bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Height‐Dependent Delayed Ionospheric Response to Solar EUV
Authors: Schmölter Erik , Heymann Frank , von Savigny Christian , Berdermann Jens 
Published: March 2022

AbstractBased on the analysis of electron density Ne profiles (Grahamstown ionosonde), a case study of the height‐dependent ionospheric response to two 27‐day solar rotation periods in 2019 is performed. A well‐defined sinusoidal response is observed for the period from 27 April 2019 to 24 May 2019 and reproduced with a Thermosphere‐Ionosphere‐Electrodynamics General Circulation Model simulation. The occurring differences between model and observations as well as the driving physical and chemical processes are discussed based on the height‐dependent variations of Ne and major species. Further simulations with an artificial noise free sinusoidal solar flux input show that the Ne delay is defined by contributions due to accumulation of O+ at the Ne peak (positive delay) and continuous loss of in the lower ionosphere (negative delay). The neutral parts' 27‐day signatures show stronger phase shifts. The time‐dependent and height‐dependent impact of the processes responsible for the delayed ionospheric response can therefore be described by a joint analysis of the neutral and ionized parts. The return to the initial ionospheric state (and thus the loss of the accumulated O+) is driven by an increase of downward transport in the second half of the 27‐day solar rotation period. For this reason, the neutral vertical winds (upwards and downwards) and their different height‐dependent 27‐day signatures are discussed. Finally, the importance of a wavelength‐dependent analysis, statistical methods (superposed epoch analysis), and coupling with the middle atmosphere is discussed to outline steps for future analysis.
Parental feeding and childhood genetic risk for obesity: exploring hypothetical interventions with causal inference methods
Authors: Herle Moritz , Pickles Andrew , Micali Nadia , Abdulkadir Mohamed , De Stavola Bianca L. 
Published: March 2022

Abstract
Background
Parental-feeding behaviors are common intervention targets for childhood obesity, but often only deliver small changes. Childhood BMI is partly driven by genetic effects, and the extent to which parental-feeding interventions can mediate child genetic liability is not known. Here we aim to examine how potential interventions on parental-feeding behaviors can mitigate some of the association between child genetic liability and BMI in early adolescence, using causal inference methods.

Methods
Data from the Avon Longitudinal Study of Parents and Children were used to estimate an interventional disparity measure for a child polygenic score for BMI (PGS-BMI) on BMI at 12 years. The approach compares counterfactual outcomes for different hypothetical interventions on parental-feeding styles applied when children are 10–11 years (n = 4248). Results are presented as adjusted total association (Adj-Ta) between genetic liability (PGS-BMI) and BMI at 12 years, versus the interventional disparity measure-direct effect (IDM-DE), which represents the association that would remain, had we intervened on parental-feeding under different scenarios.

Results
For children in the top quintile of genetic liability, an intervention shifting parental feeding to the levels of children with lowest genetic risk, resulted in a difference of 0.81 kg/m2 in BMI at 12 years (Adj-Ta = 3.27, 95% CI: 3.04, 3.49; versus IDM-DE = 2.46, 95% CI: 2.24, 2.67).

Conclusions
Findings suggest that parental-feeding interventions have the potential to buffer some of the genetic liability for childhood obesity. Further, we highlight a novel way to analyze potential interventions for health conditions only using secondary data analyses, by combining methodology from statistical genetics and social epidemiology.
Towards standardizing retinal optical coherence tomography angiography: a review
Authors: Sampson Danuta M. , Dubis Adam M. , Chen Fred K. , Zawadzki Robert J. , Sampson David D. 
Published: March 2022

AbstractThe visualization and assessment of retinal microvasculature are important in the study, diagnosis, monitoring, and guidance of treatment of ocular and systemic diseases. With the introduction of optical coherence tomography angiography (OCTA), it has become possible to visualize the retinal microvasculature volumetrically and without a contrast agent. Many lab-based and commercial clinical instruments, imaging protocols and data analysis methods and metrics, have been applied, often inconsistently, resulting in a confusing picture that represents a major barrier to progress in applying OCTA to reduce the burden of disease. Open data and software sharing, and cross-comparison and pooling of data from different studies are rare. These inabilities have impeded building the large databases of annotated OCTA images of healthy and diseased retinas that are necessary to study and define characteristics of specific conditions. This paper addresses the steps needed to standardize OCTA imaging of the human retina to address these limitations. Through review of the OCTA literature, we identify issues and inconsistencies and propose minimum standards for imaging protocols, data analysis methods, metrics, reporting of findings, and clinical practice and, where this is not possible, we identify areas that require further investigation. We hope that this paper will encourage the unification of imaging protocols in OCTA, promote transparency in the process of data collection, analysis, and reporting, and facilitate increasing the impact of OCTA on retinal healthcare delivery and life science investigations.
CD4 expression in effector T cells depends on DNA demethylation over a developmentally established stimulus-responsive element
Authors: Teghanemt Athmane , Pulipati Priyanjali , Misel-Wuchter Kara , Day Kenneth , Yorek Matthew S. , Yi Ren , Keen Henry L. , Au Christy , Maretzky Thorsten , Gurung Prajwal , Littman Dan R. , Issuree Priya D. 
Published: March 2022

AbstractThe epigenetic patterns that are established during early thymic development might determine mature T cell physiology and function, but the molecular basis and topography of the genetic elements involved are not fully known. Here we show, using the Cd4 locus as a paradigm for early developmental programming, that DNA demethylation during thymic development licenses a novel stimulus-responsive element that is critical for the maintenance of Cd4 gene expression in effector T cells. We document the importance of maintaining high CD4 expression during parasitic infection and show that by driving transcription, this stimulus-responsive element allows for the maintenance of histone H3K4me3 levels during T cell replication, which is critical for preventing de novo DNA methylation at the Cd4 promoter. A failure to undergo epigenetic programming during development leads to gene silencing during effector T cell replication. Our study thus provides evidence of early developmental events shaping the functional fitness of mature effector T cells.
Carbonate complexation enhances hydrothermal transport of rare earth elements in alkaline fluids
Authors: Louvel Marion , Etschmann Barbara , Guan Qiushi , Testemale Denis , Brugger Joël 
Published: March 2022

AbstractRare earth elements (REE), essential metals for the transition to a zero-emission economy, are mostly extracted from REE-fluorcarbonate minerals in deposits associated with carbonatitic and/or peralkaline magmatism. While the role of high-temperature fluids (100 < T < 500 °C) in the development of economic concentrations of REE is well-established, the mechanisms of element transport, ore precipitation, and light (L)REE/heavy (H)REE fractionation remain a matter of debate. Here, we provide direct evidence from in-situ X-ray Absorption Spectroscopy (XAS) that the formation of hydroxyl-carbonate complexes in alkaline fluids enhances hydrothermal mobilization of LREE at T ≥ 400 °C and HREE at T ≤ 200 °C, even in the presence of fluorine. These results not only reveal that the modes of REE transport in alkaline fluids differ fundamentally from those in acidic fluids, but further underline that alkaline fluids may be key to the mineralization of hydrothermal REE-fluorcarbonates by promoting the simultaneous transport of (L)REE, fluoride and carbonate, especially in carbonatitic systems.
Hypervalency in amorphous chalcogenides
Authors: Lee T. H. , Elliott S. R. 
Published: March 2022

AbstractThe concept of hypervalency emerged as a notion for chemical bonding in molecules to explain the atomic coordination in hypervalent molecules that violates the electron-octet rule. Despite its significance, however, hypervalency in condensed phases, such as amorphous solids, remains largely unexplored. Using ab initio molecular-dynamics simulations, we report here the underlying principles of hypervalency in amorphous chalcogenide materials, in terms of the behaviour of hypervalent structural units, and its implicit relationship with material properties. The origin of a material-dependent tendency towards hypervalency is made evident with the multi-centre hyperbonding model, from which its relationship to abnormally large Born effective charges is also unambiguously revealed. The hyperbonding model is here extended to include interactions with cation s2 lone pairs (LPs); such deep-lying LPs can also play a significant role in determining the properties of these chalcogenide materials. The role of hypervalency constitutes an indispensable and important part of chemical interactions in amorphous and crystalline chalcogenide solids.
Structures of a deltacoronavirus spike protein bound to porcine and human receptors
Authors: Ji Weiwei , Peng Qi , Fang Xueqiong , Li Zehou , Li Yaxin , Xu Cunfa , Zhao Shuqing , Li Jizong , Chen Rong , Mo Guoxiang , Wei Zhanyong , Xu Ying , Li Bin , Zhang Shuijun 
Published: March 2022

AbstractPorcine deltacoronavirus (PDCoV) can experimentally infect a variety of animals. Human infection by PDCoV has also been reported. Consistently, PDCoV can use aminopeptidase N (APN) from different host species as receptors to enter cells. To understand this broad receptor usage and interspecies transmission of PDCoV, we determined the crystal structures of the receptor binding domain (RBD) of PDCoV spike protein bound to human APN (hAPN) and porcine APN (pAPN), respectively. The structures of the two complexes exhibit high similarity. PDCoV RBD binds to common regions on hAPN and pAPN, which are different from the sites engaged by two alphacoronaviruses: HCoV-229E and porcine respiratory coronavirus (PRCoV). Based on structure guided mutagenesis, we identified conserved residues on hAPN and pAPN that are essential for PDCoV binding and infection. We report the detailed mechanism for how a deltacoronavirus recognizes homologous receptors and provide insights into the cross-species transmission of PDCoV.
Real-time nanomechanical property modulation as a framework for tunable NEMS
Authors: Ali Utku Emre , Modi Gaurav , Agarwal Ritesh , Bhaskaran Harish 
Published: March 2022

AbstractPhase-change materials (PCMs) can switch between amorphous and crystalline states permanently yet reversibly. However, the change in their mechanical properties has largely gone unexploited. The most practical configuration using suspended thin-films suffer from filamentation and melt-quenching. Here, we overcome these limitations using nanowires as active nanoelectromechanical systems (NEMS). We achieve active modulation of the Young’s modulus in GeTe nanowires by exploiting a unique dislocation-based route for amorphization. These nanowire NEMS enable power-free tuning of the resonance frequency over a range of 30%. Furthermore, their high quality factors ($$Q$$
Q
> 104) are retained after phase transformation. We utilize their intrinsic piezoresistivity with unprecedented gauge factors (up to 1100) to facilitate monolithic integration. Our NEMS demonstrate real-time frequency tuning in a frequency-hopping spread spectrum radio prototype. This work not only opens up an entirely new area of phase-change NEMS but also provides a novel framework for utilizing functional nanowires in active mechanical systems.
Vibrational fingerprints of ferroelectric HfO2
Authors: Fan Shiyu , Singh Sobhit , Xu Xianghan , Park Kiman , Qi Yubo , Cheong S. W. , Vanderbilt David , Rabe Karin M. , Musfeldt J. L. 
Published: March 2022

AbstractHafnia (HfO2) is a promising material for emerging chip applications due to its high-κdielectric behavior, suitability for negative capacitance heterostructures, scalable ferroelectricity, and silicon compatibility. The lattice dynamics along with phononic properties such as thermal conductivity, contraction, and heat capacity are under-explored, primarily due to the absence of high quality single crystals. Herein, we report the vibrational properties of a series of HfO2crystals stabilized with yttrium (chemical formula HfO2: xY, wherex = 20, 12, 11, 8, and 0%) and compare our findings with a symmetry analysis and lattice dynamics calculations. We untangle the effects of Y by testing our calculations against the measured Raman and infrared spectra of the cubic, antipolar orthorhombic, and monoclinic phases and then proceed to reveal the signature modes of polar orthorhombic hafnia. This work provides a spectroscopic fingerprint for several different phases of HfO2and paves the way for an analysis of mode contributions to high-κdielectric and ferroelectric properties for chip technologies.
Tamoxifen treatment ameliorates contractile dysfunction of Duchenne muscular dystrophy stem cell-derived cardiomyocytes on bioengineered substrates
Authors: Birnbaum Foster , Eguchi Asuka , Pardon Gaspard , Chang Alex C. Y. , Blau Helen M. 
Published: March 2022

AbstractDuchenne muscular dystrophy (DMD) is a progressive genetic myopathy that leads to heart failure from dilated cardiomyopathy by early adulthood. Recent evidence suggests that tamoxifen, a selective estrogen receptor modulator widely used to treat breast cancer, ameliorates DMD cardiomyopathy. However, the mechanism of action of 4-hydroxytamoxifen, the active metabolite of tamoxifen, on cardiomyocyte function remains unclear. To examine the effects of chronic 4-hydroxytamoxifen treatment, we used state-of-the-art human-induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) and a bioengineered platform to model DMD. We assessed the beating rate and beating velocity of iPSC-CMs in monolayers and as single cells on micropatterns that promote a physiological cardiomyocyte morphology. We found that 4-hydroxytamoxifen treatment of DMD iPSC-CMs decreased beating rate, increased beating velocity, and ameliorated calcium-handling deficits, leading to prolonged viability. Our study highlights the utility of a bioengineered iPSC-CM platform for drug testing and underscores the potential of repurposing tamoxifen as a therapy for DMD cardiomyopathy.
Transcriptomic analysis of human sensory neurons in painful diabetic neuropathy reveals inflammation and neuronal loss
Authors: Hall Bradford E. , Macdonald Emma , Cassidy Margaret , Yun Sijung , Sapio Matthew R. , Ray Pradipta , Doty Megan , Nara Pranavi , Burton Michael D. , Shiers Stephanie , Ray-Chaudhury Abhik , Mannes Andrew J. , Price Theodore J. , Iadarola Michael J. , Kulkarni Ashok B. 
Published: March 2022

AbstractPathological sensations caused by peripheral painful neuropathy occurring in Type 2 diabetes mellitus (T2DM) are often described as ‘sharp’ and ‘burning’ and are commonly spontaneous in origin. Proposed etiologies implicate dysfunction of nociceptive sensory neurons in dorsal root ganglia (DRG) induced by generation of reactive oxygen species, microvascular defects, and ongoing axonal degeneration and regeneration. To investigate the molecular mechanisms contributing to diabetic pain, DRGs were acquired postmortem from patients who had been experiencing painful diabetic peripheral neuropathy (DPN) and subjected to transcriptome analyses to identify genes contributing to pathological processes and neuropathic pain. DPN occurs in distal extremities resulting in the characteristic “glove and stocking” pattern. Accordingly, the L4 and L5 DRGs, which contain the perikarya of primary afferent neurons innervating the foot, were analyzed from five DPN patients and compared with seven controls. Transcriptome analyses identified 844 differentially expressed genes. We observed increases in levels of inflammation-associated transcripts from macrophages in DPN patients that may contribute to pain hypersensitivity and, conversely, there were frequent decreases in neuronally-related genes. The elevated inflammatory gene profile and the accompanying downregulation of multiple neuronal genes provide new insights into intraganglionic pathology and mechanisms causing neuropathic pain in DPN patients with T2DM.
Nonequilibrium band occupation and optical response of gold after ultrafast XUV excitation
Authors: Ndione Pascal D. , Weber Sebastian T. , Gericke Dirk O. , Rethfeld Baerbel 
Published: March 2022

AbstractFree electron lasers offer unique properties to study matter in states far from equilibrium as they combine short pulses with a large range of photon energies. In particular, the possibility to excite core states drives new relaxation pathways that, in turn, also change the properties of the optically and chemically active electrons. Here, we present a theoretical model for the dynamics of the nonequilibrium occupation of the different energy bands in solid gold driven by exciting deep core states. The resulting optical response is in excellent agreement with recent measurements and, combined with our model, provides a quantitative benchmark for the description of electron–phonon coupling in strongly driven gold. Focusing on sub-picosecond time scales, we find essential differences between the dynamics induced by XUV and visible light.
Anti-inflammatory effects of mesenchymal stem cell-conditioned media inhibited macrophages activation in vitro
Authors: Jin Quan-He , Kim Hyung-Keun , Na Ju-Yong , Jin Cheng , Seon Jong-Keun 
Published: March 2022

AbstractThe immunomodulatory effects of mesenchymal stem cells (MSCs) on macrophages have been reported, however, the underlying mechanism remains unknown. Therefore, this study aimed to investigate the anti-inflammatory effects of MSCs on lipopolysaccharide (LPS)-stimulated macrophages and the subsequent downregulation of their inflammatory mediators. Macrophages were treated with conditioned media from MSCs, without a subsequent change of MSCs responding to the inflammation state. This study also evaluated whether the interleukin (IL) 4 stimulation of MSCs can improve their anti-inflammatory effects. Results demonstrated that the MSC-conditioned medium (MSC-CM) stimulated with IL4 significantly inhibited inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2) protein expression of LPS-activated macrophages. MSC-CM treatment inhibited the mRNA transcription of the cytokines IL1β and IL6, the chemokines C–C motif ligand (CCL) 2, CCL3, CCL4, and CCL5, and the chemokine receptors CCR2 and CCR5, in LPS-stimulated macrophages. As revealed through western blot and immunofluorescence analyses, the phosphorylation of p38, JNK, and ERK MAPKs, as well as phosphorylation of NF-κB in stimulated macrophages, were also inhibited by the MSC-CM. Further, more potent anti-inflammatory effects were observed with the IL4-stimulated cells, compared with those observed with the non-stimulated cells. The MSC-CM demonstrated a potent anti-inflammatory effect on LPS-activated macrophages, while the IL4 stimulation improved this effect. These findings indicate that MSCs could exert anti-inflammatory effects on macrophages, and may be considered as a therapeutic agent in inflammation treatment.
A knowledge graph of clinical trials ($$\mathop {\mathtt {CTKG}}\limits$$)
Authors: Chen Ziqi , Peng Bo , Ioannidis Vassilis N. , Li Mufei , Karypis George , Ning Xia 
Published: March 2022

AbstractEffective and successful clinical trials are essential in developing new drugs and advancing new treatments. However, clinical trials are very expensive and easy to fail. The high cost and low success rate of clinical trials motivate research on inferring knowledge from existing clinical trials in innovative ways for designing future clinical trials. In this manuscript, we present our efforts on constructing the first publicly available Clinical Trials Knowledge Graph, denoted as$$\mathop {\mathtt {CTKG}}\limits$$CTKG.$$\mathop {\mathtt {CTKG}}\limits$$CTKGincludes nodes representing medical entities in clinical trials (e.g., studies, drugs and conditions), and edges representing the relations among these entities (e.g., drugs used in studies). Our embedding analysis demonstrates the potential utilities of$$\mathop {\mathtt {CTKG}}\limits$$CTKGin various applications such as drug repurposing and similarity search, among others.
Genetic and morphological variation of Vespa velutina nigrithorax which is an invasive species in a mountainous area
Authors: Do Yuno , Park Woong-Bae , Park Jun-Kyu , Kim Chang‐Jun , Choi Moon Bo 
Published: March 2022

AbstractThe yellow-legged hornet (Vespa velutina nigrithorax) is an invasive species in South Korea with negative economic, ecological, and public health impacts. We investigated genetic and morphological variation in the species populations on Mt. Jiri, the tallest mountain in South Korea. We hypothesized that a high-altitude would be negatively correlated with the genetic diversity of the hornet population, and hornet wing morphology would change with an increase in altitude. Our results showed that the genetic diversity of yellow-legged hornets did not decrease as altitude increased. Regardless of the altitude, the inbreeding coefficient was high at the newly colonized sites. A single genetic population occurred in the mountainous areas examined and gradually expanded its range. Wing morphology, especially shape, did not change with an increase in altitude or decrease in temperature. Although snow cover and cool temperatures at high altitudes could limit nest-building activities, they did not prevent the extension of the range of the species. Therefore, the yellow-legged hornet cannot be controlled naturally by climate or topography; combined approaches, including chemical control, nest removal, and bait-trapping techniques should be implemented.