bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association between dietary patterns and metabolic syndrome in Chinese adults: a propensity score-matched case-control study
Authors: Xia Yang , Gu Yeqing , Yu Fei , Zhang Qing , Liu Li , Meng Ge , Wu Hongmei , Du Huanmin , Shi Hongbin , Guo Xiaoyan , Liu Xing , Li Chunlei , Han Peipei , Dong Renwei , Wang Xiuyang , Bao Xue , Su Qian , Fang Liyun , Liu Fangfang , Yang Huijun , Kang Li , Ma Yixuan , Yu Bin , Sun Shaomei , Wang Xing , Zhou Ming , Jia Qiyu , Guo Qi , Wu Yuntang , Song Kun , Huang Guowei , Wang Guolin , Niu Kaijun 
Published: October 2016

AbstractPrevious studies indicated that dietary patterns were associated with metabolic syndrome (MS), but little is known in Chinese. We design this case-control study to evaluate the associations between dietary patterns and MS in Chinese adults. In this study, 1492 participants with MS were matched with 1492 controls using the 1:1 ratio propensity score matching methods. Dietary intake was assessed using a valid self-administered food frequency questionnaire, and MS was defined in accordance with the criteria of the American Heart Association scientific statement of 2009. Higher scores for the high-protein/cholesterol pattern were associated with higher prevalence of MS. Compared with the participants in the lowest quartile, the odds ratio (OR) for the extreme quartile was 1.36 (95% confidence interval (CI), 1.10–1.68) and the P for trend <0.01 after adjusted for the other two dietary pattern scores. We also found a moderate consumption of the balanced pattern was associated with the lowest prevalence of MS. The ORs across quartiles of the balanced pattern were 1 (reference), 0.83 (95% CI, 0.68–1.02), 0.69 (95% CI, 0.56–0.85), and 0.84 (95% CI, 0.68–1.04) after adjustment. Our study demonstrates that there is a strong association between a diet rich in animal offal, animal blood, meat, and sausage and a higher prevalence of MS.
The Important Role of Halogen Bond in Substrate Selectivity of Enzymatic Catalysis
Authors: Jiang Shuiqin , Zhang Lujia , Cui Dongbin , Yao Zhiqiang , Gao Bei , Lin Jinping , Wei Dongzhi 
Published: October 2016

AbstractThe use of halogen bond is widespread in drug discovery, design, and clinical trials, but is overlooked in drug biosynthesis. Here, the role of halogen bond in the nitrilase-catalyzed synthesis of ortho-, meta-, and para-chlorophenylacetic acid was investigated. Different distributions of halogen bond induced changes of substrate binding conformation and affected substrate selectivity. By engineering the halogen interaction, the substrate selectivity of the enzyme changed, with the implication that halogen bond plays an important role in biosynthesis and should be used as an efficient and reliable tool in enzymatic drug synthesis.
Plant growth promoting rhizobacteria Dietzia natronolimnaea modulates the expression of stress responsive genes providing protection of wheat from salinity stress
Authors: Bharti Nidhi , Pandey Shiv Shanker , Barnawal Deepti , Patel Vikas Kumar , Kalra Alok 
Published: October 2016

AbstractPlant growth promoting rhizobacteria (PGPR) hold promising future for sustainable agriculture. Here, we demonstrate a carotenoid producing halotolerant PGPR Dietzia natronolimnaea STR1 protecting wheat plants from salt stress by modulating the transcriptional machinery responsible for salinity tolerance in plants. The expression studies confirmed the involvement of ABA-signalling cascade, as TaABARE and TaOPR1 were upregulated in PGPR inoculated plants leading to induction of TaMYB and TaWRKY expression followed by stimulation of expression of a plethora of stress related genes. Enhanced expression of TaST, a salt stress-induced gene, associated with promoting salinity tolerance was observed in PGPR inoculated plants in comparison to uninoculated control plants. Expression of SOS pathway related genes (SOS1 and SOS4) was modulated in PGPR-applied wheat shoots and root systems. Tissue-specific responses of ion transporters TaNHX1, TaHAK, and TaHKT1, were observed in PGPR-inoculated plants. The enhanced gene expression of various antioxidant enzymes such as APX, MnSOD, CAT, POD, GPX and GR and higher proline content in PGPR-inoculated wheat plants contributed to increased tolerance to salinity stress. Overall, these results indicate that halotolerant PGPR-mediated salinity tolerance is a complex phenomenon that involves modulation of ABA-signalling, SOS pathway, ion transporters and antioxidant machinery.
Temperature controls organic carbon sequestration in a subarctic lake
Authors: Rantala Marttiina V. , Luoto Tomi P. , Nevalainen Liisa 
Published: October 2016

AbstractWidespread ecological reorganizations and increases in organic carbon (OC) in lakes across the Northern Hemisphere have raised concerns about the impact of the ongoing climate warming on aquatic ecosystems and carbon cycling. We employed diverse biogeochemical techniques on a high-resolution sediment record from a subarctic lake in northern Finland (70°N) to examine the direction, magnitude and mechanism of change in aquatic carbon pools prior to and under the anthropogenic warming. Coupled variation in the elemental and isotopic composition of the sediment and a proxy-based summer air temperature reconstruction tracked changes in aquatic production, depicting a decline during a cool climate interval between ~1700–1900 C.E. and a subsequent increase over the 20th century. OC accumulation rates displayed similar coeval variation with temperature, mirroring both changes in aquatic production and terrestrial carbon export. Increase in sediment organic content over the 20th century together with high inferred aquatic UV exposure imply that the 20th century increase in OC accumulation is primarily connected to elevated lake production rather than terrestrial inputs. The changes in the supply of autochthonous energy sources were further reflected higher up the benthic food web, as evidenced by biotic stable isotopic fingerprints.
Attenuation of synaptic toxicity and MARK4/PAR1-mediated Tau phosphorylation by methylene blue for Alzheimer’s disease treatment
Authors: Sun Wenchao , Lee Seongsoo , Huang Xiaoran , Liu Song , Inayathullah Mohammed , Kim Kwang-Min , Tang Hongxiang , Ashford J. Wesson , Rajadas Jayakumar 
Published: October 2016

AbstractAlzheimer’s disease (AD) is a neurodegenerative disease characterized by genotypic and phenotypic heterogeneity. Critical components of the two AD pathological pathways, Aβ-amyloidosis and Tauopathy, have been considered as therapeutic targets. Among them, much effort is focused on aberrant Tau phosphorylation and targeting Tau-phosphorylating kinases. Methylene blue (MB), a phenothiazine dye that crosses the blood-brain barrier, has been shown to hit multiple molecular targets involved in AD and have beneficial effects in clinical studies. Here we present evidence that microtubule affinity-regulating kinase (MARK4) is a novel target of MB. MB partially rescued the synaptic toxicity in Drosophila larva overexpressing PAR1 (MARK analog). In 293T culture, MB decreased MARK4-mediated Tau phosphorylation in a dose dependent manner. Further studies revealed a two-fold mechanism by MB including down-regulation of MARK4 protein level through ubiquitin-proteasome pathway and inhibition of MARK4 kinase activity in vitro. This study highlights the importance of MARK4 as a viable target for Tauopathy and provides fresh insight into the complex mechanism used by MB to treat AD.
Cytoskeletal Configuration Modulates Mechanically Induced Changes in Mesenchymal Stem Cell Osteogenesis, Morphology, and Stiffness
Authors: Pongkitwitoon Suphannee , Uzer Gunes , Rubin Janet , Judex Stefan 
Published: October 2016

AbstractMesenchymal stem cells (MSC) responding to mechanical cues generated by physical activity is critical for skeletal development and remodeling. Here, we utilized low intensity vibrations (LIV) as a physiologically relevant mechanical signal and hypothesized that the confined cytoskeletal configuration imposed by 2D culture will enable human bone marrow MSCs (hBMSC) to respond more robustly when LIV is applied in-plane (horizontal-LIV) rather than out-of-plane (vertical-LIV). All LIV signals enhanced hBMSC proliferation, osteogenic differentiation, and upregulated genes associated with cytoskeletal structure. The cellular response was more pronounced at higher frequencies (100 Hz vs 30 Hz) and when applied in the horizontal plane. Horizontal but not vertical LIV realigned the cell cytoskeleton, culminating in increased cell stiffness. Our results show that applying very small oscillatory motions within the primary cell attachment plane, rather than perpendicular to it, amplifies the cell’s response to LIV, ostensibly facilitating a more effective transfer of intracellular forces. Transcriptional and structural changes in particular with horizontal LIV, together with the strong frequency dependency of the signal, emphasize the importance of intracellular cytoskeletal configuration in sensing and responding to high-frequency mechanical signals at low intensities.
Structural basis for PPAR partial or full activation revealed by a novel ligand binding mode
Authors: Capelli Davide , Cerchia Carmen , Montanari Roberta , Loiodice Fulvio , Tortorella Paolo , Laghezza Antonio , Cervoni Laura , Pochetti Giorgio , Lavecchia Antonio 
Published: October 2016

AbstractThe peroxisome proliferator-activated receptors (PPARs) are nuclear receptors involved in the regulation of the metabolic homeostasis and therefore represent valuable therapeutic targets for the treatment of metabolic diseases. The development of more balanced drugs interacting with PPARs, devoid of the side-effects showed by the currently marketed PPARγ full agonists, is considered the major challenge for the pharmaceutical companies. Here we present a structure-based virtual screening approach that let us identify a novel PPAR pan-agonist with a very attractive activity profile and its crystal structure in the complex with PPARα and PPARγ, respectively. In PPARα this ligand occupies a new pocket whose filling is allowed by the ligand-induced switching of the F273 side chain from a closed to an open conformation. The comparison between this pocket and the corresponding cavity in PPARγ provides a rationale for the different activation of the ligand towards PPARα and PPARγ, suggesting a novel basis for ligand design.
Two-photon interference of temporally separated photons
Authors: Kim Heonoh , Lee Sang Min , Moon Han Seb 
Published: October 2016

AbstractWe present experimental demonstrations of two-photon interference involving temporally separated photons within two types of interferometers: a Mach-Zehnder interferometer and a polarization-based Michelson interferometer. The two-photon states are probabilistically prepared in a symmetrically superposed state within the two interferometer arms by introducing a large time delay between two input photons; this state is composed of two temporally separated photons, which are in two different or the same spatial modes. We then observe two-photon interference fringes involving both the Hong-Ou-Mandel interference effect and the interference of path-entangled two-photon states simultaneously in a single interferometric setup. The observed two-photon interference fringes provide simultaneous observation of the interferometric properties of the single-photon and two-photon wavepackets. The observations can also facilitate a more comprehensive understanding of the origins of the interference phenomena arising from spatially bunched/anti-bunched two-photon states comprised of two temporally separated photons within the interferometer arms.
Acetylation Mimics Within a Single Nucleosome Alter Local DNA Accessibility In Compacted Nucleosome Arrays
Authors: Mishra Laxmi N. , Pepenella Sharon , Rogge Ryan , Hansen Jeffrey C. , Hayes Jeffrey J. 
Published: October 2016

AbstractThe activation of a silent gene locus is thought to involve pioneering transcription factors that initiate changes in the local chromatin structure to increase promoter accessibility and binding of downstream effectors. To better understand the molecular requirements for the first steps of locus activation, we investigated whether acetylation of a single nucleosome is sufficient to alter DNA accessibility within a condensed 25-nucleosome array. We found that acetylation mimics within the histone H4 tail domain increased accessibility of the surrounding linker DNA, with the increased accessibility localized to the immediate vicinity of the modified nucleosome. In contrast, acetylation mimics within the H3 tail had little effect, but were able to synergize with H4 tail acetylation mimics to further increase accessibility. Moreover, replacement of the central nucleosome with a nucleosome free region also resulted in increased local, but not global DNA accessibility. Our results indicate that modification or disruption of only a single target nucleosome results in significant changes in local chromatin architecture and suggest that very localized chromatin modifications imparted by pioneer transcription factors are sufficient to initiate a cascade of events leading to promoter activation.
Critical Role of Transcription Factor PU.1 in the Function of the OX40L/TNFSF4 Promoter in Dendritic Cells
Authors: Yashiro Takuya , Hara Mutsuko , Ogawa Hideoki , Okumura Ko , Nishiyama Chiharu 
Published: October 2016

AbstractPU.1 is a hematopoietic lineage-specific transcription factor belonging to the Ets family. We investigated the role of PU.1 in the expression of OX40L in dendritic cells (DCs), because the regulatory mechanism of cell type-specific expression of OX40L, which is mainly restricted to antigen-presenting cells, is largely unknown despite the critical involvement in Th2 and Tfh development. PU.1 knockdown decreased the expression of OX40L in mouse DCs. Chromatin immunoprecipitation (ChIP) assays demonstrated that PU.1 constitutively bound to the proximal region of the OX40L promoter. Reporter assays and electrophoretic mobility shift assays revealed that PU.1 transactivated the OX40L promoter through direct binding to the most-proximal Ets motif. We found that this Ets motif is conserved between mouse and human, and that PU.1 bound to the human OX40L promoter in ChIP assay using human monocyte-derived DCs. ChIP assays based on ChIP-seq datasets revealed that PU.1 binds to several sites distant from the transcription start site on the OX40L gene in addition to the most-proximal site in mouse DCs. In the present study, the structure of the OX40L promoter regulated by PU.1 is determined. It is also suggested that PU.1 is involved in mouse OX40L expression via multiple binding sites on the gene.
Unique Features of Ethnic Mongolian Gut Microbiome revealed by metagenomic analysis
Authors: Liu Wenjun , Zhang Jiachao , Wu Chunyan , Cai Shunfeng , Huang Weiqiang , Chen Jing , Xi Xiaoxia , Liang Zebin , Hou Qiangchuan , Zhou Bin , Qin Nan , Zhang Heping 
Published: October 2016

AbstractThe human gut microbiota varies considerably among world populations due to a variety of factors including genetic background, diet, cultural habits and socioeconomic status. Here we characterized 110 healthy Mongolian adults gut microbiota by shotgun metagenomic sequencing and compared the intestinal microbiome among Mongolians, the Hans and European cohorts. The results showed that the taxonomic profile of intestinal microbiome among cohorts revealed the Actinobaceria and Bifidobacterium were the key microbes contributing to the differences among Mongolians, the Hans and Europeans at the phylum level and genus level, respectively. Metagenomic species analysis indicated that Faecalibacterium prausnitzii and Coprococcus comeswere enrich in Mongolian people which might contribute to gut health through anti-inflammatory properties and butyrate production, respectively. On the other hand, the enriched genus Collinsella, biomarker in symptomatic atherosclerosis patients, might be associated with the high morbidity of cardiovascular and cerebrovascular diseases in Mongolian adults. At the functional level, a unique microbial metabolic pathway profile was present in Mongolian’s gut which mainly distributed in amino acid metabolism, carbohydrate metabolism, energy metabolism, lipid metabolism, glycan biosynthesis and metabolism. We can attribute the specific signatures of Mongolian gut microbiome to their unique genotype, dietary habits and living environment.
CXCL13/CXCR5 enhances sodium channel Nav1.8 current density via p38 MAP kinase in primary sensory neurons following inflammatory pain
Authors: Wu Xiao-Bo , Cao De-Li , Zhang Xin , Jiang Bao-Chun , Zhao Lin-Xia , Qian Bin , Gao Yong-Jing 
Published: October 2016

AbstractCXCL13 is a B lymphocyte chemoattractant and activates CXCR5 receptor in the immune system. Here we investigated whether CXCL13/CXCR5 mediates inflammatory pain in dorsal root ganglia (DRG) and the underlying mechanisms. Peripheral injection of complete Freund’s Adjuvant (CFA) increased the expression of CXCL13 and CXCR5 in DRG neurons. In Cxcr5−/− mice, CFA-induced pain hypersensitivity were attenuated. Whole-cell patch-clamp recording showed that the excitability of dissociated DRG neurons was increased after CFA injection or CXCL13 incubation from wild-type (WT) mice, but not from Cxcr5−/− mice. Additionally, sodium channel Nav1.8 was co-expressed with CXCR5 in dissociated DRG neurons, and the increased neuronal excitability induced by CFA or CXCL13 was reduced by Nav1.8 blocker. Intrathecal injection of Nav1.8 blocker also attenuated intrathecal injection of CXCL13-induced pain hypersensitivity. Furthermore, CXCL13 increased Nav1.8 current density in DRG neurons, which was inhibited by p38 MAP kinase inhibitor. CFA and CXCL13 increased p38 phosphorylation in the DRG of WT mice but not Cxcr5−/− mice. Finally, intrathecal p38 inhibitor alleviated CXCL13-induced pain hypersensitivity. Taken together, these results demonstrated that CXCL13, upregulated by peripheral inflammation, acts on CXCR5 on DRG neurons and activates p38, which increases Nav1.8 current density and further contributes to the maintenance of inflammatory pain.
lncScore: alignment-free identification of long noncoding RNA from assembled novel transcripts
Authors: Zhao Jian , Song Xiaofeng , Wang Kai 
Published: October 2016

AbstractRNA-Seq based transcriptome assembly has been widely used to identify novel lncRNAs. However, the best-performing transcript reconstruction methods merely identified 21% of full-length protein-coding transcripts from H. sapiens. Those partial-length protein-coding transcripts are more likely to be classified as lncRNAs due to their incomplete CDS, leading to higher false positive rate for lncRNA identification. Furthermore, potential sequencing or assembly error that gain or abolish stop codons also complicates ORF-based prediction of lncRNAs. Therefore, it remains a challenge to identify lncRNAs from the assembled transcripts, particularly the partial-length ones. Here, we present a novel alignment-free tool, lncScore, which uses a logistic regression model with 11 carefully selected features. Compared to other state-of-the-art alignment-free tools (e.g. CPAT, CNCI, and PLEK), lncScore outperforms them on accurately distinguishing lncRNAs from mRNAs, especially partial-length mRNAs in the human and mouse datasets. In addition, lncScore also performed well on transcripts from five other species (Zebrafish, Fly, C. elegans, Rat, and Sheep). To speed up the prediction, multithreading is implemented within lncScore, and it only took 2 minute to classify 64,756 transcripts and 54 seconds to train a new model with 21,000 transcripts with 12 threads, which is much faster than other tools. lncScore is available athttps://github.com/WGLab/lncScore.
Switchable thulium-doped fiber laser from polarization rotation vector to scalar soliton
Authors: Wu Zhichao , Fu Songnian , Jiang Kai , Song Jue , Li Huizi , Tang Ming , Shum Ping , Liu Deming 
Published: October 2016

AbstractWe experimentally demonstrate switchable temporal soliton generation from a thulium-doped fiber laser (TDFL), using carbon nanotubes as the mode-locker. With the help of residual polarization dependent loss of a wavelength division multiplexer, a weak nonlinear polarization rotation (NPR) effect can be achieved within the laser cavity, which may provide joint contribution for passive mode-locking operation. By finely adjusting the polarization to alter the strength of NPR-based saturable absorption, the TDFL either approaches the operation regime of scalar soliton with strong NPR effect, or generates polarization rotation locked vector soliton (PRLVS) with weak NPR effect. The scalar solitons and PRLVSs possess 3-dB optical spectrum bandwidth of 2.2 nm and 2 nm, pulse-width of 1.8 ps and 2 ps, respectively. Moreover, the PRLVSs demonstrate a typical energy exchange between two polarized components on optical spectra and a period-doubling feature in time domain. Such operation principle can also be used in 1550 nm band fiber lasers and other nonlinear systems.
Superantigens hyperinduce inflammatory cytokines by enhancing the B7-2/CD28 costimulatory receptor interaction
Authors: Levy Revital , Rotfogel Ziv , Hillman Dalia , Popugailo Andrey , Arad Gila , Supper Emmanuelle , Osman Farhat , Kaempfer Raymond 
Published: October 2016

SignificanceSuperantigens—bacterial virulence factors—cause toxic shock by hyperinducing inflammatory cytokines. T-cell activation is mediated both by antigen and by interaction between principal costimulatory receptors B7-2 and CD28. Superantigens must bind CD28 to elicit cytokine overexpression through a hitherto unknown mechanism. We show that, by binding not only CD28 but also its coligand B7-2 directly, superantigens potently enhance the B7-2/CD28 interaction, thereby inducing T-cell hyperactivation. Superantigens engage B7-2 and CD28 at their homodimer interfaces, far from where the receptors interact, demonstrating the regulatory properties of these interfaces. B7-2 dimer interface peptides attenuate cytokine overexpression and prevent superantigen lethality by blocking costimulatory receptor engagement by superantigen. Thus, bacterial superantigens induce a pathogenic “cytokine storm” by strongly enhancing formation of the B7-2/CD28 costimulatory axis.
Interfibrillar stiffening of echinoderm mutable collagenous tissue demonstrated at the nanoscale
Authors: Mo Jingyi , Prévost Sylvain F. , Blowes Liisa M. , Egertová Michaela , Terrill Nicholas J. , Wang Wen , Elphick Maurice R. , Gupta Himadri S. 
Published: October 2016

Significance
Collagen plays crucial biomechanical roles in a wide array of animal tissues, but its mechanical properties remain largely static over short timescales. However, echinoderms (sea cucumbers, starfish) are striking exceptions to this rule, having “mutable collagenous tissue” with changeable mechanical properties, enabling complex locomotion, postural maintenance, defense, and reproductive strategies. Using a high-resolution X-ray probe that measures how the building blocks—fibrils—of echinoderm connective tissue stretch, slide, or reorient in real time, we show that sea cucumbers achieve this remarkable property by changing the stiffness of the matrix between individual fibrils, rather than the properties of the fibrils themselves. Understanding the mechanisms of mutability in this unique tissue may help design novel mechanically tunable synthetic biomaterials.