bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ecotropic viral integration site 1 promotes metastasis independent of epithelial mesenchymal transition in colon cancer cells
Authors: Nayak Kasturi Bala , Sajitha I. S. , Kumar T. R. Santhosh , Chakraborty Soumen 
Published: January 2018

AbstractThe most indecipherable component of solid cancer is the development of metastasis which accounts for more than 90% of cancer-related mortalities. A developmental program termed epithelial-mesenchymal transition (EMT) has also been shown to play a critical role in promoting metastasis in epithelium-derived solid tumors. By analyzing publicly available microarray datasets, we observed that ecotropic viral integration site 1 (EVI1) correlates negatively with SLUG, a master regulator of EMT. This correlation was found to be relevant as we demonstrated that EVI1 binds to SLUG promoter element directly through the distal set of zinc fingers and downregulates its expression. Many studies have shown that the primary role of SLUG during EMT and EMT-like processes is the regulation of cell motility in most of the cancer cells. Knockdown of EVI1 in metastatic colon cancer cell and subsequent passage through matrigel not only increased the invading capacity but also induced an EMT-like morphological feature of the cells, such as spindle-shaped appearance and led to a significant reduction in the expression of the epithelial marker, E-CADHERIN and increase in the expression of the mesenchymal marker, N-CADHERIN. The cells, when injected into immunocompromised mice, failed to show any metastatic foci in distant organs however the ones with EVI1, metastasized in the intraperitoneal layer and also showed multiple micro metastatic foci in the lungs and spleen. These findings suggest that in colon cancer EVI1 is dispensable for epithelial-mesenchymal transition, however, is required for metastasis.
Raman spectroscopy of graphene under ultrafast laser excitation
Authors: Ferrante C. , Virga A. , Benfatto L. , Martinati M. , De Fazio D. , Sassi U. , Fasolato C. , Ott A. K. , Postorino P. , Yoon D. , Cerullo G. , Mauri F. , Ferrari A. C. , Scopigno T. 
Published: January 2018

AbstractThe equilibrium optical phonons of graphene are well characterized in terms of anharmonicity and electron–phonon interactions; however, their non-equilibrium properties in the presence of hot charge carriers are still not fully explored. Here we study the Raman spectrum of graphene under ultrafast laser excitation with 3 ps pulses, which trade off between impulsive stimulation and spectral resolution. We localize energy into hot carriers, generating non-equilibrium temperatures in the ~1700–3100 K range, far exceeding that of the phonon bath, while simultaneously detecting the Raman response. The linewidths of both G and 2D peaks show an increase as function of the electronic temperature. We explain this as a result of the Dirac cones’ broadening and electron–phonon scattering in the highly excited transient regime, important for the emerging field of graphene-based photonics and optoelectronics.
An integrated multi-layer 3D-fabrication of PDA/RGD coated graphene loaded PCL nanoscaffold for peripheral nerve restoration
Authors: Qian Yun , Zhao Xiaotian , Han Qixin , Chen Wei , Li Hui , Yuan Weien 
Published: January 2018

AbstractAs a conductive nanomaterial, graphene has huge potentials in nerve function restoration by promoting electrical signal transduction and metabolic activities with unique topological properties. Polydopamine (PDA) and arginylglycylaspartic acid (RGD) can improve cell adhesion in tissue engineering. Here we report an integrated 3D printing and layer-by-layer casting (LBLC) method in multi-layered porous scaffold fabrication. The scaffold is composed of single-layered graphene (SG) or multi-layered graphene (MG) and polycaprolactone (PCL). The electrically conductive 3D graphene scaffold can significantly improve neural expression both in vitro and in vivo. It promotes successful axonal regrowth and remyelination after peripheral nerve injury. These findings implicate that graphene-based nanotechnology have great potentials in peripheral nerve restoration in preclinical and clinical application.
Quantitative proteomics identifies redox switches for global translation modulation by mitochondrially produced reactive oxygen species
Authors: Topf Ulrike , Suppanz Ida , Samluk Lukasz , Wrobel Lidia , Böser Alexander , Sakowska Paulina , Knapp Bettina , Pietrzyk Martyna K. , Chacinska Agnieszka , Warscheid Bettina 
Published: January 2018

AbstractThe generation of reactive oxygen species (ROS) is inevitably linked to life. However, the precise role of ROS in signalling and specific targets is largely unknown. We perform a global proteomic analysis to delineate the yeast redoxome to a depth of more than 4,300 unique cysteine residues in over 2,200 proteins. Mapping of redox-active thiols in proteins exposed to exogenous or endogenous mitochondria-derived oxidative stress reveals ROS-sensitive sites in several components of the translation apparatus. Mitochondria are the major source of cellular ROS. We demonstrate that increased levels of intracellular ROS caused by dysfunctional mitochondria serve as a signal to attenuate global protein synthesis. Hence, we propose a universal mechanism that controls protein synthesis by inducing reversible changes in the translation machinery upon modulating the redox status of proteins involved in translation. This crosstalk between mitochondria and protein synthesis may have an important contribution to pathologies caused by dysfunctional mitochondria.
Functional genomics study of acute heat stress response in the small yellow follicles of layer-type chickens
Authors: Cheng Chuen-Yu , Tu Wei-Lin , Chen Chao-Jung , Chan Hong-Lin , Chen Chih-Feng , Chen Hsin-Hsin , Tang Pin-Chi , Lee Yen-Pai , Chen Shuen-Ei , Huang San-Yuan 
Published: January 2018

AbstractThis study investigated global gene and protein expression in the small yellow follicle (SYF; 6–8 mm in diameter) tissues of chickens in response to acute heat stress. Twelve 30-week-old layer-type hens were divided into four groups: control hens were maintained at 25 °C while treatment hens were subjected to acute heat stress at 36 °C for 4 h without recovery, with 2-h recovery, and with 6-h recovery. SYFs were collected at each time point for mRNA and protein analyses. A total of 176 genes and 93 distinct proteins with differential expressions were identified, mainly associated with the molecular functions of catalytic activity and binding. The upregulated expression of heat shock proteins and peroxiredoxin family after acute heat stress is suggestive of responsive machineries to protect cells from apoptosis and oxidative insults. In conclusion, both the transcripts and proteins associated with apoptosis, stress response, and antioxidative defense were upregulated in the SYFs of layer-type hens to alleviate the detrimental effects by acute heat stress. However, the genomic regulations of specific cell type in response to acute heat stress of SYFs require further investigation.
Characterization of Carbon-Contaminated B4C-Coated Optics after Chemically Selective Cleaning with Low-Pressure RF Plasma
Authors: Moreno Fernández H. , Rogler D. , Sauthier G. , Thomasset M. , Dietsch R. , Carlino V. , Pellegrin E. 
Published: January 2018

AbstractBoron carbide (B4C) is one of the few materials that is expected to be most resilient with respect to the extremely high brilliance of the photon beam generated by free electron lasers (FELs) and is thus of considerable interest for optical applications in this field. However, as in the case of many other optics operated at light source facilities, B4C-coated optics are subject to ubiquitous carbon contaminations. Carbon contaminations represent a serious issue for the operation of FEL beamlines due to severe reduction of photon flux, beam coherence, creation of destructive interference, and scattering losses. A variety of B4C cleaning technologies were developed at different laboratories with varying success. We present a study regarding the low-pressure RF plasma cleaning of carbon contaminated B4C test samples via inductively coupled O2/Ar, H2/Ar, and pure O2 RF plasma produced following previous studies using the same ibss GV10x downstream plasma source. Results regarding the chemistry, morphology as well as other aspects of the B4C optical coating before and after the plasma cleaning are reported. We conclude that among the above plasma processes only plasma based on pure O2 feedstock gas exhibits the required chemical selectivity for maintaining the integrity of the B4C optical coatings.
PI3K induces B-cell development and regulates B cell identity
Authors: Abdelrasoul Hend , Werner Markus , Setz Corinna S. , Okkenhaug Klaus , Jumaa Hassan 
Published: January 2018

AbstractPhosphoinositide-3 kinase (PI3K) signaling is important for the survival of numerous cell types and class IA of PI3K is specifically required for the development of B cells but not for T cell development. Here, we show that class IA PI3K-mediated signals induce the expression of the transcription factor Pax5, which plays a central role in B cell commitment and differentiation by activating the expression of central B cell-specific signaling proteins such as SLP-65 and CD19. Defective class IA PI3K function leads to reduction in Pax5 expression and prevents B cell development beyond the stage expressing the precursor B cell receptor (pre-BCR). Investigating the mechanism of PI3K-induced Pax5 expression revealed that it involves a network of transcription factors including FoxO1 and Irf4 that directly binds to the Pax5 gene. Together, our results suggest that PI3K signaling links survival and differentiation of developing B cells with B cell identity and that decreased PI3K activity in pre-B cells results in reduced Pax5 expression and lineage plasticity.
Core promoter information content correlates with optimal growth temperature
Authors: Aptekmann Ariel A. , Nadra Alejandro D. 
Published: January 2018

AbstractThe subtle mechanisms by which protein-DNA interactions remain functional across a wide range of temperatures are largely unknown. In this work, we manually curated available information relating fully sequenced archaeal genomes with organism growth temperatures. We built a motif that represents the core promoter of each species and calculated its information content. We then studied the relation between optimal growth temperature (OGT) and information content (IC) in the promoter region.We found a positive correlation between G + C content and OGT in tRNA regions and not in overall genome. Furthermore, we found that there is a positive correlation between information content and optimal growth temperatures in Archaea. This can’t be explained by an increased C+G composition nor by other obvious mechanisms. These findings suggest that increased information content could produce a positive fitness in organisms living at high temperatures. We suggest that molecular information theory may need to be adapted for hyperthermophiles.
New Insight into Mixing Fluoride and Chloride in Bioactive Silicate Glasses
Authors: Chen Xiaojing , Chen Xiaohui , Pedone Alfonso , Apperley David , Hill Robert G. , Karpukhina Natalia 
Published: January 2018

AbstractAdding fluoride into bioactive glasses leads to fluorapatite formation and a decrease in glass transition temperature. Recently, chloride has been introduced into glasses as an alternative to fluoride. The presence of the large chloride ion lowers glass crystallisation tendency and increases glass molar volume, which effectively facilitates glass degradation and bone-bonding apatite-like layer formation. However, there is no information regarding the effect of mixing fluoride and chloride on the glass structure and properties. This study aims to synthesize mixed fluoride and chloride containing bioactive glasses; investigate the structural role of fluoride and chloride and their effects on glass properties. The chloride content measurements reveal that 77–90% of chloride was retained in these Q2 type glasses. Glass transition temperature reduced markedly with an increase in CaX2 (X = F + Cl) content, while the glass molar volume increased. 29Si MAS-NMR results show that the incorporation of mixed fluoride and chloride did not cause significant change in the polymerization of the silicate network and no detectable concentration of Si-F/Cl bands were present. This agrees with 19F NMR spectra showing that F existed as F-Ca(n) species.
Emergence of a substrate-temperature-dependent dielectric process in a prototypical vapor deposited hole-transport glass
Authors: Rodríguez-Tinoco Cristian , Rams-Baron Marzena , Rodríguez-Viejo Javier , Paluch Marian 
Published: January 2018

AbstractSince the discovery of ultrastability, vapor deposition has emerged as a relevant tool to further understand the nature of glasses. By this route, the density and average orientation of glasses can be tuned by selecting the proper deposition conditions. Dielectric spectroscopy, on the other hand, is a basic technique to study the properties of glasses at a molecular level, probing the dynamics of dipoles or charge carriers. Here, and for the first time, we explore the dielectric behavior of vapor deposited N,N-Diphenyl-N,N’bis(methylphenyl)-1,1′-biphenyl-4,4′-diamines (TPD), a prototypical hole-transport material, prepared at different deposition temperatures. We report the emergence of a new relaxation process which is not present in the ordinary glass. We associate this process to the Maxwell-Wagner polarization observed in heterogeneous systems, and induced by the enhanced mobility of charge carriers in the more ordered vapor deposited glasses. Furthermore, the associated activation energy establishes a clear distinction between two families of glasses, depending on the selected substrate-temperature range. This finding positions dielectric spectroscopy as a unique tool to investigate the structural and electronic properties of charge transport materials and remarks the importance of controlling the deposition conditions, historically forgotten in the preparation of optoelectronic devices.
Network of proteins, enzymes and genes linked to biomass degradation shared by Trichoderma species
Authors: Horta Maria Augusta Crivelente , Filho Jaire Alves Ferreira , Murad Natália Faraj , de Oliveira Santos Eidy , dos Santos Clelton Aparecido , Mendes Juliano Sales , Brandão Marcelo Mendes , Azzoni Sindelia Freitas , de Souza Anete Pereira 
Published: January 2018

AbstractUnderstanding relationships between genes responsible for enzymatic hydrolysis of cellulose and synergistic reactions is fundamental for improving biomass biodegradation technologies. To reveal synergistic reactions, the transcriptome, exoproteome, and enzymatic activities of extracts from Trichoderma harzianum, Trichoderma reesei and Trichoderma atroviride under biodegradation conditions were examined. This work revealed co-regulatory networks across carbohydrate-active enzyme (CAZy) genes and secreted proteins in extracts. A set of 80 proteins and respective genes that might correspond to a common system for biodegradation from the studied species were evaluated to elucidate new co-regulated genes. Differences such as one unique base pair between fungal genomes might influence enzyme-substrate binding sites and alter fungal gene expression responses, explaining the enzymatic activities specific to each species observed in the corresponding extracts. These differences are also responsible for the different architectures observed in the co-expression networks.
Aminode: Identification of Evolutionary Constraints in the Human Proteome
Authors: Chang Kevin T. , Guo Junyan , di Ronza Alberto , Sardiello Marco 
Published: January 2018

AbstractEvolutionarily constrained regions (ECRs) are a hallmark for sites of critical importance for a protein’s structure or function. ECRs can be inferred by comparing the amino acid sequences from multiple protein homologs in the context of the evolutionary relationships that link the analyzed proteins. The compilation and analysis of the datasets required to infer ECRs, however, are time consuming and require skills in coding and bioinformatics, which can limit the use of ECR analysis in the biomedical community. Here, we developed Aminode, a user-friendly webtool for the routine and rapid inference of ECRs. Aminode is pre-loaded with the results of the analysis of the whole human proteome compared with proteomes from 62 additional vertebrate species. Profiles of the relative rates of amino acid substitution and ECR maps of human proteins are available for immediate search and download on the Aminode website. Aminode can also be used for custom analyses of protein families of interest. Interestingly, mapping of known missense variants shows great enrichment of pathogenic variants and depletion of non-pathogenic variants in Aminode-generated ECRs, suggesting that ECR analysis may help evaluate the potential pathogenicity of variants of unknown significance. Aminode is freely available at http://www.aminode.org.
Volcanic dust veils from sixth century tree-ring isotopes linked to reduced irradiance, primary production and human health
Authors: Helama Samuli , Arppe Laura , Uusitalo Joonas , Holopainen Jari , Mäkelä Hanna M. , Mäkinen Harri , Mielikäinen Kari , Nöjd Pekka , Sutinen Raimo , Taavitsainen Jussi-Pekka , Timonen Mauri , Oinonen Markku 
Published: January 2018

AbstractThe large volcanic eruptions of AD 536 and 540 led to climate cooling and contributed to hardships of Late Antiquity societies throughout Eurasia, and triggered a major environmental event in the historical Roman Empire. Our set of stable carbon isotope records from subfossil tree rings demonstrates a strong negative excursion in AD 536 and 541–544. Modern data from these sites show that carbon isotope variations are driven by solar radiation. A model based on sixth century isotopes reconstruct an irradiance anomaly for AD 536 and 541–544 of nearly three standard deviations below the mean value based on modern data. This anomaly can be explained by a volcanic dust veil reducing solar radiation and thus primary production threatening food security over a multitude of years. We offer a hypothesis that persistently low irradiance contributed to remarkably simultaneous outbreaks of famine and Justinianic plague in the eastern Roman Empire with adverse effects on crop production and photosynthesis of the vitamin D in human skin and thus, collectively, human health. Our results provide a hitherto unstudied proxy for exploring the mechanisms of ‘volcanic summers’ to demonstrate the post-eruption deficiencies in sunlight and to explain the human consequences during such calamity years.
Impact of a motivational resistance-training programme on adherence and body composition in the elderly
Authors: Marcos-Pardo Pablo Jorge , Martínez-Rodríguez Alejandro , Gil-Arias Alexander 
Published: January 2018

AbstractLack of physical activity is one of the major causes for obesity and functional disability in the elderly. Including regular exercise in the elderly’s lifestyle is not an easy task. The main objective was to analyse the effect of a motivational resistance-training programme on satisfying the individual’s psychological needs, level of self-determination and body composition. A quasi-experimental study was performed with 47 volunteers (29 females, 18 males) of 67–75 years of age, divided into two groups: experimental (n = 27) and control (n = 20). A 12-week intervention programme was performed, with a total of 36 sessions. The results of the inter-group analysis indicated significant differences in the post-test measurement between the experimental group and the control group (in favour of the experimental group) regarding basic psychological needs. The experimental group, in comparison to the control group, significantly decreased their percentage of fat mass and increased muscle mass. Body weight and BMI values increased in the control group, while significantly decreasing in the experimental group. In conclusion, the motivational resistance-training programme in the elderly gave rise to positive significant changes at the physical, psychological and social levels, according to the definition of health by the World Health Organization.
Four-week individual caging of male ICR mice alters body composition without change in body mass
Authors: Shin Jisu , Woo Jiwan , Cho Yakdol , Choi Yoon Hee , Shin Naewoo Neo , Kim YoungSoo 
Published: January 2018

AbstractUnderstanding the physiological implications of caging conditions for mice is crucial in improving the replicability and reliability of animal research. Individual caging of mice is known to alter mouse psychology, such as triggering depression-like symptoms in mice, suggesting that caging conditions could have negative effects on mice. Therefore, we hypothesized that individual caging could affect the physical composition of outbred mice. To investigate this, dual X-ray absorptiometry (DXA) was used to compare the mass, bone mineral content (BMC), bone mineral density (BMD), lean tissue percentage and fat tissue percentage between group and individual caged mice. We also conducted open field test to compare mouse activities in different caging conditions. Our results showed significantly reduced BMD and lean tissue percentage and significantly increased fat tissue percentage in individually-caged male mice. Furthermore, there were no differences in body mass and activity between the grouped and individual mice, suggesting that these physical alterations were not induced by group-related activity. In this study, we conclude that individual caging could alter the body composition of mice without affecting external morphology.
Development of matrix metalloproteinase-targeted probes for lung inflammation detection with positron emission tomography
Authors: Kondo Naoya , Temma Takashi , Aita Kazuki , Shimochi Saeka , Koshino Kazuhiro , Senda Michio , Iida Hidehiro 
Published: January 2018

AbstractAs matrix metalloproteinases (MMPs), especially MMP-9 and MMP-12 are involved in the pathological processes associated with chronic obstructive pulmonary disease (COPD), we developed a novel radiofluorinated probe, 18F-IPFP, for MMPs-targeted positron emission tomography (PET). 18F-IPFP was designed by iodination of MMP inhibitor to enhance the affinity, and labelled with a compact prosthetic agent, 4-nitrophenyl 2-18F-fluoropropionate (18F-NFP). As a result, IPFP demonstrated the highest affinity toward MMP-12 (IC50 = 1.5 nM) among existing PET probes. A COPD model was employed by exposing mice to cigarette smoke and the expression levels of MMP-9 and MMP-12 were significantly increased in the lungs. Radioactivity accumulation in the lungs 90 min after administration of 18F-IPFP was 4× higher in COPD mice than normal mice, and 10× higher than in the heart, muscle, and blood. Ex vivo PET confirmed the radioactivity distribution in the tissues and autoradiography analysis demonstrated that accumulation differences in the lungs of COPD mice were 2× higher than those of normal mice. These results suggest that 18F-IPFP is a promising probe for pulmonary imaging and expected to be applied to various MMP-related diseases for early diagnosis, tracking of therapeutic effects, and new drug development in both preclinical and clinical applications.