bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficient solution of linear inverse problems using an iterative linear neural network with a generalization training approach
Authors: Tieng Quang M , Su Jiasheng , Vegh Viktor , Reutens David C 
Published: March 2021

Abstract
Inverse problems are some of the most important mathematical problems in science and mathematics because their solution yields information about parameters that are not directly observable. Artificial neural networks have long been used as a mathematical modelling method and have been used successfully to solve inverse problems for application including denoising and medical image reconstruction. Many inverse problems result from integral processes that can be modelled using a linear formulation. These can be efficiently solved via simple networks which are easily trained with reasonable datasets. An innovative simple neural network architecture, the iterative linear neural network (ILNN), consisting of two non-hidden layer networks, one for the forward model and one for the inverse model, is proposed to solve linear inverse problems. Iteration between the two models refines network outcomes with greater accuracy than a network with only the inverse model. A training procedure accompanying the network is also introduced. The network needs to train only the inverse model with one-hot vectors as targets. The training inputs of the inverse model define the weights of the forward model. The number of targets is finite and equal to the length of the vector. With the defined targets, the training process ensures that the inverse model is at least a left inverse of the forward model. This leads to generalizable networks. The experimental results show that the ILNN produces good results even if its inverse model is not perfectly trained. The proposed network is applied to solve two linear inverse problems, deconvolution and the inverse Radon transform. The network successfully reconstructed original data following blurring and Radon transformation.
Sharp nonzero lower bounds for the Schur product theorem
Authors: Khare Apoorva 
Published: March 2021

By a result of Schur [J. Reine Angew. Math. 140 (1911), pp. 1–28], the entrywise product

M
∘
N

M \circ N

of two positive semidefinite matrices

M
,
N

M,N

is again positive. Vybíral [Adv. Math. 368 (2020), p. 9] improved on this by showing the uniform lower bound

M
∘

M
¯

≥

E
n

/

n

M \circ \overline {M} \geq E_n / n

for all

n
×
n

n \times n

real or complex correlation matrices

M
M

, where

E
n

E_n

is the all-ones matrix. This was applied to settle a conjecture of Novak [J. Complexity 15 (1999), pp. 299–316] and to positive definite functions on groups. Vybíral (in his original preprint) asked if one can obtain similar uniform lower bounds for higher entrywise powers of

M
M

, or for

M
∘
N

M \circ N

when

N
≠
M
,

M
¯

N \neq M, \overline {M}

. A natural third question is to ask for a tighter lower bound that does not vanish as

n
→
∞

n \to \infty

, i.e., over infinite-dimensional Hilbert spaces.

In this note, we affirmatively answer all three questions by extending and refining Vybíral’s result to lower-bound

M
∘
N

M \circ N

, for arbitrary complex positive semidefinite matrices

M
,
N

M,N

. Specifically: we provide tight lower bounds, improving on Vybíral’s bounds. Second, our proof is ‘conceptual’ (and self-contained), providing a natural interpretation of these improved bounds via tracial Cauchy–Schwarz inequalities. Third, we extend our tight lower bounds to Hilbert–Schmidt operators. As an application, we settle Open Problem 1 of Hinrichs–Krieg–Novak–Vybíral [J. Complexity 65 (2021), Paper No. 101544, 20 pp.], which yields improvements in the error bounds in certain tensor product (integration) problems.
Commodifying Mexico: OnAmerican Dirtand the Cultural Politics of a Manufactured Bestseller
Authors: Sánchez Prado* Ignacio M 
Published: March 2021

AbstractFollowing the publication and controversy surrounding American Dirt (2020) by Jeanine Cummins, this essay discusses the process by which American Dirt'&#x99;s bestseller status was manufactured in correlation with Flatiron☳ aim to capitalize on a growing Latinx market and on the political visibility of the questions of immigration. It argues that the misrepresentation and commodification of Mexico in the book's form and construction is a central feature of its marketability and success and studies the ways in which the book☳ errors align themselves with representations in Hollywood cinema and television that forward a negative view of Mexico aligned with anti-immigrant and anti-Mexican politics. Finally, the essay discusses the coexistence of these two factors with a growing infrastructure of Hispanophone and translated Latin American literature that competes with, and seeks to challenge, the existence of books like American Dirt.
eQTLHap: a tool for comprehensive eQTL analysis considering haplotypic and genotypic effects
Authors: Al Bkhetan Ziad , Chana Gursharan , Soon Ong Cheng , Goudey Benjamin , Ramamohanarao Kotagiri 
Published: March 2021

Abstract

Motivation
The high accuracy of recent haplotype phasing tools is enabling the integration of haplotype (or phase) information more widely in genetic investigations. One such possibility is phase-aware expression quantitative trait loci (eQTL) analysis, where haplotype-based analysis has the potential to detect associations that may otherwise be missed by standard SNP-based approaches.

Results
We present eQTLHap, a novel method to investigate associations between gene expression and genetic variants, considering their haplotypic and genotypic effect. Using multiple simulations based on real data, we demonstrate that phase-aware eQTL analysis significantly outperforms typical SNP-based methods when the causal genetic architecture involves multiple SNPs. We show that phase-aware eQTL analysis is robust to phasing errors, showing only a minor impact ($&lt;4\%$) on sensitivity. Applying eQTLHap to real GEUVADIS and GTEx datasets detects numerous novel eQTLs undetected by a single-SNP approach, with 22 eQTLs replicating across studies or tissue types, highlighting the utility of phase-aware eQTL analysis.

Availability and implementation
https://github.com/ziadbkh/eQTLHap.

Contact
ziad.albkhetan@gmail.com

Supplementary information
Supplementary data are available at Briefings in Bioinformatics online.
Pandemic and Social Work: Exploring Finnish Social Workers’ Experiences through a SWOT Analysis
Authors: Harrikari Timo , Romakkaniemi Marjo , Tiitinen Laura , Ovaskainen Sanna 
Published: March 2021

Abstract
This article addresses the experiences of Finnish frontline social workers during the first wave of the COVID-19 pandemic in the spring of 2020. Two questions are addressed. First, ‘what types of challenges social work professionals faced’ in their everyday, ‘glocal’ pandemic setting and, second, what types of solutions they developed to meet these challenges. The data consist of 33 personal diaries that social work professionals created from mid-March to the end of May 2020. The diaries are analysed by a thematic content analysis and placed within the framework of a strengths, weaknesses, opportunities and threats analysis. The results suggest that the pandemic challenged social work at all levels, from face-to-face interactions to its global relations. The pandemic revealed not only the number of existing problems of social work, but also created new types of challenges. It demanded ultimate resilience from social workers and a new type of adaptive governance from social welfare institutions.
Biallelic loss-of-function variations in PRDX3 cause cerebellar ataxia
Authors: Rebelo Adriana P , Eidhof Ilse , Cintra Vivian P , Guillot-Noel Léna , Pereira Claudia V , Timmann Dagmar , Traschütz Andreas , Schöls Ludger , Coarelli Giulia , Durr Alexandra , Anheim Mathieu , Tranchant Christine , van de Warrenburg Bart , Guissart Claire , Koenig Michel , Howell Jack , Moraes Carlos T , Schenck Annette , Stevanin Giovanni , Züchner Stephan , Synofzik Matthis ,   the PREPARE network
Published: March 2021

Abstract
Peroxiredoxin 3 (PRDX3) belongs to a superfamily of peroxidases that function as protective antioxidant enzymes. Among the six isoforms (PRDX1–PRDX6), PRDX3 is the only protein exclusively localized to the mitochondria, which are the main source of reactive oxygen species. Excessive levels of reactive oxygen species are harmful to cells, inducing mitochondrial dysfunction, DNA damage, lipid and protein oxidation and ultimately apoptosis. Neuronal cell damage induced by oxidative stress has been associated with numerous neurodegenerative disorders including Alzheimer’s and Parkinson’s diseases. Leveraging the large aggregation of genomic ataxia datasets from the PREPARE (Preparing for Therapies in Autosomal Recessive Ataxias) network, we identified recessive mutations in PRDX3 as the genetic cause of cerebellar ataxia in five unrelated families, providing further evidence for oxidative stress in the pathogenesis of neurodegeneration. The clinical presentation of individuals with PRDX3 mutations consists of mild-to-moderate progressive cerebellar ataxia with concomitant hyper- and hypokinetic movement disorders, severe early-onset cerebellar atrophy, and in part olivary and brainstem degeneration. Patient fibroblasts showed a lack of PRDX3 protein, resulting in decreased glutathione peroxidase activity and decreased mitochondrial maximal respiratory capacity. Moreover, PRDX3 knockdown in cerebellar medulloblastoma cells resulted in significantly decreased cell viability, increased H2O2 levels and increased susceptibility to apoptosis triggered by reactive oxygen species. Pan-neuronal and pan-glial in vivo models of Drosophila revealed aberrant locomotor phenotypes and reduced survival times upon exposure to oxidative stress. Our findings reveal a central role for mitochondria and the implication of oxidative stress in PRDX3 disease pathogenesis and cerebellar vulnerability and suggest targets for future therapeutic approaches.
Effect of concentration and duration of particulate matter exposure on the transcriptome and DNA methylome of bronchial epithelial cells
Authors: Huang Steven K , Tripathi Priya , Koneva Lada A , Cavalcante Raymond G , Craig Nathan , Scruggs Anne M , Sartor Maureen A , Deng Furong , Chen Yahong 
Published: March 2021

Abstract
Exposure to particulate matter (PM) from ambient air pollution is a well-known risk factor for many lung diseases, but the mechanism(s) for this is not completely understood. Bronchial epithelial cells, which line the airway of the respiratory tract, undergo genome-wide level changes in gene expression and DNA methylation particularly when exposed to fine (&lt;2.5 µm) PM (PM2.5). Although some of these changes have been reported in other studies, a comparison of how different concentrations and duration of exposure affect both the gene transcriptome and DNA methylome has not been done. Here, we exposed BEAS-2B, a bronchial epithelial cell line, to different concentrations of PM2.5, and compared how single or repeated doses of PM2.5 affect both the transcriptome and methylome of cells. Widespread changes in gene expression occurred after cells were exposed to a single treatment of high-concentration (30 µg/cm2) PM2.5 for 24 h. These genes were enriched in pathways regulating cytokine–cytokine interactions, Mitogen-Activated Protein Kinase (MAPK) signaling, PI3K-Akt signaling, IL6, and P53. DNA methylomic analysis showed that nearly half of the differentially expressed genes were found to also have DNA methylation changes, with just a slightly greater trend toward overall hypomethylation across the genome. Cells exposed to a lower concentration (1 µg/cm2) of PM2.5 demonstrated a comparable, but more attenuated change in gene expression compared to cells exposed to higher concentrations. There were also many genes affected by lower concentrations of PM2.5, but not higher concentrations. Additionally, repeated exposure to PM2.5 (1 µg/cm2) for seven days resulted in transcriptomic and DNA methylomic changes that were distinct from cells treated with PM2.5 for only one day. Compared to single exposure, repeated exposure to PM2.5 caused a more notable degree of hypomethylation across the genome, though certain genes and regions demonstrated increased DNA methylation. The overall increase in hypomethylation, especially with repeated exposure to PM2.5, was associated with an increase in expression of ten–eleven translocation enzymes. These data demonstrate how variations in concentration and duration of PM2.5 exposure induce distinct differences in the transcriptomic and DNA methylomic profile of bronchial epithelial cells, which may have important implications in the development of both acute and chronic lung disease.
Management of aortic stenosis: a systematic review of clinical practice guidelines and recommendations
Authors: Khanji Mohammed Y , Ricci Fabrizio , Galusko Victor , Sekar Baskar , Chahal C Anwar A , Ceriello Laura , Gallina Sabina , Kennon Simon , Awad Wael I , Ionescu Adrian 
Published: March 2021

Abstract
Multiple guidelines exist for the management of aortic stenosis (AS). We systematically reviewed current guidelines and recommendations, developed by national or international medical organizations, on management of AS to aid clinical decision-making. Publications in MEDLINE and EMBASE between 1 June 2010 and 15 January 2021 were identified. Additionally, the International Guideline Library, National Guideline Clearinghouse, National Library for Health Guidelines Finder, Canadian Medical Association Clinical Practice Guidelines Infobase, and websites of relevant organizations were searched. Two reviewers independently screened titles and abstracts. Two reviewers assessed rigour of guideline development and extracted the recommendations. Of the seven guidelines and recommendations retrieved, five showed considerable rigour of development. Those rigourously developed, agreed on the definition of severe AS and diverse haemodynamic phenotypes, indications and contraindications for intervention in symptomatic severe AS, surveillance intervals in asymptomatic severe AS, and the importance of multidisciplinary teams (MDTs) and shared decision-making. Discrepancies exist in age and surgical risk cut-offs for recommending surgical aortic valve replacement (SAVR) vs. transcatheter aortic valve implantation (TAVI), the use of biomarkers and complementary multimodality imaging for decision-making in asymptomatic patients and surveillance intervals for non-severe AS. Contemporary guidelines for AS management agree on the importance of MDT involvement and shared decision-making for individualized treatment and unanimously indicate valve replacement in severe, symptomatic AS. Discrepancies exist in thresholds for age and procedural risk used in choosing between SAVR and TAVI, role of biomarkers and complementary imaging modalities to define AS severity and risk of progression in asymptomatic patients.
The incidence and management of shoulder complaints in general practice: a retrospective cohort study
Authors: van Doorn Pieter F , de Schepper Evelien I T , Rozendaal Rianne M , Ottenheijm Ramon P G , van der Lei Johan , Bindels Patrick J , Schiphof Dieuwke 
Published: March 2021

Abstract

Background
Shoulder pain is the third most common musculoskeletal complaint in primary care. The international guidelines for general practitioners (GPs) recommend a stepwise treatment of shoulder pain. Little is known about the actual distribution of these treatments in current practice.

Objective
To gain insight in the incidence and current management of shoulder complaints in Dutch general practice.

Methods
A retrospective cohort study was conducted using a health care database containing the full electronic medical records of approximately 200 000 patients in Dutch general practice. A search algorithm was constructed to identify incident cases of shoulder complaints from January 2012 to December 2017. Data on the management of shoulder complaints were manually validated in a random sample of 1000 cases.

Results
The overall incidence of shoulder complaints was 30.3 (95% confidence interval 29.9–30.7) per 1000 person-years. More than half of the patients (58.6%) consulted their GP only once, 44.4% two times or more and 19.7% three times or more. For most patients (58.1%), the GP applied a wait-and-see policy or prescription of oral medication in the first consultation. However, no less than 42.9% of the patients were referred or received an injection already in the first consultation.

Conclusions
There is a wide variety of treatments for shoulder complaints applied by the GP. Some patients are referred or received an injection already in the first consultation. The stepwise approach recommended by the guideline, might not always be applicable due to the diversity of patient- and shoulder characteristics presented in general practice.
Scoping review: Development and assessment of evaluation frameworks of mobile health apps for recommendations to consumers
Authors: Hensher Martin , Cooper Paul , Dona Sithara Wanni Arachchige , Angeles Mary Rose , Nguyen Dieu , Heynsbergh Natalie , Chatterton Mary Lou , Peeters Anna 
Published: March 2021

Abstract

Objective
The study sought to review the different assessment items that have been used within existing health app evaluation frameworks aimed at individual, clinician, or organizational users, and to analyze the scoring and evaluation methods used in these frameworks.

Materials and Methods
We searched multiple bibliographic databases and conducted backward searches of reference lists, using search terms that were synonyms of “health apps,” “evaluation,” and “frameworks.” The review covered publications from 2011 to April 2020. Studies on health app evaluation frameworks and studies that elaborated on the scaling and scoring mechanisms applied in such frameworks were included.

Results
Ten common domains were identified across general health app evaluation frameworks. A list of 430 assessment criteria was compiled across 97 identified studies. The most frequently used scaling mechanism was a 5-point Likert scale. Most studies have adopted summary statistics to generate the total scoring of each app, and the most popular approach taken was the calculation of mean or average scores. Other frameworks did not use any scaling or scoring mechanism and adopted criteria-based, pictorial, or descriptive approaches, or “threshold” filter.

Discussion
There is wide variance in the approaches to evaluating health apps within published frameworks, and this variance leads to ongoing uncertainty in how to evaluate health apps.

Conclusions
A new evaluation framework is needed that can integrate the full range of evaluative criteria within one structure, and provide summative guidance on health app rating, to support individual app users, clinicians, and health organizations in choosing or recommending the best health app.
Iron metabolism strategies in diatoms
Authors: Gao Xia , Bowler Chris , Kazamia Elena 
Published: March 2021

Abstract
Diatoms are one of the most successful group of photosynthetic eukaryotes in the contemporary ocean. They are ubiquitously distributed and are the most abundant primary producers in polar waters. Equally remarkable is their ability to tolerate iron deprivation and respond to periodic iron fertilization. Despite their relatively large cell sizes, diatoms tolerate iron limitation and frequently dominate iron-stimulated phytoplankton blooms, both natural and artificial. Here, we review the main iron use strategies of diatoms, including their ability to assimilate and store a range of iron sources, and the adaptations of their photosynthetic machinery and architecture to iron deprivation. Our synthesis relies on published literature and is complemented by a search of 82 diatom transcriptomes, including information collected from seven representatives of the most abundant diatom genera in the world’s oceans.
Negative Vaccine Attitudes and Intentions to Vaccinate Against Covid-19 in Relation to Smoking Status: A Population Survey of UK Adults
Authors: Jackson Sarah E , Paul Elise , Brown Jamie , Steptoe Andrew , Fancourt Daisy 
Published: March 2021

Abstract

Introduction
We examined differences in negative attitudes toward vaccines in general, and intentions to vaccinate against Covid-19 specifically, by smoking status in a large sample of adults in the UK.

Method
Data were from 29 148 adults participating in the Covid-19 Social Study in September–October 2020. Linear regression analyses examined associations between smoking status (current/former/never) and four types of general negative vaccine attitudes: mistrust of vaccine benefit, worries about unforeseen effects, concerns about commercial profiteering, and preference for natural immunity. Multinomial logistic regression examined associations between smoking status and uncertainty and unwillingness to be vaccinated for Covid-19. Covariates included sociodemographic characteristics and diagnosed health conditions.

Results
Relative to never and former smokers, current smokers reported significantly greater mistrust of vaccine benefit, were more worried about unforeseen future effects, had greater concerns about commercial profiteering, and had a stronger preference for natural immunity (Badjs 0.16–0.36, p &lt; .001). Current smokers were more likely to be uncertain (27.6% vs. 22.7% of never smokers, RRadj 1.43 [95% confidence interval = 1.31–1.56]; vs. 19.3% of former smokers, RRadj 1.55 [1.41–1.73]) or unwilling (21.5% vs. 11.6% of never smokers, RRadj 2.12 [1.91–2.34]; vs. 14.7% of former smokers, RRadj 1.53 [1.37–1.71]) to receive a Covid-19 vaccine.

Conclusions
Current smokers hold more negative attitudes toward vaccines in general, and are more likely to be undecided or unwilling to vaccinate against Covid-19, compared with never and former smokers. With a disproportionately high number of smokers belonging to socially clustered and disadvantaged socioeconomic groups, lower vaccine uptake in this group could also exacerbate health inequalities.

Implications
These results suggest that without intervention, smokers will be less likely than nonsmokers to take up the offer of a Covid-19 vaccine when offered. Targeted policy action may be required to ensure that low uptake of Covid-19 vaccination programs does not compound health inequalities between smokers and nonsmokers.
Changes in astaxanthin and fatty acid concentrations during the developmental process in the calanoidArctodiaptomus walterianusin an alpine lake at low latitudes
Authors: Cui Suzhen , Li Yun , Liu Le , Wang Qianhong , Chen Feizhou 
Published: March 2021

AbstractAstaxanthin is ubiquitous in calanoid copepods in high latitude or altitude regions and is well studied. However, the dynamics of astaxanthin in calanoids at low latitudes are less studied. We collected samples during the ice-free season from Lake Mubanghai, an alpine lake located in a low-latitude and high-altitude region, and analyzed astaxanthin content changes among different developmental stages in Arctodiaptomus walterianus. The total astaxanthin content in A. walterianus varied from 1.66 to 4.49 μg/mg dry weight and was highest in October, the month with the lowest temperature among the three sampling dates. Both free astaxanthin and astaxanthin esters content per biomass and the ratio of free astaxanthin increased from the nauplius to adult stage, and astaxanthin esters dominated in total astaxanthin in all developmental stages. The concentrations of polyunsaturated fatty acids were low in seston but were the main fatty acids in the calanoid. The total fatty acid concentration was positively correlated with the concentrations of total astaxanthin, free astaxanthin and astaxanthin esters in the calanoid. These results suggested that astaxanthin may be beneficial to the accumulation of fatty acids. This strategy may benefit calanoids in adaptation to high mountain environments at low latitudes.