bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiple helical configuration and quantity threshold of graphene nanoribbons inside a single-walled carbon nanotube
Authors: Li Yifan , Chen Wei , Ren Hongru , Zhou Xuyan , Li Hui 
Published: September 2015

AbstractMolecular dynamics simulation has been carried out to explore the configuration and quantity threshold of multiple graphene nanoribbons (GNRs) in single-walled carbon nanotube (SWCNT). The simulation results showed that several GNRs tangled together to form a perfect spiral structure to maximize the π-π stacking area when filling inside SWCNT. The formation of multiple helical configuration is influenced by the combined effect of structure stability, initial arrangement and tube space, meanwhile its forming time is related to helical angle. The simulated threshold of GNRs in SWCNT decreases with GNR width but increases with SWCNT diameter and two formulas have come up in this study to estimate the quantity threshold for GNRs. It has been found that multilayered graphite is hard to be stripped in SWCNT because the special helical configuration with incompletely separated GNRs is metastable. This work provides a possibility to control the configuration of GNR@SWCNT.
Complete mitochondrial genome of the medicinal fungus Ophiocordyceps sinensis
Authors: Li Yi , Hu Xiao-Di , Yang Rui-Heng , Hsiang Tom , Wang Ke , Liang De-Quan , Liang Fan , Cao De-Ming , Zhou Fan , Wen Ge , Yao Yi-Jian 
Published: September 2015

AbstractAs part of a genome sequencing project for Ophiocordyceps sinensis, strain 1229, a complete mitochondrial (mt) genome was assembled as a single circular dsDNA of 157,510 bp, one of the largest reported for fungi. Conserved genes including the large and small rRNA subunits, 27 tRNA and 15 protein-coding genes, were identified. In addition, 58 non-conserved open reading frames (ncORFs) in the intergenic and intronic regions were also identified. Transcription analyses using RNA-Seq validated the expression of most conserved genes and ncORFs. Fifty-two introns (groups I and II) were found within conserved genes, accounting for 68.5% of the genome. Thirty-two homing endonucleases (HEs) with motif patterns LAGLIDADG (21) and GIY-YIG (11) were identified in group I introns. The ncORFs found in group II introns mostly encoded reverse transcriptases (RTs). As in other hypocrealean fungi, gene contents and order were found to be conserved in the mt genome of O. sinensis, but the genome size was enlarged by longer intergenic regions and numerous introns. Intergenic and intronic regions were composed of abundant repetitive sequences usually associated with mobile elements. It is likely that intronic ncORFs, which encode RTs and HEs, may have contributed to the enlarged mt genome of O. sinensis.
RETRACTED ARTICLE: Anti-aging Effect of Transplanted Amniotic Membrane Mesenchymal Stem Cells in a Premature Aging Model of Bmi-1 Deficiency
Authors: Xie Chunfeng , Jin Jianliang , Lv Xianhui , Tao Jianguo , Wang Rong , Miao Dengshun 
Published: September 2015

AbstractTo determine whether transplanted amniotic membrane mesenchymal stem cells (AMSCs) ameliorated the premature senescent phenotype of Bmi-1-deficient mice, postnatal 2-day-old Bmi-1−/− mice were injected intraperitoneally with the second-passage AMSCs from amniotic membranes of β-galactosidase (β-gal) transgenic mice or wild-type (WT) mice labeled with DiI. Three reinjections were given, once every seven days. Phenotypes of 5-week-old β-gal+ AMSC-transplanted or 6-week-old DiI+ AMSC-transplanted Bmi-1−/− mice were compared with vehicle-transplanted Bmi-1−/− and WT mice. Vehicle-transplanted Bmi-1−/− mice displayed growth retardation and premature aging with decreased cell proliferation and increased cell apoptosis; a decreased ratio and dysmaturity of lymphocytic series; premature osteoporosis with reduced osteogenesis and increased adipogenesis; redox imbalance and DNA damage in multiple organs. Transplanted AMSCs carried Bmi-1 migrated into multiple organs, proliferated and differentiated into multiple tissue cells, promoted growth and delayed senescence in Bmi-1−/− transplant recipients. The dysmaturity of lymphocytic series were ameliorated, premature osteoporosis were rescued by promoting osteogenesis and inhibiting adipogenesis, the oxidative stress and DNA damage in multiple organs were inhibited by the AMSC transplantation in Bmi-1−/− mice. These findings indicate that AMSC transplantation ameliorated the premature senescent phenotype of Bmi-1-deficient mice and could be a novel therapy to delay aging and prevent aging-associated degenerative diseases.
Molecular Mechanism of Switching of TrkA/p75NTR Signaling in Monocrotophos Induced Neurotoxicity
Authors: Kumar Vivek , Gupta Amit Kumar , Shukla Rajendra Kumar , Tripathi Vinay Kumar , Jahan Sadaf , Pandey Ankita , Srivastava Akriti , Agrawal Megha , Yadav Sanjay , Khanna Vinay Kumar , Pant Aditya Bhushan 
Published: September 2015

AbstractWe demonstrate the role of molecular switching of TrkA/p75NTR signaling cascade in organophosphate pesticide-Monocrotophos (MCP) induced neurotoxicity in stem cell derived cholinergic neurons and in rat brain. Our in-silico studies reveal that MCP followed the similar pattern of binding as staurosporine and AG-879 (known inhibitors of TrkA) with TrkA protein (PDB ID: 4AOJ) at the ATP binding sites. This binding of MCP to TrkA led to the conformational change in this protein and triggers the cell death cascades. The in-silico findings are validated by observing the down regulated levels of phosphorylated TrkA and its downstream molecules viz., pERK1/2, pAkt and pCREB in MCP-exposed cells. We observe that these MCP induced alterations in pTrkA and downstream signaling molecules are found to be associated with apoptosis and injury to neurons. The down-regulation of TrkA could be linked to increased p75NTR. The in-vitro studies could be correlated in the rat model. The switching of TrkA/p75NTR signaling plays a central role in MCP-induced neural injury in rBNSCs and behavioral changes in exposed rats. Our studies significantly advance the understanding of the switching of TrkA/p75NTR that may pave the way for the application of TrkA inducer/p75NTR inhibitor for potential therapeutic intervention in various neurodegenerative disorders.
Simulated Interactive Research Experiments as Educational Tools for Advanced Science
Authors: Tomandl Mathias , Mieling Thomas , Losert-Valiente Kroon Christiane M. , Hopf Martin , Arndt Markus 
Published: September 2015

AbstractExperimental research has become complex and thus a challenge to science education. Only very few students can typically be trained on advanced scientific equipment. It is therefore important to find new tools that allow all students to acquire laboratory skills individually and independent of where they are located. In a design-based research process we have investigated the feasibility of using a virtual laboratory as a photo-realistic and scientifically valid representation of advanced scientific infrastructure to teach modern experimental science, here, molecular quantum optics. We found a concept based on three educational principles that allows undergraduate students to become acquainted with procedures and concepts of a modern research field. We find a significant increase in student understanding using our Simulated Interactive Research Experiment (SiReX), by evaluating the learning outcomes with semi-structured interviews in a pre/post design. This suggests that this concept of an educational tool can be generalized to disseminate findings in other fields.
MicroRNA125b-mediated Hedgehog signaling influences liver regeneration by chorionic plate-derived mesenchymal stem cells
Authors: Hyun Jeongeun , Wang Sihyung , Kim Jieun , Kim Gi Jin , Jung Youngmi 
Published: September 2015

AbstractAlthough chorionic plate-derived mesenchymal stem cells (CP-MSCs) were shown to promote liver regeneration, the mechanisms underlying the effect remain unclear. Hedgehog (Hh) signaling orchestrates tissue reconstruction in damaged liver. MSCs release microRNAs mediating various cellular responses. Hence, we hypothesized that microRNAs from CP-MSCs regulated Hh signaling, which influenced liver regeneration. Livers were obtained from carbon tetrachloride (CCl4)-treated rats transplanted with human CP-MSCs (Tx) or saline (non-Tx). Sonic Hh, one of Hh ligands, increased in CCl4-treated liver, whereas it decreased in CP-MSC-treated liver with CCl4. The expression of Hh-target genes was significantly downregulated in the Tx. Reduced expansion of progenitors and regressed fibrosis were observed in the liver of the Tx rats. CP-MSCs suppressed the expression of Hh and profibrotic genes in co-cultured LX2 (human hepatic stellate cell) with CP-MSCs. MicroRNA-125b targeting smo was retained in exosomes of CP-MSCs. CP-MSCs with microRNA-125b inhibitor failed to attenuate the expression of Hh signaling and profibrotic genes in the activated HSCs. Therefore, these results demonstrated that microRNA-125b from CP-MSCs suppressed the activation of Hh signaling, which promoted the reduced fibrosis, suggesting that microRNA-mediated regulation of Hh signaling contributed to liver regeneration by CP-MSCs.
OPN gene polymorphisms, rs17524488 GG/G, rs11730582 T/C and rs9138 C/A and cancer risk in a Chinese population
Authors: Mi Yuanyuan , Ren Kewei , Dai Feng , Zhu Lijie , Feng Ninghan 
Published: September 2015

AbstractPrevious studies have investigated the association between osteopontin (OPN) gene polymorphisms, rs17524488 (−156 GG/G), rs11730582 (−443 T/C) and rs9138 (C/A) and cancer risk in the Chinese population. However, the results are controversial and indefinite. We therefore carried out a meta-analysis to derive a more precise estimation of these associations. The PubMed database was systematically searched to identify potentially eligible reports. Crude odds ratios (OR) and 95% confidence intervals (CI) were used to assess the strength of associations between 3 OPN gene polymorphisms and cancer risk in a Chinese population. A total of 10 articles involving 2,391 cases and 3,007 controls were evaluated. The pooled OR indicated that OPN rs17524488 (−156 GG/G) polymorphism was significantly associated with cancer risk in Chinese population. In a stratified analysis by source of control, significant associations were also observed among rs17524488 (−156 GG/G) and rs11730582 (−443 T/C) polymorphisms and cancer. In addition, a stronger association was observed between rs9138 (C/A) polymorphism and cancer risk. In conclusion, this meta-analysis suggests that OPN rs17524488 (−156 GG/G), rs11730582 (−443 T/C) and rs9138 (C/A) polymorphisms may be associated with cancer susceptibility in the Chinese population. Nevertheless, further investigation on a larger population covering different ethnicities are warranted.
Fracture of Jammed Colloidal Suspensions
Authors: Smith M.I. 
Published: September 2015

AbstractConcentrated colloidal suspensions display dramatic rises in viscosity, leading to jamming and granulation, with increasing shear rate. It has been proposed that these effects result from inter particle friction, as lubrication forces are overcome. This suggests the jamming of concentrated colloidal suspensions should exhibit some shared phenomenology with macroscopic granular systems where friction leads to two different types of jammed state. Here we show that transient rheological measurements can be used to probe the processes of granulation in concentrated colloidal suspensions. Our results support the idea that frictional contacts are created between jammed particles. The jamming behaviour displays two qualitatively different regimes separated by a critical strain rate with qualitatively different types of fracture/break up behaviour. In the lower strain rate regime, it is found that vibrations can be used to control jamming and granulation, resulting in a flowable fluid.
Distribution of Cenozoic plant relicts in China explained by drought in dry season
Authors: Huang Yongjiang , Jacques Frédéric M. B. , Su Tao , Ferguson David K. , Tang Hui , Chen Wenyun , Zhou Zhekun 
Published: September 2015

AbstractCenozoic plant relicts are those groups that were once widespread in the Northern Hemisphere but are now restricted to some small isolated areas as a result of drastic climatic changes. They are good proxies to study how plants respond to climatic changes since their modern climatic requirements are known. Herein we look at the modern distribution of 65 palaeoendemic genera in China and compare it with the Chinese climatic pattern, in order to find a link between the plant distribution and climate. Central China and Taiwan Island are shown to be diversity centres of Cenozoic relict genera, consistent with the fact that these two regions have a shorter dry season with comparatively humid autumn and spring in China. Species distribution models indicate that the precipitation parameters are the most important variables to explain the distribution of relict genera. The Cenozoic wide-scale distribution of relict plants in the Northern Hemisphere is therefore considered to be linked to the widespread humid climate at that time and the subsequent contraction of their distributional ranges was probably caused by the drying trend along with global cooling.
Delayed emergence of behavioral and electrophysiological effects following juvenile ketamine exposure in mice
Authors: Nagy L R , Featherstone R E , Hahn C G , Siegel S J 
Published: September 2015

AbstractFrequent ketamine abuse in adulthood correlates with increased risk of psychosis, as well as cognitive deficits, including disruption of higher-order executive function and memory formation. Although the primary abusers of ketamine are adolescents and young adults, few studies have evaluated its effects on juvenile cognition. Therefore, the current study analyzes the effect of adolescent ketamine exposure on cognitive development. Juvenile mice (4 weeks of age) were exposed to chronic ketamine (20 mg kg−1, i.p. daily) for 14 days. Mice were tested immediately after exposure in the juvenile period (7 weeks of age) and again as adults (12 weeks of age). Measures included electroencephalography (EEG) in response to auditory stimulation, the social choice test, and a 6-arm radial water maze task. Outcome measures include low-frequency EEG responses, event-related potential (ERP) amplitudes, indices of social behavior and indices of spatial working memory. Juvenile exposure to ketamine was associated with electrophysiological abnormalities in adulthood, particularly in induced theta power and the P80 ERP. The social choice test revealed that ketamine-exposed mice failed to exhibit the same age-related decrease in social interaction time as controls. Ketamine-exposed mice outperformed control mice as juveniles on the radial water maze task, but did not show the same age-related improvement as adult controls. These data support the hypothesis that juvenile exposure to ketamine produces long-lasting changes in brain function that are characterized by a failure to progress along normal developmental trajectories.
Orphan nuclear receptor oestrogen-related receptor γ (ERRγ) plays a key role in hepatic cannabinoid receptor type 1-mediated induction of CYP7A1 gene expression
Authors: Zhang Yaochen , Kim Don-Kyu , Lee Ji-Min , Park Seung Bum , Jeong Won-IL , Kim Seong Heon , Lee In-Kyu , Lee Chul-Ho , Chiang John Y.L. , Choi Hueng-Sik 
Published: September 2015

Bile acids are primarily synthesized from cholesterol in the liver and have important roles in dietary lipid absorption and cholesterol homoeostasis. Detailed roles of the orphan nuclear receptors regulating cholesterol 7α-hydroxylase (CYP7A1), the rate-limiting enzyme in bile acid synthesis, have not yet been fully elucidated. In the present study, we report that oestrogen-related receptor γ (ERRγ) is a novel transcriptional regulator of CYP7A1 expression. Activation of cannabinoid receptor type 1 (CB1 receptor) signalling induced ERRγ-mediated transcription of the CYP7A1 gene. Overexpression of ERRγ increased CYP7A1 expression in vitro and in vivo, whereas knockdown of ERRγ attenuated CYP7A1 expression. Deletion analysis of the CYP7A1 gene promoter and a ChIP assay revealed an ERRγ-binding site on the CYP7A1 gene promoter. Small heterodimer partner (SHP) inhibited the transcriptional activity of ERRγ and thus regulated CYP7A1 expression. Overexpression of ERRγ led to increased bile acid levels, whereas an inverse agonist of ERRγ, GSK5182, reduced CYP7A1 expression and bile acid synthesis. Finally, GSK5182 significantly reduced hepatic CB1 receptor-mediated induction of CYP7A1 expression and bile acid synthesis in alcohol-treated mice. These results provide the molecular mechanism linking ERRγ and bile acid metabolism.
Increased ubiquitination and reduced plasma membrane trafficking of placental amino acid transporter SNAT-2 in human IUGR
Authors: Chen Yi-Yung , Rosario Fredrick J. , Shehab Majida Abu , Powell Theresa L. , Gupta Madhulika B. , Jansson Thomas 
Published: September 2015

Placental amino acid transport is decreased in intrauterine growth restriction (IUGR); however, the underlying mechanisms remain largely unknown. We have shown that mechanistic target of rapamycin (mTOR) signalling regulates system A amino acid transport by modulating the ubiquitination and plasma membrane trafficking of sodium-coupled neutral amino acid transporter 2 (SNAT-2) in cultured primary human trophoblast cells. We hypothesize that IUGR is associated with (1) inhibition of placental mTORC1 and mTORC2 signalling pathways, (2) increased amino acid transporter ubiquitination in placental homogenates and (3) decreased protein expression of SNAT-2 in the syncytiotrophoblast microvillous plasma membrane (MVM). To test this hypothesis, we collected placental tissue and isolated MVM from women with pregnancies complicated by IUGR (n=25) and gestational age-matched women with appropriately grown control infants (n=19, birth weights between the twenty-fifth to seventy-fifth percentiles). The activity of mTORC1 and mTORC2 was decreased whereas the protein expression of the ubiquitin ligase NEDD4-2 (neural precursor cell expressed developmentally down-regulated protein 4-2; +72%, P&lt;0.0001) and the ubiquitination of SNAT-2 (+180%, P&lt;0.05) were increased in homogenates of IUGR placentas. Furthermore, IUGR was associated with decreased system A amino acid transport activity (–72%, P&lt;0.0001) and SNAT-1 (–42%, P&lt;0.05) and SNAT-2 (–31%, P&lt;0.05) protein expression in MVM. In summary, these findings are consistent with the possibility that decreased placental mTOR activity causes down-regulation of placental system A activity by shifting SNAT-2 trafficking towards proteasomal degradation, thereby contributing to decreased fetal amino acid availability and restricted fetal growth in IUGR.
Backward multiple imputation estimation of the conditional lifetime expectancy function with application to censored human longevity data
Authors: Kong Jing , Klein Barbara E. K. , Klein Ronald , Wahba Grace 
Published: September 2015

SignificanceThe expected lifetime of a subject given survival past a certain time, denoted as lifetime expectancy, is often estimated in the data context with right censoring, which is a form of missing data problem commonly arising in biomedical applications, e.g., clinical trials, meaning that time-to-event is observed only if it occurs prior to some prespecified time. We report an advanced and more flexible method where users are free to choose a base model to estimate lifetime expectancy by imputing the right-censored times in backward order to address data “missingness.” We use this innovative tool to explore the interesting and important issue of human aging providing individual attributes including gender, smoking, body mass index, socioeconomic status, and diseases.
Sustaining the world's large marine ecosystems
Authors: Sherman Kenneth 
Published: September 2015

Abstract
In this essay, I review nearly six decades of a career in marine science and fisheries considering scientific contributions, successes, failures, and changes in my field of practice. My body of work has been in plankton research to support fisheries assessments, and in ecosystems programme development and implementation. I describe my early studies on Pacific plankton oceanography in relation to fisheries assessment, and subsequent studies of plankton oceanography and fisheries in relation to coastal ocean fisheries and management. Early in my career, realizing that applications of my published results and those of other fisheries ecologists were generally not included in fish stock assessments, I participated in a national planning group that introduced a system for marine resources monitoring, assessment, and prediction (MARMAP) that included primary productivity, ichthyoplankton, zooplankton, and oceanographic assessments as important components for large-scale fisheries ecology assessment. I joined with European colleagues in ICES to advance fisheries ecology studies in fish stock assessments in the 1970s and 1980s. In 1983, I conceived with Professor Lewis Alexander of the University of Rhode Island a system for assessing and managing marine resources within the spatial domain of ecologically delineated large marine ecosystems (LMEs). On behalf of the National Oceanic and Atmospheric Administration, and in partnership with developing countries, international financial organizations, UN agencies, and NGOs, I am currently contributing scientific and technical advice to a global network of assessment and management projects in 22 LMEs with 110 developing countries and $3.1 billion in financial support. The participating countries are applying a modular framework of natural science and social science indicators for assessing the changing states of LMEs. I conclude the essay with a retrospective viewpoint on my career and changes over half a century of practicing the application of marine science in relation to sustaining the goods and services of the ocean Commons.
Open Globe Injuries Presenting With Normal or High Intraocular Pressure
Authors: Margo Jordan A. , Feldman Samantha , Addis Hampton , Bodanapally Uttam K. , Ellish Nancy , Saeedi Osamah 
Published: September 2015

Objectives:
To determine the frequency, clinical characteristics, and visual outcomes of patients who present with high or normal intraocular pressure (IOP) and open globe injuries.

Design:
Retrospective chart review.

Setting:
University of Maryland Medical Center, a level 1 trauma center.

Patient or Study Population:
All cases of open globe injury presenting to The University of Maryland Medical Center from July 2005 to January 2014.

Observation:
Demographics, initial physical examination, computed tomography findings, IOP of the affected and unaffected eyes, and follow-up evaluations.

Main Outcome Measures:
(1) IOP 10 mm Hg or greater and (2) visual acuity.

Results:
Of 132 eyes presenting with open globe injury, IOP was recorded in 38 (28%). Mean IOP for the affected and unaffected eyes was 14±10.3 mm Hg and 16.6±4.1 mm Hg, respectively. Twenty-three (59.4%) eyes had IOP greater than 10 mm Hg. Six eyes (16.2%) had IOP greater than 21 mm Hg. Using bivariate analysis, IOP greater than 10 mm Hg was associated with posterior open globe injury (P=0.01), posterior hemorrhage (P=0.04), and intraconal retrobulbar hemorrhage (P=0.05). Adjusting for age, sex, and race, IOP greater than 10 mm Hg was associated with the presence of posterior open globe injury on clinical examination (P=0.04). Higher presenting IOP was found to predict light perception or worse vision (P=0.01). Multivariate analysis showed that poor presenting vision was the best predictor of poor final vision (P<0.01).

Conclusions:
High IOP does not exclude open globe injury. It is a frequent finding in patients with open globe injuries and may be associated with posterior injury and poor visual prognosis.