bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of toxic Microcystis aeruginosa on the silver carp Hypophthalmichtys molitrix revealed by hepatic RNA-seq and miRNA-seq
Authors: Hu Menghong , Qu Xiancheng , Pan Lisha , Fu Chunxue , Jia Peixuan , Liu Qigen , Wang Youji 
Published: August 2017

AbstractHigh-throughput sequencing was applied to analyze the effects of toxic Microcystis aeruginosa on the silver carp Hypophthalmichthys molitrix. Silver carps were exposed to two cyanobacteria species (toxic and non-toxic) for RNA-seq and miRNA-seq analysis. RNA-seq revealed that the liver tissue contained 105,379 unigenes. Of these genes, 143 were significantly differentiated, 82 were markedly up-regulated, and 61 were remarkably down-regulated. GO term enrichment analysis indicated that 35 of the 154 enriched GO terms were significantly enriched. KEGG pathway enrichment analysis demonstrated that 17 of the 118 enriched KEGG pathways were significantly enriched. A considerable number of disease/immune-associated GO terms and significantly enriched KEGG pathways were also observed. The sequence length determined by miRNA-seq was mainly distributed in 20–23 bp and composed of 882,620 unique small RNAs, and 53% of these RNAs were annotated to miRNAs. As confirmed, 272 known miRNAs were differentially expressed, 453 novel miRNAs were predicted, 112 miRNAs were well matched with 7,623 target genes, and 203 novel miRNAs were matched with 15,453 target genes. qPCR also indicated that Steap4, Cyp7a1, CABZ01088134.1, and PPP1R3G were significantly differentially expressed and might play major roles in the toxic, detoxifying, and antitoxic mechanisms of microcystin in fish.
A rare-earth free magnesium alloy with improved intrinsic ductility
Authors: Sandlöbes S. , Friák M. , Korte-Kerzel S. , Pei Z. , Neugebauer J. , Raabe D. 
Published: August 2017

AbstractMetals are the backbone of manufacturing owing to their strength and formability. Compared to polymers they have high mass density. There is, however, one exception: magnesium. It has a density of only 1.7 g/cm3, making it the lightest structural material, 4.5 times lighter than steels, 1.7 times lighter than aluminum, and even slightly lighter than carbon fibers. Yet, the widespread use of magnesium is hampered by its intrinsic brittleness. While other metallic alloys have multiple dislocation slip systems, enabling their well-known ductility, the hexagonal lattice of magnesium offers insufficient modes of deformation, rendering it intrinsically brittle. We have developed a quantum-mechanically derived treasure map which screens solid solution combinations with electronic bonding, structure and volume descriptors for similarity to the ductile magnesium-rare earth alloys. Using this insight we synthesized a surprisingly simple, compositionally lean, low-cost and industry-compatible new alloy which is over 4 times more ductile and 40% stronger than pure magnesium. The alloy contains 1 wt.% aluminum and 0.1 wt.% calcium, two inexpensive elements which are compatible with downstream recycling constraints.
Innate immune activating ligand SUMOylation affects tumor cell recognition by NK cells
Authors: Zitti Beatrice , Molfetta Rosa , Fionda Cinzia , Quatrini Linda , Stabile Helena , Lecce Mario , de Turris Valeria , Ricciardi Maria Rosaria , Petrucci Maria Teresa , Cippitelli Marco , Gismondi Angela , Santoni Angela , Paolini Rossella 
Published: August 2017

AbstractNatural Killer cells are innate lymphocytes involved in tumor immunosurveillance. They express activating receptors able to recognize self-molecules poorly expressed on healthy cells but up-regulated upon stress conditions, including transformation. Regulation of ligand expression in tumor cells mainly relays on transcriptional mechanisms, while the involvement of ubiquitin or ubiquitin-like modifiers remains largely unexplored. Here, we focused on the SUMO pathway and demonstrated that the ligand of DNAM1 activating receptor, PVR, undergoes SUMOylation in multiple myeloma. Concurrently, we found that PVR is preferentially located in intracellular compartments in human multiple myeloma cell lines and malignant plasma cells and that inhibition of the SUMO pathway promotes its translocation to the cell surface, increasing tumor cell susceptibility to NK cell-mediated cytolysis. Our findings provide the first evidence of an innate immune activating ligand regulated by SUMOylation, and confer to this modification a novel role in impairing recognition and killing of tumor cells.
A functional IFN-λ4-generating DNA polymorphism could protect older asthmatic women from aeroallergen sensitization and associate with clinical features of asthma
Authors: Chinnaswamy Sreedhar , Wardzynska Aleksandra , Pawelczyk Malgorzata , Makowska Joanna , Skaaby Tea , Mercader Josep M. , Ahluwalia Tarunveer S. , Grarup Niels , Guindo-Martinez Marta , Bisgaard Hans , Torrents David , Linneberg Allan , Bønnelykke Klaus , Kowalski Marek L. 
Published: August 2017

AbstractLambda interferons (IFNLs) have immunomodulatory functions at epithelial barrier surfaces. IFN-λ4, a recent member of this family is expressed only in a subset of the population due to a frameshift-causing DNA polymorphism rs368234815. We examined the association of this polymorphism with atopy (aeroallergen sensitization) and asthma in a Polish hospital-based case-control cohort comprising of well-characterized adult asthmatics (n = 326) and healthy controls (n = 111). In the combined cohort, we saw no association of the polymorphism with asthma and/or atopy. However, the IFN-λ4-generating ΔG allele protected older asthmatic women (>50 yr of age) from atopic sensitization. Further, ΔG allele significantly associated with features of less-severe asthma including bronchodilator response and corticosteroid usage in older women in this Polish cohort. We tested the association of related IFNL locus polymorphisms (rs12979860 and rs8099917) with atopy, allergic rhinitis and presence/absence of asthma in three population-based cohorts from Europe, but saw no significant association of the polymorphisms with any of the phenotypes in older women. The polymorphisms associated marginally with lower occurrence of asthma in men/older men after meta-analysis of data from all cohorts. Functional and well-designed replication studies may reveal the true positive nature of these results.
Brain grey matter volume alterations associated with antidepressant response in major depressive disorder
Authors: Liu Jia , Xu Xin , Luo Qiang , Luo Ya , Chen Ying , Lui Su , Wu Min , Zhu Hongyan , Kemp Graham J. , Gong Qiyong 
Published: August 2017

AbstractNot all patients with major depressive disorder respond to adequate pharmacological therapy. Psychoradiological studies have reported that antidepressant responders and nonresponders show different alterations in brain grey matter, but the findings are inconsistent. The present study reports a meta-analysis of voxel-based morphometric studies of patients with major depressive disorder, both antidepressant responders and nonresponders, using the anisotropic effect size version of Seed-based D Mapping to identify brain regions correlated to clinical response. A systematic search was conducted up to June 2016 to identify studies focussing on antidepressant response. In responders across 9 datasets grey matter volume (GMV) was significantly higher in the left inferior frontal gyrus and insula, while GMV was significantly lower in the bilateral anterior cingulate cortex (ACC) and the right superior frontal gyrus (SFG). In nonresponders across 5 datasets GMV was significantly lower in the bilateral ACC, median cingulate cortex (MCC) and right SFG. Conjunction analysis confirmed significant differences in the bilateral ACC and right SFG, where GMV was significantly lower in nonresponders but higher in responders. The current study adds to psychoradiology, an evolving subspecialty of radiology mainly for psychiatry and clinical psychology.
Quantum mixed phases of a two-dimensional polarized degenerate Fermi gas in an optical cavity
Authors: Feng Yanlin , Zhang Kuang , Fan Jingtao , Mei Feng , Chen Gang , Jia Suotang 
Published: August 2017

AbstractThe coupling of ultracold fermions to a high-finesse optical cavity can result in novel many-body phenomena, and has attracted significant interests at present. Here we consider a realization of the Fermi-Dicke model with controllable parameters, based on a two-dimensional polarized degenerate Fermi gas coupled to an optical cavity. We analytically investigate the ground-state properties of such system under the mean-field approximation. We find the system can exhibit a rich phase diagram depending on the fermion-photon coupling strength and the atomic resonant frequency. Contrasting to the bosonic counterpart, a first-order quantum phase transition between the superradiant phase and the normal phase featuring two Fermi surfaces can occur for the weak atomic resonant frequency, and there is a unique mixed phase where this normal phase and the superradiant phase coexist. The experimental detection of our results is also discussed.
Cell Spheroids with Enhanced Aggressiveness to Mimic Human Liver Cancer In Vitro and In Vivo
Authors: Jung Hong-Ryul , Kang Hyun Mi , Ryu Jea-Woon , Kim Dae-Soo , Noh Kyung Hee , Kim Eun-Su , Lee Ho-Joon , Chung Kyung-Sook , Cho Hyun-Soo , Kim Nam-Soon , Im Dong-Soo , Lim Jung Hwa , Jung Cho-Rok 
Published: August 2017

AbstractWe fabricated a spheroid-forming unit (SFU) for efficient and economic production of cell spheroids. We optimized the protocol for generating large and homogenous liver cancer cell spheroids using Huh7 hepatocellular carcinoma (HCC) cells. The large Huh7 spheroids showed apoptotic and proliferative signals in the centre and at the surface, respectively. In particular, hypoxia-induced factor-1 alpha (HIF-1α) and ERK signal activation were detected in the cell spheroids. To diminish core necrosis and increase the oncogenic character, we co-cultured spheroids with 2% human umbilical vein endothelial cells (HUVECs). HUVECs promoted proliferation and gene expression of HCC-related genes and cancer stem cell markers in the Huh7 spheroidsby activating cytokine signalling, mimicking gene expression in liver cancer. HUVECs induced angiogenesis and vessel maturation in Huh7 spheroids in vivo by activating epithelial–mesenchymal transition and angiogenic pathways. The large Huh7 cell spheroids containing HUVECs survived at higher concentrations of anti-cancer drugs (doxorubicin and sorafenib) than did monolayer cells. Our large cell spheroid provides a useful in vitro HCC model to enable intuitive observation for anti-cancer drug testing.
Aging-related changes in the diversity of women’s skin microbiomes associated with oral bacteria
Authors: Shibagaki Nakako , Suda Wataru , Clavaud Cecile , Bastien Philippe , Takayasu Lena , Iioka Erica , Kurokawa Rina , Yamashita Naoko , Hattori Yasue , Shindo Chie , Breton Lionel , Hattori Masahira 
Published: August 2017

AbstractSkin aging is associated with changes in cutaneous physiology including interactions with a skin microbial community. A striking alteration and diversification in the skin microbiome with aging was observed between two different age groups of 37 healthy Japanese women, i.e. younger adults of 21–37 years old and older adults of 60–76 years old, using bacterial 16S rRNA gene sequencing. The analyses revealed that the alpha diversity/species richness was significantly higher in the older than the younger group for the cheek and forehead microbiomes, while the beta diversity in the overall structure significantly differed particularly for the forearm and scalp microbiomes between the two age groups. Taxonomic profiling showed a striking reduction in the relative abundance of the majority skin genusPropionibacteriumin the cheek, forearm and forehead microbiomes of the older adults, and identified 38 species including many oral bacteria that significantly differentiated the two age groups with a skin site dependency. Furthermore, we found chronological age-related and unrelated skin clinical parameters that correlate with the observed changes in the skin microbiome diversity. Thus, our data suggested that the diversification of skin microbiomes in adult women was largely affected by chronological and physiological skin aging in association with oral bacteria.
The Schistosoma mansoni genome encodes thousands of long non-coding RNAs predicted to be functional at different parasite life-cycle stages
Authors: Vasconcelos Elton J. R. , daSilva Lucas F. , Pires David S. , Lavezzo Guilherme M. , Pereira Adriana S. A. , Amaral Murilo S. , Verjovski-Almeida Sergio 
Published: August 2017

AbstractNext Generation Sequencing (NGS) strategies, like RNA-Seq, have revealed the transcription of a wide variety of long non-coding RNAs (lncRNAs) in the genomes of several organisms. In the present work we assessed the lncRNAs complement of Schistosoma mansoni, the blood fluke that causes schistosomiasis, ranked among the most prevalent parasitic diseases worldwide. We focused on the long intergenic/intervening ncRNAs (lincRNAs), hidden within the large amount of information obtained through RNA-Seq in S. mansoni (88 libraries). Our computational pipeline identified 7029 canonically-spliced putative lincRNA genes on 2596 genomic loci (at an average 2.7 isoforms per lincRNA locus), as well as 402 spliced lncRNAs that are antisense to protein-coding (PC) genes. Hundreds of lincRNAs showed traits for being functional, such as the presence of epigenetic marks at their transcription start sites, evolutionary conservation among other schistosome species and differential expression across five different life-cycle stages of the parasite. Real-time qPCR has confirmed the differential life-cycle stage expression of a set of selected lincRNAs. We have built PC gene and lincRNA co-expression networks, unraveling key biological processes where lincRNAs might be involved during parasite development. This is the first report of a large-scale identification and structural annotation of lncRNAs in the S. mansoni genome.
Characterization and Metabolic Diversity of Flavonoids in Citrus Species
Authors: Wang Shouchuang , Yang Chenkun , Tu Hong , Zhou Junjie , Liu Xianqing , Cheng Yunjiang , Luo Jie , Deng Xiuxin , Zhang Hongyan , Xu Juan 
Published: August 2017

AbstractFlavonoids are widely distributed in plants and play important roles in many biological processes. Citrus fruits are rich dietary sources of flavonoids. However, there have been very few reports about the comprehensive metabolic profile and natural diversity of flavonoids in different tissues of various Citrus cultivars. In this study, based on the 7416 metabolic signals detected with non-targeted metabolomics approach, Principal Component Analysis revealed the flavedo has the largest differences from other tissues in metabolite levels; as many as 198 flavonoid signals were then detected in 62 Citrus germplasms from 5 species mainly cultivated worldwide, while 117 flavonoids were identified, including 39 polymethoxylated flavonoids (PMFs), 7 flavones, 10 C-O-glycosylflavonoids, 44 O-glycosylflavonoids, 10 C-glycosylflavonoids and 7 newly annotated O-glycosylpolymethoxylated flavonoids. Tissue-specific accumulations were observed: O-glycosylated flavonoids were abundant in all fruit tissues, while PMFs were accumulated preferentially in the flavedo. Among different species, mandarins had the highest levels of PMFs and O-glycosylpolymethoxylated flavonoids, followed by sweet oranges. Based on the flavonoid profiles, 62 germplasms could be clearly grouped into five distinct clusters via hierarchical clustering analysis, which were perfectly matched with their species, with sweet oranges and mandarins clustering closely and being further away from other three species.
The overlaying oil type influences in vitro embryo production: differences in composition and compound transfer into incubation medium between oils
Authors: Martinez Cristina A. , Nohalez Alicia , Parrilla Inmaculada , Motas Miguel , Roca Jordi , Romero Inmaculada , García-González Diego L. , Cuello Cristina , Rodriguez-Martinez Heriberto , Martinez Emilio A. , Gil Maria A. 
Published: August 2017

AbstractThe oil overlay micro-drop system is widely used for cultures of mammalian gametes and embryos. We evaluated hereby the effects of two unaltered commercial oils— Sigma mineral oil (S-MO) and Nidoil paraffin oil (N-PO)—on in vitro embryo production (IVP) outcomes using a pig model. The results showed that while either oil apparently did not affect oocyte maturation and fertilization rates, S-MO negatively affected embryo cleavage rates, blastocyst formation rates, and, consequently, total blastocyst efficiency of the system. No differences in the oxidation state were found between the oils or culture media incubated under S-MO or N-PO. Although both oils slightly differed in elemental composition, there were no differences in the concentrations of elements between fresh media and media incubated under oils. By contrast, we demonstrated clear oil-type differences in both the composition of volatile organic compounds (VOC) and the transfer of some of these VOC´s (straight-chain alkanes and pentanal and 1,3-diethyl benzene) to the culture medium, which could have influenced embryonic development.
FOXO1 deletion in keratinocytes improves diabetic wound healing through MMP9 regulation
Authors: Zhang Chenying , Lim Jason , Jeon Hyeran Helen , Xu Fanxing , Tian Chen , Miao Fang , Hameedaldeen Alhassan , Graves Dana T. 
Published: August 2017

AbstractKeratinocyte migration is a key aspect of re-epithelialization during wound healing. Matrix metalloproteinase 9 (MMP9) contributes to this process and deficiencies in the MMP9 lead to impaired healing. Inappropriate expression of MMP9 also contributes to impaired re-epithelialization. Previously we demonstrated that FOXO1 was activated in wound healing but to higher levels in diabetic wounds. To address mechanisms of impaired re-epithelialization we examined MMP9 expression in vivo in full thickness dermal scalp wounds created in experimental K14.Cre
+
.Foxo1
L/L
mice with lineage-specific Cre recombinase deletion of floxed FOXO1 and compared the results to control littermates. MMP9 was induced during wound healing but at a significantly higher level in diabetic compared to normal wounds. FOXO1 deletion substantially blocked this increase. By chromatin immunoprecipitation FOXO1 was shown to bind to the MMP9 promoter, FOXO1 overexpression increased MMP9 transcriptional activity and increased MMP9 expression stimulated by high glucose was blocked by FOXO1 deletion or FOXO1 knockdown. We also show for the first time that high glucose impairs keratinocyte migration by inducing high levels of MMP9 expression and establish that it involves FOXO1. Thus, FOXO1 drives high levels of MMP9 expression in diabetic wound healing, which represents a novel mechanism for impaired re-epithelization in diabetic wounds.
Structural and pharmacological basis for the induction of mitochondrial biogenesis by formoterol but not clenbuterol
Authors: Cameron Robert B. , Peterson Yuri K. , Beeson Craig C. , Schnellmann Rick G. 
Published: August 2017

AbstractMitochondrial dysfunction is associated with numerous acute and chronic degenerative diseases. The beta-2 adrenergic receptor (β2AR) agonist formoterol induces mitochondrial biogenesis (MB), but other β2AR agonists, such as clenbuterol, do not. We sought to identify the MB signaling pathway of formoterol and the differences in signaling between these two ligands that result in the differential induction of MB. While formoterol and clenbuterol increased cAMP, only formoterol increased the phosphorylation of Akt and its downstream target eNOS. The increase in Akt phosphorylation was Gβγ- and PI3K-dependent, and the increase in eNOS phosphorylation was Gβγ- and Akt-dependent. Only formoterol increased cGMP. Formoterol induced MB as measured by increases in uncoupled cellular respiration and PGC-1α and NDUFS1 mRNA expression and was blocked by inhibitors of Gβγ, Akt, NOS, and soluble guanylate cyclase. To identify distinct receptor-ligand interactions leading to these differences in signaling, we docked formoterol and clenbuterol to six structures of the β2AR. Compared to clenbuterol, the methoxyphenyl group of formoterol interacted more frequently with V114 and F193, while its formamide group interacted more frequently with C191. These data indicate that the unique structural features of formoterol allow it to interact with the β2AR to activate the Gβγ-Akt-eNOS-sGC pathway to induce MB.
Epiphyseal bone formation occurs via thyroid hormone regulation of chondrocyte to osteoblast transdifferentiation
Authors: Aghajanian Patrick , Xing Weirong , Cheng Shaohong , Mohan Subburaman 
Published: August 2017

AbstractEndochondral ossification in the diaphysis of long bones has been studied in-depth during fetal development but not postnatally in the epiphysis. Immunohistochemical studies revealed that Sox9 and Col2 expressing immature chondrocytes in the epiphysis transition into prehypertrophic and hypetrophic chondrocytes and finally into osteoblasts expressing Col1 and BSP during postnatal day 7–10, when serum levels of thyroid hormone (TH) rise. Lineage tracing using Rosa-td tomato
Col2-Cre-ERT2
mice treated with tamoxifen indicated that the same Col2 expressing chondrocytes expressed prehypertrophic, hypertrophic, and subsequently bone formation markers in a sequential manner in euthyroid but not hypothyroid mice, thus providing evidence that chondrocyte to osteoblast transdifferentiation is TH-dependent. Vascular invasion was apparent at the time of bone formation but not earlier. In vitro studies revealed that TH acting via TRα1 promoted expression of SHH while TRβ1 activation increased IHH but inhibited SHH expression. SHH promoted expression of markers of immature chondrocytes but inhibited chondrocyte hypertrophy while IHH promoted chondrocyte hypertrophy. Based on our data, we propose a model in which TH acting through TRα1 and TRβ1, respectively, fine tune levels of SHH and IHH and, thereby control the transit of proliferating immature chondrocytes into mature hypertrophic chondrocytes to become osteoblasts at the epiphysis.
Oceanographic drivers of the vertical distribution of a highly migratory, endothermic shark
Authors: Coffey Daniel M. , Carlisle Aaron B. , Hazen Elliott L. , Block Barbara A. 
Published: August 2017

AbstractSalmon sharks Lamna ditropis are highly migratory, upper trophic level predators in North Pacific ecosystems. We analysed a multi-year satellite tag dataset to investigate the habitat use of female salmon sharks across their broad range in the eastern North Pacific (NEP) and identified key environmental factors that influence vertical distribution. Salmon sharks displayed remarkable plasticity in habitat use across disparate oceanographic regions in the NEP and increased utilization of deeper waters in offshore habitats. Diel shifts in vertical distribution and behaviour were consistently observed across their range and likely reflect shifts in their foraging ecology. Salmon sharks utilized a broad thermal niche and exhibited submergence behaviour, possibly for thermal refuge, when encountering sea surface temperatures outside their preferred temperature distribution. Moreover, the vertical distribution of salmon sharks indicates they were able to exploit low dissolved oxygen environments (<1–3 ml l−1), occasionally for extended periods of time in offshore habitats. However, salmon sharks generally reduced their use of deeper waters when encountering the combination of cold temperatures (<6 °C) and low dissolved oxygen concentrations (<1–3 ml l−1). Combining vertical distribution with high-resolution horizontal movements furthers our understanding of the ecological and environmental drivers of movement across short (diel) and long-term (migratory) scales.