bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of suitable reference gene and biomarkers of serum miRNAs for osteoporosis
Authors: Chen Jian , Li Kai , Pang Qianqian , Yang Chao , Zhang Hongyu , Wu Feng , Cao Hongqing , Liu Hongju , Wan Yumin , Xia Weibo , Wang Jinfu , Dai Zhongquan , Li Yinghui 
Published: November 2016

AbstractOur objective was to identify suitable reference genes in serum miRNA for normalization and screen potential new biomarkers for osteoporosis diagnosis by a systematic study. Two types of osteoporosis models were used like as mechanical unloading and estrogen deficiency. Through a large-scale screening using microarray, qPCR validation and statistical algorithms, we first identified miR-25-3p as a suitable reference gene for both type of osteoporosis, which also showed stability during the differentiation processes of osteoblast and osteoclast. Then 15 serum miRNAs with differential expression in OVX rats were identified by microarray and qPCR validation. We further detected these 15 miRNAs in postmenopausal women and bedrest rhesus monkeys and evaluated their diagnostic value by ROC analysis. Among these miRNAs, miR-30b-5p was significantly down-regulated in postmenopausal women with osteopenia or osteoporosis; miR-103-3p, miR-142-3p, miR-328-3p were only significantly decreased in osteoporosis. They all showed positive correlations with BMD. Except miR328-3p, the other three miRNAs were also declined in the rhesus monkeys after long-duration bedrest. Their AUC values (all >0.75) proved the diagnostic potential. Our results provided a reliable normalization reference gene and verified a group of circulating miRNAs as non-invasive biomarkers in the detection of postmenopausal- and mechanical unloading- osteoporosis.
Direct and indirect ENSO modulation of winter temperature over the Asian–Pacific–American region
Authors: Leung Marco Y. T. , Zhou Wen 
Published: November 2016

AbstractIn this study, the direct and indirect atmospheric responses over the Asian–Pacific–American region to the El Niño–Southern Oscillation (ENSO) are documented. Since ENSO is likely to induce the northward displacement of the East Asian trough (NDEAT), some of the influence of ENSO on the Asian–Pacific–American region is possibly indirect and acts by inducing NDEAT. To separate corresponding influences of ENSO and NDEAT, partial regression is utilized. It is noted that temperature variations in the East Asian–Western Pacific region are controlled mainly by NDEAT. In contrast, ENSO demonstrates a weak direct relation to the temperature variation over the East Asian–Western Pacific region. This suggests that the influence of ENSO on this region is indirect, through modulation of NDEAT. On the other hand, temperature variation over the tropical eastern Pacific is dominated by ENSO forcing. Finally, temperature variation over the eastern North American–Western Pacific region is controlled by both ENSO and NDEAT. Nevertheless, their influences on temperature and circulation over this region tend to offset each other. This implies that temperature variation is controlled by their relative strengths.
Chromosome-specific sequencing reveals an extensive dispensable genome component in wheat
Authors: Liu Miao , Stiller Jiri , Holušová Kateřina , Vrána Jan , Liu Dengcai , Doležel Jaroslav , Liu Chunji 
Published: November 2016

AbstractThe hexaploid wheat genotype Chinese Spring (CS) has been used worldwide as the reference base for wheat genetics and genomics, and significant resources have been used by the international community to generate a reference wheat genome based on this genotype. By sequencing flow-sorted 3B chromosome from a hexaploid wheat genotype CRNIL1A and comparing the obtained sequences with those available for CS, we detected that a large number of sequences in the former were missing in the latter. If the distribution of such sequences in the hexaploid wheat genome is random, CRNILA sequences missing in CS could be as much as 159.3 Mb even if only fragments of 50 bp or longer were considered. Analysing RNA sequences available in the public domains also revealed that dispensable genes are common in hexaploid wheat. Together with those extensive intra- and interchromosomal rearrangements in CS, the existence of such dispensable genes is another factor highlighting potential issues with the use of reference genomes in various studies. Strong deviation in distributions of these dispensable sequences among genotypes with different geographical origins provided the first evidence indicating that they could be associated with adaptation in wheat.
Bone augmentation after ectopic implantation of a cell-free collagen-hydroxyapatite scaffold in the mouse
Authors: Calabrese Giovanna , Giuffrida Raffaella , Forte Stefano , Salvatorelli Lucia , Fabbi Claudia , Figallo Elisa , Gulisano Massimo , Parenti Rosalba , Magro Gaetano , Colarossi Cristina , Memeo Lorenzo , Gulino Rosario 
Published: November 2016

AbstractThe bone grafting is the classical way to treat large bone defects. Among the available techniques, autologous bone grafting is still the most used but, however, it can cause complications such as infection and donor site morbidity. Alternative and innovative methods rely on the development of biomaterials mimicking the structure and properties of natural bone. In this study, we characterized a cell-free scaffold, which was subcutaneously implanted in mice and then analyzed bothin vivoandex vivoafter 1, 2, 4, 8 and 16 weeks, respectively. Two types of biomaterials, made of either collagen alone or collagen plus magnesium-enriched hydroxyapatite have been used. The results indicate that bone augmentation and angiogenesis could spontaneously occur into the biomaterial, probably by the recruitment of host cells, and that the composition of the scaffolds is crucial. In particular, the biomaterial more closely mimicking the native bone drives the process of bone augmentation more efficiently. Gene expression analysis and immunohistochemistry demonstrate the expression of typical markers of osteogenesis by the host cells populating the scaffold. Our data suggest that this biomaterial could represent a promising tool for the reconstruction of large bone defects, without using exogenous living cells or growth factors.
Chondrogenic Potential of Peripheral Blood Derived Mesenchymal Stem Cells Seeded on Demineralized Cancellous Bone Scaffolds
Authors: Wang Shao-Jie , Jiang Dong , Zhang Zheng-Zheng , Huang Ai-Bing , Qi Yan-Song , Wang Hai-Jun , Zhang Ji-Ying , Yu Jia-Kuo 
Published: November 2016

AbstractAs a cell source with large quantity and easy access, peripheral blood mesenchymal stem cells (PBMSCs) were isolated and seeded in porcine demineralized cancellous bone (DCB) scaffolds, cultured in chondrogenic medium and evaluated for in vitro chondrogenesis. Bone marrow MSCs (BMMSCs) and articular cartilage chondrocytes (ACCs) underwent the same process as controls. The morphology, viability and proliferation of PBMSCs in DCB scaffolds were similar to those of BMMSCs and ACCs. PBMSCs and BMMSCs showed similar chondrogenesis potential with consistent production of COL 2 and SOX 9 protein and increased COL 2 and AGC mRNA expressions at week 3 but the COL 2 protein production was still less than that of ACCs. Minimal increase of hypertrophic markers was found in all groups. Relatively higher ALP and lower COL 10 mRNA expressions were found in both MSCs groups at week 3 than that in ACCs, whereas no significant difference of COL 1 and SOX 9 mRNA and MMP 13 protein was found among all groups. To conclude, PBMSCs shared similar proliferation and chondrogenic potential with BMMSCs in DCB scaffolds and could be an alternative to BMMSCs for cartilage tissue engineering. Further optimization of chondrogenesis system is needed regardless of the promising results.
Significant glial alterations in response to iron loading in a novel organotypic hippocampal slice culture model
Authors: Healy Sinead , McMahon Jill , Owens Peter , FitzGerald Una 
Published: November 2016

AbstractAberrant iron deposition in the brain is associated with neurodegenerative disorders including Multiple Sclerosis, Alzheimer’s disease and Parkinson’s disease. To study the collective response to iron loading, we have used hippocampal organotypic slices as a platform to develop a novel ex vivo model of iron accumulation. We demonstrated differential uptake and toxicity of iron after 12 h exposure to 10 μM ferrous ammonium sulphate, ferric citrate or ferrocene. Having established the supremacy of ferrocene in this model, the cultures were then loaded with 0.1–100 μM ferrocene for 12 h. One μM ferrocene exposure produced the maximal 1.6-fold increase in iron compared with vehicle. This was accompanied by a 1.4-fold increase in ferritin transcripts and mild toxicity. Using dual-immunohistochemistry, we detected ferritin in oligodendrocytes, microglia, but rarely in astrocytes and never in neurons in iron-loaded slice cultures. Moreover, iron loading led to a 15% loss of olig2-positive cells and a 16% increase in number and greater activation of microglia compared with vehicle. However, there was no appreciable effect of iron loading on astrocytes. In what we believe is a significant advance on traditional mono- or dual-cultures, our novel ex vivo slice-culture model allows characterization of the collective response of brain cells to iron-loading.
Sulfated hyaluronan alters fibronectin matrix assembly and promotes osteogenic differentiation of human bone marrow stromal cells
Authors: Vogel Sarah , Arnoldini Simon , Möller Stephanie , Schnabelrauch Matthias , Hempel Ute 
Published: November 2016

AbstractExtracellular matrix (ECM) composition and structural integrity is one of many factors that influence cellular differentiation. Fibronectin (FN) which is in many tissues the most abundant ECM protein forms a unique fibrillary network. FN homes several binding sites for sulfated glycosaminoglycans (sGAG), such as heparin (Hep), which was previously shown to influence FN conformation and protein binding. Synthetically sulfated hyaluronan derivatives (sHA) can serve as model molecules with a well characterized sulfation pattern to study sGAG-FN interaction. Here is shown that the low-sulfated sHA (sHA1) interacts with FN and influences fibril assembly. The interaction of FN fibrils with sHA1 and Hep, but not with non-sulfated HA was visualized by immunofluorescent co-staining. FRET analysis of FN confirmed the presence of more extended fibrils in human bone marrow stromal cells (hBMSC)-derived ECM in response to sHA1 and Hep. Although both sHA1 and Hep affected FN conformation, exclusively sHA1 increased FN protein level and led to thinner fibrils. Further, only sHA1 had a pro-osteogenic effect and enhanced the activity of tissue non-specific alkaline phosphatase. We hypothesize that the sHA1-triggered change in FN assembly influences the entire ECM network and could be the underlying mechanism for the pro-osteogenic effect of sHA1 on hBMSC.
Dense encoding of natural odorants by ensembles of sparsely activated neurons in the olfactory bulb
Authors: Gschwend Olivier , Beroud Jonathan , Vincis Roberto , Rodriguez Ivan , Carleton Alan 
Published: November 2016

AbstractSensory information undergoes substantial transformation along sensory pathways, usually encompassing sparsening of activity. In the olfactory bulb, though natural odorants evoke dense glomerular input maps, mitral and tufted (M/T) cells tuning is considered to be sparse because of highly odor-specific firing rate change. However, experiments used to draw this conclusion were either based on recordings performed in anesthetized preparations or used monomolecular odorants presented at arbitrary concentrations. In this study, we evaluated the lifetime and population sparseness evoked by natural odorants by capturing spike temporal patterning of neuronal assemblies instead of individual M/T tonic activity. Using functional imaging and tetrode recordings in awake mice, we show that natural odorants at their native concentrations are encoded by broad assemblies of M/T cells. While reducing odorant concentrations, we observed a reduced number of activated glomeruli representations and consequently a narrowing of M/T tuning curves. We conclude that natural odorants at their native concentrations recruit M/T cells with phasic rather than tonic activity. When encoding odorants in assemblies, M/T cells carry information about a vast number of odorants (lifetime sparseness). In addition, each natural odorant activates a broad M/T cell assembly (population sparseness).
Deletion of Lkb1 in adult mice results in body weight reduction and lethality
Authors: Shan Tizhong , Xiong Yan , Kuang Shihuan 
Published: November 2016

AbstractLiver kinase B1 (Lkb1) plays crucial roles in development, metabolism and survival. As constitutive knockout of Lkb1 in mice leads to embryonic lethality, whether Lkb1 is required for the growth and survival of adult mice is unclear. Here we address this question using a tamoxifen-inducible Lkb1 knockout (KO) mouse model: Rosa26-CreER: Lkb1flox/flox (abbreviated as Rosa-Lkb1). The Rosa-Lkb1 mice exhibited body weight reduction and died within 6 weeks after tamoxifen induction. The body weight reduction was due to reduced weight of various tissues but the brown and white adipose tissues underwent much more pronounced weight reduction relative to the overall body weight reduction. Accordingly, the Rosa-Lkb1 mice had increased blood glucose levels and were intolerant to glucose challenge. Expression levels of adipogenic and lipogenic genes in adipose tissues were also dramatically reduced by Lkb1 deletion. Additionally, Lkb1 deletion reduced lipid deposition and increased expression of mitochondrial (Pgc1a, Cox5b and Cox7a) and hepatic gluconeogenesis related genes (Pepck) in liver. Finally, the Rosa-Lkb1 mice had much reduced oxygen consumption, carbon dioxide production, and energy expenditure. These results demonstrate that Lkb1 plays an important role in maintaining body weight, liver and adipose tissue function, blood glucose homeostasis and survival in adult mice.
A Comprehensive Characterization of the Function of LincRNAs in Transcriptional Regulation Through Long-Range Chromatin Interactions
Authors: Cai Liuyang , Chang Huidan , Fang Yaping , Li Guoliang 
Published: November 2016

AbstractLincRNAs are emerging as important regulators with various cellular functions. However, the mechanisms behind their role in transcriptional regulation have not yet been fully explored. In this report, we proposed to characterize the diverse functions of lincRNAs in transcription regulation through an examination of their long-range chromatin interactions. We found that the promoter regions of lincRNAs displayed two distinct patterns of chromatin states, promoter-like and enhancer-like, indicating different regulatory functions for lincRNAs. Notably, the chromatin interactions between lincRNA genes and other genes suggested a potential mechanism for lincRNAs in the regulation of other genes at the RNA level because the transcribed lincRNAs could function at local spaces on other genes that interact with the lincRNAs at the DNA level. These results represent a novel way to predict the functions of lincRNAs. The GWAS-identification of SNPs within the lincRNAs revealed that some lincRNAs were disease-associated, and the chromatin interactions with those lincRNAs suggested that they were potential target genes of these lincRNA-associated SNPs. Our study provides new insights into the roles that lincRNAs play in transcription regulation.
TiO2 nanotubes wrapped with reduced graphene oxide as a high-performance anode material for lithium-ion batteries
Authors: Zheng Peng , Liu Ting , Su Ying , Zhang Lifeng , Guo Shouwu 
Published: November 2016

AbstractThrough electrostatic interaction and high-temperature reduction methods, rGO was closely coated onto the surface of TiO2nanotubes. Even at a high temperature of 700 °C, the nanotube morphology of TiO2(anatase) was preserved because of the assistance of rGO, which provides a framework that prevents the tubes from breaking into particles and undergoing a phase transformation. The rGO/TiO2nanotubes deliver a high capacity (263 mAh g−1at the end of 100 cycles at 0.1 A g−1), excellent rate performance (151 mAh g−1at 2 A g−1and 102 mAh g−1at 5 A g−1), and good cycle stability (206 mAh g−1after 500 cycles at 0.5 A g−1). These characteristics arise from the GO/TiO2nanotubes’ advanced structure. First, the closely coated rGO and Ti3+in the tubes give rise to a high electro-conductivity of the nanotubes. Additionally, the Li+ions can rapidly transfer into the electrode via the nanotubes’ empty inner diameter and short tube wall.
Screening for diabetic retinopathy using new mydriasis-free, full-field flicker ERG recording device
Authors: Fukuo Motonobu , Kondo Mineo , Hirose Akira , Fukushima Harumi , Ikesugi Kengo , Sugimoto Masahiko , Kato Kumiko , Uchigata Yasuko , Kitano Shigehiko 
Published: November 2016

AbstractDiabetic retinopathy (DR) is a leading cause of blindness among working-age adults. Therefore, it is important to detect DR accurately during mass screening. The purpose of this study was to determine whether a small, hand-held, mydriasis-free, full-field flicker electroretinographic (ERGs) device called RETevalcan be used to screen for DR. To accomplish this, we recorded full-field flicker ERGs with this device from 48 normal eyes and 118 eyes with different severities of DR in patients with diabetes mellitus (DM). This system delivered a constant flash retinal luminance by adjusting the flash luminance that compensated for changes in the pupil size. Our results showed that there were significant correlations between the severity of DR and the implicit times (P < 0.001;r = 0.55) and the amplitudes (P = 0.001;r = −0.29). When the implicit time was used for the index, the area under the receiver operating characteristic curve was 0.84 for the detection of DR, and was 0.89 for the detection of DR requiring ophthalmic treatments. These results suggest that the implicit times of the flicker ERGs recorded by the small, mydryasis-free ERG system can be used as an adjunctive tool to screen for DR.
Mutually Exclusive Uncertainty Relations
Authors: Xiao Yunlong , Jing Naihuan 
Published: November 2016

AbstractThe uncertainty principle is one of the characteristic properties of quantum theory based on incompatibility. Apart from the incompatible relation of quantum states, mutually exclusiveness is another remarkable phenomenon in the information- theoretic foundation of quantum theory. We investigate the role of mutual exclusive physical states in the recent work of stronger uncertainty relations for all incompatible observables by Mccone and Pati and generalize the weighted uncertainty relation to the product form as well as their multi-observable analogues. The new bounds capture both incompatibility and mutually exclusiveness, and are tighter compared with the existing bounds.
Phenotypic differentiation of Streptococcus pyogenes populations is induced by recombination-driven gene-specific sweeps
Authors: Bao Yun-Juan , Shapiro B. Jesse , Lee Shaun W. , Ploplis Victoria A. , Castellino Francis J. 
Published: November 2016

AbstractGenomic recombination plays an important role in driving adaptive evolution and population differentiation in bacteria. However, controversy exists as to the effects of recombination on population diversity and differentiation, i.e., recombination is frequent enough to sweep through the population at selected gene loci (gene-specific sweeps), or the recombination rate is low without interfering genome-wide selective sweeps. Observations supporting either view are sparse. Pathogenic bacteria causing infectious diseases are promising candidates to provide observations of recombination. However, phenotype-associated differentiations are usually vague among them due to diverse disease manifestations. Here we report a population genomic study of the group A Streptococcus pyogenes (GAS), a human pathogen with highly recombining genomes. By employing a genome-wide association study on single nucleotide polymorphisms (SNPs), we demonstrate a phenotypic differentiation of GAS, represented by separate clustering of two sublineages associated with niche-specific infections, i.e., skin infection and pharyngitis-induced acute rheumatic fever. By quantifying SNPs associated with the differentiation in a statistical and phylogenetic context, we propose that the phenotype-associated differentiation arose through recombination-driven gene-specific sweeps, rather than genome-wide sweeps. Our work provides a novel paradigm of phenotype-associated differentiation induced by gene-specific sweeps in a human pathogen and has implications for understanding of driving forces of bacterial evolution.
An Innovative Metal Ions Sensitive “Test Paper” Based on Virgin Nanoporous Silicon Wafer: Highly Selective to Copper(II)
Authors: Li Shaoyuan , Chen Xiuhua , Ma Wenhui , Ding Zhao , Zhang Cong , Chen Zhengjie , He Xiao , Shang Yudong , Zou Yuxin 
Published: November 2016

AbstractDeveloping an innovative “Test Paper” based on virgin nanoporous silicon (NPSi) which shows intense visible emission and excellent fluorescence stability. The visual fluorescence quenching “Test Paper” was highly selective and sensitive recognizing Cu2+at μmol/L level. Within the concentration range of 5 × 10−7~50 × 10−7mol/L, the linear regression equation of IPL = 1226.3-13.6[CCu2+] (R = 0.99) was established for Cu2+quantitative detection. And finally, Cu2+fluorescence quenching mechanism of NPSi prober was proposed by studying the surface chemistry change of NPSi and metal ions immersed-NPSi using XPS characterization. The results indicate that SiHxspecies obviously contribute to the PL emission of NPSi, and the introduce of oxidization state and the nonradiative recombination center are responsible for the PL quenching. These results demonstrate how virgin NPSi wafer can serve as Cu2+sensor. This work is of great significant to promote the development of simple instruments that could realize rapid, visible and real-time detection of various toxic metal ions.
Continuous, One-pot Synthesis and Post-Synthetic Modification of NanoMOFs Using Droplet Nanoreactors
Authors: Jambovane Sachin R. , Nune Satish K. , Kelly Ryan T. , McGrail B. Peter , Wang Zheming , Nandasiri Manjula I. , Katipamula Shanta , Trader Cameron , Schaef Herbert T. 
Published: November 2016

AbstractMetal-organic frameworks (MOFs); also known as porous coordination polymers (PCP) are a class of porous crystalline materials constructed by connecting metal clusters via organic linkers. The possibility of functionalization leads to virtually infinite MOF designs using generic modular methods. Functionalized MOFs can exhibit interesting physical and chemical properties including accelerated adsorption kinetics and catalysis. Although there are discrete methods to synthesize well-defined nanoscale MOFs, rapid and flexible methods are not available for continuous, one-pot synthesis and post-synthetic modification (functionalization) of MOFs. Here, we show a continuous, scalable nanodroplet-based microfluidic route that not only facilitates the synthesis of MOFs at a nanoscale, but also offers flexibility for direct functionalization with desired functional groups (e.g., -COCH3, fluorescein isothiocyanate; FITC). In addition, the presented route of continuous manufacturing of functionalized nanosized MOFs takes significantly less time compared to state-of-the-art batch methods currently available (1 hrvs.several days). We envisage our approach to be a breakthrough method for synthesizing complex functionalized nanomaterials (metal, metal oxides, quantum dots and MOFs) that are not accessible by direct batch processing and expand the range of a new class of functionalized MOF-based functional nanomaterials.