bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel approach of utilization of the fungal conidia biomass to remove heavy metals from the aqueous solution through immobilization
Authors: Cai Chun-Xiang , Xu Jian , Deng Nian-Fang , Dong Xue-Wei , Tang Hao , Liang Yu , Fan Xian-Wei , Li You-Zhi 
Published: November 2016

AbstractThe biomass of filamentous fungi is an important cost-effective biomass for heavy metal biosorption. However, use of free fungal cells can cause difficulties in the separation of biomass from the effluent. In this study, we immobilized the living conidia of the heavy metal-resistant Penicillium janthinillum strain GXCR by polyvinyl alcohol (PVA)-sodium alginate (SA) beads to remove heavy metals from an aqueous solution containing a low concentration (70 mg/L) of Cu, Pb, and Cd. The PVA-SA-conidia beads showed perfect characters of appropriate mechanical strength suitable for metal removal from the dynamic wastewater environment, an ideal settleability, easy separation from the solution, and a high metal biosorption and removal rate even after four cycles of successive sorption-desorption of the beads, overcoming disadvantages when fungal biomasses alone are used for heavy metal removal from wastewater. We also discuss the major biosorption-affecting factors, biosorption models, and biosorption mechanisms.
Differential expression of TGF-β superfamily members and role of Smad1/5/9-signalling in chondral versus endochondral chondrocyte differentiation
Authors: Dexheimer Verena , Gabler Jessica , Bomans Katharina , Sims Tanja , Omlor Georg , Richter Wiltrud 
Published: November 2016

AbstractProteins of the transforming-growth-factor-β (TGF-β)-superfamily have a remarkable ability to induce cartilage and bone and the crosstalk of TGF-β - and BMP-signalling pathways appears crucial during chondrocyte development. Aim was to assess the regulation of TGF-β-superfamily members and of Smad2/3- and Smad1/5/9-signalling during endochondral in vitro chondrogenesis of mesenchymal stromal cells (MSC) relative to chondral redifferentiation of articular chondrocytes (AC) to adjust chondrocyte development of MSC towards a less hypertrophic phenotype. While MSC increased BMP4 and BMP7 and reduced TGFBR2 and TGFBR3-expression during chondrogenesis, an opposite regulation was observed during AC-redifferentiation. Antagonists CHRD and CHL2 rose significantly only in AC-cultures. AC showed higher initial BMP4, pSmad1/5/9 and SOX9 protein levels, a faster (re-)differentiation but a similar decline of pSmad2/3- and pSmad1/5/9-signalling versus MSC-cultures. BMP-4/7-stimulation of MSC-pellets enhanced SOX9 and accelerated ALP-induction but did not shift differentiation towards osteogenesis. Inhibition of BMP-signalling by dorsomorphin significantly reduced SOX9, raised RUNX2, maintained collagen-type-II and collagen-type-X lower and kept ALP-activity at levels reached at initiation of treatment. Conclusively, ALK1,2,3,6-signalling was essential for MSC-chondrogenesis and its prochondrogenic rather than prohypertrophic role may explain why inhibition of canonical BMP-signalling could not uncouple cartilage matrix production from hypertrophy as this was achieved with pulsed PTHrP-application.
Evidences for Cooperative Resonance-Assisted Hydrogen Bonds in Protein Secondary Structure Analogs
Authors: Zhou Yu , Deng Geng , Zheng Yan-Zhen , Xu Jing , Ashraf Hamad , Yu Zhi-Wu 
Published: November 2016

AbstractCooperative behaviors of the hydrogen bonding networks in proteins have been discovered for a long time. The structural origin of this cooperativity, however, is still under debate. Here we report a new investigation combining excess infrared spectroscopy and density functional theory calculation on peptide analogs, represented byN-methylformamide (NMF) andN-methylacetamide (NMA). Interestingly, addition of the strong hydrogen bond acceptor, dimethyl sulfoxide, to the pure analogs caused opposite effects, namely red- and blue-shift of the N−H stretching infrared absorption in NMF and NMA, respectively. The contradiction can be reconciled by the marked lowering of the energy levels of the self-associates between NMA molecules due to a cooperative effect of the hydrogen bonds. On the contrary, NMF molecules cannot form long-chain cooperative hydrogen bonds because they tend to form dimers. Even more interestingly, we found excellent linear relationships between changes on bond orders of N−H/N−C/C = O and the hydrogen bond energy gains upon the formation of hydrogen bonding multimers in NMA, suggesting strongly that the cooperativity originates from resonance-assisted hydrogen bonds. Our findings provide insights on the structures of proteins and may also shed lights on the rational design of novel molecular recognition systems.
Enterovirus 71 infection of motor neuron-like NSC-34 cells undergoes a non-lytic exit pathway
Authors: Too Issac Horng Khit , Yeo Huimin , Sessions October Michael , Yan Benedict , Libau Eshele Anak , Howe Josephine L. C. , Lim Ze Qin , Suku-Maran Shalini , Ong Wei-Yi , Chua Kaw Bing , Wong Boon Seng , Chow Vincent T. K. , Alonso Sylvie 
Published: November 2016

AbstractEnterovirus 71 (EV71) causing Hand, Foot and Mouth Disease, is regarded as the most important neurotropic virus worldwide. EV71 is believed to replicate in muscles and infect motor neurons to reach the central nervous system (CNS). To further investigate the mechanisms involved, we have employed the motor neuron cell line NSC-34. NSC-34 cells were permissive to EV71 and virus production yields were strain-dependent with differential efficacy at the entry, replication and egress steps. Furthermore, unlike all the other cell lines previously reported, EV71-infected NSC-34 cells neither displayed cytopathic effect nor underwent apoptosis. Instead, autophagy was markedly up-regulated and virus-containing autophagic vacuoles were isolated from the culture supernatant, providing the first experimental evidence that EV71 can adopt a non-lytic exit pathway. Finally, the ability of EV71 to infect productively NSC-34 cells correlated with its ability to invade the CNS in vivo, supporting the relevance of NSC-34 cells to study the intrinsic neurovirulence of EV71 strains.
The correlation between expression profiles measured in single cells and in traditional bulk samples
Authors: Dzamba David , Valihrach Lukas , Kubista Mikael , Anderova Miroslava 
Published: November 2016

AbstractReverse transcription quantitative PCR (RT-qPCR) is already an established tool for mRNA detection and quantification. Since recently, this technique has been successfully employed for gene expression analyses, and also in individual cells (single cell RT-qPCR). Although the advantages of single cell measurements have been proven several times, a study correlating the expression measured on single cells, and in bulk samples consisting of a large number of cells, has been missing. Here, we collected a large data set to explore the relation between gene expression measured in single cells and in bulk samples, reflected by qPCR Cq values. We measured the expression of 95 genes in 12 bulk samples, each containing thousands of astrocytes, and also in 693 individual astrocytes. Combining the data, we described the relation between Cq values measured in bulk samples with either the percentage of the single cells that express the given genes, or the average expression of the genes across the single cells. We show that data obtained with single cell RT-qPCR are fully consistent with measurements in bulk samples. Our results further provide a base for quality control in single cell expression profiling, and bring new insights into the biological process of cellular expression.
Near-Earth object hazardous impact: A Multi-Criteria Decision Making approach
Authors: Sánchez-Lozano J. M. , Fernández-Martínez M. 
Published: November 2016

AbstractThe impact of a near-Earth object (NEO) may release large amounts of energy and cause serious damage. Several NEO hazard studies conducted over the past few years provide forecasts, impact probabilities and assessment ratings, such as the Torino and Palermo scales. These high-risk NEO assessments involve several criteria, including impact energy, mass, and absolute magnitude. The main objective of this paper is to provide the first Multi-Criteria Decision Making (MCDM) approach to classify hazardous NEOs. Our approach applies a combination of two methods from a widely utilized decision making theory. Specifically, the Analytic Hierarchy Process (AHP) methodology is employed to determine the criteria weights, which influence the decision making, and the Technique for Order Performance by Similarity to Ideal Solution (TOPSIS) is used to obtain a ranking of alternatives (potentially hazardous NEOs). In addition, NEO datasets provided by the NASA Near-Earth Object Program are utilized. This approach allows the classification of NEOs by descending order of their TOPSIS ratio, a single quantity that contains all of the relevant information for each object.
Androgen receptor (AR) signaling promotes RCC progression via increased endothelial cell proliferation and recruitment by modulating AKT → NF-κB → CXCL5 signaling
Authors: Guan Zhenfeng , Li Chong , Fan Jinhai , He Dalin , Li Lei 
Published: November 2016

AbstractAndrogen receptor (AR) signaling may promote renal cell carcinoma (RCC) progression via altered HIF-2α/VEGF signaling. However, it remains unclear whether AR signaling also promotes RCC progression by recruiting vascular endothelial cells (ECs), key players in the development of blood vessels. In our study, AR increased EC proliferation and recruitment to the tumor microenvironment and promoted RCC progression. Mechanistically, AR modulated cytokine CXCL5 expression by altering AKT → NF-κB signaling, and interruption of AKT → NF-κB → CXCL5 signaling using either specific inhibitors or siRNA suppressed AR-enhanced EC recruitment and AR-EC-promoted RCC progression. The results obtained using an in vivo mouse model and a human clinical sample survey confirmed the role of AR in promoting RCC progression through enhancement of EC proliferation and/or recruitment via altered AKT → NF-κB → CXCL5 signaling. Targeting this newly identified AR-induced AKT → NF-κB → CXCL5 pathway may facilitate the development of new therapies for slowing RCC progression.
Revisiting the expression and function of follicle-stimulation hormone receptor in human umbilical vein endothelial cells
Authors: Stelmaszewska Joanna , Chrusciel Marcin , Doroszko Milena , Akerfelt Malin , Ponikwicka-Tyszko Donata , Nees Matthias , Frentsch Marco , Li Xiangdong , Kero Jukka , Huhtaniemi Ilpo , Wolczynski Slawomir , Rahman Nafis A. 
Published: November 2016

AbstractExpression of follicle-stimulation hormone receptor (FSHR) is confined to gonads and at low levels to some extragonadal tissues like human umbilical vein endothelial cells (HUVEC). FSH-FSHR signaling was shown to promote HUVEC angiogenesis and thereafter suggested to have an influential role in pregnancy. We revisited hereby the expression and functionality of FSHR in HUVECs angiogenesis, and were unable to reproduce the FSHR expression in human umbilical cord, HUVECs or immortalized HUVECs (HUV-ST). Positive controls as granulosa cells and HEK293 cells stably transfected with human FSHR cDNA expressed FSHR signal. In contrast to positive control VEGF, FSH treatment showed no effects on tube formation, nitric oxide production, wound healing or cell proliferation in HUVEC/HUV-ST. Thus, it remains open whether the FSH-FSHR activation has a direct regulatory role in the angiogenesis of HUVECs.
Robustness of replica symmetry breaking phenomenology in random laser
Authors: Tommasi Federico , Ignesti Emilio , Lepri Stefano , Cavalieri Stefano 
Published: November 2016

AbstractRandom lasers are optical sources where light is amplified by stimulated emission along random paths through an amplifying scattering medium. Connections between their physics and the one of quenched disordered nonlinear systems, notably spin glasses, have been recently suggested. Here we report a first experimental study of correlations of spectral fluctuations intensity in a random laser medium where the scatterers displacement significantly changes among consecutive shots. Remarkably, our results reveal that the replica symmetry breaking (RSB) phenomenology is robust with respect to an averaging over different realizations of the disorder. Moreover, besides opening new intriguing questions about the understanding of such a phenomenon, this work aims to clarify the connection between the RSB with the onset of the Lévy regime, i.e. the fluctuations regime that is a peculiar feature of the random lasing under critical conditions. Our results suggest that the former occurs independently of the latter and then the RSB phenomenology is a generic feature linked to the random laser threshold.
Sterile inflammation as a factor in human male infertility: Involvement of Toll like receptor 2, biglycan and peritubular cells
Authors: Mayer C. , Adam M. , Glashauser L. , Dietrich K. , Schwarzer J.U. , Köhn F.-M. , Strauss L. , Welter H. , Poutanen M. , Mayerhofer A. 
Published: November 2016

AbstractChanges in the wall of seminiferous tubules in men with impaired spermatogenesis imply sterile inflammation of the testis. We tested the hypothesis that the cells forming the wall of seminiferous tubules, human testicular peritubular cells (HTPCs), orchestrate inflammatory events and that Toll like receptors (TLRs) and danger signals from the extracellular matrix (ECM) of this wall are involved. In cultured HTPCs we detected TLRs, including TLR2. A TLR-2 ligand (PAM) augmented interleukin 6 (IL-6), monocyte chemo-attractant protein-1 (MCP-1) and pentraxin 3 (PTX3) in HTPCs. The ECM-derived proteoglycan biglycan (BGN) is secreted by HTPCs and may be a TLR2-ligand at HTPCs. In support, recombinant human BGN increased PTX3, MCP-1 and IL-6 in HTPCs. Variable endogenous BGN levels in HTPCs derived from different men and differences in BGN levels in the tubular wall in infertile men were observed. In testes of a systemic mouse model for male infertility, testicular sterile inflammation and elevated estradiol (E2) levels, BGN was also elevated. Hence we studied the role of E2 in HTPCs and observed that E2 elevated the levels of BGN. The anti-estrogen ICI 182,780 blocked this action. We conclude that TLR2 and BGN contribute to sterile inflammation and infertility in man.
The fluctuating ribosome: thermal molecular dynamics characterized by neutron scattering
Authors: Zaccai Giuseppe , Natali Francesca , Peters Judith , Řihová Martina , Zimmerman Ella , Ollivier J. , Combet J. , Maurel Marie-Christine , Bashan Anat , Yonath Ada 
Published: November 2016

AbstractConformational changes associated with ribosome function have been identified by X-ray crystallography and cryo-electron microscopy. These methods, however, inform poorly on timescales. Neutron scattering is well adapted for direct measurements of thermal molecular dynamics, the ‘lubricant’ for the conformational fluctuations required for biological activity. The method was applied to compare water dynamics and conformational fluctuations in the 30 S and 50 S ribosomal subunits from Haloarcula marismortui, under high salt, stable conditions. Similar free and hydration water diffusion parameters are found for both subunits. With respect to the 50 S subunit, the 30 S is characterized by a softer force constant and larger mean square displacements (MSD), which would facilitate conformational adjustments required for messenger and transfer RNA binding. It has been shown previously that systems from mesophiles and extremophiles are adapted to have similar MSD under their respective physiological conditions. This suggests that the results presented are not specific to halophiles in high salt but a general property of ribosome dynamics under corresponding, active conditions. The current study opens new perspectives for neutron scattering characterization of component functional molecular dynamics within the ribosome.
Materials characterisation by angle-resolved scanning transmission electron microscopy
Authors: Müller-Caspary Knut , Oppermann Oliver , Grieb Tim , Krause Florian F. , Rosenauer Andreas , Schowalter Marco , Mehrtens Thorsten , Beyer Andreas , Volz Kerstin , Potapov Pavel 
Published: November 2016

AbstractSolid-state properties such as strain or chemical composition often leave characteristic fingerprints in the angular dependence of electron scattering. Scanning transmission electron microscopy (STEM) is dedicated to probe scattered intensity with atomic resolution, but it drastically lacks angular resolution. Here we report both a setup to exploit the explicit angular dependence of scattered intensity and applications of angle-resolved STEM to semiconductor nanostructures. Our method is applied to measure nitrogen content and specimen thickness in a GaNxAs1−x layer independently at atomic resolution by evaluating two dedicated angular intervals. We demonstrate contrast formation due to strain and composition in a Si- based metal-oxide semiconductor field effect transistor (MOSFET) with GexSi1−x stressors as a function of the angles used for imaging. To shed light on the validity of current theoretical approaches this data is compared with theory, namely the Rutherford approach and contemporary multislice simulations. Inconsistency is found for the Rutherford model in the whole angular range of 16–255 mrad. Contrary, the multislice simulations are applicable for angles larger than 35 mrad whereas a significant mismatch is observed at lower angles. This limitation of established simulations is discussed particularly on the basis of inelastic scattering.
Irigenin, a novel lead from Western Himalayan chemiome inhibits Fibronectin-Extra Domain A induced metastasis in Lung cancer cells
Authors: Amin Asif , Chikan Naveed Anjum , Mokhdomi Taseem A. , Bukhari Shoiab , Koul Aabid M. , Shah Basit Amin , Gharemirshamlu Fatemeh Rahimi , Wafai Asrar H. , Qadri Ayub , Qadri Raies A. 
Published: November 2016

AbstractSeveral lines of evidence indicate that Fibronectin Extra Domain A (EDA) promotes metastatic capacity of tumor cells by engaging cell surface α9β1 integrins. This interaction mediated by the C-C loop of EDA activates pro-oncogenic signaling pathways leading to epithelial to mesenchymal transition (EMT) of tumor cells, thus signifying its importance in control of metastatic progression. In this context the present study was designed to explore the active compounds from selected ethno-medicinal plants of western Himalayan region for targeting EDA of Fibronectin in lung carcinoma cells. Structure based informatics for drug designing and screening was employed to generate a lead compound(s) feed that were conformationally and energetically viable. Out of 120 compounds selected, Irigenin showed best binding-affinity with C-C loop of EDA. Irigenin specifically targeted α9β1 and α4β1 integrin binding sites on EDA comprising LEU46, PHE47, PRO48, GLU58, LEU59 and GLN60 in its C-C loop as evaluated by energy decomposition per residue of Irigenin–EDA complex. In-vitro cell motility assays complemented with EDA knock-in and knockdown assays distinctively demonstrated that Irigenin prevents metastatic capacity of lung cancer cells by selectively blocking EDA. The results presented thus project Irigenin as a lead compound to overcome Fibronectin EDA induced metastatic progression in lung carcinoma cells.
Atmospheric oxidation and carbon contamination of silver and its effect on surface-enhanced Raman spectroscopy (SERS)
Authors: Matikainen Antti , Nuutinen Tarmo , Itkonen Tommi , Heinilehto Santtu , Puustinen Jarkko , Hiltunen Jussi , Lappalainen Jyrki , Karioja Pentti , Vahimaa Pasi 
Published: November 2016

AbstractSurface-enhanced Raman spectroscopy (SERS) is considered a highly promising technology for different analytical purposes. The applications of SERS are still quite limited due its relatively poor quantitative repeatability and the fact that SERS is very sensitive to oxidation, which is a challenge especially with silver based SERS substrates. Here, the link between these phenomena is investigated by exposing silver SERS substrates to ambient laboratory air. We show that SERS intensity decreases exponentially after the exposure, which consequently leads to an increasing standard deviation (σ) in intensity. Within a five-hour measurement window, the SERS intensity already drops by 60%, while σ triples from 7% to 21%. The SERS results are supplemented by elemental analysis, which shows that oxidation and atmospheric carbon contamination coincide with the rapid SERS intensity decrease. The results emphasize how sensitive SERS is towards atmospheric contamination and how it can also reduce the measurement repeatability – even if the substrates are exposed to air just for a very short period of time.
The disruption of GDP-fucose de novo biosynthesis suggests the presence of a novel fucose-containing glycoconjugate in Plasmodium asexual blood stages
Authors: Sanz Sílvia , López-Gutiérrez Borja , Bandini Giulia , Damerow Sebastian , Absalon Sabrina , Dinglasan Rhoel R. , Samuelson John , Izquierdo Luis 
Published: November 2016

AbstractGlycosylation is an important posttranslational protein modification in all eukaryotes. Besides glycosylphosphatidylinositol (GPI) anchors and N-glycosylation, O-fucosylation has been recently reported in key sporozoite proteins of the malaria parasite. Previous analyses showed the presence of GDP-fucose (GDP-Fuc), the precursor for all fucosylation reactions, in the blood stages of Plasmodium falciparum. The GDP-Fuc de novo pathway, which requires the action of GDP-mannose 4,6-dehydratase (GMD) and GDP-L-fucose synthase (FS), is conserved in the parasite genome, but the importance of fucose metabolism for the parasite is unknown. To functionally characterize the pathway we generated a PfGMD mutant and analyzed its phenotype. Although the labelling by the fucose-binding Ulex europaeus agglutinin I (UEA-I) was completely abrogated, GDP-Fuc was still detected in the mutant. This unexpected result suggests the presence of an alternative mechanism for maintaining GDP-Fuc in the parasite. Furthermore, PfGMD null mutant exhibited normal growth and invasion rates, revealing that the GDP-Fuc de novo metabolic pathway is not essential for the development in culture of the malaria parasite during the asexual blood stages. Nonetheless, the function of this metabolic route and the GDP-Fuc pool that is generated during this stage may be important for gametocytogenesis and sporogonic development in the mosquito.
Alterations in the airborne bacterial community during Asian dust events occurring between February and March 2015 in South Korea
Authors: Cha Seho , Lee Dongwook , Jang Jun Hyeong , Lim Sora , Yang Dahye , Seo Taegun 
Published: November 2016

AbstractDuring Asian dust events, a relatively high concentration of particulate matter is transported by wind from arid and semi-arid regions, such as the Gobi and Taklamakan deserts, to nearby countries, including China, Korea, and Japan. The dust particles contain various microorganisms, which can affect human health as well as the environmental microbe population. In the current study, we investigated the characteristics of the airborne bacterial community during Asian dust events between February and March 2015 in South Korea. Bacterial diversity indexes such as operational taxonomic units, Chao1 and Inverse Simpson index were increased, along with total 16S rRNA gene copy number during Asian dust events. The bacterial community structure during Asian dust events was clearly distinguishable from that during non-Asian dust days. The genera Bacillus and Modestobacter were increased 3.9- and 2.7-fold, respectively, while Escherichia-Shigella was decreased by 89.8%. A non-metric multidimensional scaling plot with metadata analysis revealed association of particulate matter concentration, but not temperature, humidity or wind speed, with bacterial community structure, suggesting that the newly transported dust particles contain various microorganisms that influence the airborne bacterial environment.