bluuebunny/crossref_metadata_2025_split huggingface dataset:
CD4+ T cells from children with active juvenile idiopathic arthritis show altered chromatin features associated with transcriptional abnormalities
Authors: Tarbell Evan , Jiang Kaiyu , Hennon Teresa R. , Holmes Lucy , Williams Sonja , Fu Yao , Gaffney Patrick M. , Liu Tao , Jarvis James N. 
Published: February 2021

AbstractJuvenile idiopathic arthritis (JIA) is one of the most common chronic diseases in children. While clinical outcomes for patients with juvenile JIA have improved, the underlying biology of the disease and mechanisms underlying therapeutic response/non-response are poorly understood. We have shown that active JIA is associated with distinct transcriptional abnormalities, and that the attainment of remission is associated with reorganization of transcriptional networks. In this study, we used a multi-omics approach to identify mechanisms driving the transcriptional abnormalities in peripheral blood CD4+ T cells of children with active JIA. We demonstrate that active JIA is associated with alterations in CD4+ T cell chromatin, as assessed by ATACseq studies. However, 3D chromatin architecture, assessed by HiChIP and simultaneous mapping of CTCF anchors of chromatin loops, reveals that normal 3D chromatin architecture is largely preserved. Overlapping CTCF binding, ATACseq, and RNAseq data with known JIA genetic risk loci demonstrated the presence of genetic influences on the observed transcriptional abnormalities and identified candidate target genes. These studies demonstrate the utility of multi-omics approaches for unraveling important questions regarding the pathobiology of autoimmune diseases.
Embryonic fate after somatic cell nuclear transfer in non-enucleated goldfish oocytes is determined by first cleavages and DNA methylation patterns
Authors: Depincé Alexandra , Le Bail Pierre-Yves , Rouillon Charlène , Labbé Catherine 
Published: February 2021

AbstractReducing the variability in nuclear transfer outcome requires a better understanding of its cellular and epigenetic determinants, in order to ensure safer fish regeneration from cryobanked somatic material. In this work, clones from goldfish were obtained using cryopreserved fin cells as donor and non-enucleated oocytes as recipients. We showed that the high variability of clones survival was not correlated to spawn quality. Clones were then characterized for their first cleavages pattern in relation to their developmental fate up to hatching. The first cell cycle duration was increased in clones with abnormal first cleavage, and symmetric first two cleavages increased clone probability to reach later on 24 h- and hatching-stages. At 24 h-stage, 24% of the clones were diploids and from donor genetic origin only. However, ploidy and genetic origin did not determine clones morphological quality. DNA methylation reprogramming in the promoter region of pou2, nanog, and notail marker genes was highly variable, but clones with the nicest morphologies displayed the best DNA methylation reprogramming. To conclude, non-enucleated oocytes did allow authentic clones production. The first two cell cycles were a critical determinant of the clone ability to reach hatching-stage, and DNA methylation reprogramming significantly influenced clones morphological quality.
Breath analysis based early gastric cancer classification from deep stacked sparse autoencoder neural network
Authors: Aslam Muhammad Aqeel , Xue Cuili , Chen Yunsheng , Zhang Amin , Liu Manhua , Wang Kan , Cui Daxiang 
Published: February 2021

AbstractDeep learning is an emerging tool, which is regularly used for disease diagnosis in the medical field. A new research direction has been developed for the detection of early-stage gastric cancer. The computer-aided diagnosis (CAD) systems reduce the mortality rate due to their effectiveness. In this study, we proposed a new method for feature extraction using a stacked sparse autoencoder to extract the discriminative features from the unlabeled data of breath samples. A Softmax classifier was then integrated to the proposed method of feature extraction, to classify gastric cancer from the breath samples. Precisely, we identified fifty peaks in each spectrum to distinguish the EGC, AGC, and healthy persons. This CAD system reduces the distance between the input and output by learning the features and preserve the structure of the input data set of breath samples. The features were extracted from the unlabeled data of the breath samples. After the completion of unsupervised training, autoencoders with Softmax classifier were cascaded to develop a deep stacked sparse autoencoder neural network. In last, fine-tuning of the developed neural network was carried out with labeled training data to make the model more reliable and repeatable. The proposed deep stacked sparse autoencoder neural network architecture exhibits excellent results, with an overall accuracy of 98.7% for advanced gastric cancer classification and 97.3% for early gastric cancer detection using breath analysis. Moreover, the developed model produces an excellent result for recall, precision, and f score value, making it suitable for clinical application.
Urbanization and economic complexity
Authors: Di Clemente Riccardo , Strano Emanuele , Batty Michael 
Published: February 2021

AbstractUrbanization plays a crucial role in the economic development of every country. The mutual relationship between the urbanization of any country and its economic productive structure is far from being understood. We analyzed the historical evolution of product exports for all countries using the World Trade Web with respect to patterns of urbanization from 1995 to 2010. Using the evolving framework of economic complexity, we reveal that a country’s economic development in terms of its production and export of goods, is interwoven with the urbanization process during the early stages of its economic development and growth. Meanwhile in urbanized countries, the reciprocal relation between economic growth and urbanization fades away with respect to its later stages, becoming negligible for countries highly dependent on the export of resources where urbanization is not linked to any structural economic transformation.
Prenatal and postnatal maternal anxiety and amygdala structure and function in young children
Authors: Donnici Claire , Long Xiangyu , Dewey Deborah , Letourneau Nicole , Landman Bennett , Huo Yuankai , Lebel Catherine 
Published: February 2021

AbstractAnxiety symptoms are relatively common during pregnancy and are associated with behavioural problems in children. The amygdala is involved in emotion regulation, and its volume and function are associated with exposure to prenatal maternal depression. The associations between perinatal maternal anxiety and children’s amygdala structure and function remain unclear. The objective of this study was to determine associations between prenatal and postnatal maternal anxiety and amygdala structure and function in children. Maternal anxiety was measured during the second trimester of pregnancy and 12 weeks postpartum. T1-weighted anatomical data and functional magnetic resonance imaging data were collected from 54 children (25 females), between the ages of 3–7 years. Amygdala volume was calculated and functional connectivity maps were created between the amygdalae and the rest of the brain. Spearman correlations were used to test associations between amygdala volume/functional connectivity and maternal anxiety symptoms, controlling for maternal depression symptoms. Second trimester maternal anxiety symptoms were negatively associated with functional connectivity between the left amygdala and clusters in bilateral parietal regions; higher maternal anxiety was associated with increased negative connectivity. Postnatal maternal anxiety symptoms were positively associated with child amygdala volume, but this finding did not remain significant while controlling for total brain volume. These functional connectivity differences may underlie behavioral outcomes in children exposed to maternal anxiety during pregnancy.
Lactobacillus plantarum 299v probiotic supplementation in men with stable coronary artery disease suppresses systemic inflammation
Authors: Hofeld Benjamin C. , Puppala Venkata K. , Tyagi Sudhi , Ahn Kwang Woo , Anger Amberly , Jia Shuang , Salzman Nita H. , Hessner Martin J. , Widlansky Michael E. 
Published: February 2021

AbstractRecent trials demonstrate that systemic anti-inflammatory therapy reduces cardiovascular events in coronary artery disease (CAD) patients. We recently demonstrated Lactobacillus plantarum 299v (Lp299v) supplementation improved vascular endothelial function in men with stable CAD. Whether this favorable effect is in part due to anti-inflammatory action remains unknown. Testing this hypothesis, we exposed plasma obtained before and after Lp299v supplementation from these subjects to a healthy donor’s PBMCs and measured differences in the PBMC transciptome, performed gene ontological analyses, and compared Lp299v-induced transcriptome changes with changes in vascular function. Daily alcohol users (DAUs) (n = 4) had a significantly different response to Lp299v and were separated from the main analyses. Non-DAUs- (n = 15) showed improved brachial flow-mediated dilation (FMD) and reduced circulating IL-8, IL-12, and leptin. 997 genes were significantly changed. I.I.com decreased (1.01 ± 0.74 vs. 0.22 ± 0.51; P < 0.0001), indicating strong anti-inflammatory effects. Pathway analyses revealed downregulation of IL-1β, interferon-stimulated pathways, and toll-like receptor signaling, and an increase in regulator T-cell (Treg) activity. Reductions in GBP1, JAK2, and TRAIL expression correlated with improved FMD. In non-DAU men with stable CAD, post-Lp299v supplementation plasma induced anti-inflammatory transcriptome changes in human PBMCs that could benefit CAD patients. Future studies should delineate changes in circulating metabolites responsible for these effects.
Experimental characterization of speech aerosol dispersion dynamics
Authors: Tan Zu Puayen , Silwal Lokesh , Bhatt Surya P. , Raghav Vrishank 
Published: February 2021

AbstractContact and inhalation of virions-carrying human aerosols represent the primary transmission pathway for airborne diseases including the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Relative to sneezing and coughing, non-symptomatic aerosol-producing activities such as speaking are highly understudied. The dispersions of aerosols from vocalization by a human subject are hereby quantified using high-speed particle image velocimetry. Syllables of different aerosol production rates were tested and compared to coughing. Results indicate aerosol productions and penetrations are not correlated. E.g. ‘ti’ and ‘ma’ have similar production rates but only ‘ti’ penetrated as far as coughs. All cases exhibited a rapidly penetrating “jet phase” followed by a slow “puff phase.” Immediate dilution of aerosols was prevented by vortex ring flow structures that concentrated particles toward the plume-front. A high-fidelity assessment of risks to exposure must account for aerosol production rate, penetration, plume direction and the prevailing air current.
Harvest time affects antioxidant capacity, total polyphenol and flavonoid content of Polish St John’s wort’s (Hypericum perforatum L.) flowers
Authors: Makarova Katerina , Sajkowska-Kozielewicz Joanna J. , Zawada Katarzyna , Olchowik-Grabarek Ewa , Ciach Michał Aleksander , Gogolewski Krzysztof , Dobros Natalia , Ciechowicz Paulina , Freichels Hélène , Gambin Anna 
Published: February 2021

AbstractThe polyphenol content and antioxidant capacity of hyperforin and hypericin-standardized H. perforatum L. extracts may vary due to the harvest time. In this work, ethanol and ethanol–water extracts of air-dried and lyophilized flowers of H. perforatum L., collected throughout a vegetation season in central Poland, were studied. Air-dried flowers extracts had higher polyphenol (371 mg GAE/g) and flavonoid (160 mg CAE/g) content, DPPH radical scavenging (1672 mg DPPH/g), ORAC (5214 µmol TE/g) and FRAP (2.54 mmol Fe2+/g) than lyophilized flowers extracts (238 mg GAE/g, 107 mg CAE/g, 1287 mg DPPH/g, 3313 µmol TE/g and 0.31 mmol Fe2+/g, respectively). Principal component analysis showed that the collection date influenced the flavonoid and polyphenol contents and FRAP of ethanol extracts, and DPPH and ORAC values of ethanol–water extracts. The ethanol extracts with the highest polyphenol and flavonoid content protected human erythrocytes against bisphenol A-induced damage. Both high field and benchtop NMR spectra of selected extracts, revealed differences in composition caused by extraction solvent and raw material collection date. Moreover, we have shown that benchtop NMR can be used to detect the compositional variation of extracts if the assignment of signals is done previously.
Paternal exposure to a common pharmaceutical (Ritalin) has transgenerational effects on the behaviour of Trinidadian guppies
Authors: De Serrano Alex R. , Hughes Kimberly A. , Rodd F. Helen 
Published: February 2021

AbstractEvidence is emerging that paternal effects, the nongenetic influence of fathers on their offspring, can be transgenerational, spanning several generations. Methylphenidate hydrochloride (MPH; e.g. Ritalin) is a dopaminergic drug that is highly prescribed to adolescent males for the treatment of Attention-deficit/hyperactivity disorder. It has been suggested that MPH could cause transgenerational effects because MPH can affect the male germline in rodents and because paternal effects have been observed in individuals taking similar drugs (e.g. cocaine). Despite these concerns, the transgenerational effects of paternal MPH exposure are unknown. Therefore, we exposed male and female Trinidadian guppies (Poecilia reticulata) to a low, chronic dose of MPH and observed that MPH affected the anxiety/exploratory behaviour of males, but not females. Because of this male-specific effect, we investigated the transgenerational effects of MPH through the paternal line. We observed behavioural effects of paternal MPH exposure on offspring and great-grandoffspring that were not directly administered the drug, making this the first study to demonstrate that paternal MPH exposure can affect descendants. These effects were not due to differential mortality or fecundity between control and MPH lines. These results highlight the transgenerational potential of MPH.
Distribution of absorbed photons in the tunneling ionization process
Authors: Ivanov I. A. , Kim Kyung Taec 
Published: February 2021

AbstractWe describe a procedure that allows us to solve the three-dimensional time-dependent Schrödinger equation for an atom interacting with a quantized one-mode electromagnetic field. Atom-field interaction is treated in an ab initio way prescribed by quantum electrodynamics. We use the procedure to calculate probability distributions of absorbed photons in the regime of tunneling ionization. We analyze evolution of the reduced photon density matrix describing the state of the field. We show that non-diagonal density matrix elements decay quickly, as a result of the decoherence process. A stochastic model, viewing ionization as a Markovian birth-death process, reproduces the main features of the calculated photon distributions.
Investigation of allele specific expression in various tissues of broiler chickens using the detection tool VADT
Authors: Tomlinson M. Joseph , Polson Shawn W. , Qiu Jing , Lake Juniper A. , Lee William , Abasht Behnam 
Published: February 2021

AbstractDifferential abundance of allelic transcripts in a diploid organism, commonly referred to as allele specific expression (ASE), is a biologically significant phenomenon and can be examined using single nucleotide polymorphisms (SNPs) from RNA-seq. Quantifying ASE aids in our ability to identify and understandcis-regulatory mechanisms that influence gene expression, and thereby assist in identifying causal mutations. This study examines ASE in breast muscle, abdominal fat, and liver of commercial broiler chickens using variants called from a large sub-set of the samples (n = 68). ASE analysis was performed using a custom software called VCF ASE Detection Tool (VADT), which detects ASE of biallelic SNPs using a binomial test. On average ~ 174,000 SNPs in each tissue passed our filtering criteria and were considered informative, of which ~ 24,000 (~ 14%) showed ASE. Of all ASE SNPs, only 3.7% exhibited ASE in all three tissues, with ~ 83% showing ASE specific to a single tissue. When ASE genes (genes containing ASE SNPs) were compared between tissues, the overlap among all three tissues increased to 20.1%. Our results indicate that ASE genes show tissue-specific enrichment patterns, but all three tissues showed enrichment for pathways involved in translation.
Fabrication, micro-structure characteristics and transport properties of co-evaporated thin films of Bi2Te3 on AlN coated stainless steel foils
Authors: Ahmed Aziz , Han Seungwoo 
Published: February 2021

AbstractN-type bismuth telluride (Bi2Te3) thin films were prepared on an aluminum nitride (AlN)-coated stainless steel foil substrate to obtain optimal thermoelectric performance. The thermal co-evaporation method was adopted so that we could vary the thin film composition, enabling us to investigate the relationship between the film composition, microstructure, crystal preferred orientation and thermoelectric properties. The influence of the substrate temperature was also investigated by synthesizing two sets of thin film samples; in one set the substrate was kept at room temperature (RT) while in the other set the substrate was maintained at a high temperature, of 300 °C, during deposition. The samples deposited at RT were amorphous in the as-deposited state and therefore were annealed at 280 °C to promote crystallization and phase development. The electrical resistivity and Seebeck coefficient were measured and the results were interpreted. Both the transport properties and crystal structure were observed to be strongly affected by non-stoichiometry and the choice of substrate temperature. We observed columnar microstructures with hexagonal grains and a multi-oriented crystal structure for the thin films deposited at high substrate temperatures, whereas highly (00 l) textured thin films with columns consisting of in-plane layers were fabricated from the stoichiometric annealed thin film samples originally synthesized at RT. Special emphasis was placed on examining the nature of tellurium (Te) atom based structural defects and their influence on thin film properties. We report maximum power factor (PF) of 1.35 mW/m K2 for near-stoichiometric film deposited at high substrate temperature, which was the highest among all studied cases.
Cerebral arterial architectonics and CFD simulation in mice with type 1 diabetes mellitus of different duration
Authors: Yankova Galina , Tur Darya , Parshin Daniil , Cherevko Alexander , Akulov Andrey 
Published: February 2021

AbstractType 1 diabetes is a chronic autoimmune disease that affects tens of millions of people. Diabetes mellitus is one of the strongest factors in the development of cerebrovascular diseases. In this study we used NOD.CB17 Prkdcscid mice and the pharmacological model of type 1 diabetes mellitus of different duration to study changes in the cerebral vasculature. We used two combined approaches using magnetic resonance angiography both steady and transient CFD blood flow modeling. We identified the influence of type 1 diabetes on the architectonics and hemodynamics of the large blood vessels of the brain as the disease progresses. For the first time, we detected a statistically significant change in angioarchitectonics (the angles between the vessels of the circle of Willis, cross-sections areas of vessels) and hemodynamic (maximum blood flow rate, hydraulic resistance) in animals with diabetes duration of 2 months, that is manifested by the development of asymmetry of cerebral blood flow. The result shows the negative effect of diabetes on cerebral circulation as well as the practicability of CFD modeling. This may be of extensive interest, in pharmacological and preclinical studies.
Self-propelled Leidenfrost droplets on a heated glycerol pool
Authors: Matsumoto Ryo , Hasegawa Koji 
Published: February 2021

AbstractThe development of contactless sample manipulation for microfluidic purposes has attracted significant attention within the physicochemical fields. Most existing studies focus on the interactions of unheated liquid substrates and on heated/unheated solid substrates. Therefore, the dynamics of droplets on heated liquid pools have yet to be explored. Here, we present an experimental investigation on the levitated and self-propelled droplets on a heated pool. We aim to identify the effect of the pool temperature and the thermophysical properties of droplets on the dynamics of a self-propelled Leidenfrost droplet on a heated pool. The motion of droplets after levitation on the heated pool is visualized. To elucidate the self-propulsion of Leidenfrost droplets, we quantify the thickness of the vapour film between the approaching droplet and the pool surface. Our experimental results show a quantitative agreement with the simple model prediction for self-propelled Leidenfrost droplets. Our results provide deeper physical insights into the dynamics of Leidenfrost droplets on a heated pool for contactless and contamination-free sample manipulation.
Universal quantum simulation of single-qubit nonunitary operators using duality quantum algorithm
Authors: Zheng Chao 
Published: February 2021

AbstractQuantum information processing enhances human’s power to simulate nature in quantum level and solve complex problem efficiently. During the process, a series of operators is performed to evolve the system or undertake a computing task. In recent year, research interest in non-Hermitian quantum systems, dissipative-quantum systems and new quantum algorithms has greatly increased, which nonunitary operators take an important role in. In this work, we utilize the linear combination of unitaries technique for nonunitary dynamics on a single qubit to give explicit decompositions of the necessary unitaries, and simulate arbitrary time-dependent single-qubit nonunitary operator F(t) using duality quantum algorithm. We find that the successful probability is not only decided by F(t) and the initial state, but also is inversely proportional to the dimensions of the used ancillary Hilbert subspace. In a general case, the simulation can be achieved in both eight- and six-dimensional Hilbert spaces. In phase matching conditions, F(t) can be simulated by only two qubits. We illustrate our method by simulating typical non-Hermitian systems and single-qubit measurements. Our method can be extended to high-dimensional case, such as Abrams–Lloyd’s two-qubit gate. By discussing the practicability, we expect applications and experimental implementations in the near future.