bluuebunny/crossref_metadata_2025 huggingface dataset:
Presence of Chronic Obstructive Pulmonary Disease (COPD) Impair Survival in Lung Cancer Patients Receiving Epidermal Growth Factor Receptor-Tyrosine Kinase Inhibitor (EGFR-TKI): A Nationwide, Population-Based Cohort Study
Authors: Wu Chia-Che , Rau Kun-Ming , Lee Wei-Chieh , Hsieh Meng-Che , Liu Jia-Sin , Chen Yen-Yang , Su Harvey Yu-Li
Published: July 2019

The emergence of epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI) caused a paradigm shift in the treatment of non-small cell lung cancer (NSCLC). Although several clinicopathologic factors to predict the response to and survival on EGFR-TKI were recognized, its efficacy has not been confirmed for patients with underlying pulmonary disease, such as chronic obstructive pulmonary disease (COPD). We conducted the study to evaluate the impact of COPD on survival for NSCLC patients that underwent EGFR-TKI treatment. The nationwide study obtained clinicopathologic data from the National Health Insurance Research Database in Taiwan between 1995 and 2013. Patients receiving EGRR-TKI were divided into COPD and non-COPD groups, and adjusted for age, sex, comorbidities, premium level and cancer treatments. Overall survival (OS) and progression-free survival (PFS) were calculated by Kaplan–Meier analysis. In total, 21,026 NSCLC patients were enrolled, of which 47.6% had COPD. After propensity score (PS) matching, all covariates were adjusted and balanced except for age (p < 0.001). In the survival analysis, the median OS (2.04 vs. 2.28 years, p < 0.001) and PFS (0.62 vs. 0.69 years, p < 0.001) of lung cancer with COPD were significantly worse than those without COPD. Lung cancer patients on EGFR-TKI treatment had a worse survival outcome if patients had pre-existing COPD.
The Immunomodulatory Functions of Mesenchymal Stromal/Stem Cells Mediated via Paracrine Activity
Authors: Zhou Yueyuan , Yamamoto Yusuke , Xiao Zhongdang , Ochiya Takahiro
Published: July 2019

Mesenchymal stromal/stem cells (MSCs) exist in almost all tissues, possessing the potential to differentiate into specialized cell types and exert immunomodulatory functions. Thus, they have attracted much attention as a promising therapeutic candidate. Recent studies have demonstrated that paracrine signaling is mainly responsible for the involvement of MSCs in the modulation of immune responses and the progression of diseases. Through release of secretome consisting of a diverse range of cytokines, chemokines, and extracellular vesicles (EVs), MSCs convey regulatory messages to recipient immune cells in the microenvironment. In this review, we focus on the recent advances in how MSCs contribute to immunomodulation through the secretion of paracrine factors. The further improved understanding of the molecular mechanism underlying the interactions between MSCs and immune cells highlights the paracrine biology of MSCs in the modulation of the immune microenvironment and promotes the clinical application of MSCs in regenerative medicine and immune diseases.
Fractional Excretion of Phosphate (FeP) Is Associated with End-Stage Renal Disease Patients with CKD 3b and 5
Authors: Bellasi Antonio , Di Micco Lucia , Russo Domenico , De Simone Emanuele , Di Iorio Mattia , Vigilante Raffaella , Di Lullo Luca , Di Iorio Biagio Raffaele
Published: July 2019

Background: The perturbation of phosphate homeostasis portends unfavorable outcomes in chronic kidney disease (CKD). However, the absence of randomized clinical trials (RCT) fuels the discussion of whether phosphate or some other phosphorous-related factor(s) such as fibroblast growth factor 23 (FGF-23) mediates the cardiovascular and systemic toxicity. We herein test whether the fractional excretion of phosphate (FeP) as a marker of renal stress to excrete phosphorous predicts unfavorable outcomes in CKD patients. Methods: Retrospective, cross-sectional observational study. For current analysis, an historical cohort of 407 records of CKD stage 3b-5 patients attending between January 2010 and October 2015 at the Nephrology Unit of Solofra (AV), Italy were utilized. Demographic, clinical, laboratory, and outcome data were identified through the subjects’ medical records. We tested whether quartiles of FeP are associated with the risk of CKD progression or all causes of death. Parametric as well as non-parametric tests, linear and logistic regression, as well as survival analysis were utilized. Results: Overall, we investigated middle-age (mean 66.0, standard deviation 12.3 years) men and women (male 43%) with CKD stage 3b to 5 (creatinine clearance 32.0 (13.3) mL/min). Older age, lower diastolic blood pressure, poor renal function, as well as higher serum phosphate were associated with FeP. Patients with higher FeP were at an increased risk of starting dialysis or dying (hazard ratio 2.40; 95% confidence interval (1.44, 3.99)). Notably, when the two endpoints were analyzed separately, FeP was associated with renal but not all-cause survival. Conclusion: FeP is associated with ESRD, but not all-cause mortality risk in a large cohort of moderate to advanced CKD patients. Future efforts are required to validate FeP as a marker of nephron stress and risk factor for CKD progression in this high-risk population.
Reliability Analysis of CFRP-Strengthened RC Bridges Considering Size Effect of CFRP
Authors: Xie Hui-Bing , Wang Yuan-Feng
Published: July 2019

A reliability analysis of an existing structure and a carbon fiber-reinforced plastic (CFRP)-strengthened structure is commonly used to evaluate the effectiveness of strengthening. It also provides the basis for the calibration of the partial factors involved in strengthening design codes. As the fundamental data, the statistical characteristics of the CFRP tensile strength affect the evaluation result. In general, the statistical characteristics of the CFRP strength were obtained from laboratory experiments with small-scale specimens, which resulted in errors caused by the size effect. In this study, a probabilistic series-parallel model is developed to describe the size effect of CFRP. The CFRP fabric is divided into a set of representative volume elements. By numerically simulating the CFRP strength, the relationship between the number of representative volume elements and the mean and coefficient of variation (COV) of the CFRP strength is analyzed. A chi-square test is carried out to determine the distribution type of the CFRP strength. An analytical expression of the mean, COV, and the cumulated density function of the CFRP strength are derived. Finally, an existing bridge, which has operated for 41 years, is selected for the case study; it is strengthened by using CFRP fabric. Reliability indexes of the existing and the strengthened bridges are calculated to analyze the size effect on the reliability of the strengthened structure.
Novel Synthesis of Holey Reduced Graphene Oxide/Polystyrene (HRGO/PS) Nanocomposites by Microwave Irradiation as Anodes for High-Temperature Lithium-Ion Batteries
Authors: Aldawsari Yazeed , Mussa Yasmin , Ahmed Faheem , Arsalan Muhammad , Alsharaeh Edreese
Published: July 2019

To overcome the risk of exothermic lithium-ion battery overheating reactions, we fabricated a novel, high-temperature-stable anode material composed of holey reduced graphene oxide/polystyrene (HRGO/PS) nanocomposites synthesized through in situ bulk polymerization in the presence of HRGO via microwave irradiation. The HRGO/PS nanocomposites were characterized by Fourier transform infrared spectroscopy, X-ray diffraction, Raman spectroscopy, and electron microscopy analyses including field-emission scanning electron microscopy and transmission electron microscopy. All characterization studies demonstrated homogenous dispersion of HRGO in the PS matrix, which enhanced the thermal and electrical properties of the overall nanocomposites. These novel HRGO/PS nanocomposites exhibited excellent electrochemical responses, with reversible charge/discharge capacities of 92.1/92.78 mA·h/g at a current density of 500 mA/g with ~100% capacity retention and ~100% coulombic efficiency at room temperature. Furthermore, an examination of the electrochemical properties of these nanocomposites at 110 °C showed that HRGO/PS nanocomposites still displayed good charge/discharge capacities with stable cycle performances for 150 cycles.
Improvement of Thermal Cycling Resistance of AlxSi1−xN Coatings on Cu Substrates by Optimizing Al/Si Ratio
Authors: Panin Alexey , Shugurov Artur , Kazachenok Marina , Sergeev Victor
Published: July 2019

The effect of the elemental composition of AlxSi1−xN coatings deposited on Cu substrates by magnetron sputtering on their structure, mechanical properties and thermal cycling performance is studied. The coatings with Al-Si-N solid solution, two-phase (AlxSi1−xN nanocrystallites embedded in the SixNy tissue phase) and amorphous structure were obtained by varying Al/Si ratio. It is shown that polycrystalline coatings with a low Si content (Al0.88Si0.12N) are characterized by the highest thermal cycling resistance. While the coatings with a high and intermediate Si content (Al0.11Si0.89N and Al0.74Si0.26N) were subjected to cracking and spallation after the first cycle of annealing at a temperature of 1000 °C, delamination of the Al0.88Si0.12N coating was observed after 25 annealing cycles. The Al0.88Si0.12N coating also exhibited the best barrier performance against copper diffusion from the substrate. The effect of thermal stresses on the diffusion barrier performance of the coatings against copper diffusion is discussed.
Finite Element Prediction of Residual Stress and Deformation Induced by Double-Pass TIG Welding of Al 2219 Plate
Authors: Ahmad Abdulrahaman Shuaibu , Wu Yunxin , Gong Hai , Nie Lin
Published: July 2019

Finite element (FE) analysis of welding residual stress and deformation is one of the essential stages in the manufacturing process of mechanical structures and parts. It aids in reducing the production cost, minimizing errors, and optimizing the manufactured component. This paper presents a numerical prediction of residual stress and deformation induced by two-pass TIG welding of Al 2219 plates. The FE model was developed using ABAQUS and FORTRAN packages, Goldak’s heat source model was implemented by coding the nonuniform distributed flux (DFLUX) in user subroutine to represent the ellipsoidal moving weld torch, having front and rear power density distribution. Radiation and convection heat losses were taken into account. The mechanical boundary condition was applied to prevent the model from rotation and displacement in all directions while allowing material deformation. The FE model was experimentally validated and the compared results show good agreement with average variations of 18.8% and 17.4% in residual stresses and deformation, respectively.
A Seventh-Order Scheme for Computing the Generalized Drazin Inverse
Authors: Ahmed Dilan , Hama Mudhafar , Jwamer Karwan Hama Faraj , Shateyi Stanford
Published: July 2019

One of the most important generalized inverses is the Drazin inverse, which is defined for square matrices having an index. The objective of this work is to investigate and present a computational tool in the form of an iterative method for computing this task. This scheme reaches the seventh rate of convergence as long as a suitable initial matrix is chosen and by employing only five matrix products per cycle. After some analytical discussions, several tests are provided to show the efficiency of the presented formulation.
Statistical Workflow for Feature Selection in Human Metabolomics Data
Authors: Antonelli Joseph , Claggett Brian L. , Henglin Mir , Kim Andy , Ovsak Gavin , Kim Nicole , Deng Katherine , Rao Kevin , Tyagi Octavia , Watrous Jeramie D. , Lagerborg Kim A. , Hushcha Pavel V. , Demler Olga V. , Mora Samia , Niiranen Teemu J. , Pereira Alexandre C. , Jain Mohit , Cheng Susan
Published: July 2019

High-throughput metabolomics investigations, when conducted in large human cohorts, represent a potentially powerful tool for elucidating the biochemical diversity underlying human health and disease. Large-scale metabolomics data sources, generated using either targeted or nontargeted platforms, are becoming more common. Appropriate statistical analysis of these complex high-dimensional data will be critical for extracting meaningful results from such large-scale human metabolomics studies. Therefore, we consider the statistical analytical approaches that have been employed in prior human metabolomics studies. Based on the lessons learned and collective experience to date in the field, we offer a step-by-step framework for pursuing statistical analyses of cohort-based human metabolomics data, with a focus on feature selection. We discuss the range of options and approaches that may be employed at each stage of data management, analysis, and interpretation and offer guidance on the analytical decisions that need to be considered over the course of implementing a data analysis workflow. Certain pervasive analytical challenges facing the field warrant ongoing focused research. Addressing these challenges, particularly those related to analyzing human metabolomics data, will allow for more standardization of as well as advances in how research in the field is practiced. In turn, such major analytical advances will lead to substantial improvements in the overall contributions of human metabolomics investigations.
Experimental Study of Pyrite Oxidation at 100 °C: Implications for Deep Geological Radwaste Repository in Claystone
Authors: Verron Héloïse , Sterpenich Jérôme , Bonnet Julien , Bourdelle Franck , Mosser-Ruck Régine , Lorgeoux Catherine , Randi Aurélien , Michau Nicolas
Published: July 2019

The oxidation of pyrite is one of the near field processes of the chemical evolution of clay rock planned to host a deep geological radioactive waste repository during operation. Indeed, this process can lead to transitory acidic conditions in the medium (i.e., production of sulphuric acid, carbonic acid) which may influence the corrosion kinetics of the carbon steel components of some disposal cells. In order to improve the geochemical modelling of the long-term disposal, the oxidation of pyrite in contact with clays and carbonates at 100 °C must be evaluated. In this study, special attention was paid to the pyrite oxidation rate thanks to an original experimental set-up, involving several pyrite/mineral mixtures and a reactor coupled to a micro gas chromatograph (PO2 and PCO2 monitoring). Although thermodynamic modelling expects that hematite is the most stable phase in a pure pyrite heated system (low pH), experiments show the formation of native sulfur as an intermediate product of the reaction. In the presence of calcite, the pH is neutralized and drives the lower reactivity of pyrite in the absence of native sulfur. The addition of clay phases or other detrital silicates from the claystone had no impact on pyrite oxidation rate. The discrepancies between experiments and thermodynamic modelling are explained by kinetic effects. Two laws were deduced at 100 °C. The first concerns a pure pyrite system, with the following law: r P y =   10 − 4.8 · P O 2 0.5 · t − 0.5 . The second concerns a pyrite/carbonates system: r P y + C a =   10 − 5.1 · P O 2 0.5 · t − 0.5 where PO2 corresponds to the partial pressure of O2 (in bar) and t is time in seconds. Different mechanisms are proposed to explain the evolution with time of the O2 consumption during pyrite oxidation: (i) decrease of the specific or reactive surface area after oxidation of fine grains of pyrite, (ii) decrease of O2 pressure, (iii) growing up of secondary minerals (Fe-oxides or anhydrite in the presence of calcium in the system) on the surface of pyrite limiting the access of O2 to the fresh surface of pyrite, and (iv) change in the pH of the solution.
The Nervous System Relevance of the Calcium Sensing Receptor in Health and Disease
Authors: Giudice Maria Lo , Mihalik Balázs , Dinnyés András , Kobolák Julianna
Published: July 2019

The calcium sensing receptor (CaSR) was first identified in parathyroid glands, and its primary role in controlling systemic calcium homeostasis by the regulation of parathyroid hormone (PTH) secretion has been extensively described in literature. Additionally, the receptor has also been investigated in cells and tissues not directly involved in calcium homeostasis, e.g., the nervous system (NS), where it plays crucial roles in early neural development for the differentiation of neurons and glial cells, as well as in the adult nervous system for synaptic transmission and plasticity. Advances in the knowledge of the CaSR’s function in such physiological processes have encouraged researchers to further broaden the receptor’s investigation in the neuro-pathological conditions of the NS. Interestingly, pre-clinical data suggest that receptor inhibition by calcilytics might be effective in counteracting the pathomechanism underlying Alzheimer’s disease and ischemia, while a CaSR positive modulation with calcimimetics has been proposed as a potential approach for treating neuroblastoma. Importantly, such promising findings led to the repurposing of CaSR modulators as novel pharmacological alternatives for these disorders. Therefore, the aim of this review article is to critically appraise evidence which, so far, has been yielded from the investigation of the role of the CaSR in physiology of the nervous system and to focus on the most recent emerging concepts which have reported the receptor as a therapeutic target for neurodegeneration and neuroblastic tumors.
Velutin, an Aglycone Extracted from Korean Mistletoe, with Improved Inhibitory Activity against Melanin Biosynthesis
Authors: Jung Se-Hui , Kim Jaehyun , Eum Juneyong , Choe Jung Won , Kim Hak Hyun , Kee Yun , Lee Kooyeon
Published: July 2019

The abnormal regulation of melanin synthesis leads to a wide range of pigmentary disorders. Although various melanin biosynthesis inhibitors have been developed, their efficacy and long-term safety needs to be further improved, and thus the goal of this study is to develop promising natural compound inhibitors of melanin biosynthesis. Here, we obtained aglycone flavonoid extract through the microwave-assisted hydrolysis of glycoside extract from Korean mistletoe in acidic condition. The aglycone extract inhibited tyrosinase activity more efficiently with better antioxidant activity than glycoside extract in vitro. The microwave-assisted aglycone extract of mistletoe was further analyzed for in vivo activity, and the results showed the aglycone extract inhibited both early melanocyte development and melanin synthesis more efficiently in zebrafish embryo in a dose-dependent manner. Our in vivo toxicity assay quantitatively measured cell death in zebrafish embryos and showed that the microwave-assisted aglycone extract of mistletoe had no significant effect on cell death (p < 0.001), indicating that aglycone extract is more biocompatible than glycoside extract. Furthermore, our in vitro and in vivo analyses successfully identified and characterized velutin, an aglycone of a homoflavoyadorinin B glycoside, as a major inhibitory component in the microwave-assisted mistletoe extract. Ultimately, this study showed that the novel natural compound inhibitor velutin, which was generated through microwave-assisted extraction from mistletoe, improved the efficacy of melanin biosynthesis inhibition with little toxicity.
Serum Vitamin D is Differentially Associated with Socioemotional Adjustment in Early School-Aged Ugandan Children According to Perinatal HIV Status and In Utero/Peripartum Antiretroviral Exposure History
Authors: Yakah William , Fenton Jenifer I. , Sikorskii Alla , Zalwango Sarah K. , Tuke Robert , Musoke Philippa , Boivin Michael J. , Giordani Bruno , Ezeamama Amara E.
Published: July 2019

An impact of vitamin D in neurocognitive function has been theorized but it remains unknown whether vitamin-D insufficiency (VDI) is associated with worse socio-emotional adjustment (SEA) in vulnerable early school-aged children. This study examines the thesis that deficits in SEA are related to VDI using longitudinal data from 254 children that are perinatally HIV-infected (PHIV), exposed-uninfected (HEU), or unexposed-uninfected (HUU). In utero/peripartum antiretroviral (IPA) exposure was established per medical record documentation of biological mother’s ART regimen in pregnancy. Four caregiver-reported age- and sex-standardized measures of SEA were obtained at months 0, 6, and 12 for dependent children aged 6–10 years: externalizing problems (EPC), internalizing problems (IPC), behavioral symptoms index (BSI), and adaptive skills index (ASI). VDI was highly prevalent (74%, n = 188), and its association with change in SEA measures over 12 months varied by HIV-status (VDI*HIV, all p-values < 0.03). There was further variation in relationship of vitamin-D to SEA by IPA among PHIV (for ASI, BSI, and EPC, vitamin-D*IPA, p-value ≤ 0.01) and HEU (for BSI and EPC, vitamin-D*IPA, p-value ≤ 0.04). Among HUU, BSI (β = −0.32, 95% CI: −0.50, −0.13), IPC (β = −0.28, 95% CI: −0.47, −0.09), and EPC (β = −0.20, 95% CI: −0.37, −0.02) all declined moderately per quartile increment in VD. Among PHIV, on the one hand higher vitamin D predicted ASI gains (moderate vs. low VD, β = 0.52, p = 0.002), but this protective association was absent for BSI, EPC, and IPC (β = 0.36–0.77, p < 0.05). In absence of IPA-exposure, increasing vitamin-D predicted declines in BSI and EPC (moderate vs. low Vitamin D, β = −0.56 to −0.71, p ≤ 0.02) among HEU. However, given IPA exposure among HEU, higher VDI predicted moderate elevation in BSI (β = 0.39, 95% CI: 0.00, 0.78) and IPC (β = 0.48, 95% CI: 0.05, 0.92). Interaction between VD and IPA exposure for SEA outcomes among HEU and PHIV children warrants further investigation. The vitamin-D associated SEA improvement among HUU and HEU without IPA exposure suggests vitamin-D supplementation may remediate behavioral and adaptive deficits in this groups.
Consumer Perceptions and Acceptability of Traditional Dishes Prepared with Provitamin A-Biofortified Maize and Sweet Potato
Authors: Govender Laurencia , Pillay Kirthee , Siwela Muthulisi , Modi Albert Thembinkosi , Mabhaudhi Tafadzwanashe
Published: July 2019

Vitamin A deficiency (VAD) is prevalent in South Africa, particularly among predominantly poor rural communities. Provitamin A (PVA)-biofortified crops could be used to address VAD; however, there are challenges of poor consumer acceptability. This study investigated the effect of replacing white maize and cream-fleshed sweet potato (CFSP) with PVA-biofortified maize and orange-fleshed sweet potato (OFSP), respectively, on consumer acceptability and perceptions of traditional dishes of rural communities in South Africa. Consumer acceptability of PVA-biofortified phutu (a crumbly maize porridge) served with either curried cabbage, chicken or bambara groundnut, separately, and boiled OFSP was evaluated by black South African adults (n = 120) using a five-point facial hedonic scale. Focus group discussions (FGDs) were conducted with 56 subjects recruited from the consumer panel to assess consumer perceptions of the food samples. The majority of the participants rated the composite dishes containing PVA-biofortified phutu as “4 = good” and the acceptability of the composite dishes varied significantly (p < 0.05). Compared to other age groups, the 50–59-year age group showed higher preference for white phutu and chicken curry, whereas the 30–39-year age group showed higher preference for PVA-biofortified phutu and chicken curry. The acceptability of OFSP and CFSP was similar. The study participants showed positive perceptions of the OFSP, as well as PVA-biofortified phutu if served with either curried chicken or cabbage. The findings suggest that PVA-biofortified maize and OFSP can replace white maize and CFSP, respectively, in selected traditional dishes of the rural communities studied to alleviate VAD.
Rectal Cancer: 20% Risk Reduction Thanks to Dietary Fibre Intake. Systematic Review and Meta-Analysis
Authors: Gianfredi Vincenza , Nucci Daniele , Salvatori Tania , Dallagiacoma Giulia , Fatigoni Cristina , Moretti Massimo , Realdon Stefano
Published: July 2019

The aim of this systematic review and meta-analysis was to evaluate the association between dietary fibre intake and rectal cancer (RC) risk. In January 2019, a structured computer search on PubMed/Medline, Excerpta Medica dataBASE (EMBASE) and Scopus was performed for studies reporting the results of primary research evaluating dietary fibre intake in women and men as well as the risk of developing RC. Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) recommendations were followed. Highest vs. lowest fibre concentrations was compared. The Egger test was used to estimate publication bias. Heterogeneity between studies was evaluated with I2 statistics. The search strategy identified 912 papers, 22 of which were included in our meta-analysis. Having evaluated a total of 2,876,136 subjects, the results suggest a protective effect of dietary fibre intake on RC prevention. The effect Size (ES) was [0.77 (95% CI = 0.66–0.89), p-value = 0.001)]. Moderate statistical heterogeneity (Chi2 = 51.36, df = 21, I2 = 59.11%, p-value = 0.000) was found. However, no publication bias was found, as confirmed by Egger’s linear regression test (Intercept −0.21, t = −0.24, p = 0.816). The findings suggest that dietary fibre intake could be protective against RC, with a clinically relevant reduction of RC risk. Identifying preventive measures to avoid the development of RC, especially by following a healthy lifestyle including healthy diet, is pivotal.
Philosophy in the Artworld: Some Recent Theories of Contemporary Art
Authors: Smith Terry
Published: July 2019

“The contemporary” is a phrase in frequent use in artworld discourse as a placeholder term for broader, world-picturing concepts such as “the contemporary condition” or “contemporaneity”. Brief references to key texts by philosophers such as Giorgio Agamben, Jacques Rancière, and Peter Osborne often tend to suffice as indicating the outer limits of theoretical discussion. In an attempt to add some depth to the discourse, this paper outlines my approach to these questions, then explores in some detail what these three theorists have had to say in recent years about contemporaneity in general and contemporary art in particular, and about the links between both. It also examines key essays by Jean-Luc Nancy, Néstor García Canclini, as well as the artist-theorist Jean-Phillipe Antoine, each of whom have contributed significantly to these debates. The analysis moves from Agamben’s poetic evocation of “contemporariness” as a Nietzschean experience of “untimeliness” in relation to one’s times, through Nancy’s emphasis on art’s constant recursion to its origins, Rancière’s attribution of dissensus to the current regime of art, Osborne’s insistence on contemporary art’s “post-conceptual” character, to Canclini’s preference for a “post-autonomous” art, which captures the world at the point of its coming into being. I conclude by echoing Antoine’s call for artists and others to think historically, to “knit together a specific variety of times”, a task that is especially pressing when presentist immanence strives to encompasses everything.
A Linear Model to Describe Branching and Allometry in Root Architecture
Authors: Colchado-López Joel , Cervantes R. Cristian , Rosas Ulises
Published: July 2019

Root architecture is a complex structure that comprises multiple traits of the root phenotype. Novel platforms and models have been developed to better understand root architecture. In this methods paper, we introduce a novel allometric model, named rhizochron index (m), which describes lateral root (LR) branching and elongation patterns across the primary root (PR). To test our model, we obtained data from 16 natural accessions of Arabidopsis thaliana at three stages of early root development to measure conventional traits of root architecture (e.g., PR and LR length), and extracted the rhizochron index (m). In addition, we tested previously published datasets to assess the utility of the rhizochron index (m) to distinguish mutants and environmental effects on root architecture. Our results indicate that rhizochron index (m) is useful to distinguish the natural variations of root architecture between A. thaliana accessions, but not across early stages of root development. Correlation analyses in these accessions showed that m is a novel trait that partially captures information from other root architecture traits such as total lateral root length, and the ratio between lateral root and primary root lengths. Moreover, we found that the rhizochron index was useful to distinguish ABA effect on root architecture, as well as the mutant pho1 phenotype. We propose the rhizochron index (m) as a new feature of the root architectural system to be considered, in addition to conventional traits in future investigations.
Using Game Theory to Understand Systemic Acquired Resistance as a Bet-Hedging Option for Increasing Fitness When Disease Is Uncertain
Authors: Reynolds Gregory J. , Gordon Thomas R. , McRoberts Neil
Published: July 2019

Systemic acquired resistance (SAR) is a mechanism through which plants may respond to initial challenge by a pathogen through activation of inducible defense responses, thereby increasing resistance to subsequent infection attempts. Fitness costs are assumed to be incurred by plants induced for SAR, and several studies have attempted to quantify these costs. We developed a mathematical model, motivated by game-theoretic concepts, to simulate competition between hypothetical plant populations with and without SAR to examine conditions under which the phenomenon of SAR may have evolved. Data were gathered from various studies on fitness costs of induced resistance on life history traits in different plant hosts and scaled as a proportion of the values in control cohorts in each study (i.e., healthy plants unprimed for SAR). With unprimed healthy control plants set to a fitness value of 1, primed healthy plants incurred a fitness cost of about 10.4% (0.896, n = 157), primed diseased plants incurred a fitness cost of about 15.5% (0.845, n = 54), and unprimed diseased plants incurred a fitness cost of about 28.9% (0.711, n = 69). Starting from a small proportion of the population (0.5%) and competing against a population with constitutive defenses alone in stochastic simulations, the SAR phenotype almost always dominated the population after 1000 generations when the probability of disease was greater than or equal to 0.5 regardless of the probability for priming errors.
Lignin Biopolymers in the Age of Controlled Polymerization
Authors: Ganewatta Mitra S. , Lokupitiya Hasala N. , Tang Chuanbing
Published: July 2019

Polymers made from natural biomass are gaining interest due to the rising environmental concerns and depletion of petrochemical resources. Lignin isolated from lignocellulosic biomass is the second most abundant natural polymer next to cellulose. The paper pulp process produces industrial lignin as a byproduct that is mostly used for energy and has less significant utility in materials applications. High abundance, rich chemical functionalities, CO2 neutrality, reinforcing properties, antioxidant and UV blocking abilities, as well as environmental friendliness, make lignin an interesting substrate for materials and chemical development. However, poor processability, low reactivity, and intrinsic structural heterogeneity limit lignins′ polymeric applications in high-performance advanced materials. With the advent of controlled polymerization methods such as ATRP, RAFT, and ADMET, there has been a great interest in academia and industry to make value-added polymeric materials from lignin. This review focuses on recent investigations that utilize controlled polymerization methods to generate novel lignin-based polymeric materials. Polymers developed from lignin-based monomers, various polymer grafting technologies, copolymer properties, and their applications are discussed.
Structure–Property Relationships of Pure Cellulose and GO/CEL Membranes Regenerated from Ionic Liquid Solutions
Authors: Ślusarczyk Czesław , Fryczkowska Beata
Published: July 2019

Two types of cellulose membranes were produced by a classical wet phase inversion method from a solution of the polymer in 1-ethyl-3-methylimidazolium acetate (EMIMAc) by coagulation in water and selected primary alcohols. The first type were membranes made from pure cellulose (CEL). The second type were membranes obtained by adding nanosized graphene oxide (GO) to the cellulose solution. The process of precipitation and selection of the coagulant affected the structure of the membranes, which in turn affected their usability and applicability. The results of the presented studies show that the physicochemical properties of the coagulant used (e.g., molecular mass and dipole moment) play important roles in this process. It was found that both the content and dimensions of the pores depended on the molecular mass of the coagulant used. It was also found that the dipole moment of coagulant molecules had a large influence on the volume content of the pores (e.g., the 1-octanol (Oc) membrane had a dipole moment of 1.71 D; Φ = 1.82%). We investigated the effect of the type of coagulant on the porous structure of CEL membranes and how this affected the transport properties of the membranes (e.g., for the distilled water (W) membrane, Jv = 5.24 ± 0.39 L/m2 h; for the Oc membrane, Jv = 92.19 ± 1.51 L/m2 h). The paper presents the results of adding GO nanoparticles in terms of the structure, morphology, and transport properties of GO/CEL membranes (e.g., for composite membrane F (containing 20% GO), Jv = 40.20 ± 2.33 L/m2 h). In particular, it describes their extremely high ability to remove heavy metal ions.
Polymeric Foams
Authors: Antunes Marcelo , Velasco José Ignacio
Published: July 2019

Advances in nanotechnology have boosted the development of more efficient materials, with emerging sectors (electronics, energy, aerospace, among others) demanding novel materials to fulfill the complex technical requirements of their products [...]
Individual Loss Reserving Using a Gradient Boosting-Based Approach
Authors: Duval Francis , Pigeon Mathieu
Published: July 2019

In this paper, we propose models for non-life loss reserving combining traditional approaches such as Mack’s or generalized linear models and gradient boosting algorithm in an individual framework. These claim-level models use information about each of the payments made for each of the claims in the portfolio, as well as characteristics of the insured. We provide an example based on a detailed dataset from a property and casualty insurance company. We contrast some traditional aggregate techniques, at the portfolio-level, with our individual-level approach and we discuss some points related to practical applications.
Comparison of Mature Douglas-Firs’ Crown Structures Developed with Two Quantitative Structural Models Using TLS Point Clouds for Neighboring Trees in a Natural Regime Stand
Authors: Fang Rong , Strimbu Bogdan M.
Published: July 2019

The Douglas fir crown structure serves important ecological functions in regulating the ecosystem of the Pacific Northwest (PNW). Mapping and modeling of the Douglas-fir crown has traditionally focused on young plantations or old-growth forests. The crown description in natural regime forests is limited by data availability. Terrestrial laser scanning (TLS) enables the acquisition of crown structural attributes, even in dense forests, at a fine scale. The certical and horizontal distributions of the fine-scale branch attributes, such as branch diameter, branch length, and branch insertion angle, will reflect the crown behaviors towards light resources availability, as a result of neighborhood competition. The main objective of the study is to compare crown structural models of a group of neighboring trees developed with two TLS-based procedures, namely: semi-automatic (Cyclone software) and automatic (TreeQSM) procedures. The estimated crown attributes are the branch diameter, branch length, branch insertion angle, height of branch insertion point, and branch azimuth. The results show that branch azimuth distribution does not differ between TreeQSM and Cyclone for most of the sample trees. However, the TreeQSM and Cyclone identified branches exhibit different distributions of insertion height. A paired t-test indicates no difference between the mean branch diameter of Cyclone and TreeQSM at an individual tree level. However, Cyclone estimated that the branch length and branch insertion angle are 0.49 m and 9.9° greater than the TreeQSM estimates, respectively. Repeat measurements of the analysis of variance (ANOVA) suggest that the height along the stem is an influential factor of the difference between the Cyclone and TreeQSM branch diameter estimates. To test whether TLS-based estimates are within the ranges of the previous observations, we computed the tree crown attributes of second- and old-growth trees using Monte Carlo simulations for diameter at breast height (DBH) class 50–55 cm, 60–65 cm, and 85–105 cm. We found that the crown attributes estimated from both of the TLS-based methods are between the simulated second- and old-growth trees, except for DBH 85–105 cm. The TLS-based crown structural models show increasingly diverse distributions of branch insertion angles and increasing branch exclusion as DBH increases. Cyclone-based crown structural models are consistent with previous studies. However, TreeQSM-based crown structural models omitted a significant number of branches and generated crown structures with reduced plausibility.
Applying Machine Learning and Statistical Approaches for Travel Time Estimation in Partial Network Coverage
Authors: Alrukaibi Fahad , Alsaleh Rushdi , Sayed Tarek
Published: July 2019

The objective of this study is to estimate the real time travel times on urban networks that are partially covered by moving sensors. The study proposes two machine learning approaches; the random forest (RF) model and the multi-layer feed forward neural network (MFFN) to estimate travel times on urban networks which are partially covered by moving sensors. A MFFN network with three hidden layers was developed and trained using the back-propagation learning algorithm, and the neural weights were optimized using the Levenberg–Marquardt optimization technique. A case study of an urban network with 100 links is considered in this study. The performance of the proposed models was compared to a statistical model, which uses the empirical Bayes (EB) method and the spatial correlation between travel times. The models’ performances were evaluated using data generated from VISSIM microsimulation model. Results show that the machine learning algorithms, e.g., RF and ANN, achieve average improvements of about 4.1% and 2.9% compared with the statistical approach. The RF, MFFN, and the statistical approach models correctly predict real time travel times with estimation accuracies reaching 90.7%, 89.5%, and 86.6% respectively. Moreover, results show that at low moving sensor penetration rate, the RF and MFFN achieve higher estimation accuracy compared with the statistical approach. At probe penetration rate of 1%, the RF, MFFN, and the statistical approach models correctly predict real time travel times with estimation accuracy of 85.6%, 84.4%, and 80.9% respectively. Furthermore, the study investigated the impact of the probe penetration rate on real time neighbor links coverage. Results show that at probe penetration rates of 1%, 3%, and 5%, the models cover the estimation of real time travel times on 73.8%, 94.8%, and 97.2% of the estimation intervals.
Commuting in Urban Kenya: Unpacking Travel Demand in Large and Small Kenyan Cities
Authors: Salon Deborah , Gulyani Sumila
Published: July 2019

In Kenya’s capital city, Nairobi, streets are regularly gridlocked. While it is clear that roads are congested at peak hours, it is not known which commuters are experiencing that congestion or what their commute times actually are. Even less is known about commuting patterns in other Kenyan cities. This paper contributes new evidence on commuting from a survey of 14,580 households, conducted in 15 Kenyan cities in 2013. Walking and matatus—privately-operated paratransit—account for 89% of all adult commuting in urban Kenya. As cities increase in size, the proportion relying on walking falls and matatu use increases. Within a city, commuters with higher income and education, and those living further from the city center, are more likely to use matatus rather than walk. Commute times are surprisingly short. In smaller Kenyan cities the median commute time is just 20 min. In Nairobi, the median commute time is 30 min, and only 5% of those surveyed reported commuting an hour or longer. These data paint a remarkably sustainable picture of urban travel patterns in Kenya. As incomes, education levels, and demand for motorized travel rise, the challenge will be to expand and improve the system while maintaining its sustainability.
Correlation Dynamics of Dipolar Bosons in 1D Triple Well Optical Lattice
Authors: Bera Sangita , Salasnich Luca , Chakrabarti Barnali
Published: July 2019

The concept of spontaneous symmetry breaking and off-diagonal long-range order (ODLRO) are associated with Bose–Einstein condensation. However, as in the system of reduced dimension the effect of quantum fluctuation is dominating, the concept of ODLRO becomes more interesting, especially for the long-range interaction. In the present manuscript, we study the correlation dynamics triggered by lattice depth quench in a system of three dipolar bosons in a 1D triple-well optical lattice from the first principle using the multiconfigurational time-dependent Hartree method for bosons (MCTDHB). Our main motivation is to explore how ODLRO develops and decays with time when the system is brought out-of-equilibrium by a sudden change in the lattice depth. We compare results of dipolar bosons with contact interaction. For forward quench ( V f > V i ) , the system exhibits the collapse–revival dynamics in the time evolution of normalized first- and second-order Glauber’s correlation function, time evolution of Shannon information entropy both for the contact as well as for the dipolar interaction which is reminiscent of the one observed in Greiner’s experiment [Nature, 415 (2002)]. We define the collapse and revival time ratio as the figure of merit ( τ ) which can uniquely distinguish the timescale of dynamics for dipolar interaction from that of contact interaction. In the reverse quench process ( V i > V f ) , for dipolar interaction, the dynamics is complex and the system does not exhibit any definite time scale of evolution, whereas the system with contact interaction exhibits collapse–revival dynamics with a definite time-scale. The long-range repulsive tail in the dipolar interaction inhibits the spreading of correlation across the lattice sites.
Prophylactic Effects of Bee Venom Phospholipase A2 in Lipopolysaccharide-Induced Pregnancy Loss
Authors: Baek Hyunjung , Yang HyeJin , Lee Jong Hoon , Kang Na-Hoon , Lee Jinwook , Bae Hyunsu , Hwang Deok-Sang
Published: July 2019

Spontaneous abortion represents a common form of embryonic loss caused by early pregnancy failure. In the present study, we investigated the prophylactic effects of bee venom phospholipase A2 (bvPLA2), a regulatory T cell (Treg) inducer, on a lipopolysaccharide (LPS)-induced abortion mouse model. Fetal loss, including viable implants, the fetal resorption rate, and the fetal weight, were measured after LPS and bvPLA2 treatment. The levels of serum and tissue inflammatory cytokines were determined. To investigate the involvement of the Treg population in bvPLA2-mediated protection against fetal loss, the effect of Treg depletion was evaluated following bvPLA2 and LPS treatment. The results clearly revealed that bvPLA2 can prevent fetal loss accompanied by growth restriction in the remaining viable fetus. When the LPS-induced abortion mice were treated with bvPLA2, Treg cells were significantly increased compared with those in the non-pregnant, PBS, and LPS groups. After LPS injection, the levels of proinflammatory cytokines were markedly increased compared with those in the PBS mouse group, while bvPLA2 treatment showed significantly decreased TNF-α and IFN-γ expression compared with that in the LPS group. The protective effects of bvPLA2 treatment were not detected in Treg-depleted abortion-prone mice. These findings suggest that bvPLA2 has protective effects in the LPS-induced abortion mouse model by regulating Treg populations.
The Activity of Isoquinoline Alkaloids and Extracts from Chelidonium majus against Pathogenic Bacteria and Candida sp.
Authors: Zielińska Sylwia , Wójciak-Kosior Magdalena , Dziągwa-Becker Magdalena , Gleńsk Michał , Sowa Ireneusz , Fijałkowski Karol , Rurańska-Smutnicka Danuta , Matkowski Adam , Junka Adam
Published: July 2019

Chelidonium majus (Papaveraceae) extracts exhibit antimicrobial activity due to the complex alkaloid composition. The aim of the research was to evaluate the antimicrobial potential of extracts from wild plants and in vitro cultures, as well as seven major individual alkaloids. Plant material derived from different natural habitats and in vitro cultures was used for the phytochemical analysis and antimicrobial tests. The composition of alkaloids was analyzed using chromatographic techniques (HPLC with DAD detection). The results have shown that roots contained higher number and amounts of alkaloids in comparison to aerial parts. All tested plant extracts manifested antimicrobial activity, related to different chemical structures of the alkaloids. Root extract used at 31.25–62.5 mg/L strongly reduced bacterial biomass. From the seven individually tested alkaloids, chelerythrine was the most effective against P. aeruginosa (MIC at 1.9 mg/L), while sanguinarine against S. aureus (MIC at 1.9 mg/L). Strong antifungal activity was observed against C. albicans when chelerythrine, chelidonine, and aerial parts extract were used. The experiments with plant extracts, individually tested alkaloids, and variable combinations of the latter allowed for a deeper insight into the potential mechanisms affecting the activity of this group of compounds.
The First Co-Opted Endogenous Foamy Viruses and the Evolutionary History of Reptilian Foamy Viruses
Authors: Aiewsakun Pakorn , Simmonds Peter , Katzourakis Aris
Published: July 2019

A recent study reported the discovery of an endogenous reptilian foamy virus (FV), termed ERV-Spuma-Spu, found in the genome of tuatara. Here, we report two novel reptilian foamy viruses also identified as endogenous FVs (EFVs) in the genomes of panther gecko (ERV-Spuma-Ppi) and Schlegel’s Japanese gecko (ERV-Spuma-Gja). Their presence indicates that FVs are capable of infecting reptiles in addition to mammals, amphibians, and fish. Numerous copies of full length ERV-Spuma-Spu elements were found in the tuatara genome littered with in-frame stop codons and transposable elements, suggesting that they are indeed endogenous and are not functional. ERV-Spuma-Ppi and ERV-Spuma-Gja, on the other hand, consist solely of a foamy virus-like env gene. Examination of host flanking sequences revealed that they are orthologous, and despite being more than 96 million years old, their env reading frames are fully coding competent with evidence for strong purifying selection to maintain expression and for them likely being transcriptionally active. These make them the oldest EFVs discovered thus far and the first documented EFVs that may have been co-opted for potential cellular functions. Phylogenetic analyses revealed a complex virus–host co-evolutionary history and cross-species transmission routes of ancient FVs.