bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of ALDH2 on Sleep Disturbances in Patients with Parkinson’s Disease
Authors: Lin Chia-Yen , Yu Rwei-Ling , Wu Ruey-Meei , Tan Chun-Hsiang 
Published: December 2019

AbstractMonoamine neurotransmitters play essential roles in the regulation of arousal and sleep. Impaired metabolism of monoamine neurotransmitters could result in the accumulation of neurotoxic aldehyde metabolites and, hence, neuronal degeneration. Aldehyde dehydrogenases play an important role in the metabolism of the neurotoxic aldehyde metabolites, including the aldehyde metabolites of dopamine, serotonin, and noradrenaline. Deficient aldehyde dehydrogenase 2 (ALDH2) has been suggested to result in the accumulation of these biogenic aldehydes. An ALDH2 single nucleotide polymorphism (SNP), rs671 (A), results in significantly reduced ALDH2 enzyme activity. A total of 83 Parkinson’s disease (PD) patients were recruited in this study. In addition to the genotypes of rs671, the patients were assessed with the PD sleep scale-2nd version (PDSS-2) and the Epworth sleepiness scale (ESS) for symptoms of daytime and nocturnal sleep disturbances. The patients carrying rs671 (A) had more frequent dozing while lying down to rest in the afternoon (ESS item5) (F = 7.308, p = 0.008) than the rs671 (GG) patients. The patients with rs671 (A) reported a trend toward more frequent difficulty staying asleep than the patients with rs671 (GG). (F = 3.278, p = 0.074). The results indicate that patients carrying allele rs671 (A) are more likely to experience impairment in the regulation of arousal and sleep. The results also support the hypothesis that the accumulation of neurotoxic monoamine neurotransmitter aldehyde metabolites secondary to reduced ALDH2 enzyme activity may cause more severe monoaminergic neuronal loss and, hence, more severe symptoms in the regulation of wakefulness and sleep.
Shape-dependent toxicity and mineralization of hydroxyapatite nanoparticles in A7R5 aortic smooth muscle cells
Authors: Huang Ling-Hong , Sun Xin-Yuan , Ouyang Jian-Ming 
Published: December 2019

AbstractVascular smooth muscle cell damage is a key step in inducing vascular calcification that yields hydroxyapatite (HAP) as a major product. The effect of the shape of HAP on the damage to vascular smooth muscle cells has yet to be investigated. In this study, we compared the differences in toxicity of four various morphological nano-HAP crystals, namely, H-Rod, H-Needle, H-Sphere, and H-Plate, in rat aortic smooth muscle cells (A7R5). The sizes of these crystals were 39 nm × 115 nm, 41 nm ×189 nm, 56 nm × 56 nm, and 91 nm × 192 nm, respectively. Results showed that all HAPs decreased cell viability, disorganized cell morphology, disrupted cell membranes, increased intracellular reactive oxygen species concentration, decreased mitochondrial membrane potential, decreased lysosome integrity, increased alkaline phosphatase activity, and increased intracellular calcium concentration, resulting in cell necrosis. The cytotoxicity of the four kinds of HAP was ranked as follows: H-Plate > H-Sphere > H-Needle > H-Rod. The cytotoxicity of each crystal was positively correlated with the following factors: large specific surface area, high electrical conductivity and low surface charge. HAP accelerated calcium deposits on the A7R5 cell surface and induced the expression of osteogenic proteins, such as BMP-2, Runx2, OCN, and ALP. The crystals with high cytotoxicity caused more calcium deposits on the cell surface, higher expression levels of osteogenic protein, and stronger osteogenic transformation abilities. These findings elucidated the relationship between crystal shape and cytotoxicity and provided theoretical references for decreasing the risks of vascular calcification.
Integrated species–phenon trees: visualizing infraspecific diversity within lineages
Authors: Zehady Abdullah Khan , Fordham Barry G. , Ogg James G. 
Published: December 2019

AbstractThe unprecedented detail with which contemporary molecular phylogenetics are visualizing infraspecific relationships within living species and species complexes cannot as yet be reliably extended into deep time. Yet paleontological systematics has routinely dealt in (mainly) morphotaxa envisaged in various ways to have been components of past species lineages. Bridging these perspectives can only enrich both. We present a visualization tool that digitally depicts infraspecific diversity within species through deep time. Our integrated species–phenon tree merges ancestor–descendant trees for fossil morphotaxa (phena) into reconstructed phylogenies of lineages (species) by expanding the latter into “species boxes” and placing the phenon trees inside. A key programming strategy to overcome the lack of a simple overall parent–child hierarchy in the integrated tree has been the progressive population of a species–phenon relationship map which then provides the graphical footprint for the overarching species boxes. Our initial case has been limited to planktonic foraminfera via Aze & others’ important macroevolutionary dataset. The tool could potentially be appropriated for other organisms, to detail other kinds of infraspecific granularity within lineages, or more generally to visualize two nested but loosely coupled trees.
Exploring inflammatory signatures in arthritic joint biopsies with Spatial Transcriptomics
Authors: Carlberg Konstantin , Korotkova Marina , Larsson Ludvig , Catrina Anca I. , Ståhl Patrik L. , Malmström Vivianne 
Published: December 2019

AbstractLately it has become possible to analyze transcriptomic profiles in tissue sections with retained cellular context. We aimed to explore synovial biopsies from rheumatoid arthritis (RA) and spondyloarthritis (SpA) patients, using Spatial Transcriptomics (ST) as a proof of principle approach for unbiased mRNA studies at the site of inflammation in these chronic inflammatory diseases. Synovial tissue biopsies from affected joints were studied with ST. The transcriptome data was subjected to differential gene expression analysis (DEA), pathway analysis, immune cell type identification using Xcell analysis and validation with immunohistochemistry (IHC). The ST technology allows selective analyses on areas of interest, thus we analyzed morphologically distinct areas of mononuclear cell infiltrates. The top differentially expressed genes revealed an adaptive immune response profile and T-B cell interactions in RA, while in SpA, the profiles implicate functions associated with tissue repair. With spatially resolved gene expression data, overlaid on high-resolution histological images, we digitally portrayed pre-selected cell types in silico. The RA displayed an overrepresentation of central memory T cells, while in SpA effector memory T cells were most prominent. Consequently, ST allows for deeper understanding of cellular mechanisms and diversity in tissues from chronic inflammatory diseases.
Using mechanistic models for the clinical interpretation of complex genomic variation
Authors: Peña-Chilet María , Esteban-Medina Marina , Falco Matias M. , Rian Kinza , Hidalgo Marta R. , Loucera Carlos , Dopazo Joaquín 
Published: December 2019

AbstractThe sustained generation of genomic data in the last decade has increased the knowledge on the causal mutations of a large number of diseases, especially for highly penetrant Mendelian diseases, typically caused by a unique or a few genes. However, the discovery of causal genes in complex diseases has been far less successful. Many complex diseases are actually a consequence of the failure of complex biological modules, composed by interrelated proteins, which can happen in many different ways, which conferring a multigenic nature to the condition that can hardly be attributed to one or a few genes. We present a mechanistic model, Hipathia, implemented in a web server that allows estimating the effect that mutations, or changes in the expression of genes, have over the whole system of human signaling and the corresponding functional consequences. We show several use cases where we demonstrate how different the ultimate impact of mutations with similar loss-of-function potential can be and how the potential pathological role of a damaged gene can be inferred within the context of a signaling network. The use of systems biology-based approaches, such as mechanistic models, allows estimating the potential impact of loss-of-function mutations occurring in proteins that are part of complex biological interaction networks, such as signaling pathways. This holistic approach provides an elegant alternative to gene-centric approaches that can open new avenues in the interpretation of the genomic variability in complex diseases.
Hierarchical habitat-use by an endangered steppe bird in fragmented landscapes is associated with large connected patches and high food availability
Authors: Gómez-Catasús Julia , Garza Vicente , Morales Manuel B. , Traba Juan 
Published: December 2019

AbstractMultidimensional approaches must be employed when addressing habitat use patterns. In this study, we aim to elucidate the hierarchical nature of space use by species inhabiting fragmented landscapes, using the threatened Dupont’s lark (Chersophilus duponti). The intensity of space use by Dupont’s lark was estimated using the Kernel Density Function on territory locations in 2015. We measured descriptors of habitat quality at metapopulation (connectivity and patch size), landscape (land-use types and anthropogenic disturbance) and microhabitat-scale (plant structure and composition, herbivore abundance and food availability) at 37 sampling stations. We fitted a Partial Least Squares Regression (PLSR) which yielded two components, accounting for 81% of total variance. Metapopulation-scale factors had the greatest explanatory power (32%), followed by microhabitat (17%) landscape (10%) and spatial predictors (3.6%). Connectivity and patch size were key factors explaining habitat use, and wind farms had a negative effect. At microhabitat-scale, space use was positively associated withColeoptera, Orthoptera, AraneaeandDipterabiomass, but negatively withFormicidaeandBlattodeabiomass, the cover ofStipa spp, Koeleria vallesianaand moss. This research highlights the hierarchical nature of habitat use in fragmented landscapes. Therefore, conservation measures should ensure connectivity, guarantee a minimum patch size, and improve habitat quality within patches.
Tunable three-way topological energy-splitter
Authors: Makwana Mehul P. , Chaplain Gregory 
Published: December 2019

AbstractStrategically combining four structured domains creates the first ever three-way topological energy-splitter; remarkably, this is only possible using a square, or rectangular, lattice, and not the graphene-like structures more commonly used in valleytronics. To achieve this effect, the two mirror symmetries, present within all fully-symmetric square structures, are broken; this leads to two nondistinct interfaces upon which valley-Hall states reside. These interfaces are related to each other via the time-reversal operator and it is this subtlety that allows us to ignite the third outgoing lead. The geometrical construction of our structured medium allows for the three-way splitter to be adiabatically converted into a wave steerer around sharp bends. Due to the tunability of the energies directionality by geometry, our results have far-reaching implications for applications such as beam-splitters, switches and filters across wave physics.
Safety and efficacy of risedronate for patients with esophageal varices and liver cirrhosis: a non-randomized clinical trial
Authors: Lima Talles Bazeia , Santos Lívia Alves Amaral , Nunes Hélio Rubens de Carvalho , Silva Giovanni Faria , Caramori Carlos Antonio , Qi Xingshun , Romeiro Fernando Gomes 
Published: December 2019

AbstractDespite the high prevalence of osteoporosis in liver cirrhosis, the indication of bisphosphonates for patients with esophageal varices has been avoided due to risk of digestive mucosal damage. Therefore, this study aimed to evaluate the safety profile of risedronate treatment for patients with osteoporosis, liver cirrhosis and esophageal varices with low risk of bleeding. A total of 120 patients were allocated into two groups according to their bone mineral density measured by dual-energy X-ray absorptiometry. In the intervention group, 57 subjects with osteoporosis received oral risedronate at 35 mg weekly plus daily calcium and vitamin D supplementation. In the control group, 63 subjects with osteopenia received only calcium and vitamin D. The groups received the treatment for one year and underwent surveillance endoscopies at six and 12 months, as well as a control dual-energy X-ray absorptiometry after a 12-month follow-up. The study received Institutional Review Board approval. The groups had not only comparable Model for End-stage Liver Disease score and esophageal varices degree, but also similar incidence of digestive adverse effects. A significant improvement was achieved in the intervention group in the lumbar spine T score (p < 0.001). The results suggest that risedronate may be safely used in liver cirrhosis and esophageal varices with low bleeding risk under endoscopic surveillance, thus allowing bone mass recovery.
Improving sentence reading performance in Chinese children with developmental dyslexia by training based on visual attention span
Authors: Zhao Jing , Liu Hanlong , Li Jiaxiao , Sun Haixia , Liu Zhanhong , Gao Jing , Liu Yuan , Huang Chen 
Published: December 2019

AbstractDeficits in the visual attention span (VAS) are thought to hamper reading performance in dyslexic individuals. However, the causal relationship between VAS deficits and reading disability remains unclear. The present study attempts to address this issue by using a VAS-based intervention to explore the possible influence of VAS on reading processes in Chinese children with dyslexia. Given the influence of the heterogeneity of dyslexia on intervention effects, VAS-impaired dyslexic and VAS-intact dyslexic individuals were separately trained. Therefore, there were five groups of participants in this study, including 10 trained dyslexic individuals with VAS deficits and 10 untrained dyslexic individuals with VAS dysfunction as the baseline reference, 10 trained and 10 untrained dyslexic individuals with an intact VAS, and fourteen age-matched normal readers for reference of normal level. All participants completed reading measures and a visual 1-back task, reflecting VAS capacity with non-verbal stimuli and non-verbal responses, before and after VAS-based training. VAS-based training tasks included a length estimation task regarding the bottom-up attention, visual search and digit cancelling tasks targeting top-down attentional modulation, and visual tracking tasks to train eye-movement control. The results showed that visual training only helped improve VAS skills in VAS-impaired dyslexic individuals receiving training. Meanwhile, their silent sentence reading accuracy improved after training, and there was a significant relationship between training improvements in VAS function and reading performance. The current findings suggest that VAS-based training has a far-transfer effect on linguistic level (i.e., fluent reading). These findings suggest the possibility that VAS-related training may help children with dyslexia improve their reading skills.
Non-contact physiological monitoring of preterm infants in the Neonatal Intensive Care Unit
Authors: Villarroel Mauricio , Chaichulee Sitthichok , Jorge João , Davis Sara , Green Gabrielle , Arteta Carlos , Zisserman Andrew , McCormick Kenny , Watkinson Peter , Tarassenko Lionel 
Published: December 2019

AbstractThe implementation of video-based non-contact technologies to monitor the vital signs of preterm infants in the hospital presents several challenges, such as the detection of the presence or the absence of a patient in the video frame, robustness to changes in lighting conditions, automated identification of suitable time periods and regions of interest from which vital signs can be estimated. We carried out a clinical study to evaluate the accuracy and the proportion of time that heart rate and respiratory rate can be estimated from preterm infants using only a video camera in a clinical environment, without interfering with regular patient care. A total of 426.6 h of video and reference vital signs were recorded for 90 sessions from 30 preterm infants in the Neonatal Intensive Care Unit (NICU) of the John Radcliffe Hospital in Oxford. Each preterm infant was recorded under regular ambient light during daytime for up to four consecutive days. We developed multi-task deep learning algorithms to automatically segment skin areas and to estimate vital signs only when the infant was present in the field of view of the video camera and no clinical interventions were undertaken. We propose signal quality assessment algorithms for both heart rate and respiratory rate to discriminate between clinically acceptable and noisy signals. The mean absolute error between the reference and camera-derived heart rates was 2.3 beats/min for over 76% of the time for which the reference and camera data were valid. The mean absolute error between the reference and camera-derived respiratory rate was 3.5 breaths/min for over 82% of the time. Accurate estimates of heart rate and respiratory rate could be derived for at least 90% of the time, if gaps of up to 30 seconds with no estimates were allowed.
Tunable super- and subradiant boundary states in one-dimensional atomic arrays
Authors: Zhang Anwei , Wang Luojia , Chen Xianfeng , Yakovlev Vladislav V. , Yuan Luqi 
Published: December 2019

AbstractEfficient manipulation of quantum states is a key step towards applications in quantum information, quantum metrology, and nonlinear optics. Recently, atomic arrays have been shown to be a promising system for exploring topological quantum optics and robust control of quantum states, where the inherent nonlinearity is included through long-range hoppings. Here we show that a one-dimensional atomic array in a periodic magnetic field exhibits characteristic properties associated with an effective two-dimensional Hofstadter-butterfly-like model. Our work points out super- and sub-radiant topological edge states localized at the boundaries of the atomic array despite featuring long-range interactions, and opens an avenue of exploring an interacting quantum optical platform with synthetic dimensions.
Regime-switching model detection map for direct exoplanet detection in ADI sequences
Authors: Dahlqvist C.-H. , Cantalloube F. , Absil O. 
Published: December 2019

Context. Beyond the choice of wavefront control systems or coronographs, advanced data processing methods play a crucial role in disentangling potential planetary signals from bright quasi-static speckles. Among these methods, angular differential imaging (ADI) for data sets obtained in pupil tracking mode (ADI sequences) is one of the foremost research avenues, considering the many observing programs performed with ADI-based techniques and the associated discoveries.
Aims. Inspired by the field of econometrics, here we propose a new detection algorithm for ADI sequences, deriving from the regime-switching model first proposed in the 1980s.
Methods. The proposed model is very versatile as it allows the use of PSF-subtracted data sets (residual cubes) provided by various ADI-based techniques, separately or together, to provide a single detection map. The temporal structure of the residual cubes is used for the detection as the model is fed with a concatenated series of pixel-wise time sequences. The algorithm provides a detection probability map by considering two possible regimes for concentric annuli, the first one accounting for the residual noise and the second one for the planetary signal in addition to the residual noise.
Results. The algorithm performance is tested on data sets from two instruments, VLT/NACO and VLT/SPHERE. The results show an overall better performance in the receiver operating characteristic space when compared with standard signal-to-noise-ratio maps for several state-of-the-art ADI-based post-processing algorithms.
First direct observation of a torsional Alfvén oscillation at coronal heights
Authors: Kohutova P. , Verwichte E. , Froment C. 
Published: December 2019

Context. Torsional Alfvén waves are promising candidates for the transport of energy across different layers of the solar atmosphere. They have been predicted theoretically for decades. Previous detections of Alfvén waves so far have however mostly relied on indirect signatures.
Aims. We present the first direct observational evidence of a fully resolved torsional Alfvén oscillation of a large-scale structure occurring at coronal heights.
Methods. We analysed IRIS imaging and spectral observation of a surge resulting from magnetic reconnection between active region prominence threads and surrounding magnetic field lines.
Results. The IRIS spectral data provide clear evidence of an oscillation in the line-of-sight velocity with a 180° phase difference between the oscillation signatures at opposite edges of the surge flux tube. This together with an alternating tilt in the Si IV and Mg II k spectra across the flux tube and the trajectories traced by the individual threads of the surge material provide clear evidence of torsional oscillation of the flux tube.
Conclusions. Our observation shows that magnetic reconnection leads to the generation of large-scale torsional Alfvén waves.
The PanEDM neutron electric dipole moment experiment at the ILL
Authors: Wurm David , Beck Douglas H. , Chupp Tim , Degenkolb Skyler , Fierlinger Katharina , Fierlinger Peter , Filter Hanno , Ivanov Sergey , Klau Christopher , Kreuz Michael , Lelièvre-Berna Eddy , Lins Tobias , Meichelböck Joachim , Neulinger Thomas , Paddock Robert , Röhrer Florian , Rosner Martin , Serebrov Anatolii P. , Singh Jaideep Taggart , Stoepler Rainer , Stuiber Stefan , Sturm Michael , Taubenheim Bernd , Tonon Xavier , Tucker Mark , Grinten Maurits van der , Zimmer Oliver 
Published: December 2019

The neutron's permanent electric dipole momentdnis constrained to below 3 × 10−26e cm (90% C.L.) [1, 2], by experiments using ultracold neutrons (UCN). We plan to improve this limit by an order of magnitude or more with PanEDM, the first experiment exploiting the ILL's new UCN source SuperSUN. SuperSUN is expected to provide a high density of UCN with energies below 80 neV, implying extended statistical reach with respect to existing sources, for experiments that rely on long storage or spin-precession times. Systematic errors in PanEDM are strongly suppressed by passive magnetic shielding, with magnetic field and gradient drifts at the single fT level. A holding-field homogeneity on the order of 10−4is achieved in low residual fields, via a high static damping factor and built-in coil system. No comagnetometer is needed for the first order-of-magnitude improvement indn, thanks to high magnetic stability and an assortment of sensors outside the UCN storage volumes. PanEDM will be commissioned and upgraded in parallel with SuperSUN, to take full advantage of the source's output in each phase. Commissioning is ongoing in 2019, and a new limit in the mid 10−27e cm range should be possible with two full reactor cycles of data in the commissioned apparatus.