bluuebunny/crossref_metadata_2025 huggingface dataset:
H3K18Ac as a Marker of Cancer Progression and Potential Target of Anti-Cancer Therapy
Authors: Hałasa Marta , Wawruszak Anna , Przybyszewska Alicja , Jaruga Anna , Guz Małgorzata , Kałafut Joanna , Stepulak Andrzej , Cybulski Marek
Published: May 2019

Acetylation and deacetylation are posttranslational modifications (PTMs) which affect the regulation of chromatin structure and its remodeling. Acetylation of histone 3 at lysine placed on position 18 (H3K18Ac) plays an important role in driving progression of many types of cancer, including breast, colon, lung, hepatocellular, pancreatic, prostate, and thyroid cancer. The aim of this review is to analyze and discuss the newest findings regarding the role of H3K18Ac and acetylation of other histones in carcinogenesis. We summarize the level of H3K18Ac in different cancer cell lines and analyze its association with patients’ outcomes, including overall survival (OS), progression-free survival (PFS), and disease-free survival (DFS). Finally, we describe future perspectives of cancer therapeutic strategies based on H3K18 modifications.
Amyloid Beta and Phosphorylated Tau-Induced Defective Autophagy and Mitophagy in Alzheimer’s Disease
Authors: Reddy P. Hemachandra , Oliver Darryll MA
Published: May 2019

Alzheimer’s disease (AD) is a progressive neurodegenerative disease characterized by memory loss and multiple cognitive impairments. Several decades of intense research have revealed that multiple cellular changes are implicated in the development and progression of AD, including mitochondrial damage, synaptic dysfunction, amyloid beta (Aβ) formation and accumulation, hyperphosphorylated tau (P-Tau) formation and accumulation, deregulated microRNAs, synaptic damage, and neuronal loss in patients with AD. Among these, mitochondrial dysfunction and synaptic damage are early events in the disease process. Recent research also revealed that Aβ and P-Tau-induced defective autophagy and mitophagy are prominent events in AD pathogenesis. Age-dependent increased levels of Aβ and P-Tau reduced levels of several autophagy and mitophagy proteins. In addition, abnormal interactions between (1) Aβ and mitochondrial fission protein Drp1; (2) P-Tau and Drp1; and (3) Aβ and PINK1/parkin lead to an inability to clear damaged mitochondria and other cellular debris from neurons. These events occur selectively in affected AD neurons. The purpose of our article is to highlight recent developments of a Aβ and P-Tau-induced defective autophagy and mitophagy in AD. This article also summarizes several aspects of mitochondrial dysfunction, including abnormal mitochondrial dynamics (increased fission and reduced fusion), defective mitochondrial biogenesis, reduced ATP, increased free radicals and lipid peroxidation, and decreased cytochrome c oxidase (COX) activity and calcium dyshomeostasis in AD pathogenesis. Our article also discusses how reduced levels of Drp1, Aβ, and P-Tau can enhance the clearance of damaged mitochondria and other cellular debris by autophagy and mitophagy mechanisms.
3D-Organotypic Cultures to Unravel Molecular and Cellular Abnormalities in Atopic Dermatitis and Ichthyosis Vulgaris
Authors: Leman Géraldine , Moosbrugger-Martinz Verena , Blunder Stefan , Pavel Petra , Dubrac Sandrine
Published: May 2019

Atopic dermatitis (AD) is characterized by dry and itchy skin evolving into disseminated skin lesions. AD is believed to result from a primary acquired or a genetically-induced epidermal barrier defect leading to immune hyper-responsiveness. Filaggrin (FLG) is a protein found in the cornified envelope of fully differentiated keratinocytes, referred to as corneocytes. Although FLG null mutations are strongly associated with AD, they are not sufficient to induce the disease. Moreover, most patients with ichthyosis vulgaris (IV), a monogenetic skin disease characterized by FLG homozygous, heterozygous, or compound heterozygous null mutations, display non-inflamed dry and scaly skin. Thus, all causes of epidermal barrier impairment in AD have not yet been identified, including those leading to the Th2-predominant inflammation observed in AD. Three dimensional organotypic cultures have emerged as valuable tools in skin research, replacing animal experimentation in many cases and precluding the need for repeated patient biopsies. Here, we review the results on IV and AD obtained with epidermal or skin equivalents and consider these findings in the context of human in vivo data. Further research utilizing complex models including immune cells and cutaneous innervation will enable finer dissection of the pathogenesis of AD and deepen our knowledge of epidermal biology.
Mitophagy in Cancer: A Tale of Adaptation
Authors: Vara-Perez Monica , Felipe-Abrio Blanca , Agostinis Patrizia
Published: May 2019

In the past years, we have learnt that tumors co-evolve with their microenvironment, and that the active interaction between cancer cells and stromal cells plays a pivotal role in cancer initiation, progression and treatment response. Among the players involved, the pathways regulating mitochondrial functions have been shown to be crucial for both cancer and stromal cells. This is perhaps not surprising, considering that mitochondria in both cancerous and non-cancerous cells are decisive for vital metabolic and bioenergetic functions and to elicit cell death. The central part played by mitochondria also implies the existence of stringent mitochondrial quality control mechanisms, where a specialized autophagy pathway (mitophagy) ensures the selective removal of damaged or dysfunctional mitochondria. Although the molecular underpinnings of mitophagy regulation in mammalian cells remain incomplete, it is becoming clear that mitophagy pathways are intricately linked to the metabolic rewiring of cancer cells to support the high bioenergetic demand of the tumor. In this review, after a brief introduction of the main mitophagy regulators operating in mammalian cells, we discuss emerging cell autonomous roles of mitochondria quality control in cancer onset and progression. We also discuss the relevance of mitophagy in the cellular crosstalk with the tumor microenvironment and in anti-cancer therapy responses.
Functionalization of Hydroxyapatite Ceramics: Raman Mapping Investigation of Silanization
Authors: Siniscalco David , Dutreilh-Colas Maggy , Hjezi Zahi , Cornette Julie , El Felss Nadia , Champion Eric , Damia Chantal
Published: May 2019

Surface modification of bioceramic materials by covalent immobilization of biomolecules is a promising way to improve their bioactivity. This approach implies the use of organic anchors to introduce functional groups on the inorganic surface on which the biomolecules will be immobilized. In this process, the density and surface distribution of biomolecules, and in turn the final biological properties, are strongly influenced by those of the anchors. We propose a new approach based on Raman 2D mapping to evidence the surface distribution of organosilanes, frequently used as anchors on biomaterial surfaces on hydroxyapatite and silicated hydroxyapatite ceramics. Unmodified and silanized ceramic surfaces were characterized by means of contact angle measurements, atomic force microscopy (AFM) and Raman mapping. Contact angle measurements and AFM topographies confirmed the surface modification. Raman mapping highlighted the influence of both the ceramic’s composition and silane functionality (i.e., the number of hydrolysable groups) on the silane surface distribution. The presence of hillocks was shown, evidencing a polymerization and/or an aggregation of the molecules whatever the silane and the substrates were. The substitution of phosphate groups by silicate groups affects the covering, and the spots are more intense on SiHA than on HA.
Improved Transition Metal Dichalcogenides-Based Surface Plasmon Resonance Biosensors
Authors: Hasib Mohammad Hasibul Hasan , Nur Jannati Nabiha , Rizal Conrad , Shushama Kamrun Nahar
Published: May 2019

Surface plasmon resonance (SPR) biosensors based on transition metal dichalcogenides (TMDC) materials have shown improved performance in terms of sensitivity, detection accuracy (DA), and quality factor (QF) over conventional biosensors. In this paper, we propose a five-layers model containing black phosphorus (BP) and TMDC (Ag/BP/WS2) in Kretschmann configuration. Using TM-polarized light at 633 nm, we numerically demonstrate the highest sensitivity (375°/RIU), DA (0.9210), and QF (65.78 1/RIU) reported so far over similar materials. Refractive index (RI) of the coupling prism has also played an essential role in enhancing the performance of these biosensors. The research on TMDC materials is still new, and these materials bring about opportunities to develop a new class of biosensor.
Development of a Stand-Alone Photovoltaic System Considering Shaded Effect for Energy Storage and Release
Authors: Chao Kuei-Hsiang , Lai Yu-Ju , Chang Wen-Ching
Published: May 2019

The purpose of this study was to develop a photovoltaic system that stores energy for use in direct current micro-grid systems or to supply electric power to consumers living in remote areas. If the photovoltaic module array is shaded, the signals of conventional maximum power point trackers (MPPT) may be trapped at the local power maxima. Therefore, this study developed a smart maximum power point tracker to track the maximum power point (MPP). The control method adopted a teaching learning based optimization (TLBO) algorithm. To adjust the energy flow direction of the direct current load terminal, this study proposed an energy accumulation and release strategy that used a high-boost/buck-ratio bidirectional converter to control the battery charge and discharge for energy accumulation and release. In addition, this study developed an inverter to convert direct current into alternating current for alternating current loads.
Integrated Building Cells for a Simple Modular Design of Electronic Circuits with Reduced External Complexity: Performance, Active Element Assembly, and an Application Example
Authors: Sotner Roman , Jerabek Jan , Polak Ladislav , Prokop Roman , Kledrowetz Vilem
Published: May 2019

This paper introduces new integrated analog cells fabricated in a C035 I3T25 0.35-μm ON Semiconductor process suitable for a modular design of advanced active elements with multiple terminals and controllable features. We developed and realized five analog cells on a single integrated circuit (IC), namely a voltage differencing differential buffer, a voltage multiplier with current output in full complementary metal–oxide–semiconductor (CMOS) form, a voltage multiplier with current output with a bipolar core, a current-controlled current conveyor of the second generation with four current outputs, and a single-input and single-output adjustable current amplifier. These cells (sub-blocks of the manufactured IC device), designed to operate in a bandwidth of up to tens of MHz, can be used as a construction set for building a variety of advanced active elements, offering up to four independently adjustable internal parameters. The performances of all individual cells were verified by extensive laboratory measurements, and the obtained results were compared to simulations in the Cadence IC6 tool. The definition and assembly of a newly specified advanced active element, namely a current-controlled voltage differencing current conveyor transconductance amplifier (CC-VDCCTA), is shown as an example of modular interconnection of the selected cells. This device was implemented in a newly synthesized topology of an electronically linearly tunable quadrature oscillator. Features of this active element were verified by simulations and experimental measurements.
An Assessment of Fire Refugia Importance Criteria Ranked by Land Managers
Authors: Martinez Anthony , Meddens Arjan , Kolden Crystal , Hudak Andrew
Published: May 2019

There is evidence that forest resiliency is declining in the western US due to recent increases in both areas burned by wildfire and the number of large fires. Fire refugia may increase forest resiliency; however, for land managers to incorporate fire refugia into their management plans, methods need to be developed to identify and rank criteria for what make fire refugia important. As part of a larger effort to build a spatially explicit ranking model for unburned islands in the inland northwestern US, we investigated the perceived importance of criteria used to inform a ranking model to identify high-value fire refugia. We developed a survey targeting land managers within the inland northwestern US. Participants were asked to score a predetermined list of criteria by their importance for determining the value of fire refugia. These scores were analyzed to identify trends among respondents that could be used to develop a fire refugia ranking model. The results indicate that respondents generally organized criteria into two groups: Human infrastructure and wildlife habitat. However, there was little consensus among respondents in their scoring of fire refugia importance criteria, suggesting that a single region-wide fire refugia ranking model may not be feasible. More research with a larger sample size is needed to develop targeted ranking models.
The Effect of Ecophysiological Traits on Live Fuel Moisture Content
Authors: Pivovaroff Alexandria L. , Emery Nathan , Sharifi M. Rasoul , Witter Marti , Keeley Jon E. , Rundel Philip W.
Published: May 2019

Live fuel moisture content (LFMC) is an important metric for fire danger ratings. However, there is limited understanding of the physiological control of LFMC or how it varies among co-occurring species. This is a problem for biodiverse yet fire-prone regions such as southern California. We monitored LFMC and water potential for 11 native woody species, and measured ecophysiological traits related to access to water, plant water status, water use regulation, and drought adaptation to answer: (1) What are the physiological mechanisms associated with changes in LFMC? and (2) How do seasonal patterns of LFMC differ among a variety of shrub species? We found that LFMC varied widely among species during the wet winter months, but converged during the dry summer months. Traits associated with LFMC patterns were those related to access to water, such as predawn and minimum seasonal water potentials (Ψ), and water use regulation, such as transpiration. The relationship between LFMC and Ψ displayed a distinct inflection point. For most species, this inflection point was also associated with the turgor loss point, an important drought-adaptation trait. Other systems will benefit from studies that incorporate physiological mechanisms into determining critical LFMC thresholds to expand the discipline of pyro-ecophysiology.
Three-Dimensional Simulation of Fluid–Structure Interaction Problems Using Monolithic Semi-Implicit Algorithm
Authors: Murea Cornel Marius
Published: May 2019

A monolithic semi-implicit method is presented for three-dimensional simulation of fluid–structure interaction problems. The updated Lagrangian framework is used for the structure modeled by linear elasticity equation and, for the fluid governed by the Navier–Stokes equations, we employ the Arbitrary Lagrangian Eulerian method. We use a global mesh for the fluid–structure domain where the fluid–structure interface is an interior boundary. The continuity of velocity at the interface is automatically satisfied by using globally continuous finite element for the velocity in the fluid–structure mesh. The method is fast because we solve only a linear system at each time step. Three-dimensional numerical tests are presented.
Smart Bioinks as de novo Building Blocks to Bioengineer Living Tissues
Authors: Blaeser Andreas , Heilshorn Sarah C. , Duarte Campos Daniela F.
Published: May 2019

In vitro tissues and 3D in vitro models have come of age [...]
Functional Characterization of Date Palm Aquaporin Gene PdPIP1;2 Confers Drought and Salinity Tolerance to Yeast and Arabidopsis
Authors: Patankar Himanshu V. , Al-Harrasi Ibtisam , Al-Yahyai Rashid , Yaish Mahmoud W.
Published: May 2019

Recent studies on salinity tolerance in date palm revealed the discovery of salt-responsive genes including PdPIP1;2, a highly conserved aquaporin gene in plants, which was functionally characterized in this study to investigate its precise role in drought and salinity tolerance. Immunoblot assay showed a high level of PIP1 protein accumulation only in the leaves of date palm plants when grown under drought, an observation which may imply the involvement of PIP1;2 in CO2 uptake. Heterologous overexpression of PdPIP1;2 in yeast (Saccharomyces cerevisiae) improved tolerance to salinity and oxidative stress. While, heterologous overexpression of PdPIP1;2 in Arabidopsis had significantly (p < 0.05) increased biomass, chlorophyll content, and root length under drought and salinity. In addition, a significantly (p < 0.05) higher percentage of transgenic plants could be recovered by rewatering after drought stress, indicating the ability of the transgenic plants to maintain water and viability under drought. Transgenic plants under drought and salinity maintained significantly (p < 0.05) higher K+/Na+ ratios than wild type (WT) plants, an observation which may represent an efficient tolerance mechanism controlled by the transgene. Collectively, this study provided an insight on the mechanism by which PdPIP1;2 conferred tolerance to salt and drought stresses in date palm.
Comparative Transcriptome Analysis in Oilseed Rape (Brassica napus) Reveals Distinct Gene Expression Details between Nitrate and Ammonium Nutrition
Authors: Tang Weijie , He Xin , Qian Lunwen , Wang Feng , Zhang Zhenhua , Sun Chao , Lin Liangbin , Guan Chunyun
Published: May 2019

Nitrate (NO3−) and ammonium (NH4+) are the main inorganic nitrogen (N) sources absorbed by oilseed rape, a plant that exhibits genotypic differences in N efficiency. In our previous study, the biomass, N accumulation, and root architecture of two oilseed rape cultivars, Xiangyou 15 (high N efficiency, denoted “15”) and 814 (low N efficiency, denoted “814”), were inhibited under NH4+ nutrition, though both cultivars grew normally under NO3− nutrition. To gain insight into the underlying molecular mechanisms, transcriptomic changes were investigated in the roots of 15 and 814 plants subjected to nitrogen-free (control, CK), NO3− (NT), and NH4+ (AT) treatments at the seedling stage. A total of 14,355 differentially expressed genes (DEGs) were identified. Among the enriched Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway categories of these DEGs, carbohydrate metabolism, lipid metabolism, protein metabolism, and cell wall biogenesis were inhibited by AT treatment. Interestingly, DEGs such as N transporters, genes involved in N assimilation and CESA genes related to cellulose synthase were also mostly downregulated in the AT treatment group. This downregulation of genes related to crucial metabolic pathways resulted in inhibition of oilseed rape growth after AT treatment.
“Why Can’t I Become a Manager?”—A Systematic Review of Gender Stereotypes and Organizational Discrimination
Authors: Castaño Ana , Fontanil Yolanda , García-Izquierdo Antonio
Published: May 2019

Women continue to lag behind for accessing managerial positions, partially due to discrimination at work. One of the main roots of such discrimination is gender stereotyping, so we aim to comprehend those biased procedures. First, we have analyzed those highlighted gender lawsuit cases in the scientific literature that have dealt with stereotypes both in the American and the European work contexts. Second, meta-analytic studies regarding organizational consequences of gender stereotypes have been synthetized. Third, gender stereotypes have been grouped by means of a content analysis of the existing literature after processing 61 articles systematically retrieved from WOS, SCOPUS, and PsycINFO databases. As a result, a taxonomy of gender stereotypes has been achieved evidencing that descriptive and prescriptive stereotypes have an impact on decision-making procedures through the apparently perception of women as less suitable for managerial positions. Moreover, we offer a deep explanation of the gender discrimination phenomenon under the umbrella of psychosocial theories, and some measures for successfully overcoming management stereotyping, showing that organizational culture can be improved from both the perspective of equal employment opportunities and the organizational justice frameworks for reaching a balanced and healthier workplace.
Istex: A Database of Twenty Million Scientific Papers with a Mining Tool Which Uses Named Entities
Authors: Maurel Denis , Morale Enza , Thouvenin Nicolas , Ringot Patrice , Turri Angel
Published: May 2019

Istex is a database of twenty million full text scientific papers bought by the French Government for the use of academic libraries. Papers are usually searched for by the title, authors, keywords or possibly the abstract. To authorize new types of queries of Istex, we implemented a system of named entity recognition on all papers and we offer users the possibility to run searches on these entities. After the presentation of the French Istex project, we detail in this paper the named entity recognition with CasEN, a cascade of graphs, implemented on the Unitex Software. CasEN exists in French, but not in English. The first challenge was to build a new cascade in a short time. The results of its evaluation showed a good Precision measure, even if the Recall was not very good. The Precision was very important for this project to ensure it did not return unwanted papers by a query. The second challenge was the implementation of Unitex to parse around twenty millions of documents. We used a dockerized application. Finally, we explain also how to query the resulting Named entities in the Istex website.
Novel Stopping Criteria for Optimization-Based Microwave Breast Imaging Algorithms
Authors: Kaye Cameron , Jeffrey Ian , LoVetri Joe
Published: May 2019

A discontinuous Galerkin formulation of the Contrast Source Inversion algorithm (DGM-CSI) for microwave breast imaging employing a frequency-cycling reconstruction technique has been modified here to include a set of automated stopping criteria that determine a suitable time to shift imaging frequencies and to globally terminate the reconstruction. Recent studies have explored the use of tissue-dependent geometrical mapping of the well-reconstructed real part to its imaginary part as initial guesses during consecutive frequency hops. This practice was shown to improve resulting 2D images of the dielectric properties of synthetic breast models, but a fixed number of iterations was used to halt DGM-CSI inversions arbitrarily. Herein, a new set of stopping conditions is introduced based on an intelligent statistical analysis of a window of past iterations of data error using the two-sample Kolmogorov-Smirnov (K-S) test. This non-parametric goodness-of-fit test establishes a pattern in the data error distribution, indicating an appropriate time to shift frequencies, or terminate the algorithm. The proposed stopping criteria are shown to improve the efficiency of DGM-CSI while yielding images of equivalent quality to assigning an often liberally overestimated number of iterations per reconstruction.
Relevance of HLA-DQB1*02 Allele in the Genetic Predisposition of Children with Celiac Disease: Additional Cues from a Meta-Analysis
Authors: Capittini Cristina , De Silvestri Annalisa , Rebuffi Chiara , Tinelli Carmine , Poddighe Dimitri
Published: May 2019

Background and Objectives: Celiac disease (CD) is a multifactorial immune-mediated disorder, triggered by the ingestion of gluten in genetically-predisposed subjects carrying MHC-DQ2 and -DQ8 heterodimers, which are encoded by four HLA-DQ allelic variants, overall. This meta-analysis aims at providing further epidemiological support to the predominant relevance of one specific allele, namely HLA-DQB1*02, in the predisposition and genetic risk of CD. Materials and Methods: We performed a search of MEDLINE/PubMed, Embase, Web of Science, and Scopus, retrieving all publications (case–control study, cross-sectional, and retrospective cohort study) on the association between HLA class II polymorphisms and first-degree relatives (FDRs) of children with CD. After a critical reading of the articles, two investigators independently performed data extraction according to the following inclusion criteria: HLA class II genes, any DQ and DR molecules, and CD diagnosed following the current clinical guidelines. A third participant was consulted for discussion to reach an agreement concerning discrepancies. Results: Our search strategy selected 14 studies as being eligible for inclusion, and those were submitted for data extraction and analysis. These studies were published between 1999 and 2016 and, collectively, enrolled 3063 FDRs. Positive and negative likelihood ratios (LR+ and LR−, respectively) for CD diagnosis, according to the presence of the HLA-DQ genotype coding a complete MHC-DQ2 and/or MHC-DQ8 molecules, were 1.449 (CI 1.279–1.642) and 0.187 (CI 0.096–0.362), respectively. If only the isolated presence of HLA-DQB1*02 allele is considered, the pooled estimation of LR+ was 1.659 (CI 1.302–2.155) and, importantly, the LR− still showed a very good discriminatory power of 0.195 (CI 0.068–0.558). Conclusions: Through our differential meta-analysis, comparing the presence of the genotype coding the full MHC-DQ2 and/or DQ8 molecules with the isolated presence of HLA-DQB1*02 allelic variant, we found that the LR− of the latter analysis maintained the same value. This observation, along with previous evidences, might be useful to consider potential cost-effective widened screening strategies for CD in children.
Discovering Biomarkers and Pathways Shared by Alzheimer’s Disease and Ischemic Stroke to Identify Novel Therapeutic Targets
Authors: Rahman Md. Rezanur , Islam Tania , Shahjaman Md. , Zaman Toyfiquz , Faruquee Hossain Md. , Jamal Mohammad Abu Hena Mostofa , Huq Fazlul , Quinn Julian M. W. , Moni Mohammad Ali
Published: May 2019

Background and objectives: Alzheimer’s disease (AD) is a progressive neurodegenerative disease that results in severe dementia. Having ischemic strokes (IS) is one of the risk factors of the AD, but the molecular mechanisms that underlie IS and AD are not well understood. We thus aimed to identify common molecular biomarkers and pathways in IS and AD that can help predict the progression of these diseases and provide clues to important pathological mechanisms. Materials and Methods: We have analyzed the microarray gene expression datasets of IS and AD. To obtain robust results, combinatorial statistical methods were used to analyze the datasets and 26 transcripts (22 unique genes) were identified that were abnormally expressed in both IS and AD. Results: Gene Ontology (GO) and KEGG pathway analyses indicated that these 26 common dysregulated genes identified several altered molecular pathways: Alcoholism, MAPK signaling, glycine metabolism, serine metabolism, and threonine metabolism. Further protein–protein interactions (PPI) analysis revealed pathway hub proteins PDE9A, GNAO1, DUSP16, NTRK2, PGAM2, MAG, and TXLNA. Transcriptional and post-transcriptional components were then identified, and significant transcription factors (SPIB, SMAD3, and SOX2) found. Conclusions: Protein–drug interaction analysis revealed PDE9A has interaction with drugs caffeine, γ-glutamyl glycine, and 3-isobutyl-1-methyl-7H-xanthine. Thus, we identified novel putative links between pathological processes in IS and AD at transcripts levels, and identified possible mechanistic and gene expression links between IS and AD.
A Comprehensive Plasma Metabolomics Dataset for a Cohort of Mouse Knockouts within the International Mouse Phenotyping Consortium
Authors: Barupal Dinesh K. , Zhang Ying , Shen Tong , Fan Sili , Roberts Bryan S. , Fitzgerald Patrick , Wancewicz Benjamin , Valdiviez Luis , Wohlgemuth Gert , Byram Gregory , Choy Ying Yng , Haffner Bennett , Showalter Megan R. , Vaniya Arpana , Bloszies Clayton S. , Folz Jacob S. , Kind Tobias , Flenniken Ann M. , McKerlie Colin , Nutter Lauryl M. J. , Lloyd Kent C. , Fiehn Oliver
Published: May 2019

Mouse knockouts facilitate the study ofgene functions. Often, multiple abnormal phenotypes are induced when a gene is inactivated. The International Mouse Phenotyping Consortium (IMPC) has generated thousands of mouse knockouts and catalogued their phenotype data. We have acquired metabolomics data from 220 plasma samples from 30 unique mouse gene knockouts and corresponding wildtype mice from the IMPC. To acquire comprehensive metabolomics data, we have used liquid chromatography (LC) combined with mass spectrometry (MS) for detecting polar and lipophilic compounds in an untargeted approach. We have also used targeted methods to measure bile acids, steroids and oxylipins. In addition, we have used gas chromatography GC-TOFMS for measuring primary metabolites. The metabolomics dataset reports 832 unique structurally identified metabolites from 124 chemical classes as determined by ChemRICH software. The GCMS and LCMS raw data files, intermediate and finalized data matrices, R-Scripts, annotation databases, and extracted ion chromatograms are provided in this data descriptor. The dataset can be used for subsequent studies to link genetic variants with molecular mechanisms and phenotypes.
Development of Piezo-Actuated Two-Degree-of-Freedom Fast Tool Servo System
Authors: Liu Yamei , Zheng Yanping , Gu Yan , Lin Jieqiong , Lu Mingming , Xu Zisu , Fu Bin
Published: May 2019

Fast tool servo (FTS) machining technology is a promising method for freeform surfaces and machining micro-nanostructure surfaces. However, limited degrees of freedom (DOF) is an inherent drawback of existing FTS technologies. In this paper, a piezo-actuated serial structure FTS system is developed to obtain translational motions along with z and x-axis directions for ultra-precision machining. In addition, the principle of the developed 2-DOF FTS is introduced and explained. A high-rigidity four-bar (HRFB) mechanism is proposed to produce motion along the z-axis direction. Additionally, through a micro-rotation motion around flexible bearing hinges (FBHs), bi-directional motions along the x-axis direction can be produced. The kinematics of the mechanism are described using a matrix-based compliance modeling (MCM) method, and then the static analysis and dynamic analysis are performed using finite element analysis (FEA). Testing experiments were conducted to investigate the actual performance of the developed system. The results show that low coupling, proper travel, and high natural frequency are obtained. Finally, a sinusoidal wavy surface is uniformly generated by the mechanism developed to demonstrate the effectiveness of the FTS system.
Comparison of Phytochemical Differences of the Pulp of Different Peach [Prunus persica (L.) Batsch] Cultivars with Alpha-Glucosidase Inhibitory Activity Variations in China Using UPLC-Q-TOF/MS
Authors: Zhang Xianan , Su Mingshen , Du Jihong , Zhou Huijuan , Li Xiongwei , Li Xin , Ye Zhengwen
Published: May 2019

In order to fully understand the variation of the fruit alpha-glucosidase inhibitory activity-related phytochemical basis in the Chinese peach [Prunus persica (L.) Batsch], mature fruit from 33 cultivars was used for the investigation of fruit phenolic phytochemical attributes, including total phenolics, flavonoids, anthocyanins, and procyanidins, as well as the alpha-glucosidase inhibitory activity in vitro. Alpha-glucosidase inhibitory activity varied significantly among tested peach cultivars and was strongly correlated with total phenolics, total procyanidins, and total flavonoids. Untargeted UPLC-Q-TOF/MS-based metabolomics were used to comprehensively discriminate between peaches with different inhibitory activity on alpha-glucosidase. Principal component analysis (PCA) and orthogonal partial least squares discrimination analysis (OPLS-DA) were used for this process. Twenty-three differential compounds were identified between peach cultivars with high and low alpha-glucosidase inhibitory activity, and nine, including procyanidin C1, procyanidin trimer isomer 1, procyanidin trimer isomer 2, procyanidin B1, procyanidin dimer, epicatechin-epicatechin-epicatechin, phloridzin, kaempferol 3-(2’’,6’’-di-(E)-p-coumarylglucoside), and luteolin 3’-methyl ether 7-malonylglucoside, were identified as marker compounds responsible for the discrimination. Overall, variations in metabolites in peach pulp reflect the diversity in peach germplasm, and these nine compounds are good candidate markers for future genetic breeding of peach fruit with high alpha-glucosidase inhibitory activity.
Silver Nanoparticles on Cellulose Surfaces: Quantitative Measurements
Authors: Carapeto Ana Patrícia , Ferraria Ana Maria , Botelho do Rego Ana Maria
Published: May 2019

In this work, cellulose films pre-activated with carbonyldiimidazole (CDI) and grafted with 1,6-hexanediamine, were decorated with silver nanoparticles (AgNPs). The generation of AgNPs was followed by quartz crystal microbalance (QCM). The obtained films were characterized by X-Ray Photoelectron Spectroscopy (XPS) and imaged by atomic force microscopy (AFM). XPS confirmed the synthesis in situ of AgNPs on the film attesting their oxidation state. The results from the three techniques were compared showing how sound the quantitative treatment of the results issued from these techniques can be. The main objective of this work is exactly to show that the quantitative exploration of the results of different characterization techniques can and should be practiced systematically instead of just comparing them qualitatively.
Plasmon Sensitized Heterojunction 2D Ultrathin Ag/AgI-δ-Bi2O3 for Enhanced Photocatalytic Nitrogen Fixation
Authors: Gao Xiaoming , Shang Yanyan , Gao Kailong , Fu Feng
Published: May 2019

A novel 2D ultrathin Ag/AgI-δ-Bi2O3 photocatalyst was constructed by a facile hydrothermal and in situ photodeposition method, which presented a uniform nanosheet structure with an average height of 6 nm. Its composition, morphology and light-harvesting properties were characterized by X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM), transmission electron microscopy (TEM), UV–vis spectrophotometer (UV–vis) and photoluminescence (PL) measurements in detail. The Ag/AgI-δ-Bi2O3 nanocomposites showed an excellent photocatalytic nitrogen fixation performance of 420 μmol L−1 g−1 h−1 in water without any sacrificial agent. The introduction of Ag/AgI nanoparticles caused the morphology modification of δ-Bi2O3, a higher concentration of oxygen vacancy, and the construction of a plasmon sensitized heterojunction, resulting in enhanced light absorption, improved separation efficiency of charge carriers and strong N2 absorption and activation ability, which are responsible for the superior photocatalytic performance of Ag/AgI-δ-Bi2O3.
Can Gut Microbiota Composition Predict Response to Dietary Treatments?
Authors: Biesiekierski Jessica R , Jalanka Jonna , Staudacher Heidi M
Published: May 2019

Dietary intervention is a challenge in clinical practice because of inter-individual variability in clinical response. Gut microbiota is mechanistically relevant for a number of disease states and consequently has been incorporated as a key variable in personalised nutrition models within the research context. This paper aims to review the evidence related to the predictive capacity of baseline microbiota for clinical response to dietary intervention in two specific health conditions, namely, obesity and irritable bowel syndrome (IBS). Clinical trials and larger predictive modelling studies were identified and critically evaluated. The findings reveal inconsistent evidence to support baseline microbiota as an accurate predictor of weight loss or glycaemic response in obesity, or as a predictor of symptom improvement in irritable bowel syndrome, in dietary intervention trials. Despite advancement in quantification methodologies, research in this area remains challenging and larger scale studies are needed until personalised nutrition is realistically achievable and can be translated to clinical practice.
Comparison of Riser-Simplified, Riser-Only, and Full-Loop Simulations for a Circulating Fluidized Bed
Authors: Wang Min , Wu Yingya , Shi Xiaogang , Lan Xingying , Wang Chengxiu , Gao Jinsen
Published: May 2019

With the development of computing power, the simulation of circulating fluidized bed (CFB) has developed from riser-simplified simulation to riser-only simulation, then to full-loop simulation. This paper compared these three methods based on pilot-scale CFB experiment data to find the scope of application of each method. All these simulations, using the Eulerian–Eulerian two-fluid model with the kinetic theory of granular theory, were conducted to simulate a pilot-scale CFB. The hydrodynamics, such as pressure balance, solids holdup distribution, solids velocity distribution, and instantaneous mass flow rates in the riser or CFB system, were investigated in different simulations. By comparing the results from different methods, it was found that riser-simplified simulation is not sufficient to obtain accurate hydrodynamics, especially in higher solids circulating rates. The riser-only simulation is able to make a reasonable prediction of time-averaged behaviors of gas–solids in most parts of riser but the entrance region. Further, the full-loop simulation can not only predict precise results, but also obtain comprehensive details and instantaneous information in the CFB system.
Influence of Lower Atmosphere on the Radiometric Quality of Unmanned Aerial Vehicle Imagery
Authors: Kedzierski Michal , Wierzbicki Damian , Sekrecka Aleksandra , Fryskowska Anna , Walczykowski Piotr , Siewert Jolanta
Published: May 2019

Unmanned aerial vehicle (UAV) imagery has been widely used in remote sensing and photogrammetry for some time. Increasingly often, apart from recording images in the red-green-blue (RGB) range, multispectral images are also recorded. It is important to accurately assess the radiometric quality of UAV imagery to eliminate interference that might reduce the interpretation potential of the images and distort the results of remote sensing analyses. Such assessment should consider the influence of the atmosphere and the seasonal and weather conditions at the time of acquiring the imagery. The assessment of the radiometric quality of images acquired in different weather conditions is crucial in terms of improving the interpretation potential of the imagery and improving the accuracy of determining the indicators used in remote sensing and in environmental monitoring. Until now, the assessment of radiometric quality of UAV imagery did not consider the influence of meteorological conditions at different times of year. This paper presents an assessment of the influence of weather conditions on the quality of UAV imagery acquired in the visible range. This study presents the methodology for assessing image quality, considering the weather conditions characteristic of autumn in Central and Eastern Europe. The proposed solution facilitates the assessment of the radiometric quality of images acquired in the visible range. Using the objective indicator of quality assessment developed in this study, images were classified into appropriate categories, allowing, at a later stage, to improve the results of vegetation indices. The obtained results confirm that the proposed quality assessment methodology enables the objective assessment of the quality of imagery acquired in different meteorological conditions.
Determinants of Smallholders’ Market Preferences: The Case of Sustainable Certified Coffee Farmers in Vietnam
Authors: Hung Anh Nguyen , Bokelmann Wolfgang
Published: May 2019

This study attempts to analyze the market preference of coffee farmers in Vietnam. Using the transaction cost approach, a seemingly unrelated regression (SUR) model was developed based on the sales volume in different markets, transaction cost attributes, socioeconomic factors, and behavioral aspects of sustainable certified coffee farmers. Factors that significantly influence farmers’ market preference include several transaction cost attributes (price uncertainty, market competition, transportation cost, speed of payment, and sale volume agreement) and characteristics of coffee farmers (age, ethnic, farming experience, location, and certificate ownership). Repeated economic transaction embedded in the social relationship indicates the largest sales volume of coffee farmers to the market of buying agents and the existence of local traders. There is a belief that formal institution brings better market access for coffee farmers, but main issues are regarding opportunistic behavior, imperfect market knowledge, traditional farming habits, and contract noncompliance, which have resulted in a lower preference for the market of processors/exporters.
Internet’s User Perception of Corporate Social Responsibility in Hotel Services
Authors: García-Pozo Alejandro , Mondéjar-Jiménez José , Sánchez-Ollero José Luis
Published: May 2019

The objective of this study was to use the perceptions of internet users to analyse the effect of the social, economic and environmental dimensions of corporate social responsibility (CSR) implemented by hotel establishments in order to determine whether those dimensions are perceived by consumers. Our analysis was based on a sample, distributed by age, sex and province segments, obtained from the Andalusian population between 16 and 74 years of age who are users of travel websites (e.g., TripAdvisor, Booking) and hotels corporate websites. A questionnaire was used to investigate each latent factor related to the three main dimensions of CSR that may affect the perceptions of accommodation service consumers. The questionnaire was statistically validated and developed in previous economic studies in this field. The data were analysed using Partial Last Square (PLS) methodology. The results confirm the validity of the three dimensions analysed, although consumers appear to play more relevance upon economic and environmental factors than upon the social components of CSR.
Numerical Solution of Non-Newtonian Fluid Flow Due to Rotatory Rigid Disk
Authors: Rehman Khalil Ur , Malik M. Y. , Khan Waqar A , Khan Ilyas , Alharbi S. O.
Published: May 2019

In this article, the non-Newtonian fluid model named Casson fluid is considered. The semi-infinite domain of disk is fitted out with magnetized Casson liquid. The role of both thermophoresis and Brownian motion is inspected by considering nanosized particles in a Casson liquid spaced above the rotating disk. The magnetized flow field is framed with Navier’s slip assumption. The Von Karman scheme is adopted to transform flow narrating equations in terms of reduced system. For better depiction a self-coded computational algorithm is executed rather than to move-on with build-in array. Numerical observations via magnetic, Lewis numbers, Casson, slip, Brownian motion, and thermophoresis parameters subject to radial, tangential velocities, temperature, and nanoparticles concentration are reported. The validation of numerical method being used is given through comparison with existing work. Comparative values of local Nusselt number and local Sherwood number are provided for involved flow controlling parameters.
Aspergillus flavus as a Model System to Test the Biological Activity of Botanicals: An Example on Citrullus colocynthis L. Schrad. Organic Extracts
Authors: Degola Francesca , Marzouk Belsem , Gori Antonella , Brunetti Cecilia , Dramis Lucia , Gelati Stefania , Buschini Annamaria , Restivo Francesco M.
Published: May 2019

Citrullus colocynthis L. Schrader is an annual plant belonging to the Cucurbitaceae family, widely distributed in the desert areas of the Mediterranean basin. Many pharmacological properties (anti-inflammatory, anti-diabetic, analgesic, anti-epileptic) are ascribed to different organs of this plant; extracts and derivatives of C. colocynthis are used in folk Berber medicine for the treatment of numerous diseases—such as rheumatism arthritis, hypertension bronchitis, mastitis, and even cancer. Clinical studies aimed at confirming the chemical and biological bases of pharmacological activity assigned to many plant/herb extracts used in folk medicine often rely on results obtained from laboratory preliminary tests. We investigated the biological activity of some C. colocynthis stem, leaf, and root extracts on the mycotoxigenic and phytopathogenic fungus Aspergillus flavus, testing a possible correlation between the inhibitory effect on aflatoxin biosynthesis, the phytochemical composition of extracts, and their in vitro antioxidant capacities.
Microcystis Chemotype Diversity in the Alimentary Tract of Bigheaded Carp
Authors: Riba Milán , Kiss-Szikszai Attila , Gonda Sándor , Boros Gergely , Vitál Zoltán , Borsodi Andrea Kériné , Krett Gergely , Borics Gábor , Ujvárosi Andrea Zsuzsanna , Vasas Gábor
Published: May 2019

Most cyanobacterial organisms included in the genus Microcystis can produce a wide repertoire of secondary metabolites. In the mid-2010s, summer cyanobacterial blooms of Microcystis sp. occurred regularly in Lake Balaton. During this period, we investigated how the alimentary tract of filter-feeding bigheaded carps could deliver different chemotypes of viable cyanobacteria with specific peptide patterns. Twenty-five Microcystis strains were isolated from pelagic plankton samples (14 samples) and the hindguts of bigheaded carp (11 samples), and three bloom samples were collected from the scums of cyanobacterial blooms. An LC-MS/MS-based untargeted approach was used to analyze peptide patterns, which identified 36 anabaenopeptin, 17 microginin, and 13 microcystin variants. Heat map clustering visualization was used to compare the identified chemotypes. A lack of separation was observed in peptide patterns of Microcystis that originated from hindguts, water samples, and bloom-samples. Except for 13 peptides, all other congeners were detected from the viable and cultivated chemotypes of bigheaded carp. This finding suggests that the alimentary tract of bigheaded carps is not simply an extreme habitat, but may also supply the cyanobacterial strains that represent the pelagic chemotypes.
Prevalent Mycotoxins in Animal Feed: Occurrence and Analytical Methods
Authors: Santos Pereira Carolina , C. Cunha Sara , Fernandes José O.
Published: May 2019

Today, we have been witnessing a steady tendency in the increase of global demand for maize, wheat, soybeans, and their products due to the steady growth and strengthening of the livestock industry. Thus, animal feed safety has gradually become more important, with mycotoxins representing one of the most significant hazards. Mycotoxins comprise different classes of secondary metabolites of molds. With regard to animal feed, aflatoxins, fumonisins, ochratoxins, trichothecenes, and zearalenone are the more prevalent ones. In this review, several constraints posed by these contaminants at economical and commercial levels will be discussed, along with the legislation established in the European Union to restrict mycotoxins levels in animal feed. In addition, the occurrence of legislated mycotoxins in raw materials and their by-products for the feeds of interest, as well as in the feeds, will be reviewed. Finally, an overview of the different sample pretreatment and detection techniques reported for mycotoxin analysis will be presented, the main weaknesses of current methods will be highlighted.