bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a Functional Glomerulus at the Organ Level on a Chip to Mimic Hypertensive Nephropathy
Authors: Zhou Mengying , Zhang Xulang , Wen Xinyu , Wu Taihua , Wang Weidong , Yang Mingzhou , Wang Jing , Fang Ming , Lin Bingcheng , Lin Hongli 
Published: August 2016

AbstractGlomerular hypertension is an important factor exacerbating glomerular diseases to end-stage renal diseases because, ultimately, it results in glomerular sclerosis (especially in hypertensive and diabetic nephropathy). The precise mechanism of glomerular sclerosis caused by glomerular hypertension is unclear, due partly to the absence of suitable in vitro or in vivo models capable of mimicking and regulating the complex mechanical forces and/or organ-level disease processes. We developed a “glomerulus-on-a-chip” (GC) microfluidic device. This device reconstitutes the glomerulus with organ-level glomerular functions to create a disease model-on-a chip that mimics hypertensive nephropathy in humans. It comprises two channels lined by closely opposed layers of glomerular endothelial cells and podocytes that experience fluid flow of physiological conditions to mimic the glomerular microenvironment in vivo. Our results revealed that glomerular mechanical forces have a crucial role in cellular cytoskeletal rearrangement as well as the damage to cells and their junctions that leads to increased glomerular leakage observed in hypertensive nephropathy. Results also showed that the GC could readily and flexibly meet the demands of a renal-disease model. The GC could provide drug screening and toxicology testing and create potential new personalized and accurate therapeutic platforms for glomerular disease.
Joint effects of pregnancy, sociocultural, and environmental factors on early life gut microbiome structure and diversity
Authors: Levin Albert M. , Sitarik Alexandra R. , Havstad Suzanne L. , Fujimura Kei E. , Wegienka Ganesa , Cassidy-Bushrow Andrea E. , Kim Haejin , Zoratti Edward M. , Lukacs Nicholas W. , Boushey Homer A. , Ownby Dennis R. , Lynch Susan V. , Johnson Christine C. 
Published: August 2016

AbstractThe joint impact of pregnancy, environmental, and sociocultural exposures on early life gut microbiome is not yet well-characterized, especially in racially and socioeconomically diverse populations. Gut microbiota of 298 children from a Detroit-based birth cohort were profiled using 16S rRNA sequencing: 130 neonates (median age = 1.2 months) and 168 infants (median age = 6.6 months). Multiple factors were associated with neonatal gut microbiome composition in both single- and multi-factor models, with independent contributions of maternal race-ethnicity, breastfeeding, mode of delivery, marital status, exposure to environmental tobacco smoke, and indoor pets. These findings were consistent in the infants, and networks demonstrating the shared impact of factors on gut microbial composition also showed notable topological similarity between neonates and infants. Further, latent groups defined by these factors explained additional variation, highlighting the importance of combinatorial effects. Our findings also have implications for studies investigating the impact of the early life gut microbiota on disease.
Polycomb-group protein SlMSI1 represses the expression of fruit-ripening genes to prolong shelf life in tomato
Authors: Liu Dan-Dan , Zhou Li-Jie , Fang Mou-Jing , Dong Qing-Long , An Xiu-Hong , You Chun-Xiang , Hao Yu-Jin 
Published: August 2016

AbstractPolycomb-group (PcG) protein MULTICOPY SUPPRESSOR OF IRA1 (MSI1) protein is an evolutionarily conserved developmental suppressor and plays a crucial role in regulating epigenetic modulations. However, the potential role and function of MSI1 in fleshy fruits remain unknown. In this study, SlMSI1 was cloned and transformed into tomato to explore its function. The quantitative real-time PCR results showed that SlMSI1 was highly expressed in flowers and fruits and that its transcript and protein levels were significantly decreased in fruits after the breaker stage. Additionally, SlMSI1-overexpressing transgenic tomatoes displayed abnormal non-ripening fruit formation, whereas its suppression promoted fruit ripening in transgenic tomatoes. Quantitative real-time PCR assays also showed that RIN and its regulons were decreased in SlMSI1 overexpression transgenic tomato fruits. Furthermore, RNA-seq analysis demonstrated that SlMSI1 inhibits fruit ripening by negatively regulating a large set of fruit-ripening genes in addition to RIN and its regulons. Finally, genetic manipulation of SlMSI1 and RIN successfully prolonged the fruit shelf life by regulating the fruit-ripening genes in tomato. Our findings reveal a novel regulatory function of SlMSI1 in fruit ripening and provide a new regulator that may be useful for genetic engineering and modification of fruit shelf life.
Single-cell RNA-seq reveals distinct injury responses in different types of DRG sensory neurons
Authors: Hu Ganlu , Huang Kevin , Hu Youjin , Du Guizhen , Xue Zhigang , Zhu Xianmin , Fan Guoping 
Published: August 2016

AbstractPeripheral nerve injury leads to various injury-induced responses in sensory neurons including physiological pain, neuronal cell death and nerve regeneration. In this study, we performed single-cell RNA-sequencing (scRNA-seq) analysis of mouse nonpeptidergic nociceptors (NP), peptidergic nociceptors (PEP) and large myelinated sensory neurons (LM) under both control and injury conditions at 3 days after sciatic nerve transection (SNT). After performing principle component and weighted gene co-expression network analysis, we categorized dorsal root ganglion (DRG) neurons into different subtypes and discovered co-regulated injury-response genes including novel regeneration associated genes (RAGs) in association with neuronal development, protein translation and cytoplasm transportation. In addition, we found significant up-regulation of the genes associated with cell death such as Pdcd2 in a subset of NP neurons after axotomy, implicating their actions in neuronal cell death upon nerve injury. Our study revealed the distinctive and sustained heterogeneity of transcriptomic responses to injury at single neuron level, implicating the involvement of different gene regulatory networks in nerve regeneration, neuronal cell death and neuropathy in different population of DRG neurons.
Space radiation exposure persistently increased leptin and IGF1 in serum and activated leptin-IGF1 signaling axis in mouse intestine
Authors: Suman Shubhankar , Kumar Santosh , Fornace Albert J. , Datta Kamal 
Published: August 2016

AbstractTravel into outer space is fraught with risk of exposure to energetic heavy ion radiation such as56Fe ions, which due to its high linear energy transfer (high-LET) characteristics deposits higher energy per unit volume of tissue traversed and thus more damaging to cells relative to low-LET radiation such as γ rays. However, estimates of human health risk from energetic heavy ion exposure are hampered due to lack of tissue specificin vivomolecular data. We investigated long-term effects of56Fe radiation on adipokines and insulin-like growth factor 1 (IGF1) signaling axis in mouse intestine and colon. Six- to eight-week-old C57BL/6J mice were exposed to 1.6 Gy of56Fe ions. Serum and tissues were collected up to twelve months post-irradiation. Serum was analyzed for leptin, adiponectin, IGF1 and IGF binding protein 3. Receptor expressions and downstream signaling pathway alterations were studied in tissues. Irradiation increased leptin and IGF1 levels in serum and IGF1R and leptin receptor expression in tissues. When considered along with upregulated Jak2/Stat3 pathways and cell proliferation, our data supports the notion that space radiation exposure is a risk to endocrine alterations with implications for chronic pathophysiologic changes in gastrointestinal tract.
Pleiotropic action of CpG-ODN on endothelium and macrophages attenuates angiogenesis through distinct pathways
Authors: Wu Jiahui , Su Wenru , Powner Michael B. , Liu Jian , Copland David A. , Fruttiger Marcus , Madeddu Paolo , Dick Andrew D. , Liu Lei 
Published: August 2016

AbstractThere is an integral relationship between vascular cells and leukocytes in supporting healthy tissue homeostasis. Furthermore, activation of these two cellular components is key for tissue repair following injury. Toll-like receptors (TLRs) play a role in innate immunity defending the organism against infection, but their contribution to angiogenesis remains unclear. Here we used synthetic TLR9 agonists, cytosine-phosphate-guanosine oligodeoxynucleotides (CpG-ODN), to investigate the role of TLR9 in vascular pathophysiology and identify potential therapeutic translation. We demonstrate that CpG-ODN stimulates inflammation yet inhibits angiogenesis. Regulation of angiogenesis by CpG-ODN is pervasive and tissue non-specific. Further, we noted that synthetic CpG-ODN requires backbone phosphorothioate but not TLR9 activation to render and maintain endothelial stalk cells quiescent. CpG-ODN pre-treated endothelial cells enhance macrophage migration but restrain pericyte mobilisation. CpG-ODN attenuation of angiogenesis, however, remains TLR9-dependent, as inhibition is lost in TLR9 deficient mice. Additionally, CpG-ODNs induce an M1 macrophage phenotype that restricts angiogenesis. The effects mediated by CpG-ODNs can therefore modulate both endothelial cells and macrophages through distinct pathways, providing potential therapeutic application in ocular vascular disease.
Multilayer Network Analysis of Nuclear Reactions
Authors: Zhu Liang , Ma Yu-Gang , Chen Qu , Han Ding-Ding 
Published: August 2016

AbstractThe nuclear reaction network is usually studied via precise calculation of differential equation sets and much research interest has been focused on the characteristics of nuclides, such as half-life and size limit. In this paper, however, we adopt the methods from both multilayer and reaction networks and obtain a distinctive view by mapping all the nuclear reactions in JINA REACLIB database into a directed network with 4 layers: neutron, proton, 4He and the remainder. The layer names correspond to reaction types decided by the currency particles consumed. This combined approach reveals that, in the remainder layer, the β-stability has high correlation with node degree difference and overlapping coefficient. Moreover, when reaction rates are considered as node strength, we find that, at lower temperatures, nuclide half-life scales reciprocally with its out-strength. The connection between physical properties and topological characteristics may help to explore the boundary of the nuclide chart.
Hypomineralized Second Primary Molars as Predictor of Molar Incisor Hypomineralization
Authors: Negre-Barber A. , Montiel-Company J. M. , Boronat-Catalá M. , Catalá-Pizarro M. , Almerich-Silla J. M. 
Published: August 2016

AbstractMolar incisor hypomineralization (MIH) is a developmental defect of dental enamel that shares features with hypomineralized second primary molars (HSPM). Prior to permanent tooth eruption, second primary molars could have predictive value for permanent molar and incisor hypomineralization. To assess this possible relationship, a cross-sectional study was conducted in a sample of 414 children aged 8 and 9 years from the INMA cohort in Valencia (Spain). A calibrated examiner (linear-weighted Kappa 0.83) performed the intraoral examinations at the University of Valencia between November 2013 and 2014, applying the diagnostic criteria for MIH and HSPM adopted by the European Academy of Paediatric Dentistry. 100 children (24.2%) presented MIH and 60 (14.5%) presented HSPM. Co-occurrence of the two defects was observed in 11.1% of the children examined. The positive predictive value was 76.7% (63.9–86.6) and the negative predictive value 84.7% (80.6–88.3). The positive likelihood ratio (S/1-E) was 10.3 (5.9–17.9) and the negative likelihood ratio (1-S/E) 0.57 (0.47–0.68). The odds ratio was 18.2 (9.39–35.48). It was concluded that while the presence of HSPM can be considered a predictor of MIH, indicating the need for monitoring and control, the absence of this defect in primary dentition does not rule out the appearance of MIH.
Molecular hydrogen suppresses activated Wnt/β-catenin signaling
Authors: Lin Yingni , Ohkawara Bisei , Ito Mikako , Misawa Nobuaki , Miyamoto Kentaro , Takegami Yasuhiko , Masuda Akio , Toyokuni Shinya , Ohno Kinji 
Published: August 2016

AbstractMolecular hydrogen (H2) is effective for many diseases. However, molecular bases of H2 have not been fully elucidated. Cumulative evidence indicates that H2 acts as a gaseous signal modulator. We found that H2 suppresses activated Wnt/β-catenin signaling by promoting phosphorylation and degradation οf β-catenin. Either complete inhibition of GSK3 or mutations at CK1- and GSK3-phosphorylation sites of β-catenin abolished the suppressive effect of H2. H2 did not increase GSK3-mediated phosphorylation of glycogen synthase, indicating that H2 has no direct effect on GSK3 itself. Knock-down of adenomatous polyposis coli (APC) or Axin1, which form the β-catenin degradation complex, minimized the suppressive effect of H2 on β-catenin accumulation. Accordingly, the effect of H2 requires CK1/GSK3-phosphorylation sites of β-catenin, as well as the β-catenin degradation complex comprised of CK1, GSK3, APC and Axin1. We additionally found that H2 reduces the activation of Wnt/β-catenin signaling in human osteoarthritis chondrocytes. Oral intake of H2 water tended to ameliorate cartilage degradation in a surgery-induced rat osteoarthritis model through attenuating β-catenin accumulation. We first demonstrate that H2 suppresses abnormally activated Wnt/β-catenin signaling, which accounts for the protective roles of H2 in a fraction of diseases.
Epsin1 modulates synaptic vesicle retrieval capacity at CNS synapses
Authors: Kyung Jae Won , Bae Jae Ryul , Kim Dae-Hwan , Song Woo Keun , Kim Sung Hyun 
Published: August 2016

AbstractSynaptic vesicle retrieval is an essential process for continuous maintenance of neural information flow after synaptic transmission. Epsin1, originally identified as an EPS15-interacting protein, is a major component of clathrin-mediated endocytosis. However, the role of Epsin1 in synaptic vesicle endocytosis at CNS synapses remains elusive. Here, we showed significantly altered synaptic vesicle endocytosis in neurons transfected with shRNA targeting Epsin1 during/after neural activity. Endocytosis was effectively restored by introducing shRNA-insensitive Epsin1 into Epsin1-depleted neurons. Domain studies performed on neurons in which domain deletion mutants of Epsin1 were introduced after Epsin1 knockdown revealed that ENTH, CLAP, and NPFs are essential for synaptic vesicle endocytosis, whereas UIMs are not. Strikingly, the efficacy of the rate of synaptic vesicle retrieval (the “endocytic capacity”) was significantly decreased in the absence of Epsin1. Thus, Epsin1 is required for proper synaptic vesicle retrieval and modulates the endocytic capacity of synaptic vesicles.
Investigation of mechanism: spoof SPPs on periodically textured metal surface with pyramidal grooves
Authors: Tian Lili , Liu Jianlong , Zhou Keya , Gao Yang , Liu Shutian 
Published: August 2016

AbstractIn microwave and terahertz frequency band, a textured metal surface can support spoof surface plasmon polaritons (SSPPs). In this paper, we explore a SSPPs waveguide composed of a metal block with pyramidal grooves. Under the deep subwavelength condition, theoretical formulas for calculation of dispersion relations are derived based on the modal expansion method (MEM). Using the obtained formulas, a general analysis is given about the properties of the SSPPs in the waveguides with upright and downward pyramidal grooves. It is demonstrated that the SSPPs waveguides with upright pyramidal grooves give better field-confinement. Numerical simulations are used to check the theoretical analysis and show good agreement with the analytical results. In addition, the group velocity of the SSPPs propagating along the waveguide is explored and two structures are designed to show how to trap the SSPPs on the metal surface. The calculation methodology provided in this paper can also be used to deal with the SSPPs waveguides with irregular grooves.
Frobenius-norm-based measures of quantum coherence and asymmetry
Authors: Yao Yao , Dong G. H. , Xiao Xing , Sun C. P. 
Published: August 2016

AbstractWe formulate the Frobenius-norm-based measures for quantum coherence and asymmetry respectively. In contrast to the resource theory of coherence and asymmetry, we construct a natural measure of quantum coherence inspired from optical coherence theory while the group theoretical approach is employed to quantify the asymmetry of quantum states. Besides their simple structures and explicit physical meanings, we observe that these quantities are intimately related to the purity (or linear entropy) of the corresponding quantum states. Remarkably, we demonstrate that the proposed coherence quantifier is not only a measure of mixedness, but also an intrinsic (basis-independent) quantification of quantum coherence contained in quantum states, which can also be viewed as a normalized version of Brukner-Zeilinger invariant information. In our context, the asymmetry of N-qubit quantum systems is considered under local independent and collective"Equation missing" transformations. In- triguingly, it is illustrated that the collective effect has a significant impact on the asymmetry measure and quantum correlation between subsystems plays a non-negligible role in this circumstance.
The emergence of superstructural order in insulin amyloid fibrils upon multiple rounds of self-seeding
Authors: Surmacz-Chwedoruk Weronika , Babenko Viktoria , Dec Robert , Szymczak Piotr , Dzwolak Wojciech 
Published: August 2016

AbstractTypically, elongation of an amyloid fibril entails passing conformational details of the mother seed to daughter generations of fibrils with high fidelity. There are, however, several factors that can potentially prevent such transgenerational structural imprinting from perpetuating, for example heterogeneity of mother seeds or so-calledconformational switching. Here, we examine phenotypic persistence of bovine insulin amyloid ([BI]) upon multiple rounds of self-seeding under quiescent conditions. According to infrared spectroscopy, with the following passages of homologous seeding, daughter fibrils gradually depart from the mother seed’s spectral characteristics. We note that this transgenerational structural drift in [BI] amyloid leads toward fibrils with infrared, chiroptical and morphological traits similar to those of the superstructural variant of fibrils which normally forms upon strong agitation of insulin solutions. However, in contrast to agitation-induced insulin amyloid, the superstructural assemblies of daughter fibrils isolated through self-seeding are sonication-resistant. Our results suggest that formation of single amyloid fibrils is not a dead-end of the amyloidogenic self-assembly. Instead, the process appears to continue toward the self-assembly of higher-order structures although on longer time-scales. From this perspective, the fast agitation-induced aggregation of insulin appears to be a shortcut to amyloid superstructures whose formation under quiescent conditions is slow.
Understanding music with cochlear implants
Authors: Bruns Lisa , Mürbe Dirk , Hahne Anja 
Published: August 2016

AbstractDirect stimulation of the auditory nerve via a Cochlear Implant (CI) enables profoundly hearing-impaired people to perceive sounds. Many CI users find language comprehension satisfactory, but music perception is generally considered difficult. However, music contains different dimensions which might be accessible in different ways. We aimed to highlight three main dimensions of music processing in CI users which rely on different processing mechanisms: (1) musical discrimination abilities, (2) access to meaning in music and (3) subjective music appreciation. All three dimensions were investigated in two CI user groups (post- and prelingually deafened CI users, all implanted as adults) and a matched normal hearing control group. The meaning of music was studied by using event-related potentials (with the N400 component as marker) during a music-word priming task while music appreciation was gathered by a questionnaire. The results reveal a double dissociation between the three dimensions of music processing. Despite impaired discrimination abilities of both CI user groups compared to the control group, appreciation was reduced only in postlingual CI users. While musical meaning processing was restorable in postlingual CI users, as shown by a N400 effect, data of prelingual CI users lack the N400 effect and indicate previous dysfunctional concept building.
Diagnostic performance of serum IgG4 level for IgG4-related disease: a meta-analysis
Authors: Xu Wen-long , Ling Ying-chun , Wang Zhi-kai , Deng Fang 
Published: August 2016

AbstractAn elevated serum IgG4 level is one of the most useful factors in the diagnosis of IgG4-related disease (IgG4-RD). In this study, we performed a meta-analysis of the published articles assessing the diagnostic accuracy of serum IgG4 concentrations for IgG4-RD. The databases of MEDLINE/PubMed, EMBASE and Web of Science were systematically searched for relevant studies. Sensitivities and specificities of serum IgG4 in each study were calculated, and the hierarchical summary receiver operating characteristic (HSROC) model with a random effects model were employed to obtain the individual and pooled estimates of sensitivities and specificities. In total, twenty-three studies comprising 6048 patients with IgG4-RD were included in the meta-analysis. The pooled sensitivity was 85% with a 95% confidence interval (CI) of 78–90%; the pooled specificity was 93% with a 95% CI of 90–95%. The HSROC curve for quantitative serum IgG4 lies closer to the upper left corner of the plot, and the area under the curve (AUC) was 0.95 (95% CI 0.93, 0.97), which suggested a high diagnostic accuracy of serum IgG4 for the entity of IgG4-RD. Our study suggests that serum IgG4 has high sensitivity and specificity in the diagnosis of IgG4-RD.
Werner syndrome through the lens of tissue and tumour genomics
Authors: Tokita Mari , Kennedy Scott R. , Risques Rosa Ana , Chun Stephen G. , Pritchard Colin , Oshima Junko , Liu Yan , Bryant-Greenwood Peter K. , Welcsh Piri , Monnat Raymond J. 
Published: August 2016

AbstractWerner syndrome (WS) is the canonical adult human progeroid (‘premature aging’) syndrome. Patients with this autosomal recessive Mendelian disorder display constitutional genomic instability and an elevated risk of important age-associated diseases including cancer. Remarkably few analyses of WS patient tissue and tumors have been performed to provide insight into WS disease pathogenesis or the high risk of neoplasia. We used autopsy tissue from four mutation-typed WS patients to characterize pathologic and genomic features of WS, and to determine genomic features of three neoplasms arising in two of these patients. The results of these analyses provide new information on WS pathology and genomics; provide a first genomic characterization of neoplasms arising in WS; and provide new histopathologic and genomic data to test several popular models of WS disease pathogenesis.