bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multi-faceted epigenetic dysregulation of gene expression promotes esophageal squamous cell carcinoma
Authors: Cao Wei , Lee Hayan , Wu Wei , Zaman Aubhishek , McCorkle Sean , Yan Ming , Chen Justin , Xing Qinghe , Sinnott-Armstrong Nasa , Xu Hongen , Sailani M. Reza , Tang Wenxue , Cui Yuanbo , liu Jia , Guan Hongyan , Lv Pengju , Sun Xiaoyan , Sun Lei , Han Pengli , Lou Yanan , Chang Jing , Wang Jinwu , Gao Yuchi , Guo Jiancheng , Schenk Gundolf , Shain Alan Hunter , Biddle Fred G. , Collisson Eric , Snyder Michael , Bivona Trever G. 
Published: July 2020

AbstractEpigenetic landscapes can shape physiologic and disease phenotypes. We used integrative, high resolution multi-omics methods to delineate the methylome landscape and characterize the oncogenic drivers of esophageal squamous cell carcinoma (ESCC). We found 98% of CpGs are hypomethylated across the ESCC genome. Hypo-methylated regions are enriched in areas with heterochromatin binding markers (H3K9me3, H3K27me3), while hyper-methylated regions are enriched in polycomb repressive complex (EZH2/SUZ12) recognizing regions. Altered methylation in promoters, enhancers, and gene bodies, as well as in polycomb repressive complex occupancy and CTCF binding sites are associated with cancer-specific gene dysregulation. Epigenetic-mediated activation of non-canonical WNT/β-catenin/MMP signaling and a YY1/lncRNA ESCCAL-1/ribosomal protein network are uncovered and validated as potential novel ESCC driver alterations. This study advances our understanding of how epigenetic landscapes shape cancer pathogenesis and provides a resource for biomarker and target discovery.
Transmission phase read-out of a large quantum dot in a nanowire interferometer
Authors: Borsoi Francesco , Zuo Kun , Gazibegovic Sasa , Op het Veld Roy L. M. , Bakkers Erik P. A. M. , Kouwenhoven Leo P. , Heedt Sebastian 
Published: July 2020

AbstractDetecting the transmission phase of a quantum dot via interferometry can reveal the symmetry of the orbitals and details of electron transport. Crucially, interferometry will enable the read-out of topological qubits based on one-dimensional nanowires. However, measuring the transmission phase of a quantum dot in a nanowire has not yet been established. Here, we exploit recent breakthroughs in the growth of one-dimensional networks and demonstrate interferometric read-out in a nanowire-based architecture. In our two-path interferometer, we define a quantum dot in one branch and use the other path as a reference arm. We observe Fano resonances stemming from the interference between electrons that travel through the reference arm and undergo resonant tunnelling in the quantum dot. Between consecutive Fano peaks, the transmission phase exhibits phase lapses that are affected by the presence of multiple trajectories in the interferometer. These results provide critical insights for the design of future topological qubits.
Burst-tree decomposition of time series reveals the structure of temporal correlations
Authors: Jo Hang-Hyun , Hiraoka Takayuki , Kivelä Mikko 
Published: July 2020

AbstractComprehensive characterization of non-Poissonian, bursty temporal patterns observed in various natural and social processes is crucial for understanding the underlying mechanisms behind such temporal patterns. Among them bursty event sequences have been studied mostly in terms of interevent times (IETs), while the higher-order correlation structure between IETs has gained very little attention due to the lack of a proper characterization method. In this paper we propose a method of representing an event sequence by a burst tree, which is then decomposed into a set of IETs and an ordinal burst tree. The ordinal burst tree exactly captures the structure of temporal correlations that is entirely missing in the analysis of IET distributions. We apply this burst-tree decomposition method to various datasets and analyze the structure of the revealed burst trees. In particular, we observe that event sequences show similar burst-tree structure, such as heavy-tailed burst-size distributions, despite of very different IET distributions. This clearly shows that the IET distributions and the burst-tree structures can be separable. The burst trees allow us to directly characterize the preferential and assortative mixing structure of bursts responsible for the higher-order temporal correlations. We also show how to use the decomposition method for the systematic investigation of such correlations captured by the burst trees in the framework of randomized reference models. Finally, we devise a simple kernel-based model for generating event sequences showing appropriate higher-order temporal correlations. Our method is a tool to make the otherwise overwhelming analysis of higher-order correlations in bursty time series tractable by turning it into the analysis of a tree structure.
Divergence in the metabolome between natural aging and Alzheimer’s disease
Authors: Hunsberger Holly C. , Greenwood Bennett P. , Tolstikov Vladimir , Narain Niven R. , Kiebish Michael A. , Denny Christine Ann 
Published: July 2020

AbstractAlzheimer’s disease (AD) is a progressive and debilitating neurodegenerative disorder and one of the leading causes of death in the United States. Although amyloid plaques and fibrillary tangles are hallmarks of AD, research suggests that pathology associated with AD often begins 20 or more years before symptoms appear. Therefore, it is essential to identify early-stage biomarkers in those at risk for AD and age-related cognitive decline (ARCD) in order to develop preventative treatments. Here, we used an untargeted metabolomics analysis to define system-level alterations following cognitive decline in aged and APP/PS1 (AD) mice. At 6, 12, and 24 months of age, both control (Ctrl) and AD mice were tested in a 3-shock contextual fear conditioning (CFC) paradigm to assess memory decline. AD mice exhibited memory deficits across age and these memory deficits were also seen in naturally aged mice. Prefrontal cortex (PFC), hippocampus (HPC), and spleen were then collected and analyzed for metabolomic alterations. A number of significant pathways were altered between Ctrl and AD mice and naturally aged mice. By identifying systems-level alterations following ARCD and AD, these data could provide insights into disease mechanisms and advance the development of biomarker panels.
LSD-induced increases in social adaptation to opinions similar to one’s own are associated with stimulation of serotonin receptors
Authors: Duerler Patricia , Schilbach Leonhard , Stämpfli Philipp , Vollenweider Franz X. , Preller Katrin H. 
Published: July 2020

AbstractAdapting one’s attitudes and behaviors to group norms is essential for successful social interaction and, thus, participation in society. Yet, despite its importance for societal and individual functioning, the underlying neuropharmacology is poorly understood. We therefore investigated its neurochemical and neural correlates in a pharmacological functional magnetic resonance imaging study. Lysergic acid diethylamide (LSD) has been shown to alter social processing and therefore provides the unique opportunity to investigate the role of the 5-HT2A receptor in social influence processing. Twenty-four healthy human volunteers received either (1) placebo + placebo, (2) placebo + LSD (100 µg), or (3) the 5-HT2A receptor antagonist ketanserin (40 mg) + LSD (100 µg) at three different occasions in a double-blind, randomized, counterbalanced, cross-over design. LSD increases social adaptation but only if the opinions of others are similar to the individual’s own. These increases were associated with increased activity in the medial prefrontal cortex while participants received social feedback. Furthermore, pretreatment with the 5-HT2A antagonist ketanserin fully blocked LSD-induced changes during feedback processing, indicating a key role of the 5-HT2A system in social feedback processing. Our results highlight the crucial role of the 5-HT-system in social influence and, thus, provide important insight into the neuropharmacological basis of social cognition and behavior.
Chronic cement dust load induce novel damages in foliage and buds of Malus domestica
Authors: Shah Kamran , An Na , Ma Wenchun , Ara Gulshan , Ali Kawsar , Kamanova Svetlana , Zuo Xiya , Han Mingyu , Ren Xiaolin , Xing Libo 
Published: July 2020

AbstractCement industry-derived pollutants appear to play multiple roles in stimulating abiotic stress responses in plants. Cement dust deposition on agriculture fields can affect soils, photosynthesis, transpiration and respiration of plants. Here, we characterised the acute physiological responses of Malus × domestica leaves to different cement dust concentrations. The cement dust was sprinkled over plants daily for 2 months at 10 and 20 g/plant, with 0 g/plant serving as the control. Leaf physiological responses revealed significant increases in oxidative stress and antioxidant enzyme activity levels. Additionally, ascorbic acid, soluble sugar, free amino acid, and pigment levels decreased after exposure to cement dust. Macroscopic morphometric parameters, such as weight, dry matter content, and lengths and widths of leaves and buds, were significantly reduced in the cement-treated groups. A histological analysis of leaves and buds revealed decreased cellular areas, cellular damage, and abridged leaf thickness, while an ion leakage assay confirmed the negative effects on tissue integrity. These results provide evidence that cement dust is a hazardous pollutant that induces abiotic stress responses and has degradative effects on leaf health, pigment and biochemical metabolite levels, and anatomical features. Studies to determine the elemental residues of cement dust present in edible plant parts and the adverse impacts of their consumption on human health are strongly recommended.
Hydrogen-rich water reduces inflammatory responses and prevents apoptosis of peripheral blood cells in healthy adults: a randomized, double-blind, controlled trial
Authors: Sim Minju , Kim Chong-Su , Shon Woo-Jeong , Lee Young-Kwan , Choi Eun Young , Shin Dong-Mi 
Published: July 2020

AbstractThe evidence for the beneficial effects of drinking hydrogen-water (HW) is rare. We aimed to investigate the effects of HW consumption on oxidative stress and immune functions in healthy adults using systemic approaches of biochemical, cellular, and molecular nutrition. In a randomized, double-blind, placebo-controlled study, healthy adults (20–59 y) consumed either 1.5 L/d of HW (n = 20) or plain water (PW, n = 18) for 4 weeks. The changes from baseline to the 4th week in serum biological antioxidant potential (BAP), derivatives of reactive oxygen, and 8-Oxo-2′-deoxyguanosine did not differ between groups; however, in those aged ≥ 30 y, BAP increased greater in the HW group than the PW group. Apoptosis of peripheral blood mononuclear cells (PBMCs) was significantly less in the HW group. Flow cytometry analysis of CD4+, CD8+, CD20+, CD14+ and CD11b+ cells showed that the frequency of CD14+ cells decreased in the HW group. RNA-sequencing analysis of PBMCs demonstrated that the transcriptomes of the HW group were clearly distinguished from those of the PW group. Most notably, transcriptional networks of inflammatory responses and NF-κB signaling were significantly down-regulated in the HW group. These finding suggest HW increases antioxidant capacity thereby reducing inflammatory responses in healthy adults.
Glycolaldehyde-modified proteins cause adverse functional and structural aortic remodeling leading to cardiac pressure overload
Authors: Haesen Sibren , Cöl Ümare , Schurgers Wouter , Evens Lize , Verboven Maxim , Driesen Ronald B. , Bronckaers Annelies , Lambrichts Ivo , Deluyker Dorien , Bito Virginie 
Published: July 2020

AbstractGrowing evidence supports the role of advanced glycation end products (AGEs) in the development of diabetic vascular complications and cardiovascular diseases (CVDs). We have shown that high-molecular-weight AGEs (HMW-AGEs), present in our Western diet, impair cardiac function. Whether HMW-AGEs affect vascular function remains unknown. In this study, we aimed to investigate the impact of chronic HMW-AGEs exposure on vascular function and structure. Adult male Sprague Dawley rats were daily injected with HMW-AGEs or control solution for 6 weeks. HMW-AGEs animals showed intracardiac pressure overload, characterized by increased systolic and mean pressures. The contraction response to PE was increased in aortic rings from the HMW-AGEs group. Relaxation in response to ACh, but not SNP, was impaired by HMW-AGEs. This was associated with reduced plasma cyclic GMP levels. SOD restored ACh-induced relaxation of HMW-AGEs animals to control levels, accompanied by a reduced half-maximal effective dose (EC50). Finally, collagen deposition and intima-media thickness of the aortic vessel wall were increased with HMW-AGEs. Our data demonstrate that chronic HMW-AGEs exposure causes adverse vascular remodelling. This is characterised by disturbed vasomotor function due to increased oxidative stress and structural changes in the aorta, suggesting an important contribution of HMW-AGEs in the development of CVDs.
Contradictory effects of leaf rolls in a leaf-mining weevil
Authors: Kobayashi Chisato , Matsuo Kazunori , Kawata Masakado 
Published: July 2020

AbstractLeaf rolls by herbivorous insects evolved in various lepidopteran groups, aphids, and some attelabid weevil species. Leaf rolls are known to have a positive effect on the survival of immature insects, protecting them from natural enemies such as birds, ants, predatory wasps, and parasitoids as well as environmental stress. On the other hand, leaf rolls are considered to have a negative effect on immature survival, attracting natural enemies because of their noticeability and subsequent learning or specialization. In this study, we directly tested the effects of leaf rolls using an attelabid species by comparing the fate of immature insects between artificial leaf rolls and unrolled leaves. The results showed the following positive effects of leaf rolls: avoidance of parasitism by eulophid wasps and avoidance of egg predation by unknown predators. On the other hand, a negative effect of leaf rolls was also detected, specifically and increase in mortality via leaf roll herbivory. This study indicated that leaf shelters are not only protective refuges but are also sometimes risky hiding places, although total survival rates increased in leaf shelters.
Vitamin D protects against immobilization-induced muscle atrophy via neural crest-derived cells in mice
Authors: Nakamura Satoshi , Sato Yuiko , Kobayashi Tami , Kaneko Yosuke , Ito Eri , Soma Tomoya , Okada Hiroyuki , Miyamoto Kana , Oya Akihito , Matsumoto Morio , Nakamura Masaya , Kanaji Arihiko , Miyamoto Takeshi 
Published: July 2020

AbstractVitamin D deficiency is a recognized risk factor for sarcopenia development, but mechanisms underlying this outcome are unclear. Here, we show that low vitamin D status worsens immobilization-induced muscle atrophy in mice. Mice globally lacking vitamin D receptor (VDR) exhibited more severe muscle atrophy following limb immobilization than controls. Moreover, immobilization-induced muscle atrophy was worse in neural crest-specific than in skeletal muscle-specific VDR-deficient mice. Tnfα expression was significantly higher in immobilized muscle of VDR-deficient relative to control mice, and was significantly elevated in neural crest-specific but not muscle-specific VDR-deficient mice. Furthermore, muscle atrophy induced by limb immobilization in low vitamin D mice was significantly inhibited in Tnfα-deficient mice. We conclude that vitamin D antagonizes immobilization-induced muscle atrophy via VDR expressed in neural crest-derived cells.
Comparative assessment of mouse models for experimental orthodontic tooth movement
Authors: Kirschneck Christian , Bauer Maria , Gubernator Joshua , Proff Peter , Schröder Agnes 
Published: July 2020

AbstractAnimal experiments are essential for the elucidation of biological-cellular mechanisms in the context of orthodontic tooth movement (OTM). So far, however, no studies comparatively assess available mouse models regarding their suitability. OTM of first upper molars was induced in C57BL/6 mice either via an elastic band or a NiTi coil spring for three, seven or 12 days. We assessed appliance survival rate, OTM and periodontal bone loss (µCT), root resorptions, osteoclastogenesis (TRAP+ area) and local expression of OTM-related genes (RT-qPCR). Seven days after the elastic bands were inserted, 87% were still in situ, but only 27% after 12 days. Survival rate for the NiTi coil springs was 100% throughout, but 8.9% of the animals did not survive. Both methods induced significant OTM, which was highest after 12 (NiTi spring) and 7 days (band), with a corresponding increase in local gene expression of OTM-related genes and osteoclastogenesis. Periodontal bone loss and root resorptions were not induced at a relevant extent by neither of the two procedures within the experimental periods. To induce reliable OTM in mice beyond 7 days, a NiTi coil spring is the method of choice. The elastic band method is recommended only for short-term yes/no-questions regarding OTM.
Pro-inflammatory properties of H-ferritin on human macrophages, ex vivo and in vitro observations
Authors: Ruscitti Piero , Di Benedetto Paola , Berardicurti Onorina , Panzera Noemi , Grazia Nicolò , Lizzi Anna Rita , Cipriani Paola , Shoenfeld Yehuda , Giacomelli Roberto 
Published: July 2020

AbstractFerritin is an iron-binding molecule, which comprises 24 subunits, heavy (FeH) and light (FeL) subunits, suggested to have a pathogenic role by the ‘hyperferritinemic syndrome’. In this work, we tested (1) FeH and FeL in bone marrow (BM) and sera in patients with macrophage activation syndrome (MAS); (2) pro-inflammatory effects of ferritin, FeL, and FeH on macrophages; (3) ability of FeH-stimulated macrophages to stimulate the proliferation of peripheral blood mononuclear cells (PBMCs); (4) production of mature IL-1β and IL-12p70 in extracellular compartments of FeH-stimulated macrophages. Immunofluorescence analysis and liquid chromatography mass spectrometry (LC–MS/MS) based proteomics were performed to identify FeL and FeH in BM and sera, respectively, in the same patients. Macrophages were stimulated with ferritin, FeH, and FeL to assess pro-inflammatory effects by RT-PCR and western blot. The proliferation of co-cultured PBMCs with FeH-stimulated macrophages was tested. Immunofluorescence showed an increased FeH expression in BMs, whereas LC–MS/MS identified that FeL was mainly represented in sera. FeH induced a significant increase of gene expressions of IL-1β, IL-6, IL-12, and TNF-α, more marked with FeH, which also stimulated NLRP3. FeH-stimulated macrophages enhanced the proliferation of PBMCs. The ELISA assays showed that mature form of IL-1β and IL-12p70 were increased, in extracellular compartments of FeH-stimulated macrophages. Our results showed FeH in BM biopsies of MAS patients, whereas, LC–MS/MS identified FeL in the sera. FeH showed pro-inflammatory effects on macrophages, stimulated NLRP3, and increased PBMCs proliferation.
Recombinant expression, purification and PEGylation of Paneth cell peptide (cryptdin-2) with value added attributes against Staphylococcus aureus
Authors: Kaur Navneet , Dilawari Rahul , Kaur Amrita , Sahni Girish , Rishi Praveen 
Published: July 2020

AbstractCryptdins are disulfide-rich cationic antimicrobial peptides secreted by mouse Paneth cells and are known to exhibit potent antimicrobial activity against various deadly pathogens. Keeping in view the extremely low yield obtained from mouse Paneth cells and high cost of synthetic peptide(s), herein, we have attempted to produce cryptdin-2 in Escherichia coli using recombinant technology. To avoid lethal effects of peptide on the host cells, cryptdin-2 was expressed as a fusion protein with thioredoxin as fusion partner which yielded 40 mg/L protein in the soluble fraction. Subsequently, mature cryptdin-2 was cleaved from the fusion partner and purified by cation exchange chromatography. Since conjugation of poly(ethylene) glycol (PEG) has been known to improve the biological properties of biomolecules, therefore, we further attempted to prepare PEG-conjugated variant of cryptdin-2 using thiol specific PEGylation. Though the antimicrobial activity of PEGylated cryptdin-2 was compromised to some extent, but it was found to have enhanced serum stability for longer duration as compared to its un-modified forms. Also, it was found to exhibit reduced toxicity to the host cells. Further, its synergism with gentamicin suggests that PEGylated cryptdin-2 can be used with conventional antibiotics, thereby indicating its possibility to be used as an adjunct therapy.
Illuminating nature’s beauty: modular, scalable and low-cost LED dome illumination system using 3D-printing technology
Authors: Bäumler Fabian , Koehnsen Alexander , Tramsen Halvor T. , Gorb Stanislav N. , Büsse Sebastian 
Published: July 2020

AbstractPresenting your research in the proper light can be exceptionally challenging. Meanwhile, dome illumination systems became a standard for micro- and macrophotography in taxonomy, morphology, systematics and especially important in natural history collections. However, proper illumination systems are either expensive and/or laborious to use. Nowadays, 3D-printing technology revolutionizes lab-life and will soon find its way into most people’s everyday life. Consequently, fused deposition modelling printers become more and more available, with online services offering personalized printing options. Here, we present a 3D-printed, scalable, low-cost and modular LED illumination dome system for scientific micro- and macrophotography. We provide stereolithography ('.stl') files and print settings, as well as a complete list of necessary components required for the construction of three differently sized domes. Additionally, we included an optional iris diaphragm and a sliding table, to arrange the object of desire inside the dome. The dome can be easily scaled and modified by adding customized parts, allowing you to always present your research object in the best light.
Optimal SSSC-based power damping inter-area oscillations using firefly and harmony search algorithms
Authors: Naderipour Amirreza , Abdul-Malek Zulkurnain , Ramachandaramurthy Vigna K. , Miveh Mohammad Reza , Moghaddam Mohammad Jafar Hadidian , Guerrero Josep. M. 
Published: July 2020

AbstractThe static synchronous series compensator (SSSC) can add a series reactance to the transmission line, and when it is fed using auxiliary signals, it can participate in damping inter-area oscillations by changing the series reactance. In this paper, the effect of the SSSC on small-signal stability is investigated. The design of a controller for damping oscillations is designed and discussed. Moreover, using the firefly and the harmony search algorithms, the optimal parameters controlling SSSC are addressed. The effectiveness of these two algorithms and the rate of SSSC participation in damping inter-area oscillation are also discussed. MATLAB software was used to analyse the models and to perform simulations in the time domain. The simulation results on the sample system, in two areas, indicated the optimal accuracy and precision of the proposed controller.