bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of Simulated Microgravity on Cytoskeleton and Viscoelastic Properties of Endothelial Cell
Authors: Janmaleki M. , Pachenari M. , Seyedpour S. M. , Shahghadami R. , Sanati-Nezhad A. 
Published: September 2016

AbstractThis study focused on the effects of simulated microgravity (s-μg) on mechanical properties, major cytoskeleton biopolymers, and morphology of endothelial cells (ECs). The structural and functional integrity of ECs are vital to regulate vascular homeostasis and prevent atherosclerosis. Furthermore, these highly gravity sensitive cells play a key role in pathogenesis of many diseases. In this research, impacts of s-μg on mechanical behavior of human umbilical vein endothelial cells were investigated by utilizing a three-dimensional random positioning machine (3D-RPM). Results revealed a considerable drop in cell stiffness and viscosity after 24 hrs of being subjected to weightlessness. Cortical rigidity experienced relatively immediate and significant decline comparing to the stiffness of whole cell body. The cells became rounded in morphology while western blot analysis showed reduction of the main cytoskeletal components. Moreover, fluorescence staining confirmed disorganization of both actin filaments and microtubules (MTs). The results were compared statistically among test and control groups and it was concluded that s-μg led to a significant alteration in mechanical behavior of ECs due to remodeling of cell cytoskeleton.
Co-expression of LASS2 and TGF-β1 predicts poor prognosis in hepatocellular carcinoma
Authors: Ruan Haoyu , Wang Ting , Yang Chen , Jin Guangzhi , Gu Dishui , Deng Xuan , Wang Cun , Qin Wenxin , Jin Haojie 
Published: September 2016

AbstractLongevity assurance homolog 2 of yeast LAG1 (LASS2) has been reported to act as an important tumor suppressor in the development of human cancers. However, little is known about the prognostic value of LASS2 in hepatocellular carcinoma (HCC) . In the present study, we analyzed correlation between LASS2 and TGF-β1 levels, and evaluated their prognostic values in HCC patients. We first analyzed the expression of LASS2 and TGF-β1 in two independent cohorts (test cohort: 184 HCC patients; validation cohort: 118 HCC patients) using immunohistochemistry (IHC). Kaplan-Meier survival and Cox regression analyses were executed to evaluate the prognosis of HCC. The results of IHC analysis revealed a positive correlation between the expression of LASS2 and TGF-β1. HCC Patients with low expression of LASS2 and TGF-β1 had shorter overall survival (OS) and time to recurrence (TTR) than patients with high expression of LASS2 and TGF-β1. Furthermore, combination of LASS2 and TGF-β1 was an independent and significant risk factor for OS and TTR. In conclusion, low expression of LASS2 and TGF-β1 contributes to the aggressiveness and poor prognosis of HCC, and may represent a novel prognostic biomarker for HCC patients.
Longitudinal in vivo MRI in a Huntington’s disease mouse model: Global atrophy in the absence of white matter microstructural damage
Authors: Steventon Jessica J. , Trueman Rebecca C. , Ma Da , Yhnell Emma , Bayram-Weston Zubeyde , Modat Marc , Cardoso Jorge , Ourselin Sebastian , Lythgoe Mark , Stewart Andrew , Rosser Anne E. , Jones Derek K. 
Published: September 2016

AbstractHuntington’s disease (HD) is a genetically-determined neurodegenerative disease. Characterising neuropathology in mouse models of HD is commonly restricted to cross-sectional ex vivo analyses, beset by tissue fixation issues. In vivo longitudinal magnetic resonance imaging (MRI) allows for disease progression to be probed non-invasively. In the HdhQ150 mouse model of HD, in vivo MRI was employed at two time points, before and after the onset of motor signs, to assess brain macrostructure and white matter microstructure. Ex vivo MRI, immunohistochemistry, transmission electron microscopy and behavioural testing were also conducted. Global brain atrophy was found in HdhQ150 mice at both time points, with no neuropathological progression across time and a selective sparing of the cerebellum. In contrast, no white matter abnormalities were detected from the MRI images or electron microscopy images alike. The relationship between motor function and MR-based structural measurements was different for the HdhQ150 and wild-type mice, although there was no relationship between motor deficits and histopathology. Widespread neuropathology prior to symptom onset is consistent with patient studies, whereas the absence of white matter abnormalities conflicts with patient data. The myriad reasons for this inconsistency require further attention to improve the translatability from mouse models of disease.
Location and Visualization of Working p-n and/or n-p Junctions by XPS
Authors: Copuroglu Mehmet , Caliskan Deniz , Sezen Hikmet , Ozbay Ekmel , Suzer Sefik 
Published: September 2016

AbstractX-ray photoelectron spectroscopy (XPS) is used to follow some of the electrical properties of a segmented silicon photodetector, fabricated in a p-n-p configuration, during operation under various biasing configurations. Mapping of the binding energy position of Si2p reveals the shift in the position of the junctions with respect to the polarity of the DC bias applied. Use of squared and triangular shaped wave excitations, while recording XPS data, allows tapping different electrical properties of the device under normal operational conditions, as well as after exposing parts of it to harsh physical and chemical treatments. Unique and chemically specific electrical information can be gained with this noninvasive approach which can be useful especially for localized device characterization and failure analyses.
FolR1: a novel cell surface marker for isolating midbrain dopamine neural progenitors and nascent dopamine neurons
Authors: Gennet Nicole , Tamburini Claudia , Nan Xinsheng , Li Meng 
Published: September 2016

AbstractCell type-specific surface markers offer a powerful tool for purifying defined cell types for restorative therapies and drug screenings. Midbrain dopaminergic neurons (mesDA) are the nerve cells preferentially lost in the brains of Parkinson’s disease patients. Clinical trials of transplantation of fetal neural precursors suggest that cell therapy may offer a cure for this devastating neurological disease. Many lines of preclinical studies demonstrate that neural progenitors committed to dopaminergic fate survive and integrate better than postmitotic DA neurons. We show that the folate-receptor 1 (FolR1), a GPI-anchored cell surface molecule, specifically marks mesDA neural progenitors and immature mesDA neurons. FolR1 expression superimposes with Lmx1a, a bona-fide mesDA lineage marker, during the active phase of mesDA neurogenesis from E9.5 to E14.5 during mouse development, as well as in ESC-derived mesDA lineage. FolR1+ neural progenitors can be isolated by FACS or magnetic sorting (MAC) which give rise to dopamine neurons expressing TH and Pitx3, whilst FolR1 negative cells generate non-dopaminergic neurons and glia cells. This study identifies FolR1 as a new cell surface marker selectively expressed in mesDA progenitors in vivo and in vitro and that can be used to enrich in vitro differentiated TH neurons.
The Na+/Ca2+, K+ exchanger 2 modulates mammalian cone phototransduction
Authors: Sakurai Keisuke , Vinberg Frans , Wang Tian , Chen Jeannie , Kefalov Vladimir J. 
Published: September 2016

AbstractCalcium ions (Ca2+) modulate the phototransduction cascade of vertebrate cone photoreceptors to tune gain, inactivation, and light adaptation. In darkness, the continuous current entering the cone outer segment through cGMP-gated (CNG) channels is carried in part by Ca2+, which is then extruded back to the extracellular space. The mechanism of Ca2+extrusion from mammalian cones is not understood. The dominant view has been that the cone-specific isoform of the Na+/Ca2+, K+exchanger, NCKX2, is responsible for removing Ca2+from their outer segments. However, indirect evaluation of cone function in NCKX2-deficient (Nckx2−/−) mice by electroretinogram recordings revealed normal photopic b-wave responses. This unexpected result suggested that NCKX2 may not be involved in the Ca2+homeostasis of mammalian cones. To address this controversy, we examined the expression of NCKX2 in mouse cones and performed transretinal recordings fromNckx2−/−mice to determine the effect of NCKX2 deletion on cone function directly. We found thatNckx2−/−cones exhibit compromised phototransduction inactivation, slower response recovery and delayed background adaptation. We conclude that NCKX2 is required for the maintenance of efficient Ca2+extrusion from mouse cones. However, surprisingly,Nckx2−/−cones adapted normally in steady background light, indicating the existence of additional Ca2+-extruding mechanisms in mammalian cones.
Describing synchronization and topological excitations in arrays of magnetic spin torque oscillators through the Kuramoto model
Authors: Flovik Vegard , Macià Ferran , Wahlström Erik 
Published: September 2016

AbstractThe collective dynamics in populations of magnetic spin torque oscillators (STO) is an intensely studied topic in modern magnetism. Here, we show that arrays of STO coupled via dipolar fields can be modeled using a variant of the Kuramoto model, a well-known mathematical model in non-linear dynamics. By investigating the collective dynamics in arrays of STO we find that the synchronization in such systems is a finite size effect and show that the critical coupling—for a complete synchronized state—scales with the number of oscillators. Using realistic values of the dipolar coupling strength between STO we show that this imposes an upper limit for the maximum number of oscillators that can be synchronized. Further, we show that the lack of long range order is associated with the formation of topological defects in the phase field similar to the two-dimensional XY model of ferromagnetism. Our results shed new light on the synchronization of STO, where controlling the mutual synchronization of several oscillators is considered crucial for applications.
A role of CB1R in inducing θ-rhythm coordination between the gustatory and gastrointestinal insula
Authors: Kang Youngnam , Sato Hajime , Saito Mitsuru , Yin Dong Xu , Park Sook Kyung , Oh Seog Bae , Bae Yong Chul , Toyoda Hiroki 
Published: September 2016

AbstractAnandamide (AEA) and N-oleoylethanolamine (OEA) are produced in the intestine and brain during fasting and satiety, respectively. Subsequently, AEA facilitates food intake via activation of cannabinoid type-1 receptors (CB1Rs) while OEA decreases food intake via activation of peroxisome proliferator-activated receptor-α (PPARα) and/or G-protein-coupled receptor 119 (GPR119). Neuronal activity in the gastrointestinal region of the autonomic insula (GI-Au-I) that rostrally adjoins the gustatory insula (Gu-I) increases during fasting, enhancing appetite while umami and sweet taste sensations in Gu-I enhances appetite in GI-Au-I, strongly suggesting the presence of a neural interaction between the Gu-I and GI-Au-I which changes depending on the concentrations of AEA and OEA. However, this possibility has never been investigated. In rat slice preparations, we demonstrate with voltage-sensitive dye imaging that activation of CB1Rs by AEA induces θ-rhythm oscillatory synchronization in the Gu-I which propagates into the GI-Au-I but stops at its caudal end, displaying an oscillatory coordination. The AEA-induced oscillation was abolished by a CB1R antagonist or OEA through activation of GPR119. Our results demonstrate that the neural coordination between the Gu-I and GI-Au-I is generated or suppressed by the opposing activities between CB1R and GPR119. This mechanism may be involved in the feeding behavior based on taste recognition.
Purple foliage coloration in tea (Camellia sinensis L.) arises from activation of the R2R3-MYB transcription factor CsAN1
Authors: Sun Binmei , Zhu Zhangsheng , Cao Panrong , Chen Hao , Chen Changming , Zhou Xin , Mao Yanhui , Lei Jianjun , Jiang Yanpin , Meng Wei , Wang Yingxi , Liu Shaoqun 
Published: September 2016

AbstractPurple foliage always appears in Camellia sinensis families; however, the transcriptional regulation of anthocyanin biosynthesis is unknown. The tea bud sport cultivar ‘Zijuan’ confers an abnormal pattern of anthocyanin accumulation, resulting in a mutant phenotype that has a striking purple color in young foliage and in the stem. In this study, we aimed to unravel the underlying molecular mechanism of anthocyanin biosynthetic regulation in C. sinensis. Our results revealed that activation of the R2R3-MYB transcription factor (TF) anthocyanin1 (CsAN1) specifically upregulated the bHLH TF CsGL3 and anthocyanin late biosynthetic genes (LBGs) to confer ectopic accumulation of pigment in purple tea. We found CsAN1 interacts with bHLH TFs (CsGL3 and CsEGL3) and recruits a WD-repeat protein CsTTG1 to form the MYB-bHLH-WDR (MBW) complex that regulates anthocyanin accumulation. We determined that the hypomethylation of a CpG island in the CsAN1 promoter is associated with the purple phenotype. Furthermore, we demonstrated that low temperature and long illumination induced CsAN1 promoter demethylation, resulting in upregulated expression to promote anthocyanin accumulation in the foliage. The successful isolation of CsAN1 provides important information on the regulatory control of anthocyanin biosynthesis in C. sinensis and offers a genetic resource for the development of new varieties with enhanced anthocyanin content.
Network analysis reveals common host protein/s modulating pathogenesis of neurotropic viruses
Authors: Ghosh Sourish , Mukherjee Sriparna , Sengupta Nabonita , Roy Arunava , Dey Dhritiman , Chakraborty Surajit , Chattopadhyay Dhrubajyoti , Banerjee Arpan , Basu Anirban 
Published: September 2016

AbstractNetwork analysis through graph theory provides a quantitative approach to characterize specific proteins and their constituent assemblies that underlie host-pathogen interactions. In the present study, graph theory was used to analyze the interactome designed out of 50 differentially expressing proteins from proteomic analysis of Chandipura Virus (CHPV, Family: Rhabdoviridae) infected mouse brain tissue to identify the primary candidates for intervention. Using the measure of degree centrality, that quantifies the connectedness of a single protein within a milieu of several other interacting proteins, DJ-1 was selected for further molecular validation. To elucidate the generality of DJ-1’s role in propagating infection its role was also monitored in another RNA virus, Japanese Encephalitis Virus (JEV, Family: Flaviviridae) infection. Concurrently, DJ-1 got over-expressed in response to reactive oxygen species (ROS) generation following viral infection which in the early phase of infection migrated to mitochondria to remove dysfunctional mitochondria through the process of mitophagy. DJ-1 was also observed to modulate the viral replication and interferon responses along with low-density lipoprotein (LDL) receptor expression in neurons. Collectively these evidences reveal a comprehensive role for DJ-1 in neurotropic virus infection in the brain.
One-pot synthesis of (−)-Ambrox
Authors: Yang Shaoxiang , Tian Hongyu , Sun Baoguo , Liu Yongguo , Hao Yanfeng , Lv Yanyu 
Published: September 2016

Abstract(−)-Ambrox is recognised as the prototype of all ambergris odorants. Widely used in perfumery, (−)-Ambrox is an important ingredient due to its unique scent and excellent fixative function. An environmentally friendly and practical preparation of (−)-Ambrox is still unavailable at present although a lot of attention has been paid to this hot research topic for many years. A one-pot synthesis of (−)-Ambrox was studied starting from (−)-sclareol through oxidation with hydrogen peroxide in the presence of a quaternary ammonium phosphomolybdate catalyst {[C5H5NC16H33] [H2PMo12O40]}, which gave the product a 20% overall yield.
Acute trauma induced disc displacement without reduction and its sequelae
Authors: He DongMei , Yang XiuJuan , Wang FeiYu , Yang Chi , Dong MinJun 
Published: September 2016

AbstractAcute traumatic temporomandibular joint disc displacement (ATDD) and its sequelae are not familiar for most surgeons. This study is to discuss its sequelae in cases without disc reduction after failed conservative treatment. From 2010 to 2015, 26 patients with 34 joints were included in the study. All patients had at least 3 months conservative treatment. Their maximal incisor opening (MIO) was measured during follow-ups and MRI examination was used to check the condylar bone degeneration. The mean follow-up for conservative treatment after admission was 8.69 months, the patients reached an average of 25.7 mm MIO. MRI showed condylar bone intact in 8 joints (23.5%), condylar surface bone destruction (Wilks IV, V stages) in 14 joints (41.2%), and severe bone resorption in 12 joints (35.3%). 15 patients with 23 joints were asked for surgical treatment after a mean conservative treatment of 5.4 months (3–12 months) to improve mouth opening and relieve chronic pain. 12 joints had total joint replacement (TJR). 11 joints had disc repositioning. Their mean MIO before operation was 19.8 mm and significantly improved to 33.9 mm after operation (p = 0.0000). ATDD may cause severe osteoarthritis or ankylosis. Disc repositioning and TJR could significantly improve MIO.
OX40 regulates pressure overload-induced cardiac hypertrophy and remodelling via CD4+ T-cells
Authors: Wu Qing-Qing , Yuan Yuan , Jiang Xiao-Han , Xiao Yang , Yang Zheng , Ma Zhen-Guo , Liao Hai-Han , Liu Yuan , Chang Wei , Bian Zhou-Yan , Tang Qi-Zhu 
Published: September 2016

OX40, which belongs to the tumour necrosis factor (TNF)-receptor family, is a costimulatory receptor that can potentiate T-cell receptor signalling on the surface of T-lymphocytes. The role of OX40 in non-immune systems, particularly the cardiovascular system, has not been defined. In the present study, we observed a noticeable increase in OX40 expression during cardiac remodelling in rodent heart. In the present study, cardiac hypertrophy was induced by aortic banding (AB) in OX40 knockout (KO) mice and wild-type (WT) mice. After 8 weeks, the OX40 KO mice showed significantly attenuated cardiac hypertrophy, fibrosis and inflammation as well as preserved cardiac function compared with the WT mice. Follow-up in vitro studies suggested that CD4+ T-lymphocyte proliferation and pro-inflammatory cytokine release were significantly decreased, whereas anti-inflammatory cytokine release was considerably increased in OX40 KO mice compared with WT mice as assessed by Cell Counting Kit-8 (CCK-8) assay and ELISA. Co-culturing neonatal rat cardiomyocytes with the activated supernatant of CD4+ T-lymphocytes from OX40 KO mice reduced the hypertrophy response. Interestingly, OX40 KO mice with reconstituted CD4+ T-lymphocytes presented deteriorated cardiac remodelling. Collectively, our data indicate that OX40 regulates cardiac remodelling via the modulation of CD4+ T-lymphocytes.
DNA and RNA topoisomerase activities of Top3β are promoted by mediator protein Tudor domain-containing protein 3
Authors: Siaw Grace Ee-Lu , Liu I-Fen , Lin Po-Yen , Been Michael D. , Hsieh Tao-shih 
Published: September 2016

Significance
Tudor domain-containing protein 3 (TDRD3), a multidomain scaffold protein functions as an epigenetic reader on nuclear chromatin and binds with fragile X mental retardation protein on mRNA. It forms a conserved complex with topoisomerase 3β (Top3β), a type IA topoisomerase, and participates in both transcription and translation. The mechanism of how TDRD3 acts as Top3β’s partner in regulating these cellular processes is unknown. Here, we demonstrated that TDRD3 is able to stimulate Top3β’s DNA and RNA topoisomerase catalytic activities, through binding and stabilizing single-stranded regions in DNA and RNA substrates. Because these regions are the preferred site for Top3β, TDRD3 therefore acts as a regulator to provide access of the enzyme to these nucleic acid substrates and to act upon them.
Stability of the solution of stochastic differential equation driven by time-changed Lévy noise
Authors: Nane Erkan , Ni Yinan 
Published: September 2016

This paper studies stabilities of the solution of stochastic differential equations (SDE) driven by time-changed Lévy noise in both probability and moment sense. This provides more flexibility in modeling schemes in application areas including physics, biology, engineering, finance and hydrology. Necessary conditions for the solution of time-changed SDE to be stable in different senses will be established. The connection between stability of the solution to time-changed SDE and that to corresponding original SDE will be disclosed. Examples related to different stabilities will be given. We study SDEs with time-changed Lévy noise, where the time-change processes are the inverse of general Lévy subordinators. These results are an important generalization of the results of Q. Wu (2016).
DeepChrome: deep-learning for predicting gene expression from histone modifications
Authors: Singh Ritambhara , Lanchantin Jack , Robins Gabriel , Qi Yanjun 
Published: September 2016

Abstract

Motivation
Histone modifications are among the most important factors that control gene regulation. Computational methods that predict gene expression from histone modification signals are highly desirable for understanding their combinatorial effects in gene regulation. This knowledge can help in developing ‘epigenetic drugs’ for diseases like cancer. Previous studies for quantifying the relationship between histone modifications and gene expression levels either failed to capture combinatorial effects or relied on multiple methods that separate predictions and combinatorial analysis. This paper develops a unified discriminative framework using a deep convolutional neural network to classify gene expression using histone modification data as input. Our system, called DeepChrome, allows automatic extraction of complex interactions among important features. To simultaneously visualize the combinatorial interactions among histone modifications, we propose a novel optimization-based technique that generates feature pattern maps from the learnt deep model. This provides an intuitive description of underlying epigenetic mechanisms that regulate genes.

Results
We show that DeepChrome outperforms state-of-the-art models like Support Vector Machines and Random Forests for gene expression classification task on 56 different cell-types from REMC database. The output of our visualization technique not only validates the previous observations but also allows novel insights about combinatorial interactions among histone modification marks, some of which have recently been observed by experimental studies.

Availability and Implementation
Codes and results are available at www.deepchrome.org

Contact
yanjun@virginia.edu

Supplementary information
Supplementary data are available at Bioinformatics online.