bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of microRNA and Gene Expression Profiles in Alzheimer’s Disease: A Meta-Analysis Approach
Authors: Moradifard Shirin , Hoseinbeyki Moslem , Ganji Shahla Mohammad , Minuchehr Zarrin 
Published: March 2018

AbstractUnderstanding the molecular mechanisms underlying Alzheimer’s disease (AD) is necessary for the diagnosis and treatment of this neurodegenerative disorder. It is therefore important to detect the most important genes and miRNAs, which are associated with molecular events, and studying their interactions for recognition of AD mechanisms. Here we focus on the genes and miRNAs expression profile, which we have detected the miRNA target genes involved in AD. These are the most quintessential to find the most important miRNA, to target genes and their important pathways. A total of 179 differentially expressed miRNAs (DEmiRs) and 1404 differentially expressed genes (DEGs) were obtained from a comprehensive meta-analysis. Also, regions specific genes with their molecular function in AD have been demonstrated. We then focused on miRNAs which regulated most genes in AD, alongside we analyzed their pathways. The miRNA-30a-5p and miRNA-335 elicited a major function in AD after analyzing the regulatory network, we showed they were the most regulatory miRNAs in the AD. In conclusion, we demonstrated the most important genes, miRNAs, miRNA-mRNA interactions and their related pathways in AD using Bioinformatics methods. Accordingly, our defined genes and miRNAs could be used for future molecular studies in the context of AD.
Clinical and genetic characteristics of 251 consecutive patients with macular and cone/cone-rod dystrophy
Authors: Birtel Johannes , Eisenberger Tobias , Gliem Martin , Müller Philipp L. , Herrmann Philipp , Betz Christian , Zahnleiter Diana , Neuhaus Christine , Lenzner Steffen , Holz Frank G. , Mangold Elisabeth , Bolz Hanno J. , Charbel Issa Peter 
Published: March 2018

AbstractMacular and cone/cone-rod dystrophies (MD/CCRD) demonstrate a broad genetic and phenotypic heterogeneity, with retinal alterations solely or predominantly involving the central retina. Targeted next-generation sequencing (NGS) is an efficient diagnostic tool for identifying mutations in patient with retinitis pigmentosa, which shows similar genetic heterogeneity. To detect the genetic causes of disease in patients with MD/CCRD, we implemented a two-tier procedure consisting of Sanger sequencing and targeted NGS including genes associated with clinically overlapping conditions. Disease-causing mutations were identified in 74% of 251 consecutive MD/CCRD patients (33% of the variants were novel). Mutations in ABCA4, PRPH2 and BEST1 accounted for 57% of disease cases. Further mutations were identified in CDHR1, GUCY2D, PROM1, CRX, GUCA1A, CERKL, MT-TL1, KIF11, RP1L1, MERTK, RDH5, CDH3, C1QTNF5, CRB1, JAG1, DRAM2, POC1B, NPHP1 and RPGR. We provide detailed illustrations of rare phenotypes, including autofluorescence and optical coherence tomography imaging. Targeted NGS also identified six potential novel genotype-phenotype correlations for FAM161A, INPP5E, MERTK, FBLN5, SEMA4A and IMPDH1. Clinical reassessment of genetically unsolved patients revealed subgroups with similar retinal phenotype, indicating a common molecular disease cause in each subgroup.
Accelerated seed dispersal along linear disturbances in the Canadian oil sands region
Authors: Roberts David , Ciuti Simone , Barber Quinn E. , Willier Caitlin , Nielsen Scott E. 
Published: March 2018

AbstractHabitat fragmentation is typically seen as inhibiting movement via erosion in connectivity, although some patterns of early-phase disturbance, such as narrow linear disturbances in otherwise undisturbed forests, may actually facilitate the dispersal of certain species. Such features are common in Alberta’s oil sands region as legacies from seismic hydrocarbon exploration used to map oil reserves. Many of the ecological implications of these disturbances are unknown. Here, we investigate the effect of these forest dissections by experimentally testing dispersal patterns along seismic lines compared with adjacent forests using two proxy materials for wind-dispersed seeds, Typha latifolia seed and goose down feathers. We found that wind speeds were up to seven times higher and 95th percentile seed dispersal distances nearly four times farther on seismic lines compared with undisturbed forests and the corresponding effect of these features on seed dispersal distances can be substantial, potentially facilitating future changes in composition and ecological processes in boreal forests. This raises important considerations for native and invasive species, particularly in the context of climate change and the associated importance of seed movement and migration.
A Modular Microfluidic Device via Multimaterial 3D Printing for Emulsion Generation
Authors: Ji Qinglei , Zhang Jia Ming , Liu Ying , Li Xiying , Lv Pengyu , Jin Dongping , Duan Huiling 
Published: March 2018

Abstract3D-printing (3DP) technology has been developing rapidly. However, limited studies on the contribution of 3DP technology, especially multimaterial 3DP technology, to droplet-microfluidics have been reported. In this paper, multimaterial 3D-printed devices for the pneumatic control of emulsion generation have been reported. A 3D coaxial flexible channel with other rigid structures has been designed and printed monolithically. Numerical and experimental studies have demonstrated that this flexible channel can be excited by the air pressure and then deform in a controllable way, which can provide the active control of droplet generation. Furthermore, a novel modular microfluidic device for double emulsion generation has been designed and fabricated, which consists of three modules: function module, T-junction module, and co-flow module. The function module can be replaced by (1) Single-inlet module, (2) Pneumatic Control Unit (PCU) module and (3) Dual-inlet module. Different modules can be easily assembled for different double emulsion production. By using the PCU module, double emulsions with different number of inner droplets have been successfully produced without complicated operation of flow rates of different phases. By using single and dual inlet module, various double emulsions with different number of encapsulated droplets or encapsulated droplets with different compositions have been successfully produced, respectively.
Frataxin overexpression in Müller cells protects retinal ganglion cells in a mouse model of ischemia/reperfusion injury in vivo
Authors: Schultz Rowena , Krug Melanie , Precht Michel , Wohl Stefanie G. , Witte Otto W. , Schmeer Christian 
Published: March 2018

AbstractMüller cells are critical for retinal function and neuronal survival but can become detrimental in response to retinal ischemia and increased oxidative stress. Elevated oxidative stress increases expression of the mitochondrial enzyme frataxin in the retina, and its overexpression is neuroprotective after ischemia. Whether frataxin expression in Müller cells might improve their function and protect neurons after ischemia is unknown. The aim of this study was to evaluate the effect of frataxin overexpression in Müller cells on neuronal survival after retinal ischemia/reperfusion in the mouse in vivo. Retinal ischemia/reperfusion was induced in mice overexpressing frataxin in Müller cells by transient elevation of intraocular pressure. Retinal ganglion cells survival was determined 14 days after lesion. Expression of frataxin, antioxidant enzymes, growth factors and inflammation markers was determined with qRT-PCR, Western blotting and immunohistochemistry 24 hours after lesion. Following lesion, there was a 65% increase in the number of surviving RGCs in frataxin overexpressing mice. Improved survival was associated with increased expression of the antioxidant enzymes Gpx1 and Sod1 as well as the growth factors Cntf and Lif. Additionally, microglial activation was decreased in these mice. Therefore, support of Müller cell function constitutes a feasible approach to reduce neuronal degeneration after ischemia.
Self-assembling asymmetric peptide-dendrimer micelles – a platform for effective and versatile in vitro nucleic acid delivery
Authors: Kokil Ganesh R. , Veedu Rakesh N. , Le Bao Tri , Ramm Grant A. , Parekh Harendra S. 
Published: March 2018

AbstractDespite advancements in the development of high generation cationic-dendrimer systems for delivery of nucleic acid-based therapeutics, commercially available chemical agents suffer from major drawbacks such as cytotoxicity while being laborious and costly to synthesize. To overcome the aforementioned limitations, low-generation cationic peptide asymmetric dendrimers with side arm lipid (cholic and decanoic acid) conjugation were designed, synthesized and systematically screened for their ability to self-assemble into micelles using dynamic light scattering. Cytotoxicity profiling revealed that our entire asymmetric peptide dendrimer library when trialled alone, or as asymmetric dendrimer micelle-nucleic acid complexes, were non-cytotoxic across a broad concentration range. Further, the delivery efficiency of asymmetric peptide dendrimers in H-4-II-E (rat hepatoma), H2K (mdx mouse myoblast), and DAOY (human medulloblastoma) cells demonstrated that cholic acid-conjugated asymmetric dendrimers possess far superior delivery efficiency when compared to the commercial standards, Lipofectamine 2000 or Lipofectin®.
Non-equilibrium synergistic effects in atmospheric pressure plasmas
Authors: Guo Heng , Zhang Xiao-Ning , Chen Jian , Li He-Ping , Ostrikov Kostya 
Published: March 2018

AbstractNon-equilibrium is one of the important features of an atmospheric gas discharge plasma. It involves complicated physical-chemical processes and plays a key role in various actual plasma processing. In this report, a novel complete non-equilibrium model is developed to reveal the non-equilibrium synergistic effects for the atmospheric-pressure low-temperature plasmas (AP-LTPs). It combines a thermal-chemical non-equilibrium fluid model for the quasi-neutral plasma region and a simplified sheath model for the electrode sheath region. The free-burning argon arc is selected as a model system because both the electrical-thermal-chemical equilibrium and non-equilibrium regions are involved simultaneously in this arc plasma system. The modeling results indicate for the first time that it is the strong and synergistic interactions among the mass, momentum and energy transfer processes that determine the self-consistent non-equilibrium characteristics of the AP-LTPs. An energy transfer process related to the non-uniform spatial distributions of the electron-to-heavy-particle temperature ratio has also been discovered for the first time. It has a significant influence for self-consistently predicting the transition region between the “hot” and “cold” equilibrium regions of an AP-LTP system. The modeling results would provide an instructive guidance for predicting and possibly controlling the non-equilibrium particle-energy transportation process in various AP-LTPs in future.
Comparison of twelve liver functional reserve models for outcome prediction in patients with hepatocellular carcinoma undergoing surgical resection
Authors: Ho Shu-Yein , Liu Po-Hong , Hsu Chia-Yang , Hsia Cheng-Yuan , Su Chien-Wei , Lee Yun-Hsuan , Huang Yi-Hsiang , Lee Fa-Yauh , Hou Ming-Chih , Huo Teh-Ia 
Published: March 2018

AbstractVarious noninvasive liver functional reserve models have been proposed, but their prognostic ability in patients with hepatocellular carcinoma (HCC) is unclear. We aimed to investigate the performance of twelve noninvasive liver reserve models in HCC patients undergoing surgical resection. A total of 645 patients undergoing resection were prospectively identified and retrospectively analyzed. Tumor recurrence, overall survival, and independent prognostic factors were evaluated by the Cox proportional hazards model. Of the twelve models, the King’s score showed the highest homogeneity and lowest corrected Akaike information criterion (AICc) value, suggesting a better predictive ability for tumor recurrence. In multivariate Cox analysis, we confirmed that King’s score, tumor size and serum alpha-fetoprotein level were independent predictors associated with recurrence. In survival prediction, albumin-bilirubin (ALBI) revealed the highest homogeneity and lowest value among twelve invasive models, indicating a better prognostic performance. In the Cox model, ALBI grade, tumor burden, alpha-fetoprotein, vascular invasion, diabetes mellitus and performance status were independent predictors linked with overall survival. In summary, the currently used liver function models have differential predictive ability for HCC patients undergoing surgical resection. The King’s score is a feasible tool to predict tumor recurrence, whereas ALBI grade is a more robust model for prognostic prediction.
Evidence from EXAFS for Different Ta/Ti Site Occupancy in High Critical Current Density Nb3Sn Superconductor Wires
Authors: Heald Steve M. , Tarantini Chiara , Lee Peter J. , Brown Michael D. , Sung ZuHawn , Ghosh Arup K. , Larbalestier David C. 
Published: March 2018

AbstractTo meet critical current density, J
c
, targets for the Future Circular Collider (FCC), the planned replacement for the Large Hadron Collider (LHC), the high field performance of Nb3Sn must be improved, but champion J
c
values have remained static for the last 10 years. Making the A15 phase stoichiometric and enhancing the upper critical field H
c2
by Ti or Ta dopants are the standard strategies for enhancing high field performance but detailed recent studies show that even the best modern wires have broad composition ranges. To assess whether further improvement might be possible, we employed Extended X-ray Absorption Fine Structure (EXAFS) to determine the lattice site location of dopants in modern high-performance Nb3Sn strands with J
c
values amongst the best so far achieved. Although Ti and Ta primarily occupy the Nb sites in the A15 structure, we also find significant Ta occupancy on the Sn site. These findings indicate that the best performing Ti-doped stand is strongly sub-stoichiometric in Sn and that antisite disorder likely explains its high average H
c2
behavior. These new results suggest an important role for dopant and antisite disorder in minimizing superconducting property distributions and maximizing high field J
c
properties.
Mechanisms underlying the lack of endogenous processing and CLIP-mediated binding of the invariant chain by HLA-DP84Gly
Authors: Anczurowski Mark , Yamashita Yuki , Nakatsugawa Munehide , Ochi Toshiki , Kagoya Yuki , Guo Tingxi , Wang Chung-Hsi , Rahman Muhammed A. , Saso Kayoko , Butler Marcus O. , Hirano Naoto 
Published: March 2018

AbstractWhile the principles of classical antigen presentation via MHC class II are well-established, the mechanisms for the many routes of cross-presentation by which endogenous antigens become associated with class II molecules are not fully understood. We have recently demonstrated that the single amino acid polymorphism HLA-DPβ84Gly(DP84Gly) is critical to abrogate class II invariant chain associated peptide (CLIP) region-mediated binding of invariant chain (Ii) to DP, allowing endoplasmic reticulum (ER)-resident endogenous antigens to constitutively associate with DP84Glysuch as DP4. In this study, we demonstrate that both the CLIP and N-terminal non-CLIP Ii regions cooperatively generate an Ii conformation that cannot associate with DP84Glyvia the CLIP region. We also demonstrate the ability of DP4 to efficiently process and present antigens encoded in place of CLIP in a chimeric Ii, regardless of wild type Ii and HLA-DM expression. These data highlight the complex interplay between DP polymorphisms and the multiple Ii regions that cooperatively regulate this association, ultimately controlling the presentation of endogenous antigens on DP molecules. These results may also offer a mechanistic explanation for recent studies identifying the differential effects between DP84Glyand DP84Aspas clinically relevant in human disease.
Molecular Insights into the Interaction of RONS and Thieno[3,2-c]pyran Analogs with SIRT6/COX-2: A Molecular Dynamics Study
Authors: Yadav Dharmendra K. , Kumar Surendra , Saloni  , Misra Sanjeev , Yadav Lalit , Teli Mahesh , Sharma Praveen , Chaudhary Sandeep , Kumar Naresh , Choi Eun Ha , Kim Hyung Sik , Kim Mi-hyun 
Published: March 2018

AbstractSIRT6 and COX-2 are oncogenes target that promote the expression of proinflammatory and pro-survival proteins through a signaling pathway, which leads to increased survival and proliferation of tumor cells. However, COX-2 also suppresses skin tumorigenesis and their relationship with SIRT6, making it an interesting target for the discovery of drugs with anti-inflammatory and anti-cancer properties. Herein, we studied the interaction of thieno[3,2-c]pyran analogs and RONS species with SIRT6 and COX-2 through the use of molecular docking and molecular dynamic simulations. Molecular docking studies revealed the importance of hydrophobic and hydrophilic amino acid residues for the stability. The molecular dynamics study examined conformational changes in the enzymes caused by the binding of the substrates and how those changes affected the stability of the protein-drug complex. The average RMSD values of the backbone atoms in compounds 6 and 10 were calculated from 1000 ps to 10000 ps and were found to be 0.13 nm for both compounds. Similarly, the radius of gyration values for compounds 6 and 10 were found to be 1.87 ± 0.03 nm and 1.86 ± 0.02 nm, respectively. The work presented here, will be of great help in lead identification and optimization for early drug discovery.
The effects of crystalloid versus synthetic colloid in vitro on immune cells, co-cultured with mouse splenocytes
Authors: Lee Seung Hyun , Seo Eun-Hye , Park Hyun Jun , Oh Chung-Sik , Kim Cho Long , Park Sewon , Kim Seong-Hyop 
Published: March 2018

AbstractThis study assessed the effects of crystalloid versus synthetic colloid in vitro on immune cells co-cultured with mouse splenocytes. Mouse splenocytes were co-cultured with three different types of fluid: Plasma solution-A® (CJ HealthCare, Seoul, Korea; the crystalloid group); Tetraspan 6%® (B. Braun Medical, Melsungen, Germany; the Colloid-T group); and Volulyte 6%® (Fresenius Kabi, Bad Homburg vor dér-Höhe, Germany; Colloid-V group). To evaluate the acquired immune response, cluster of differentiation (CD) 4+ T cells and CD8+ T cells were measured. To evaluate the innate immune response, neutrophils were measured. The frequencies of CD4+ and CD8+ T cells did not differ significantly among the three groups on day 1 or 3. However, the frequencies of CD4+ and CD8+ T cells in the two synthetic colloid groups were significantly higher than those in the crystalloid group on day 7. On day 1, the frequency of neutrophils was significantly lower in the two synthetic colloid groups, compared with the crystalloid group. However, the values on the other days were similar among all three groups. In conclusion, crystalloid had a limited effect on the immune response; on the other hand, synthetic colloid increased the acquired immune response, although it temporarily inhibited the innate immune response.
Structural and magnetic properties of cobalt iron disulfide (CoxFe1−xS2) nanocrystals
Authors: Gabold Henrik , Luan Zhongyue , Paul Neelima , Opel Matthias , Müller-Buschbaum Peter , Law Matt , Paul Amitesh 
Published: March 2018

AbstractWe report on synthesis and investigation of nanocrystalline cobalt-iron-pyrites with an emphasis on nanocrystal structure, morphology and magnetic behavior. The nanocrystals (NCs) were 5–25 nm in diameter as characterized using scanning electron microscopy (SEM) and transmission electron microscopy (TEM). With an increase in Fe fraction, X-ray diffraction and small-angle-X-ray scattering (SAXS) showed a systematic decrease in lattice constant, primary grain/NC size (15 to 7 nm), and nanoparticle (NP) size (70 to 20 nm), respectively. The temperature dependence of the DC magnetization and AC susceptibility versus frequency revealed a number of magnetic phases in Co
x
Fe1−xS2. Samples with x = 1 and x = 0.875–0.625 showed evidence of superspin glass (SSG) behavior with embedded ferromagnetic (FM) clusters of NPs. For x = 0.5, samples retained their mixed phases, but showed superparamagnetic (SPM) behavior with antiferromagnetic clusters suppressing magnetic dipolar interactions. Below x = 0.5, the pyrites show increasing paramagnetic character. We construct a phase diagram, which can be understood in terms of competition between the various dipolar, exchange, inter- and intracluster interactions. Our results suggest that NC size and shape can be tuned to engineer spin-polarized ferromagnetism of n-doped iron pyrite.
Parallel opsin switches in multiple cone types of the starry flounder retina: tuning visual pigment composition for a demersal life style
Authors: Savelli Ilaria , Novales Flamarique Iñigo , Iwanicki Tom , Taylor John S. 
Published: March 2018

AbstractVariable expression of visual pigment proteins (opsins) in cone photoreceptors of the vertebrate retina is a primary determinant of vision plasticity. Switches in opsin expression or variable co-expression of opsins within differentiated cones have been documented for a few rodents and fishes, but the extent of photoreceptor types affected and potential functional significance are largely unknown. Here, we show that both single and double cones in the retina of a flatfish, the starry flounder (Platichthys stellatus), undergo visual pigment changes through opsin switches or variable opsin co-expression. As the post-metamorphic juvenile (i.e., the young asymmetric flatfish with both eyes on one side of the body) grows from ~5 g to ~196 g, some single cones and one member of unequal double cones switched from a visual pigment with maximum wavelength of absorbance, λmax, at shorter wavelengths (437 nm and 527 nm) to one with longer λmax (456 nm and 545 nm, respectively) whereas other cones had intermediate visual pigments (λmax at 445 nm or 536 nm) suggesting co-expression of two opsins. The shift toward longer wavelength absorbing visual pigments was in line with maximizing sensitivity to the restricted light spectrum at greater depths and achromatic detection of overhead targets.
Potential role of new molecular plasma signatures on cardiovascular risk stratification in asymptomatic individuals
Authors: Baldan-Martin Montserrat , Lopez Juan A. , Corbacho-Alonso Nerea , Martinez Paula J. , Rodriguez-Sanchez Elena , Mourino-Alvarez Laura , Sastre-Oliva Tamara , Martin-Rojas Tatiana , Rincón Raul , Calvo Eva , Vazquez Jesus , Vivanco Fernando , Padial Luis R. , Alvarez-Llamas Gloria , Ruiz-Hurtado Gema , Ruilope Luis M. , Barderas Maria G. 
Published: March 2018

AbstractThe evaluation of cardiovascular (CV) risk is based on equations derived from epidemiological data in individuals beyond the limits of middle age such as the Framingham and SCORE risk assessments. Lifetime Risk calculator (QRisk®), estimates CV risk throughout a subjects’ lifetime, allowing those. A more aggressive and earlier intervention to be identified and offered protection from the consequences of CV and renal disease. The search for molecular profiles in young people that allow a correct stratification of CV risk would be of great interest to adopt preventive therapeutic measures in individuals at high CV risk. To improve the selection of subjects susceptible to intervention with aged between 30–50 years, we have employed a multiple proteomic strategy to search for new markers of early CV disease or reported CV events and to evaluate their relationship with Lifetime Risk. Blood samples from 71 patients were classified into 3 groups according to their CV risk (healthy, with CV risk factors and with a previously reported CV event subjects) and they were analyzed using a high through quantitative proteomics approach. This strategy allowed three different proteomic signatures to be defined, two of which were related to CV stratification and the third one involved markers of organ damage.