bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neoepitopes prediction strategies: an integration of cancer genomics and immunoinformatics approaches
Authors: Dhanda Sandeep Kumar , Mahajan Swapnil , Manoharan Malini 
Published: November 2022

Abstract
A major near-term medical impact of the genomic technology revolution will be the elucidation of mechanisms of cancer pathogenesis, leading to improvements in the diagnosis of cancer and the selection of cancer treatment. Next-generation sequencing technologies have accelerated the characterization of a tumor, leading to the comprehensive discovery of all the major alterations in a given cancer genome, followed by the translation of this information using computational and immunoinformatics approaches to cancer diagnostics and therapeutic efforts. In the current article, we review various components of cancer immunoinformatics applied to a series of fields of cancer research, including computational tools for cancer mutation detection, cancer mutation and immunological databases, and computational vaccinology.
WDR45 variants cause ferrous iron loss due to impaired ferritinophagy associated with nuclear receptor coactivator 4 and WD repeat domain phosphoinositide interacting protein 4 reduction
Authors: Tsukida Kiwako , Muramatsu Shin-ichi , Osaka Hitoshi , Yamagata Takanori , Muramatsu Kazuhiro 
Published: November 2022

Abstract
Static encephalopathy of childhood with neurodegeneration in adulthood/β-propeller protein-associated neurodegeneration is a neurodegenerative disorder with brain iron accumulation caused by the variants of WDR45, a core autophagy-related gene that encodes WD repeat domain phosphoinositide interacting protein 4. However, the pathophysiology of the disease, particularly the function of WDR45/WD repeat domain phosphoinositide interacting protein 4 in iron metabolism, is largely unknown. As no other variants of core autophagy-related genes show abnormalities in iron metabolism, the relation between autophagy and iron metabolism remains to be elucidated. Since iron deposition in the brain is the hallmark of static encephalopathy of childhood with neurodegeneration in adulthood/β-propeller protein-associated neurodegeneration, iron chelation therapy has been attempted, but it was found to worsen the symptoms; thus, the establishment of a curative treatment is essential. Here, we evaluated autophagy and iron metabolism in patient-derived cells. The expression of ferritin and ferric iron increased and that of ferrous iron decreased in the patient cells with WDR45 variants. In addition, the expression of nuclear receptor coactivator 4 was markedly reduced in patient-derived cells. Furthermore, divalent metal transporter 1, which takes in ferrous iron, was upregulated, while ferroportin, which exports ferrous iron, was downregulated in patient-derived cells. The transfer of WDR45 via an adeno-associated virus vector restored WD repeat domain phosphoinositide interacting protein 4 and nuclear receptor coactivator 4 expression, reduced ferritin levels, and improved other phenotypes observed in patient-derived cells. As nuclear receptor coactivator 4 mediates the ferritin-specific autophagy, i.e. ferritinophagy, its deficiency impaired ferritinophagy, leading to the accumulation of ferric iron-containing ferritin and insufficiency of ferrous iron. Because ferrous iron is required for various essential biochemical reactions, the changes in divalent metal transporter 1 and ferroportin levels may indicate a compensatory response for maintaining the intracellular levels of ferrous iron. Our study revealed that the pathophysiology of static encephalopathy of childhood with neurodegeneration in adulthood/β-propeller protein-associated neurodegeneration involves ferrous iron insufficiency via impaired ferritinophagy through nuclear receptor coactivator 4 expression reduction. Our findings could aid in developing a treatment strategy involving WDR45 manipulation, which may have clinical applications.
Labor force participation during COVID-19 and risk of depression: a Danish register study
Authors: Hellmann Sophie S , Møller Sanne P , Ersbøll Annette K , Santini Ziggi I , Nielsen Maj Britt D , Grønbæk Morten K , Ekholm Ola , Thygesen Lau C 
Published: November 2022

Abstract

Background
COVID-19 caused economic insecurity for businesses and their employees. Understanding effects of changes in labor force participation on depression risk during economic recession is fundamental for early diagnosis. The study evaluates if changes in labor force participation are associated with depression risk during COVID-19 in Denmark.

Methods
A register-based longitudinal study of Danes aged 25–67 years without depression 2 years prior to baseline defined as February 2020. An eight-level categorical variable on stable or changing labor force participation was defined from monthly employment percentage gradients in the Danish Register-based Evaluation and Marginalization Database from February 2020. The cohort was followed until 31 December 2020 for depressions overall and mild-, moderate- and severe depression. Sex-stratified cox regression models with hazard ratios (HR) and 95% confidence intervals (95% CI) were performed accounting for important confounders.

Results
In total, 1 619 240 (50.3%) men of mean age 45.6 years and 1 598 587 (49.7%) women of mean age 45.9 years were included. Becoming unemployed implied an increased HR of depression in men (HR 2.02; 95% CI 1.94–2.10) and women (2.19; 2.12–2.26) compared to a steady-state full-time employment. Being outside the labor force or employed part-time implied an elevated HR in men (3.02; 2.82–3.23 and 2.41; 2.35–2.48) and women (3.13; 2.30–3.31 and 2.30; 2.26–2.35), respectively, compared to a steady-state full-time employment.

Conclusions
Changes in labor force participation were associated with higher risk of depression relative to a steady-state full-time employment particularly among individuals with low labor force participation during COVID-19.
Chronic, Mild Hypothermic Environmental Temperature Does Not Ameliorate Cognitive Deficits in an Alzheimer’s Disease Mouse
Authors: McFadden Samuel , Sime Lindsey N , Cox MaKayla F , Findley Caleigh A , Peck Mackenzie R , Quinn Kathleen , Fang Yimin , Bartke Andrzej , Hascup Erin R , Hascup Kevin N 
Published: November 2022

Abstract
Metabolic dysfunction increases with age and is a contributing factor to Alzheimer’s disease (AD) development. We have previously observed impaired insulin sensitivity and glucose homeostasis in the APP/PS1 model of AD. To improve these parameters, we chronically exposed male and female mice to mild hypothermic environmental temperature (eT), which positively modulates metabolism. Although a hypothermic eT normalized insulin sensitivity, glucose tolerance was still impaired in both sexes of AD mice. We observed increased plasma glucagon and B-cell activating factor in both sexes, but additional sexually dimorphic mechanisms may explain the impaired glucose homeostasis in AD mice. Hepatic Glut2 was decreased in females while visceral adipose tissue TNFα was increased in male APP/PS1 mice. A mild hypothermic eT did not improve spatial learning and memory in either sex and increased amyloid plaque burden in male APP/PS1 mice. Overall, plasma markers of glucose homeostasis and AD pathology were worse in females compared to male APP/PS1 mice suggesting a faster disease progression. This could affect the therapeutic outcomes if interventional strategies are administered at the same chronological age to male and female APP/PS1 mice. Furthermore, this data suggests a dichotomy exists between mechanisms to improve metabolic function and cognitive health that may be further impaired in AD.
Defining the characteristics of interferon-alpha–stimulated human genes: insight from expression data and machine learning
Authors: Chai Haiting , Gu Quan , Robertson David L , Hughes Joseph 
Published: November 2022

Abstract

Background
A virus-infected cell triggers a signalling cascade, resulting in the secretion of interferons (IFNs), which in turn induces the upregulation of the IFN-stimulated genes (ISGs) that play a role in antipathogen host defence. Here, we conducted analyses on large-scale data relating to evolutionary gene expression, sequence composition, and network properties to elucidate factors associated with the stimulation of human genes in response to IFN-α.

Results
We find that ISGs are less evolutionary conserved than genes that are not significantly stimulated in IFN experiments (non-ISGs). ISGs show obvious depletion of GC content in the coding region. This influences the representation of some compositions following the translation process. IFN-repressed human genes (IRGs), downregulated genes in IFN experiments, can have similar properties to the ISGs. Additionally, we design a machine learning framework integrating the support vector machine and novel feature selection algorithm that achieves an area under the receiver operating characteristic curve (AUC) of 0.7455 for ISG prediction. Its application in other IFN systems suggests the similarity between the ISGs triggered by type I and III IFNs.

Conclusions
ISGs have some unique properties that make them different from the non-ISGs. The representation of some properties has a strong correlation with gene expression following IFN-α stimulation, which can be used as a predictive feature in machine learning. Our model predicts several genes as putative ISGs that so far have shown no significant differential expression when stimulated with IFN-α in the cell/tissue types in the available databases. A web server implementing our method is accessible at http://isgpre.cvr.gla.ac.uk/. The docker image at https://hub.docker.com/r/hchai01/isgpre can be downloaded to reproduce the prediction.
Partitions among elastic waves for dynamic surface loads in a layered medium
Authors: Piña-Flores José , Cárdenas-Soto Martín , García-Jerez Antonio , Sánchez-Sesma Francisco J 
Published: November 2022

SUMMARY
The relationship between the Green's function and the average correlations of the elastic displacements within a diffuse field has been firmly established. The energies of horizontal and vertical motion in such a field are proportional to the imaginary part of the corresponding diagonal components of the Green's tensor for coincident source and receiver. Given this remarkable connection, we examine the partitions of elastic waves due to dynamic horizontal and vertical surface loads in a layered elastic media. The elastic radiation characteristics for horizontally layered media are much more complicated than for the homogeneous half-space. While the corresponding power partitions of the different types of waves in a half-space do not vary with respect to frequency, even in an elastic medium consisting of layers over a half-space, the modal structure shows strong variations in the frequency, mainly around the main peak and the minimum of the horizontal-to-vertical spectral ratio (HVSR). Using a test model with a moderately high impedance contrast, we find that most of the energy density of the horizontal displacements is concentrated in the fundamental mode of the Love waves, reaching ∼80 per cent of the power in the horizontal components. The vertical displacement of the P-SV body waves reaches a maximum of ∼85 per cent, while the fundamental mode of Rayleigh waves reaches a maximum of ∼99 per cent of the available power in the vertical motion. With this analysis, it is possible to analyse the multimodal effects in the dispersion diagrams and explicitly relate the partition of the energy density with the dispersion curves and the HVSR under the diffuse field assumption.
Prevalence of Parvovirus B19 Viremia Among German Blood Donations and the Relationship to ABO and Rhesus Blood Group Antigens
Authors: Healy Katie , Aulin Linda B S , Freij Urban , Ellerstad Marie , Brückle Lena , Hillmering Helen , Svae Tor-Einar , Broliden Kristina , Gustafsson Rasmus 
Published: November 2022

Abstract

Background
Asymptomatic blood donors can transmit human parvovirus B19 (B19V).

Methods
We assessed the B19V prevalence among a large cohort of blood donations collected in Germany during 2015–2018.

Results
In total, 167 123 donations were screened for B19V deoxyribonucleic acid with 22 cases of viremia identified (0.013% positive). Infections peaked at a 4-year interval and the highest number of cases occurred in the summer months. All 22 infections were found in rhesus D-antigen-positive donations, suggesting a protective factor in donors who lack this antigen.

Conclusions
These findings contribute to our understanding of risk factors for B19V infection among central European blood and plasma donors.
Integrating Structural and Reduced-Form Methods in Empirical Finance
Authors: Whited Toni M 
Published: November 2022

Abstract
I discuss various ways in which inference based on the estimation of the parameters of statistical models (reduced-form estimation) can be combined with inference based on the estimation of the parameters of economic models (structural estimation). I discuss five basic categories of integration: directly combining the two methods, using statistical models to simplify structural estimation, using structural estimation to extend the validity of reduced-form results, using reduced-form techniques to assess the external validity of structural estimations, and using structural estimation as a sample selection remedy. I illustrate each of these methods with examples from corporate finance, banking, and personal finance. I conclude by exploring the role of robust estimation techniques in structural estimation in corporate finance.
The social determinants of health, law, and urban development: using human rights to address structural health inequalities in our cities
Authors: Montel Lisa 
Published: November 2022

Abstract
The COVID-19 pandemic exacerbated profound inequalities in the conditions in which people live, work, and age. Law plays a critical role in shaping these structural health inequalities, which have existed for decades. This dynamic can be observed at the local level, with cities operating as environments unequally distributing the risks of non-communicable diseases between population groups. This article first focuses on urban development to explore the conceptual links between health inequalities and the role of law. I expand this observation and I posit that the social determinants of health are about human rights. With that in mind, I argue that human rights are necessary to address the issue of unequally unhealthy urban environments, hence recognising that people are entitled to a minimum essential level of the conditions in which they live, work, and age, which the State is responsible to fulfil. By way of strengthening my argument, I lay out how a human rights framework can improve these conditions and ameliorate unfair inequalities. Finally, I recognise and respond to the limits of a human rights approach.
Magnetic fluxes of solar active regions of different magneto-morphological classes – I. Cyclic variations
Authors: Abramenko Valentina I , Suleymanova Regina A , Zhukova Anastasija V 
Published: November 2022

ABSTRACT
Data for 3046 solar active regions (ARs) observed since 1996 May 12 to 2021 December 27 were utilized to explore how the magnetic fluxes from ARs of different complexity follow the solar cycle. Magnetograms from the Michelson Doppler Imager instrument on the Solar and Heliospheric Observatory and from the Helioseismic and Magnetic Imager instrument on the Solar Dynamics Observatory were utilized. Each AR was classified as a regular bipolar AR (classes A1 or A2), or as an irregular bipolar AR (class B1), or as a multipolar AR (classes B2 or B3). Unipolar ARs were segregated into a specific class U. We found the following results. Unsigned magnetic fluxes from ARs of different classes evolve synchronously following the cycle, the correlation coefficient between the flux curves varies in a range of 0.70–0.99. The deepest solar minimum is observed simultaneously for all classes. Only the most simple ARs were observed during a deepest minimum: A1- and B1-class ARs. The overall shape of a cycle is governed by the regular ARs, whereas the fine structure of a solar maximum is determined by the most complex irregular ARs. Approximately equal amount of flux (45–50 per cent of the total flux) is contributed by the A-class and B-class ARs during a solar maximum. Thus, observations allow us to conclude that the appearance of ARs with the magnetic flux above 1021 Mx is caused by the solar dynamo that operates as a unique process displaying the properties of a non-linear dynamical dissipative system with a cyclic behaviour and unavoidable fluctuations.
Discovery of δ Sct components in eclipsing binary systems IQ CMa, AW men and W Vol
Authors: Ulaş Burak , Ulusoy Ceren 
Published: November 2022

ABSTRACT
We present the first evidence on the δ Sct type pulsations of the primary components of three eclipsing binaries IQ CMa, AW Men, and W Vol in the Transiting Exoplanet Survey Satellite (TESS) field. A comprehensive investigation of the binary properties is conducted. The light curves of the systems are analysed and the frequency analyses are performed to residual data. The systems are compared to the binaries of the same morphological types, and the primaries are examined in contrast to the δ Sct type pulsators. The results show that the systems are oscillating eclipsing Algol-type systems.
From Galactic chemical evolution to cosmic supernova rates synchronized with core-collapse supernovae limited to the narrow progenitor mass range
Authors: Tsujimoto T 
Published: November 2022

ABSTRACT
Massive (≥8 M⊙) stars perish via one of two fates: core-collapse supernovae (CCSNe), which release synthesized heavy elements, or failed supernovae, thereby forming black holes. In the conventional Galactic chemical evolution (GCE) scheme, a substantial portion of massive stars, e.g. all stars in the mass range of 8–100 M⊙, are assumed to enrich the Galaxy with their nucleosynthetic products. However, this hypothesis conflicts with the observations, namely, few CCSNe whose progenitor stars are more massive than ∼18 M⊙. Here, we show that the chemical characteristics shaped by local thin disc stars are compatible with the predictions by enrichment via CCSNe limited to less massive progenitors in the new paradigm of Galactic dynamics that allows stars to migrate from the inner disc. This renewed GCE model predicts that the bursting star formation events − which are considered to take place in the Galactic bulge and in the thick disc − generate more numerous low-mass CCSNe than those expected from the locally determined canonical initial mass function. This finding suggests a high rate of CCSNe in early-type galaxies, which reflects a unique cosmic history of the CCSN rate. With considerable contributions from these galaxies to the cosmic star formation rates in the early Universe, we predict a more steeply increasing slope of the CCSN rate with increasing redshift than that in proportion to cosmic star formation. This predicted redshift evolution agrees well with the measured rates for $0 \lesssim z \lesssim 0.8$; however, its predicted CCSN rate for higher z calls for more precise data from future surveys.
Evolution of massive black hole binaries in collisionally relaxed nuclear star clusters – Impact of mass segregation
Authors: Mukherjee Diptajyoti , Zhu Qirong , Ogiya Go , Rodriguez Carl L , Trac Hy 
Published: November 2022

ABSTRACT
Massive Black Hole (MBH) binaries are considered to be one of the most important sources of Gravitational Waves (GW) that can be detected by GW detectors like LISA. However, there are a lot of uncertainties in the dynamics of MBH binaries in the stages leading up to the GW-emission phase. It has been recently suggested that Nuclear Star Clusters (NSCs) could provide a viable route to overcome the final parsec problem for MBH binaries at the centre of galaxies. NSCs are collisional systems where the dynamics would be altered by the presence of a mass spectrum. In this study, we use a suite of high-resolution N-body simulations with over 1 million particles to understand how collisional relaxation under the presence of a mass spectrum of NSC particles affects the dynamics of the MBH binary under the merger of two NSCs. We consider MBH binaries with different mass ratios and additional non-relaxed models. We find that mass-segregation driven by collisional relaxation can lead to accelerated hardening in lower mass ratio binaries but has the opposite effect in higher mass ratio binaries. Crucially, the relaxed models also demonstrate much lower eccentricities at binary formation and negligible growth during hardening stages leading to longer merger time-scales. The results are robust and highlight the importance of collisional relaxation on changing the dynamics of the binary. Our models are state-of-the-art, use zero softening, and high enough particle numbers to model NSCs realistically.
Mapping separase-mediated cleavage in situ
Authors: Boukaba Abdelhalim , Wu Qiongfang , Liu Jian , Chen Cheng , Liang Jierong , Li Jingjing , Strunnikov Alexander V 
Published: November 2022

Abstract
Separase is a protease that performs critical functions in the maintenance of genetic homeostasis. Among them, the cleavage of the meiotic cohesin during meiosis is a key step in producing gametes in eukaryotes. However, the exact chromosomal localization of this proteolytic cleavage was not addressed due to the lack of experimental tools. To this end, we developed a method based on monoclonal antibodies capable of recognizing the predicted neo-epitopes produced by separase-mediated proteolysis in the RAD21 and REC8 cohesin subunits. To validate the epigenomic strategy of mapping cohesin proteolysis, anti-RAD21 neo-epitopes antibodies were used in ChIP-On-ChEPseq analysis of human cells undergoing mitotic anaphase. Second, a similar analysis applied for mapping of REC8 cleavage in germline cells in Macaque showed a correlation with a subset of alpha-satellites and other repeats, directly demonstrating that the site-specific mei-cohesin proteolysis hotspots are coincident but not identical with centromeres. The sequences for the corresponding immunoglobulin genes show a convergence of antibodies with close specificity. This approach could be potentially used to investigate cohesin ring opening events in other chromosomal locations, if applied to single cells.
Identity, immigration, and subjective well-being: why are natives so sharply divided on immigration issues?
Authors: Howley Peter , Waqas Muhammad 
Published: November 2022

Abstract
We put forward differences in the form of national identity across natives as a key mechanism explaining the sharp public divide on immigration issues. We show that inflows of migrants into local areas can be harmful for the self-reported well-being of natives, but this is only true for natives who self-identify with an ethnic form of national identity. On the other hand, we provide some evidence to suggest that immigration may be utility enhancing for natives with a civic form of national identity. We also show how differences in national identity significantly predict voting preferences in the UK referendum on European Union membership where concern with immigration issues were a salient factor. Drawing on identity economics, our proposed explanation is that for natives with an ethnic form of national identity, any positive economic benefits associated with immigration may not be enough to outweigh losses in identity-based utility.