessment tool for monitoring health promotion in secondary schools (SS). The ultimate aim is to improve adolescents’ well-being and quality of life in their reference environment. The design and validation of the instrument were based on participatory action research (involving students, professors, parents, health professionals, youth workers, youth directors, youth managers). A mixed quantitative and qualitative approach was adopted. The construction process included the following five consecutive stages: (i) steering-group creation and definition of objectives; (ii) diagnosing students’ health and well-being in SS (case study); (iii) initial design and construction of health promotion indicators; (iv) validation based on expert judgement and (v) validation by means of a pilot test. The final construction of the self-assessment tool included 5 areas (healthy habits, affectivity and socialization, emotional well-being, safety and risks, and specific health situations), 9 objectives and 18 indicators deployed through a rubric. Each indicator is discussed in depth, specifying the most appropriate resources and health promotion activities for its application. The final self-assessment tool is designed to be sensitive to and effective for self-assessment of health promotion in SS. It contributes to improving adolescent health on an individual basis and also has an impact on the school environment. Finally, it also promotes analysis of the health content on the curriculum and the teaching-learning method(s) employed at the school. The self-assessment tool has been published open access and its implementation will continue to increase health promotion in SS in Catalonia.
Onshore biological sampling of landings by species and size category within auction sites can be more efficient than trip-based concurrent sampling
Authors: Azevedo Manuela , Silva Cristina , Vølstad Jon Helge 
Published: July 2021

Abstract
Since 1996, the European Union has required that fishery products of 35 fish species or groups of species, including crustaceans and cephalopods, be graded before being landed on the basis of commercial size-categories. A multi-stage sampling scheme to estimate catch-at-length and catch-at-age compositions of total annual landings has been conducted in Portuguese waters since 2009. All species and their size-categories are sampled concurrently from random trips within representatively selected site-days annually. In an effort to improve cost-efficiency of the biological catch sampling of commercial landings in Portugal, a size- category sampling scheme was tested during 2017, taking advantage of the stratification of horse mackerel landings, induced by the mandatory grading of landings by size-category. The total number of site-days (primary sampling units), fish boxes sampled, and specimens of horse mackerel sampled for length and age across strata during the pilot study were 30%, 57%, and 12% of the sampling carried out under the standard concurrent scheme, respectively. The assignment of horse mackerel length to the six commercial size-categories was highly consistent across site-days. Our study shows that the concurrent sampling, where trips are subsampled within site-days, could miss some size-categories by chance, resulting in poor estimates of catch-at-length especially for small fish present at the market during a site-day. The size-category sampling scheme ensured subsamples of fish from all size-categories within a site-day, and achieved data on catch-at-age that are fit-for purpose at 24% of the total cost for the standard concurrent sampling. The effect of sampling designs and sample sizes on horse mackerel stock assessment outputs showed that the onshore biological sampling to estimate catch-at-age compositions for stock assessment is optimized with the size-category sampling scheme. Pilot field experiments should be carried out for selected species that evidence consistent size grading among commercial categories.
Kinetics of the Severe Acute Respiratory Syndrome Coronavirus 2 Antibody Response and Serological Estimation of Time Since Infection
Authors: Pelleau Stéphane , Woudenberg Tom , Rosado Jason , Donnadieu Françoise , Garcia Laura , Obadia Thomas , Gardais Soazic , Elgharbawy Yasmine , Velay Aurelie , Gonzalez Maria , Nizou Jacques Yves , Khelil Nizar , Zannis Konstantinos , Cockram Charlotte , Merkling Sarah Hélène , Meola Annalisa , Kerneis Solen , Terrier Benjamin , de Seze Jerome , Planas Delphine , Schwartz Olivier , Dejardin François , Petres Stéphane , von Platen Cassandre , Pellerin Sandrine Fernandes , Arowas Laurence , de Facci Louise Perrin , Duffy Darragh , Cheallaigh Clíona Ní , Dunne Jean , Conlon Niall , Townsend Liam , Duong Veasna , Auerswald Heidi , Pinaud Laurie , Tondeur Laura , Backovic Marija , Hoen Bruno , Fontanet Arnaud , Mueller Ivo , Fafi-Kremer Samira , Bruel Timothée , White Michael 
Published: July 2021

Abstract

Background
Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induces a complex antibody response that varies by orders of magnitude between individuals and over time.

Methods
We developed a multiplex serological test for measuring antibodies to 5 SARS-CoV-2 antigens and the spike proteins of seasonal coronaviruses. We measured antibody responses in cohorts of hospitalized patients and healthcare workers followed for up to 11 months after symptoms. A mathematical model of antibody kinetics was used to quantify the duration of antibody responses. Antibody response data were used to train algorithms for estimating time since infection.

Results
One year after symptoms, we estimate that 36% (95% range, 11%–94%) of anti-Spike immunoglobulin G (IgG) remains, 31% (95% range, 9%–89%) anti-RBD IgG remains, and 7% (1%–31%) of anti-nucleocapsid IgG remains. The multiplex assay classified previous infections into time intervals of 0–3 months, 3–6 months, and 6–12 months. This method was validated using data from a seroprevalence survey in France, demonstrating that historical SARS-CoV-2 transmission can be reconstructed using samples from a single survey.

Conclusions
In addition to diagnosing previous SARS-CoV-2 infection, multiplex serological assays can estimate the time since infection, which can be used to reconstruct past epidemics.
Value-based drug price schemes: a welfare analysis
Authors: Levaggi Laura , Levaggi Rosella 
Published: July 2021

AbstractObjectivesThe market for innovative drugs is characterized by high levels of regulation, whose impact on the market is not neutral. On the one hand, strict regulation may in fact adversely affect incentives to develop new and better products; on the other hand, high prices may drive an unsustainable increase in healthcare costs. This trade-off is particularly important in Europe, where about 75% of drugs costs are financed by the public sector.MethodsWe develop a simple model that allows to compare the impact of different listing and pricing strategies on the social value of innovative drugs, the consumer surplus and the expected profit of the industry.Key findingsUncertainty in the expected price, as well as other forms of access regulation, may lead to a fairer division of the social value between patients and the industry, at the cost of leaving some of the potential value of the drug unexploited.ConclusionsThe regulator may improve value for money if it is prepared either to restrict access to the drug or to reduce the expected price. In both cases, the number of groups of patients treated may be different from the social optimum.
Clues from 4U 0142+61 on supernova fallback disc formation and precession
Authors: Grimani Catia 
Published: July 2021

ABSTRACT
The Nuclear Spectroscopic Telescope Array (NuSTAR) experiment detected a hard X-ray emission (10–70 keV) with a period of 8.68917 s and a pulse-phase modulation at 55 ks, or half this value, from the anomalous X-ray pulsar (AXP) 4U 0142+61. It is shown here that this evidence is naturally explained by the precession of a Keplerian supernova fallback disc surrounding this AXP. It is also found that the precession of discs formed around young neutron stars at distances larger than those considered in the past, may constitute almost neglected sources of gravitational waves with frequencies belonging to the sensitivity bands of the future space interferometers: Laser Interferometer Space Antenna (LISA), Advanced Laser Interferometer Antenna (ALIA), DECi-hertz Interferometer Gravitational wave Observatory (DECIGO), and Big Bang Observer (BBO). In this work, the gravitational wave emission from precessing fallback discs possibly formed around young pulsars such as Crab in a region extending beyond 8 × 107 m from the pulsar surface is estimated. It is also evaluated the role that infrared radiation emission from circumpulsar discs may play in contributing to inverse Compton scattering of TeV energy positrons and electrons. Extensive observational campaigns of disc formation around young and middle-aged pulsars may also contribute to solve the long-standing problem of a pulsar origin for the excess of positrons in cosmic rays observed near the Earth above 7 GeV. In the near future the James Webb Space Telescope, with unprecedented near- and mid-infrared observation capabilities, may provide direct evidence of a large sample of supernova fallback discs.