bluuebunny/crossref_metadata_2025 huggingface dataset:
Genome-Wide Identification and Expression Analyses of the bZIP Transcription Factor Genes in moso bamboo (Phyllostachys edulis)
Authors: Pan Feng , Wu Min , Hu Wenfang , Liu Rui , Yan Hanwei , Xiang Yan
Published: May 2019

The basic leucine zipper (bZIP) transcription factor (TF) family is one of the largest gene families, and play crucial roles in many processes, including stress responses, hormone effects. The TF family also participates in plant growth and development. However, limited information is available for these genes in moso bamboo (Phyllostachys edulis), one of the most important non-timber forest products in the world. In the present study, 154 putative PhebZIP genes were identified in the moso bamboo genome. The phylogenetic analyses indicate that the PhebZIP gene proteins classify into 9 subfamilies and the gene structures and conserved motifs that analyses identified among all PhebZIP proteins suggested a high group-specificity. Microsynteny and evolutionary patterns analyses of the non-synonymous (Ka) and synonymous (Ks) substitution rates and their ratios indicated that paralogous pairs of PhebZIP genes in moso bamboo underwent a large-scale genome duplication event that occurred 7–15 million years ago (MYA). According to promoter sequence analysis, we further selected 18 genes which contain the higher number of cis-regulatory elements for expression analysis. The result showed that these genes are extensively involved in GA-, ABA- and MeJA-responses, with possibly different mechanisms. The tissue-specific expression profiles of PhebZIP genes in five plant tissues/organs/developmental stages suggested that these genes are involved in moso bamboo organ development, especially seed development. Subcellular localization and transactivation activity analysis showed that PhebZIP47 and PhebZIP126 were localized in the nucleus and PhebZIP47 with no transcriptional activation in yeast. Our research provides a comprehensive understanding of PhebZIP genes and may aid in the selection of appropriate candidate genes for further cloning and functional analysis in moso bamboo growth and development, and improve their resistance to stress during their life.
Functional Analysis of Peptidyl-prolyl cis-trans Isomerase from Aspergillus flavus
Authors: Ahmad Saleem , Wang Sen , Wu Weizhong , Yang Kunlong , Zhang YanFeng , Tumukunde Elisabeth , Wang Shihua , Wang Yu
Published: May 2019

Aspergillus flavus, a ubiquitous filamentous fungus found in soil, plants and other substrates has been reported not only as a pathogen for plants, but also a carcinogen producing fungus for human. Peptidyl-Prolyl Isomerase (PPIases) plays an important role in cell process such as protein secretion cell cycle control and RNA processing. However, the function of PPIase has not yet been identified in A. flavus. In this study, the PPIases gene from A. flavus named ppci1 was cloned into expression vector and the protein was expressed in prokaryotic expression system. Activity of recombinant ppci1 protein was particularly inhibited by FK506, CsA and rapamycin. 3D-Homology model of ppci1 has been constructed with the template, based on 59.7% amino acid similarity. The homologous recombination method was used to construct the single ppci1 gene deletion strain Δppci1. We found that, the ppci1 gene plays important roles in A. flavus growth, conidiation, and sclerotia formation, all of which showed reduction in Δppci1 and increased in conidiation compared with the wild-type and complementary strains in A. flavus. Furthermore, aflatoxin and peanut seeds infection assays indicated that ppci1 contributes to virulence of A. flavus. Furthermore, we evaluated the effect of PPIase inhibitors on A. flavus growth, whereby these were used to treat wild-type strains. We found that the growths were inhibited under every inhibitor. All, these results may provide valuable information for designing inhibitors in the controlling infections of A. flavus.
Nanostructured SL9-CpG Lipovaccines Elicit Immune Response for the Treatment of Melanoma
Authors: Mu Li-Min , Liu Lei , Liu Rui , Du Ya-Fei , Luo Qian , Xu Jia-Rui , Xie Ying , Lu Wan-Liang
Published: May 2019

Antigen peptides and adjuvants have been extensively investigated for cancer immunotherapy, and they are expected to elicit specific immune responses for cancer treatment. However, the anti-cancer efficacy of antigen peptide and adjuvant-based cancer vaccines has been limited due to the inefficient delivery to draining lymph nodes after administration. Therefore, it is necessary to develop a suitable delivery system to transport antigen peptides and adjuvants. Here, we report a novel type of nanostructured lipovaccines for the treatment of melanoma by delivering antigen peptide (SL9) and oligodeoxynucleotide adjuvant (CpG) to the lymphatic vessels and to the draining lymph node. The SL9-CpG lipovaccines were characterized using dynamic laser scattering (DLS) and transmission electron microscopy (TEM). The lymph uptake, immune response elicitation and treatment effects were evaluated on melanoma-bearing C57BL/6 mice using flow cytometry (FCM), enzyme-linked immunosorbent assay (ELISA) and tumor inhibitory efficacy. The SL9-CpG lipovaccines were uniform with a nanoscale size (~70 nm), had high encapsulation efficiency, and exhibited effective lymph uptake, resulting in activation of specific cytotoxic CD8+ T cells, and release of IFN-γ, and a robust inhibition of tumor growth. Therefore, the nanostructured SL9-CpG lipovaccines offer a promising strategy for melanoma treatment.
The Small GTPase Arf6: An Overview of Its Mechanisms of Action and of Its Role in Host–Pathogen Interactions and Innate Immunity
Authors: Van Acker Tim , Tavernier Jan , Peelman Frank
Published: May 2019

The small GTase Arf6 has several important functions in intracellular vesicular trafficking and regulates the recycling of different types of cargo internalized via clathrin-dependent or -independent endocytosis. It activates the lipid modifying enzymes PIP 5-kinase and phospholipase D, promotes actin polymerization, and affects several functionally distinct processes in the cell. Arf6 is used for the phagocytosis of pathogens and can be directly or indirectly targeted by various pathogens to block phagocytosis or induce the uptake of intracellular pathogens. Arf6 is also used in the signaling of Toll-like receptors and in the activation of NADPH oxidases. In this review, we first give an overview of the different roles and mechanisms of action of Arf6 and then focus on its role in innate immunity and host–pathogen interactions.
Relevance of Interactions between Starch-based Coatings and Plum Fruit Surfaces: A Physical-Chemical Analysis
Authors: Basiak Ewelina , Geyer Martin , Debeaufort Frédéric , Lenart Andrzej , Linke Manfred
Published: May 2019

In order to extend the shelf life of the fruit, improve appearance, and to keep all nutrition properties of the plum from diminishing, edible coatings comprised of wheat starch and wheat starch–whey protein isolate (in ratio 80/20) were created. Stand-alone films were produced to assess properties which helped to understand the phenomena occurring on the surface level of coated plums. The properties of coatings based on starch are similar to starch coatings containing oil because the natural epicuticular wax layer of plums merges with coating materials. Adding oil doubled the contact angle value and the dispersive component of the surface tension. The workings of adhesion and cohesion, spreading coefficient, water absorption, water content, and solubility in water of the films decreased. Similar processes were observed on the fruits’ surface. In appearance, the coating process is similar to polishing the plum surface for removing crystalline wax. The color parameters of coated fruits did not significantly change. Newly formed bonds or interactions established between starch, whey proteins, water, glycerol, and oil are displayed by Fourier transform infrared (FTIR) analysis. This work revealed how the interactions between the epicuticular wax on the fruit’s surface and the hydrocolloid-based coatings affect the efficiency of the coatings.
Overexpression of SmANS Enhances Anthocyanin Accumulation and Alters Phenolic Acids Content in Salvia miltiorrhiza and Salvia miltiorrhiza Bge f. alba Plantlets
Authors: Li Hongyan , Liu Jingling , Pei Tianlin , Bai Zhenqing , Han Ruilian , Liang Zongsuo
Published: May 2019

Flavonoids play multiple roles in plant coloration and stress resistance and are closely associated with human health. Flavonoids and non-flavonoids (such as phenolic acids) are produced via the phenylpropanoid-derived pathway. Anthocyanidin synthase (ANS) catalyzes the synthesis of anthocyanins from leucoanthocyanidin in the flavonoids branched pathway. In this study, SmANS from Salvia miltiorrhiza was cloned and mainly localized in the endoplasmic reticulum (ER), plastids, Golgi, plasma membrane, and nucleus of tobacco epidermal cells, and was most highly expressed in purple petals in S. miltiorrhiza, whereas it showed almost no expression in white petals, green calyxes, and pistils in S. miltiorrhiza Bge f. alba. Overexpressed SmANS enhanced anthocyanin accumulation but reduced salvianolic acid B (SAB) and rosmarinic acid (RA) biosynthesis in S. miltiorrhiza and S. miltiorrhiza Bge f. alba plantlets, meanwhile, it restored the purple-red phenotype in S. miltiorrhiza Bge f. alba. These changes were due to reallocation of the metabolic flow, which was influenced by the SmANS gene. These findings indicate that SmANS not only plays a key role in anthocyanin accumulation in S. miltiorrhiza, but also acts as a “switch” for the coloration of S. miltiorrhiza Bge f. alba. This study provides baseline information for further research on flavonoids metabolism and improvement of anthocyanin or phenolic acid production by genetic engineering.
Magnetodielectric Response of Soft Magnetoactive Elastomers: Effects of Filler Concentration and Measurement Frequency
Authors: Kostrov Sergei A. , Shamonin Mikhail , Stepanov Gennady V. , Kramarenko Elena Yu.
Published: May 2019

The magnetodielectric response of magnetoactive elastomers (MAEs) in its dependence on filler concentration, magnetic field, and test frequency is studied experimentally. MAEs are synthesized on the basis of a silicone matrix filled with spherical carbonyl iron particles characterized by a mean diameter of 4.5 µm. The concentration of the magnetic filler within composite materials is equal to 70, 75, and 80 mass%. The effective lossless permittivity ε′ as well as the dielectric loss tanδ grow significantly when the magnetic field increases. The permittivity increases and the dielectric loss decreases with increasing filler concentration. In the measurement frequency range between 1 kHz and 200 kHz, the frequency hardly affects the values of ε′ and tanδ in the absence of a magnetic field. However, both parameters decrease considerably with the growing frequency in a constant magnetic field. The more strongly the magnetic field is applied, the larger the change in permittivity and loss tangent at the same test frequency is observed. An equivalent circuit formulation qualitatively describes the main tendencies of the magnetodielectric response.
Amniotic Fluid Cells, Stem Cells, and p53: Can We Stereotype p53 Functions?
Authors: Rodrigues Melissa , Blattner Christine , Stuppia Liborio
Published: May 2019

In recent years, great interest has been devoted to finding alternative sources for human stem cells which can be easily isolated, ideally without raising ethical objections. These stem cells should furthermore have a high proliferation rate and the ability to differentiate into all three germ layers. Amniotic fluid, ordinarily discarded as medical waste, is potentially such a novel source of stem cells, and these amniotic fluid derived stem cells are currently gaining a lot of attention. However, further information will be required about the properties of these cells before they can be used for therapeutic purposes. For example, the risk of tumor formation after cell transplantation needs to be explored. The tumor suppressor protein p53, well known for its activity in controlling Cell Prolif.eration and cell death in differentiated cells, has more recently been found to be also active in amniotic fluid stem cells. In this review, we summarize the major findings about human amniotic fluid stem cells since their discovery, followed by a brief overview of the important role played by p53 in embryonic and adult stem cells. In addition, we explore what is known about p53 in amniotic fluid stem cells to date, and emphasize the need to investigate its role, particularly in the context of cell tumorigenicity.
What Drives Symbiotic Calcium Signalling in Legumes? Insights and Challenges of Imaging
Authors: Vaz Martins Teresa , Livina Valerie N.
Published: May 2019

We review the contribution of bioimaging in building a coherent understanding of Ca 2 + signalling during legume-bacteria symbiosis. Currently, two different calcium signals are believed to control key steps of the symbiosis: a Ca 2 + gradient at the tip of the legume root hair is involved in the development of an infection thread, while nuclear Ca 2 + oscillations, the hallmark signal of this symbiosis, control the formation of the root nodule, where bacteria fix nitrogen. Additionally, different Ca 2 + spiking signatures have been associated with specific infection stages. Bioimaging is intrinsically a cross-disciplinary area that requires integration of image recording, processing and analysis. We used experimental examples to critically evaluate previously-established conclusions and draw attention to challenges caused by the varying nature of the signal-to-noise ratio in live imaging. We hypothesise that nuclear Ca 2 + spiking is a wide-range signal involving the entire root hair and that the Ca 2 + signature may be related to cytoplasmic streaming.
Digital PCR in Myeloid Malignancies: Ready to Replace Quantitative PCR?
Authors: Cilloni Daniela , Petiti Jessica , Rosso Valentina , Andreani Giacomo , Dragani Matteo , Fava Carmen , Saglio Giuseppe
Published: May 2019

New techniques are on the horizon for the detection of small leukemic clones in both, acute leukemias and myeloproliferative disorders. A promising approach is based on digital polymerase chain reaction (PCR). Digital PCR (dPCR) is a breakthrough technology designed to provide absolute nucleic acid quantification. It is particularly useful to detect a low amount of target and therefore it represents an alternative method for detecting measurable residual disease (MRD). The main advantages are the high precision, the very reliable quantification, the absolute quantification without the need for a standard curve, and the excellent reproducibility. Nowadays the main disadvantages of this strategy are the costs that are still higher than standard qPCR, the lack of standardized methods, and the limited number of laboratories that are equipped with instruments for dPCR. Several studies describing the possibility and advantages of using digital PCR for the detection of specific leukemic transcripts or mutations have already been published. In this review we summarize the available data on the use of dPCR in acute myeloid leukemia and myeloproliferative disorders.
UBA6 and Its Bispecific Pathways for Ubiquitin and FAT10
Authors: Wang Fengting , Zhao Bo
Published: May 2019

Questions have been raised since the discovery of UBA6 and its significant coexistence with UBE1 in the ubiquitin–proteasome system (UPS). The facts that UBA6 has the dedicated E2 enzyme USE1 and the E1–E2 cascade can activate and transfer both ubiquitin and ubiquitin-like protein FAT10 have attracted a great deal of attention to the regulational mechanisms of the UBA6–USE1 cascade and to how FAT10 and ubiquitin differentiate with each other. This review recapitulates the latest advances in UBA6 and its bispecific UBA6–USE1 pathways for both ubiquitin and FAT10. The intricate networks of UBA6 and its interplays with ubiquitin and FAT10 are briefly reviewed, as are their individual and collective functions in diverse physiological conditions.
A Thermostable Aspergillus fumigatus GH7 Endoglucanase Over-Expressed in Pichia pastoris Stimulates Lignocellulosic Biomass Hydrolysis
Authors: Vianna Bernardi Aline , Kimie Yonamine Deborah , Akira Uyemura Sergio , Magnani Dinamarco Taisa
Published: May 2019

In the context of avoiding the use of non-renewable energy sources, employing lignocellulosic biomass for ethanol production remains a challenge. Cellulases play an important role in this scenario: they are some of the most important industrial enzymes that can hydrolyze lignocellulose. This study aims to improve on the characterization of a thermostable Aspergillus fumigatus endo-1,4-β-glucanase GH7 (Af-EGL7). To this end, Af-EGL7 was successfully expressed in Pichia pastoris X-33. The kinetic parameters Km and Vmax were estimated and suggested a robust enzyme. The recombinant protein was highly stable within an extreme pH range (3.0–8.0) and was highly thermostable at 55 °C for 72 h. Low Cu2+ concentrations (0.1–1.0 mM) stimulated Af-EGL7 activity up to 117%. Af-EGL7 was tolerant to inhibition by products, such as glucose and cellobiose. Glucose at 50 mM did not inhibit Af-EGL7 activity, whereas 50 mM cellobiose inhibited Af-EGL7 activity by just 35%. Additionally, the Celluclast® 1.5L cocktail supplemented with Af-EGL7 provided improved hydrolysis of sugarcane bagasse “in natura”, sugarcane exploded bagasse (SEB), corncob, rice straw, and bean straw. In conclusion, the novel characterization of Af-EGL7 conducted in this study highlights the extraordinary properties that make Af-EGL7 a promising candidate for industrial applications.
Circadian Regulation in Tissue Regeneration
Authors: Paatela Ellen , Munson Dane , Kikyo Nobuaki
Published: May 2019

Circadian rhythms regulate over 40% of protein-coding genes in at least one organ in the body through mechanisms tied to the central circadian clock and to cell-intrinsic auto-regulatory feedback loops. Distinct diurnal differences in regulation of regeneration have been found in several organs, including skin, intestinal, and hematopoietic systems. Each regenerating system contains a complex network of cell types with different circadian mechanisms contributing to regeneration. In this review, we elucidate circadian regeneration mechanisms in the three representative systems. We also suggest circadian regulation of global translational activity as an understudied global regulator of regenerative capacity. A more detailed understanding of the molecular mechanisms underlying circadian regulation of tissue regeneration would accelerate the development of new regenerative therapies.
Sex-Dependent Effects of Perinatal Inflammation on the Brain: Implication for Neuro-Psychiatric Disorders
Authors: Ardalan Maryam , Chumak Tetyana , Vexler Zinaida , Mallard Carina
Published: May 2019

Individuals born preterm have higher rates of neurodevelopmental disorders such as schizophrenia, autistic spectrum, and attention deficit/hyperactivity disorders. These conditions are often sexually dimorphic and with different developmental trajectories. The etiology is likely multifactorial, however, infections both during pregnancy and in childhood have emerged as important risk factors. The association between sex- and age-dependent vulnerability to neuropsychiatric disorders has been suggested to relate to immune activation in the brain, including complex interactions between sex hormones, brain transcriptome, activation of glia cells, and cytokine production. Here, we will review sex-dependent effects on brain development, including glia cells, both under normal physiological conditions and following perinatal inflammation. Emphasis will be given to sex-dependent effects on brain regions which play a role in neuropsychiatric disorders and inflammatory reactions that may underlie early-life programming of neurobehavioral disturbances later in life.
Using Thermography to Confirm Genotypic Variation for Drought Response in Maize
Authors: Casari Raphael , Paiva Dayane , Silva Vivianny , Ferreira Thalita , Souza, Junior Manoel , Oliveira Nelson , Kobayashi Adilson , Molinari Hugo , Santos Thiago , Gomide Reinaldo , Magalhães Paulo , Sousa Carlos
Published: May 2019

The feasibility of thermography as a technique for plant screening aiming at drought-tolerance has been proven by its relationship with gas exchange, biomass, and yield. In this study, unlike most of the previous, thermography was applied for phenotyping contrasting maize genotypes whose classification for drought tolerance had already been established in the field. Our objective was to determine whether thermography-based classification would discriminate the maize genotypes in a similar way as the field selection in which just grain yield was taken into account as a criterion. We evaluated gas exchange, daily water consumption, leaf relative water content, aboveground biomass, and grain yield. Indeed, the screening of maize genotypes based on canopy temperature showed similar results to traditional methods. Nevertheless, canopy temperature only partially reflected gas exchange rates and daily water consumption in plants under drought. Part of the explanation may lie in the changes that drought had caused in plant leaves and canopy structure, altering absorption and dissipation of energy, photosynthesis, transpiration, and partitioning rates. Accordingly, although there was a negative relationship between grain yield and plant canopy temperature, it does not necessarily mean that plants whose canopies were maintained cooler under drought achieved the highest yield.
Hidden Aggregation Hot-Spots on Human Apolipoprotein E: A Structural Study
Authors: Tsiolaki Paraskevi L. , Katsafana Aikaterini D. , Baltoumas Fotis A. , Louros Nikolaos N. , Iconomidou Vassiliki A.
Published: May 2019

Human apolipoprotein E (apoE) is a major component of lipoprotein particles, and under physiological conditions, is involved in plasma cholesterol transport. Human apolipoprotein E found in three isoforms (E2; E3; E4) is a member of a family of apolipoproteins that under pathological conditions are detected in extracellular amyloid depositions in several amyloidoses. Interestingly, the lipid-free apoE form has been shown to be co-localized with the amyloidogenic Aβ peptide in amyloid plaques in Alzheimer’s disease, whereas in particular, the apoE4 isoform is a crucial risk factor for late-onset Alzheimer’s disease. Evidence at the experimental level proves that apoE self-assembles into amyloid fibrilsin vitro, although the misfolding mechanism has not been clarified yet. Here, we explored the mechanistic insights of apoE misfolding by testing short apoE stretches predicted as amyloidogenic determinants by AMYLPRED, and we computationally investigated the dynamics of apoE and an apoE–Αβ complex. Our in vitro biophysical results prove that apoE peptide–analogues may act as the driving force needed to trigger apoE aggregation and are supported by the computational apoE outcome. Additional computational work concerning the apoE–Αβ complex also designates apoE amyloidogenic regions as important binding sites for oligomeric Αβ; taking an important step forward in the field of Alzheimer’s anti-aggregation drug development.
The Role of Chemokines in the Pathophysiology of Major Depressive Disorder
Authors: Milenkovic Vladimir M. , Stanton Evan H. , Nothdurfter Caroline , Rupprecht Rainer , Wetzel Christian H.
Published: May 2019

Major depressive disorder (MDD) is a debilitating condition, whose high prevalence and multisymptomatic nature set its standing as a leading contributor to global disability. To better understand this psychiatric disease, various pathophysiological mechanisms have been proposed, including changes in monoaminergic neurotransmission, imbalance of excitatory and inhibitory signaling in the brain, hyperactivity of the hypothalamic-pituitary-adrenal (HPA) axis, and abnormalities in normal neurogenesis. While previous findings led to a deeper understanding of the disease, the pathogenesis of MDD has not yet been elucidated. Accumulating evidence has confirmed the association between chronic inflammation and MDD, which is manifested by increased levels of the C-reactive protein, as well as pro-inflammatory cytokines, such as Interleukin 1 beta, Interleukin 6, and the Tumor necrosis factor alpha. Furthermore, recent findings have implicated a related family of cytokines with chemotactic properties, known collectively as chemokines, in many neuroimmune processes relevant to psychiatric disorders. Chemokines are small (8–12 kDa) chemotactic cytokines, which are known to play roles in direct chemotaxis induction, leukocyte and macrophage migration, and inflammatory response propagation. The inflammatory chemokines possess the ability to induce migration of immune cells to the infection site, whereas their homeostatic chemokine counterparts are responsible for recruiting cells for their repair and maintenance. To further support the role of chemokines as central elements to healthy bodily function, recent studies suggest that these proteins demonstrate novel, brain-specific mechanisms including the modulation of neuroendocrine functions, chemotaxis, cell adhesion, and neuroinflammation. Elevated levels of chemokines in patient-derived serum have been detected in individuals diagnosed with major depressive disorder, bipolar disorder, and schizophrenia. Furthermore, despite the considerable heterogeneity of experimental samples and methodologies, existing biomarker studies have clearly demonstrated the important role of chemokines in the pathophysiology of psychiatric disorders. The purpose of this review is to summarize the data from contemporary experimental and clinical studies, and to evaluate available evidence for the role of chemokines in the central nervous system (CNS) under physiological and pathophysiological conditions. In light of recent results, chemokines could be considered as possible peripheral markers of psychiatric disorders, and/or targets for treating depressive disorders.
Bioinformatic Analysis of Gene Variants from Gastroschisis Recurrence Identifies Multiple Novel Pathogenetic Pathways: Implication for the Closure of the Ventral Body Wall
Authors: Salinas-Torres Víctor M. , Gallardo-Blanco Hugo L. , Salinas-Torres Rafael A. , Cerda-Flores Ricardo M. , Lugo-Trampe José J. , Villarreal-Martínez Daniel Z. , Martínez de Villarreal Laura E.
Published: May 2019

We investigated whether likely pathogenic variants co-segregating with gastroschisis through a family-based approach using bioinformatic analyses were implicated in body wall closure. Gene Ontology (GO)/Panther functional enrichment and protein-protein interaction analysis by String identified several biological networks of highly connected genes in UGT1A3, UGT1A4, UGT1A5, UGT1A6, UGT1A7, UGT1A8, UGT1A9, UGT1A10, AOX1, NOTCH1, HIST1H2BB, RPS3, THBS1, ADCY9, and FGFR4. SVS–PhoRank identified a dominant model in OR10G4 (also as heterozygous de novo), ITIH3, PLEKHG4B, SLC9A3, ITGA2, AOX1, and ALPP, including a recessive model in UGT1A7, UGT1A6, PER2, PTPRD, and UGT1A3. A heterozygous compound model was observed in CDYL, KDM5A, RASGRP1, MYBPC2, PDE4DIP, F5, OBSCN, and UGT1A. These genes were implicated in pathogenetic pathways involving the following GO related categories: xenobiotic, regulation of metabolic process, regulation of cell adhesion, regulation of gene expression, inflammatory response, regulation of vascular development, keratinization, left-right symmetry, epigenetic, ubiquitination, and regulation of protein synthesis. Multiple background modifiers interacting with disease-relevant pathways may regulate gastroschisis susceptibility. Based in our findings and considering the plausibility of the biological pattern of mechanisms and gene network modeling, we suggest that the gastroschisis developmental process may be the consequence of several well-orchestrated biological and molecular mechanisms which could be interacting with gastroschisis predispositions within the first ten weeks of development.
Methods for the Refinement of Protein Structure 3D Models
Authors: Adiyaman Recep , McGuffin Liam James
Published: May 2019

The refinement of predicted 3D protein models is crucial in bringing them closer towards experimental accuracy for further computational studies. Refinement approaches can be divided into two main stages: The sampling and scoring stages. Sampling strategies, such as the popular Molecular Dynamics (MD)-based protocols, aim to generate improved 3D models. However, generating 3D models that are closer to the native structure than the initial model remains challenging, as structural deviations from the native basin can be encountered due to force-field inaccuracies. Therefore, different restraint strategies have been applied in order to avoid deviations away from the native structure. For example, the accurate prediction of local errors and/or contacts in the initial models can be used to guide restraints. MD-based protocols, using physics-based force fields and smart restraints, have made significant progress towards a more consistent refinement of 3D models. The scoring stage, including energy functions and Model Quality Assessment Programs (MQAPs) are also used to discriminate near-native conformations from non-native conformations. Nevertheless, there are often very small differences among generated 3D models in refinement pipelines, which makes model discrimination and selection problematic. For this reason, the identification of the most native-like conformations remains a major challenge.
Show Me a Safer Way: Detecting Anomalous Driving Behavior Using Online Traffic Footage
Authors: Zheng Xiao , Wu Fumi , Chen Weizhang , Naghizade Elham , Khoshelham Kourosh
Published: May 2019

Real-time traffic monitoring is essential in many novel applications, from traffic management to smart navigation systems. The large number of traffic cameras being integrated into urban infrastructures has enabled efficient traffic monitoring as an intervention in reducing traffic accidents and related casualties. In this paper, we focus on the problem of the automatic detection of anomalous driving behaviors, e.g., speeding or stopping on a bike lane, by using the traffic-camera feed that is available online. This can play an important role in personalized route-planning applications where, for instance, a user wants find the safest paths to get to a destination. We present an integrated system that accurately detects, tracks, and classifies vehicles using online traffic-camera feed.
Comparing the Acidity of (R3P)2BH-Based Donor Groups in Iridium Pincer Complexes
Authors: Maser Leon , Schneider Christian , Alig Lukas , Langer Robert
Published: May 2019

In the current manuscript, we describe the reactivity of a series of iridium(III) pincer complexes with the general formulae [(PEP)IrCl(CO)(H)]n (n = +1, +2) towards base, where PEP is a pincer-type ligand with different central donor groups, and E is the ligating atom of this group (E = B, C, N). The donor groups encompass a secondary amine, a phosphine-stabilised borylene and a protonated carbodiphosphorane. As all ligating atoms E exhibit an E–H bond, we addressed the question of wether the coordinated donor group can be deprotonated in competition to the reductive elimination of HCl from the iridium(III) centre. Based on experimental and quantum chemical investigations, it is shown that the ability for deprotonation of the coordinated ligand decreases in the order of (R3P)2CH+ > R2NH > (R3P)2BH. The initial product of the reductive elimination of HCl from [(PBP)IrCl(CO)(H)]n (1c), the square planar iridium(I) complex, [(PBP)Ir(CO)]+ (3c), was found to be unstable and further reacts to [(PBP)Ir(CO)2]+ (5c). Comparing the C–O stretching vibrations of the latter with those of related complexes, it is demonstrated that neutral ligands based on tricoordinate boron are very strong donors.
Butyl Rubber-Based Composite: Thermal Degradation and Prediction of Service Lifetime
Authors: Nguyen-Tri Phuong , Triki Ennouri , Nguyen Tuan Anh
Published: May 2019

Butyl rubber-based composite (BRC) is one of the most popular materials for the fabrication of protective gloves against chemical and mechanical risks. However, in many workplaces, such as metal manufacturing or automotive mechanical services, its mechanical hazards usually appear together with metalworking fluids (MWFs). The presence of these contaminants, particularly at high temperatures, could modify its properties due to the scission, the plasticization and the crosslinking of the polymer network and thus lead to severe modification of the mechanical and physicochemical properties of material. This work aims to determine the effect of temperature and a metalworking fluid on the mechanical behavior of butyl rubber composite, dealing with crosslinking density, cohesion forces and the elastic constant of BRC, based on Mooney–Rivlin’s theory. The effect of temperature with and without MWFs on the thermo-dynamical properties and morphology of butyl membranes was also investigated. The prediction of service lifetime was then evaluated from the extrapolation of the Arrhenius plot at different temperatures.
Microbiological and SEM-EDS Evaluation of Titanium Surfaces Exposed to Periodontal Gel: In Vitro Study
Authors: Bernardi Sara , Bianchi Serena , Tomei Anna Rita , Continenza Maria Adelaide , Macchiarelli Guido
Published: May 2019

Inflammatory diseases affecting the soft and hard tissues surrounding an implant represent a new challenge in contemporary implant dentistry. Among several methods proposed for the decontamination of titanium surfaces, the administration of topical 14% doxycycline gel seems to be a reliable option. In the present study, we evaluated the microbial effect of 14% doxycycline gel applied on titanium surfaces and exposed to human salivary microbes in anaerobic conditions. We also examined the composition of the exposed surfaces to assess the safe use of periodontal gel on titanium surfaces. Six anatase and six type 5 alloy titanium surfaces were used and divided into two groups: The test group and the positive control group. Both were cultured with human salivary samples in anaerobic conditions. On the test groups, 240 mg of periodontal gel was applied. The microbial assessment was performed with a colony-forming unit (CFU) count and matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) to identify the species. The surface integrity was assessed using scanning electron microscopy-energy dispersive X-ray spectrometry (SEM-EDS). The results demonstrated the microbial efficacy of the 14% doxycycline periodontal gel and its safe use on titanium surfaces. However, the SEM observations revealed the permanence of the gel on the titanium surfaces due to the physical composition of the gel. This permanence needs to be further investigated in vivo and a final polishing protocol on the titanium surface is recommended.
Semisolid State Sintering Behavior of Aluminum–Stainless Steel 316L Composite Materials by Powder Metallurgy
Authors: Park Kwangjae , Kim Dasom , Kim Kyungju , Cho Seungchan , Takagi Kenta , Kwon Hansang
Published: May 2019

Aluminum (Al)-stainless steel 316L (SUS316L) composites were successfully fabricated by the spark plasma sintering process (SPS) using pure Al and SUS316L powders as raw materials. The Al-SUS316L composite powder comprising Al with 50 vol.% of SUS316L was prepared by a ball milling process. Subsequently, it was sintered at 630 °C at a pressure of 200 MPa and held for 5 min in a semisolid state. The X-ray diffraction (XRD) patterns show that intermetallic compounds such as Al13Fe4 and AlFe3 were created in the Al-SUS316L composite because the Al and SUS316L particles reacted together during the SPS process. The presence of these intermetallic compounds was also confirmed by using XRD, scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDS), and EDS mapping. The mechanical hardness of the Al-SUS316L composites was analyzed by a Vickers hardness tester. Surprisingly, the Al-SU316L composite exhibited a Vickers hardness of about 620 HV. It can be concluded that the Al-SUS316L composites fabricated by the SPS process are lightweight and high-hardness materials that could be applied in the engineering industry such as in automobiles, aerospace, and shipbuilding.
High Throughput Direct Laser Interference Patterning of Aluminum for Fabrication of Super Hydrophobic Surfaces
Authors: Lang Valentin , Voisiat Bogdan , Lasagni Andrés Fabián
Published: May 2019

This work addresses the fabrication of hydrophobic surface structures by means of direct laser interference patterning using an optical setup optimized for high throughput processing. The developed optical assembly is used to shape the laser beam intensity as well as to obtain the two sub beams required for creating the interference pattern. The resulting beam profile consists of an elongated rectangular laser spot with 5.0 mm × 0.1 mm size, which enables the optimized utilization of the laser fluence available from an ns-pulsed laser with a wavelength of 1064 nm. Depending on the pulse repetition rate applied, heating of the substrate volume generated by heat accumulation encouraged exceptionally high aspect ratios of the trench structures due to melt flow dynamic material deformation. Finally, water contact angle measurements of the produced structures permitted the demonstration of the capability of controlling the wetting angle, in which this effect does not only depend on the height of the generated surface structures but also on their morphology.
The Bio-Safety Concerns of Three Domestic Temporary Hair Dye Molecules: Fuchsin Basic, Victoria Blue B and Basic Red 2
Authors: Liu Bing , Jin Shu-Fang , Li Hua-Chao , Sun Xiang-Yu , Yan Si-Qi , Deng Shu-Jun , Zhao Ping
Published: May 2019

Hair-coloring products include permanent, semi-permanent and temporary dyes that vary by chemical formulation and are distinguished mainly by how long they last. Domestic temporary hair dyes, such as fuchsin basic, basic red 2 and Victoria blue B, are especially popular because of their cheapness and facile applications. Despite numerous studies on the relationship between permanent hair dyes and disease, there are few studies addressing whether these domestic temporary hair dyes are associated with an increased cancer risk. Herein, to ascertain the bio-safety of these temporary hair dyes, we comparatively studied their percutaneous absorption, hemolytic effect and cytotoxic effects in this paper. Furthermore, to better understand the risk of these dyes after penetrating the skin, experimental and theoretical studies were carried out examining the interactions between the dyes and serum albumins as well as calf thymus (CT)-DNA. The results showed that these domestic temporary hair dyes are cytotoxic with regard to human red blood cells and NIH/3T3 cell lines, due to intense interactions with bovine serum albumin (BSA)/DNA. We conclude that the temporary hair dyes may have risk to human health, and those who use them should be aware of their potential toxic effects.
Analysis of Volatile Compounds in Pears by HS-SPME-GC×GC-TOFMS
Authors: Wang Chenchen , Zhang Wenjun , Li Huidong , Mao Jiangsheng , Guo Changying , Ding Ruiyan , Wang Ying , Fang Liping , Chen Zilei , Yang Guosheng
Published: May 2019

Aroma plays an important role in fruit quality and varies among different fruit cultivars. In this study, a sensitive and accurate method based on headspace solid-phase microextraction (HS-SPME) coupled with comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry (GC×GC-TOFMS) was developed to comprehensively compare aroma components of five pear cultivars. In total, 241 volatile compounds were identified and the predominant volatile compounds were esters (101 compounds), followed by alcohols (20 compounds) and aldehydes (28 compounds). The longyuanyangli has the highest relative concentration (838.12 ng/g), while the Packham has the lowest (208.45 ng/g). This study provides a practical method for pear aroma analysis using SPME and GC×GC-TOFMS.
Barriers and Facilitators to Weight and Lifestyle Management in Women with Polycystic Ovary Syndrome: General Practitioners’ Perspectives
Authors: Arasu Alexis , Moran Lisa J , Robinson Tracy , Boyle Jacqueline , Lim Siew
Published: May 2019

Background: Weight and lifestyle management is advocated as the first-line treatment for polycystic ovary syndrome (PCOS) by evidence-based guidelines. Current literature describes both systems- and individual-related challenges that general practitioners (GPs) face when attempting to implement guideline recommendations for lifestyle management into clinical practice for the general population. The GPs’ perspective in relation to weight and lifestyle advice for PCOS has not been captured. Methods: Fifteen GPs were recruited to take part in semi-structured interviews. NVIVO software was used for qualitative analysis. Results: We report that GPs unanimously acknowledge the importance of weight and lifestyle management in PCOS. Practice was influenced by both systems-related and individual-related facilitators and barriers. Individual-related barriers include perceived lack of patient motivation for weight loss, time pressures, lack of financial reimbursement, and weight management being professionally unrewarding. System-related barriers include costs of accessing allied health professionals and unavailability of allied health professionals in certain locations. Individual-related facilitators include motivated patient subgroups such as those trying to get pregnant and specific communication techniques such as motivational interviewing. System-related facilitators include the GP’s role in chronic disease management. Conclusions: This study contributes to the understanding of barriers and facilitators that could be addressed to optimize weight and lifestyle management in women with PCOS in primary care.
Preparation, Structure and Properties of Acid Aqueous Solution Plasticized Thermoplastic Chitosan
Authors: Zhang Yu , Liu Biao-Lan , Wang Liang-Jie , Deng Ying-Hua , Zhou Shi-Yi , Feng Ji-Wen
Published: May 2019

This work provides a simple method for the preparation of thermoplastic chitosan using the most common dilute inorganic and organic acids in aqueous solutions, namely hydrochloric acid (HCl) and acetic acid (HAc). The melting plasticization behavior of chitosan under different concentrations and types of acid solution was investigated. By means of infrared spectra (IR), scanning electron microscope (SEM), X-ray diffraction (XRD), and other characterization methods, as well as a mechanical property test, it was found that as the acid solution concentration increased, the protonation effect was stronger and the plasticization performance showed a better trend. The structure and performance of the modified chitosan were optimal when the concentration of HCl was around 8 wt %. In addition, it was found that HCl had a better effect on the plasticization of chitosan than HAc, which was because the protonation ability of HCl was stronger than that of HAc. Unlike the casting method, the structure and properties of chitosan sheets prepared by thermoplastic processing were directly affected by protonation, however not by the interaction of anionic-cationic electrostatic attractions between the –NH3+ groups of chitosan chains and the carboxyl groups of acetic acids or the chloridoid groups of hydrochloric acid.
Three New Supramolecular Coordination Polymers Based on 1H-pyrazolo[3,4-b]pyridin-3-amine and 1,3-benzenedicarboxylate Derivatives
Authors: Xu Yun , Deng Qing-Hua , Ding Fang , An Ran , Liu Dong , Miao Ti-Fang
Published: May 2019

Three new supramolecular coordination polymers, namely [Zn(1,3-BDC)(HL)]n (Polymer 1), [Zn3(1,3,5-BTC)2(HL)2(H2O)2]n (Polymer 2), and [Zn9(5-SO3-1,3-BDC)2(L)8(OH)4]n (Polymer 3), were synthesized under solvothermal conditions, based on 1H-pyrazolo[3,4-b]pyridin-3-amine (HL) along with 1,3-benzenedicarboxylate (1,3-BDC) and its derivatives, such as 1,3,5-benzenetricarboxylate (1,3,5-BTC) and 5-sulfo-1,3-benzenedicarboxylate (5-SO3-1,3-BDC). Polymers 1–3 were characterized by elemental analysis, IR spectroscopy, powder X-ray diffraction (PXRD), and single crystal X-ray diffraction analysis. Polymer 1 exhibited a two-dimensional (2D) 4-connected sql net. The neighboring 2D nets were further linked into a 3D supramolecular network by hydrogen-bonding interactions. Polymer 2 displayed a 3D (4, 4, 4)-connected network, which was further stabilized by R 2 2 (14) and S(9) hydrogen-bonding rings along with π–π interactions. The 2D sheet structure of Polymer 3 was constructed by novel quasi-linear nonanuclear Zn(II) units, which further extended into a 3D supramolecular structure by hydrogen-bonding interactions. The solid-state photoluminescence properties of Polymers 1–3 were also investigated.
Internal Model Control for Rank-Deficient System with Time Delays Based on Damped Pseudo-Inverse
Authors: Jiang Meiying , Jiang Beiyan , Wang Qi
Published: May 2019

It is a challenge to design a satisfactory controller for a complex multivariable industrial system with minimal offsetting and a slow response. An internal model control method is proposed for rank-deficient systems with a time delay based on a damped pseudo-inverse. An internal model control was designed to obtain the desired dynamic characteristics of the system by transforming the time-delay system into a system without a time delay, following the Pade approximation approach. By introducing a damping factor, the internal model controller was designed based on a damped pseudo-inverse, since the inverse matrix of the rank-deficient system does not exist. Furthermore, a singular value decomposition was used to analyze the steady-state performance of the system. The selection of the damping factor was also presented, and a μ analysis was made to evaluate the stability of the system. To demonstrate the effectiveness of the proposed method, a crude distillation process with five inputs and four outputs was considered as an example. The simulation results illustrate that not only can the proposed strategy guarantee the system’s stability, but it also has a relatively good dynamic performance.
Exploring New Crystal Structures of Glycine via Electric Field-Induced Structural Transformations with Molecular Dynamics Simulations
Authors: Bulutoglu Pelin Su , Parks Conor , Nere Nandkishor K. , Bordawekar Shailendra , Ramkrishna Doraiswami
Published: May 2019

Being able to control polymorphism of a crystal is of great importance to many industries, including the pharmaceutical industry, since the crystal’s structure determines significant physical properties of a material. While there are many conventional methods used to control the final crystal structure that comes out of a crystallization unit, these methods fail to go beyond a few known structures that are kinetically accessible. Recent studies have shown that externally applied fields have the potential to effectively control polymorphism and to extend the set of observable polymorphs that are not accessible through conventional methods. This computational study focuses on the application of high-intensity dc electric fields (e-fields) to induce solid-state transformation of glycine crystals to obtain new polymorphs that have not been observed via experiments. Through molecular dynamics simulations of solid-state α -, β -, and γ -glycine crystals, it has been shown that the new polymorphs sustain their structures within 125 ns after the electric field has been turned off. It was also demonstrated that strength and direction of the electric field and the initial structure of the crystal are parameters that affect the resulting polymorph. Our results showed that application of high-intensity dc electric fields on solid-state crystals can be an effective crystal structure control method for the exploration of new crystal structures of known materials and to extend the range of physical properties a material can have.