bluuebunny/crossref_metadata_2025_split huggingface dataset:
Longitudinal Prediction of the Infant Gut Microbiome with Dynamic Bayesian Networks
Authors: McGeachie Michael J. , Sordillo Joanne E. , Gibson Travis , Weinstock George M. , Liu Yang-Yu , Gold Diane R. , Weiss Scott T. , Litonjua Augusto 
Published: February 2016

AbstractSequencing of the 16S rRNA gene allows comprehensive assessment of bacterial community composition from human body sites. Previously published and publicly accessible data on 58 preterm infants in the Neonatal Intensive Care Unit who underwent frequent stool collection was used. We constructed Dynamic Bayesian Networks from the data and analyzed predictive performance and network characteristics. We constructed a DBN model of the infant gut microbial ecosystem, which explicitly captured specific relationships and general trends in the data: increasing amounts of Clostridia, residual amounts of Bacilli and increasing amounts of Gammaproteobacteria that then give way to Clostridia. Prediction performance of DBNs with fewer edges were overall more accurate, although less so on harder-to-predict subjects (p = 0.045). DBNs provided quantitative likelihood estimates for rare abruptions events. Iterative prediction was less accurate (p < 0.001), but showed remarkable insensitivity to initial conditions and predicted convergence to a mix of Clostridia, Gammaproteobacteria and Bacilli. DBNs were able to identify important relationships between microbiome taxa and predict future changes in microbiome composition from measured or synthetic initial conditions. DBNs also provided likelihood estimates for sudden, dramatic shifts in microbiome composition, which may be useful in guiding further analysis of those samples.
Dissolved organic carbon from the upper Rio Negro protects zebrafish (Danio rerio) against ionoregulatory disturbances caused by low pH exposure
Authors: Duarte Rafael M. , Smith D. Scott , Val Adalberto L. , Wood Chris M. 
Published: February 2016

AbstractThe so-called “blackwaters” of the Amazonian Rio Negro are rich in highly coloured dissolved organic carbon (DOC), but ion-poor and very acidic, conditions that would cause fatal ionoregulatory failure in most fish. However these blackwaters support 8% of the world’s ichthyofauna. We tested the hypothesis that native DOC provides protection against ionoregulatory dysfunction in this extreme environment. DOCs were isolated by reverse-osmosis from two Rio Negro sites. Physico-chemical characterization clearly indicated a terrigenous origin, with a high proportion of hydroxyl and phenolic sites, high chemical reactivity to protons and unusual proteinaceous fluorescence. When tested using zebrafish (a model organism), Rio Negro DOC provided almost perfect protection against ionoregulatory disturbances associated with acute exposure to pH 4.0 in ion-poor water. DOC reduced diffusive losses of Na+ and Cl− and promoted a remarkable stimulation of Na+ uptake that otherwise would have been completely inhibited. Additionally, prior acclimation to DOC at neutral pH reduced rates of branchial Na+ turnover and provided similar protection against acid-induced ionoregulatory disturbances, even if the DOC was no longer present. These results reinforce the important roles that DOC molecules can play in the regulation of gill functions in freshwater fish, particularly in ion-poor, acidic blackwaters.
Mortality prediction in patients with severe septic shock: a pilot study using a target metabolomics approach
Authors: Ferrario Manuela , Cambiaghi Alice , Brunelli Laura , Giordano Silvia , Caironi Pietro , Guatteri Luca , Raimondi Ferdinando , Gattinoni Luciano , Latini Roberto , Masson Serge , Ristagno Giuseppe , Pastorelli Roberta 
Published: February 2016

AbstractSeptic shock remains a major problem in Intensive Care Unit, with high lethality and high-risk second lines treatments. In this preliminary retrospective investigation we examined plasma metabolome and clinical features in a subset of 20 patients with severe septic shock (SOFA score >8), enrolled in the multicenter Albumin Italian Outcome Sepsis study (ALBIOS, NCT00707122). Our purpose was to evaluate the changes of circulating metabolites in relation to mortality as a pilot study to be extended in a larger cohort. Patients were analyzed according to their 28-days and 90-days mortality. Metabolites were measured using a targeted mass spectrometry-based quantitative metabolomic approach that included acylcarnitines, aminoacids, biogenic amines, glycerophospholipids, sphingolipids and sugars. Data-mining techniques were applied to evaluate the association of metabolites with mortality. Low unsaturated long-chain phosphatidylcholines and lysophosphatidylcholines species were associated with long-term survival (90-days) together with circulating kynurenine. Moreover, a decrease of these glycerophospholipids was associated to the event at 28-days and 90-days in combination with clinical variables such as cardiovascular SOFA score (28-day mortality model) or renal replacement therapy (90-day mortality model). Early changes in the plasma levels of both lipid species and kynurenine associated with mortality have potential implications for early intervention and discovering new target therapy.
Validation of a risk prediction score for proximal neoplasia in colorectal cancer screening: a prospective colonoscopy study
Authors: Wong Martin C.S. , Ching Jessica Y.L. , Chan Victor C.W. , Tang Raymond S.Y. , Luk Arthur K.C. , Lam Thomas Y.T. , Wong Sunny S.H. , Ng Siew C. , Ng Simon S.M. , Wu Justin C.Y. , Chan Francis K.L. , Sung Joseph J.Y. 
Published: February 2016

AbstractThis study developed a clinical scoring system to predict the risks of PN among screening participants for colorectal cancer. We recruited 5,789 Chinese asymptomatic screening participants who received colonoscopy in Hong Kong (2008–2014). From random sampling of 2,000 participants, the independent risk factors were evaluated for PN using binary regression analysis. The odds ratios for significant risk factors were used to develop a scoring system, with scores stratified into ‘average risk’ (AR):0–2 and ‘high risk’ (HR):3–5. The other 3,789 subjects formed an independent validation cohort. Each participant received a score calculated based on their risk factors. The performance of the scoring system was evaluated. The proportion of PN in the derivation and validation cohorts was 12.6% and 12.9%, respectively. Based on age, gender, family history, body mass index and self-reported ischaemic heart disease, 85.0% and 15.0% in the validation cohort were classified as AR and HR, respectively. Their prevalence of PN was 12.0% and 18.1%, respectively. Participants in the HR group had 1.51-fold (95% CI = 1.24–1.84, p < 0.001) higher risk of PN than the AR group. The overall c-statistics of the prediction model was 0.71(0.02). The scoring system is useful in predicting the risk of PN to prioritize patients for colonoscopy.
Role of autophagy in cadmium-induced apoptosis of primary rat osteoblasts
Authors: Liu Wei , Dai Nannan , Wang Yi , Xu Chao , Zhao Hongyan , Xia Pengpeng , Gu Jianhong , Liu Xuezhong , Bian Jianchun , Yuan Yan , Zhu Jiaqiao , Liu Zongping 
Published: February 2016

AbstractCadmium (Cd) is a common environmental pollutant that can damage many organs and the fetus. We previously reported that Cd induced apoptosis in primary rat osteoblasts (OBs). OB apoptosis induced by Cd will eventually lead to osteoporosis. In this study, a novel pharmacotherapeutic approach was investigated involving the regulation of autophagy to prevent Cd osteoporosis. The results showed that Cd treatment induced apoptosis in OBs, as demonstrated by the ratio of Bax/Bcl-2, activation of poly (ADP-ribose) polymerase (PARP) and nuclear condensation. In addition, cells treated with Cd were observed to undergo autophagic cell death by monitoring the induction of the beclin 1, autophagy gene 5 (Atg5) and the expression of microtubule-associated protein 1 light chain 3 (LC3). The results indicated that promotion of apoptotic cell death by Cd is accompanied by induction of autophagy in OBs. Interestingly, Cd-mediated apoptotic cell death was suppressed by pretreatment with the autophagy activator rapamycin (RAP) and potentiated by the autophagy inhibitor chloroquine (CQ) or small interfering RNA against beclin 1. These findings suggest that the autophagic response plays a protective role that impedes eventual cell death. Activation of autophagy could therefore be an adjunctive strategy for treatment of Cd-induced osteoporosis.
Targeting arginase-II protects mice from high-fat-diet-induced hepatic steatosis through suppression of macrophage inflammation
Authors: Liu Chang , Rajapakse Angana G. , Riedo Erwin , Fellay Benoit , Bernhard Marie-Claire , Montani Jean-Pierre , Yang Zhihong , Ming Xiu-Fen 
Published: February 2016

AbstractNonalcoholic fatty liver disease (NAFLD) associates with obesity and type 2 diabetes. Hypoactive AMP-activated protein kinase (AMPK), hyperactive mammalian target of rapamycin (mTOR) signaling and macrophage-mediated inflammation are mechanistically linked to NAFLD. Studies investigating roles of arginase particularly the extrahepatic isoform arginase-II (Arg-II) in obesity-associated NAFLD showed contradictory results. Here we demonstrate that Arg-II−/− mice reveal decreased hepatic steatosis, macrophage infiltration, TNF-α and IL-6 as compared to the wild type (WT) littermates fed high fat diet (HFD). A higher AMPK activation (no difference in mTOR signaling), lower levels of lipogenic transcription factor SREBP-1c and activity/expression of lipogenic enzymes were observed in the Arg-II−/− mice liver. Moreover, release of TNF-α and IL-6 from bone marrow-derived macrophages (BMM) of Arg-II−/− mice is decreased as compared to WT-BMM. Conditioned medium from Arg-II−/−-BMM exhibits weaker activity to facilitate triglyceride synthesis paralleled with lower expression of SREBP-1c and SCD-1 and higher AMPK activation in hepatocytes as compared to that from WT-BMM. These effects of BMM conditioned medium can be neutralized by neutralizing antibodies against TNF-α and IL-6. Thus, Arg-II-expressing macrophages facilitate diet-induced NAFLD through TNF-α and IL-6 in obesity.
Upward shift of the vortex solid phase in high-temperature-superconducting wires through high density nanoparticle addition
Authors: Miura Masashi , Maiorov Boris , Balakirev Fedor F. , Kato Takeharu , Sato Michio , Takagi Yuji , Izumi Teruo , Civale Leonardo 
Published: February 2016

AbstractWe show a simple and effective way to improve the vortex irreversibility line up to very high magnetic fields (60T) by increasing the density of second phase BaZrO3 nanoparticles. (Y0.77,Gd0.23)Ba2Cu3Oy films were grown on metal substrates with different concentration of BaZrO3 nanoparticles by the metal organic deposition method. We find that upon increase of the BaZrO3 concentration, the nanoparticle size remains constant but the twin-boundary density increases. Up to the highest nanoparticle concentration (n ~ 1.3 × 1022/m3), the irreversibility field (Hirr) continues to increase with no sign of saturation up to 60 T, although the vortices vastly outnumber pinning centers. We find extremely high Hirr, namely Hirr = 30 T (H||45°) and 24 T (H||c) at 65 K and 58 T (H||45°) and 45 T (H||c) at 50K. The difference in pinning landscape shifts the vortex solid-liquid transition upwards, increasing the vortex region useful for power applications, while keeping the upper critical field, critical temperature and electronic mass anisotropy unchanged.
Unusual dimensionality effects and surface charge density in 2D Mg(OH)2
Authors: Suslu Aslihan , Wu Kedi , Sahin Hasan , Chen Bin , Yang Sijie , Cai Hui , Aoki Toshihiro , Horzum Seyda , Kang Jun , Peeters Francois M. , Tongay Sefaattin 
Published: February 2016

AbstractWe present two-dimensional Mg(OH)2 sheets and their vertical heterojunctions with CVD-MoS2 for the first time as flexible 2D insulators with anomalous lattice vibration and chemical and physical properties. New hydrothermal crystal growth technique enabled isolation of environmentally stable monolayer Mg(OH)2 sheets. Raman spectroscopy and vibrational calculations reveal that the lattice vibrations of Mg(OH)2 have fundamentally different signature peaks and dimensionality effects compared to other 2D material systems known to date. Sub-wavelength electron energy-loss spectroscopy measurements and theoretical calculations show that Mg(OH)2 is a 6 eV direct-gap insulator in 2D and its optical band gap displays strong band renormalization effects from monolayer to bulk, marking the first experimental confirmation of confinement effects in 2D insulators. Interestingly, 2D-Mg(OH)2 sheets possess rather strong surface polarization (charge) effects which is in contrast to electrically neutral h-BN materials. Using 2D-Mg(OH)2 sheets together with CVD-MoS2 in the vertical stacking shows that a strong change transfer occurs from n-doped CVD-MoS2 sheets to Mg(OH)2, naturally depleting the semiconductor, pushing towards intrinsic doping limit and enhancing overall optical performance of 2D semiconductors. Results not only establish unusual confinement effects in 2D-Mg(OH)2, but also offer novel 2D-insulating material with unique physical, vibrational and chemical properties for potential applications in flexible optoelectronics.
Miltirone exhibits antileukemic activity by ROS-mediated endoplasmic reticulum stress and mitochondrial dysfunction pathways
Authors: Zhou Ling , Jiang Lifeng , Xu Maolei , Liu Qun , Gao Ning , Li Ping , Liu E-Hu 
Published: February 2016

AbstractIn this study, we investigated the effects of miltirone in human leukemia cell lines, primary leukemia cells and nude mice U937 xenograft. Treatment of cells with miltirone resulted in apoptosis, mitochondria membrane potential (MMP) collapses, increase of Bax/Bcl-2 ratio and cytochrome c release. Miltirone triggered the endoplasmic reticulum (ER) stress identified through several key molecules of the unfolded protein response, including phosphorylated PERK, eIF2a, GRP78, GRP94 and caspase-12. Miltrone treatment also resulted in the release of Ca2+ from the ER stores and mitochondrial Ca2+ loading in the cells. Further research revealed that miltirone resulted in dose-dependent decrease in complex III activity and elevated reactive oxygen species (ROS) production in these cells. Miltirone-induced apoptosis, dissipation of MMP and ER stress were dramatically blocked by pretreatment with antioxidant N-acetylcysteine (NAC). In contrast, treatment with ER stress inhibitor TUDCA significantly attenuated miltirone-induced ROS and apoptosis in leukemia cells. Moreover, our in vivo findings showed that administration of miltirone markedly inhibited tumor growth and induced apoptosis in U937 xenograft model with low systemic toxicity. Taken together, these findings indicate that miltirone may exert its antileukemic activity by inducing apoptosis through a ROS-dependent destructive cycle involving ER stress and mitochondrial dysfunction.
Stem cell-derived tissue-associated regulatory T cells ameliorate the development of autoimmunity
Authors: Haque Mohammad , Song Jianyong , Fino Kristin , Sandhu Praneet , Song Xinmeng , Lei Fengyang , Zheng Songguo , Ni Bing , Fang Deyu , Song Jianxun 
Published: February 2016

AbstractPluripotent stem cells (PSCs) have the potential to produce almost all of the cells in the body, including regulatory T cells (Tregs). However, the exact conditions required for the development of antigen (Ag)-specific Tregs from PSCs (i.e., PSC-Tregs) are not well delineated. Ag-specific PSC-Tregs can be tissue/organ-associated and migrate to local inflamed tissues/organs to suppress the autoimmune response after adoptive transfer, thereby avoiding potential overall immunosuppression from non-specific Tregs. In this study, we developed a new approach to generate functional Ag-specific Tregs from induced PSCs (iPSCs), i.e., iPSC-Tregs, which had the ability to generate an Ag-specific immunosuppressive response in a murine model of arthritis. We retrovirally transduced murine iPSCs with a construct containing genes of Ag-specific T cell receptor (TCR) and the transcriptional factor FoxP3. We differentiated the iPSCs into Ag-specific iPSC-Tregs using in vitro or in vivo Notch signaling and demonstrated that adoptive transfer of such Tregs dramatically suppressed autoimmunity in a well-established Ag-induced arthritis model, including the inflammation, joint destruction, cartilage prostaglandin depletion, osteoclast activity and Th17 production. Our results indicate that PSCs can be used to develop Ag-specific Tregs, which have a therapeutic potential for Treg-based therapies of autoimmune disorders.
Snakes elicit earlier, and monkey faces, later, gamma oscillations in macaque pulvinar neurons
Authors: Le Quan Van , Isbell Lynne A. , Matsumoto Jumpei , Le Van Quang , Nishimaru Hiroshi , Hori Etsuro , Maior Rafael S. , Tomaz Carlos , Ono Taketoshi , Nishijo Hisao 
Published: February 2016

AbstractGamma oscillations (30–80 Hz) have been suggested to be involved in feedforward visual information processing, and might play an important role in detecting snakes as predators of primates. In the present study, we analyzed gamma oscillations of pulvinar neurons in the monkeys during a delayed non-matching to sample task, in which monkeys were required to discriminate 4 categories of visual stimuli (snakes, monkey faces, monkey hands and simple geometrical patterns). Gamma oscillations of pulvinar neuronal activity were analyzed in three phases around the stimulus onset (Pre-stimulus: 500 ms before stimulus onset; Early: 0–200 ms after stimulus onset; and Late: 300–500 ms after stimulus onset). The results showed significant increases in mean strength of gamma oscillations in the Early phase for snakes and the Late phase for monkey faces, but no significant differences in ratios and frequencies of gamma oscillations among the 3 phases. The different periods of stronger gamma oscillations provide neurophysiological evidence that is consistent with other studies indicating that primates can detect snakes very rapidly and also cue in to faces for information. Our results are suggestive of different roles of gamma oscillations in the pulvinar: feedforward processing for images of snakes and cortico-pulvinar-cortical integration for images of faces.
Heart Rate Variability Change Before and After Hemodialysis is Associated with Overall and Cardiovascular Mortality in Hemodialysis
Authors: Chen Szu-Chia , Huang Jiun-Chi , Tsai Yi-Chun , Hsiu-Chin Mai R. N. , Jui-Hsin Chen R. N. , Kuo Po-Lin , Chang Jer-Ming , Hwang Shang-Jyh , Chen Hung-Chun 
Published: February 2016

AbstractLow heart rate variability (HRV) has been recognized to correlate with adverse cardiovascular (CV) outcomes in hemodialysis (HD) patients. It has been reported that HRV might be improved after HD, but whether the improved HRV after HD predicts a better CV prognosis remains to be determined. This study examined the ability of the change in HRV before and after HD in predicting overall and CV mortality in HD patients. This study enrolled 182 patients under maintenance HD. HRV was examined to assess changes before and after HD. The change in HRV (ΔHRV) was defined as post-HD HRV minus pre-HD HRV. During a median follow-up period of 35.2 months, 29 deaths (15.9%) were recorded. Multivariate analysis showed that decreased ΔLF% was associated with increased overall (hazard ratios [HR], 0.978; 95% confidence interval [CI], 0.961–0.996; p = 0.019) and CV mortality (HR, 0.941; 95% CI, 0.914–0.970; p < 0.001), respectively. Moreover, adding ΔLF% to a clinical model provided an additional benefit in the prediction of overall (p = 0.002) and CV mortality (p < 0.001). HRV change before and after HD (ΔHRV) is an useful clinical marker and it is stronger than HRV before HD in predicting overall and CV mortality.
Nanoquinacrine induced apoptosis in cervical cancer stem cells through the inhibition of hedgehog-GLI1 cascade: Role of GLI-1
Authors: Nayak Anmada , Satapathy Shakti Ranjan , Das Dipon , Siddharth Sumit , Tripathi Neha , Bharatam Prasad V. , Kundu ChanakyaNath 
Published: February 2016

AbstractTo improve the pharmacokinetics and to study the anti-cervical cancer and anti-stem cells (CSCs) mechanism of Quinacrine (QC), a spherical nano particle of QC (i.e. NQC) was prepared and characterized. QC and NQC showed higher cytotoxicity in multiple cancer cells than the normal epithelial cells. NQC exhibited more toxicity in cervical cancer cells and its CSCs than QC. A dose-dependent decreased expression of Hedgehog-GLI (HH-GLI) components were noted in NQC treated HeLa cells and its CSCs. NQC increased the expressions of negatively regulated HH-GLI components (GSK3β, PTEN) and caused apoptosis in CSCs. Reduction of GLI1 at mRNA and promoter level were noted after NQC exposure. The expressions of HH-GLI components, GLI1 promoter activity and apoptosis were unaltered in NQC treated GLI1-knockdown cells. In silico, cell based and in vitro reconstitution assay revealed that NQC inhibit HH-GLI cascade by binding to the consensus sequence (5′GACCACCCA3′) of GLI1 in GLI-DNA complex through destabilizing DNA-GLI1 complex. NQC reduced the tumors size and proliferation marker Ki-67 in an in vivo xenograft mice model. Thus, NQC induced apoptosis in cancers through inhibition of HH-GLI cascade by GLI1. Detail interaction of QC-DNA-GLI complex can pave path for anticancer drug design.
Intestinal Microbiota Distinguish Gout Patients from Healthy Humans
Authors: Guo Zhuang , Zhang Jiachao , Wang Zhanli , Ang Kay Ying , Huang Shi , Hou Qiangchuan , Su Xiaoquan , Qiao Jianmin , Zheng Yi , Wang Lifeng , Koh Eileen , Danliang Ho , Xu Jian , Lee Yuan Kun , Zhang Heping 
Published: February 2016

AbstractCurrent blood-based approach for gout diagnosis can be of low sensitivity and hysteretic. Here via a 68-member cohort of 33 healthy and 35 diseased individuals, we reported that the intestinal microbiota of gout patients are highly distinct from healthy individuals in both organismal and functional structures. In gout, Bacteroides caccae and Bacteroides xylanisolvens are enriched yet Faecalibacterium prausnitzii and Bifidobacterium pseudocatenulatum depleted. The established reference microbial gene catalogue for gout revealed disorder in purine degradation and butyric acid biosynthesis in gout patients. In an additional 15-member validation-group, a diagnosis model via 17 gout-associated bacteria reached 88.9% accuracy, higher than the blood-uric-acid based approach. Intestinal microbiota of gout are more similar to those of type-2 diabetes than to liver cirrhosis, whereas depletion of Faecalibacterium prausnitzii and reduced butyrate biosynthesis are shared in each of the metabolic syndromes. Thus the Microbial Index of Gout was proposed as a novel, sensitive and non-invasive strategy for diagnosing gout via fecal microbiota.
Individual Differences in Rhythmic Cortical Entrainment Correlate with Predictive Behavior in Sensorimotor Synchronization
Authors: Nozaradan Sylvie , Peretz Isabelle , Keller Peter E. 
Published: February 2016

AbstractThe current study aims at characterizing the mechanisms that allow humans to entrain the mind and body to incoming rhythmic sensory inputs in real time. We addressed this unresolved issue by examining the relationship between covert neural processes and overt behavior in the context of musical rhythm. We measured temporal prediction abilities, sensorimotor synchronization accuracy and neural entrainment to auditory rhythms as captured using an EEG frequency-tagging approach. Importantly, movement synchronization accuracy with a rhythmic beat could be explained by the amplitude of neural activity selectively locked with the beat period when listening to the rhythmic inputs. Furthermore, stronger endogenous neural entrainment at the beat frequency was associated with superior temporal prediction abilities. Together, these results reveal a direct link between cortical and behavioral measures of rhythmic entrainment, thus providing evidence that frequency-tagged brain activity has functional relevance for beat perception and synchronization.