bluuebunny/crossref_metadata_2025 huggingface dataset:
A two‐tier bioinformatic pipeline to develop probes for target capture of nuclear loci with applications in Melastomataceae
Authors: Jantzen Johanna R. , Amarasinghe Prabha , Folk Ryan A. , Reginato Marcelo , Michelangeli Fabian A. , Soltis Douglas E. , Cellinese Nico , Soltis Pamela S.
Published: May 2020

Premise

Putatively single‐copy nuclear (SCN) loci, which are identified using genomic resources of closely related species, are ideal for phylogenomic inference. However, suitable genomic resources are not available for many clades, including Melastomataceae. We introduce a versatile approach to identify SCN loci for clades with few genomic resources and use it to develop probes for target enrichment in the distantly related Memecylon and Tibouchina (Melastomataceae).

Methods

We present a two‐tiered pipeline. First, we identified putatively SCN loci using MarkerMiner and transcriptomes from distantly related species in Melastomataceae. Published loci and genes of functional significance were then added (384 total loci). Second, using HybPiper, we retrieved 689 homologous template sequences for these loci using genome‐skimming data from within the focal clades.

Results

We sequenced 193 loci common to Memecylon and Tibouchina. Probes designed from 56 template sequences successfully targeted sequences in both clades. Probes designed from genome‐skimming data within a focal clade were more successful than probes designed from other sources.

Discussion

Our pipeline successfully identified and targeted SCN loci in Memecylon and Tibouchina, enabling phylogenomic studies in both clades and potentially across Melastomataceae. This pipeline could be easily applied to other clades with few genomic resources.
Tumor Necrosis Factor Induces Obliterative Pulmonary Vascular Disease in a Novel Model of Connective Tissue Disease–Associated Pulmonary Arterial Hypertension
Authors: Bell Richard D. , White R. James , Garcia‐Hernandez Maria L. , Wu Emily , Rahimi Homaira , Marangoni Roberta G. , Slattery Pamelia , Duemmel Stacey , Nuzzo Marc , Huertas Nelson , Yee Min , O'Reilly Michael A. , Morrell Craig , Ritchlin Christopher T. , Schwarz Edward M. , Korman Benjamin D.
Published: May 2020

Objective

Connective tissue disease (CTD)–associated pulmonary arterial hypertension (PAH) is the second most common etiology of PAH and carries a poor prognosis. Recently, it has been shown that female human tumor necrosis factor (TNF)–transgenic (Tg) mice die of cardiopulmonary disease by 6 months of age. This study was undertaken to characterize this pathophysiology and assess its potential as a novel model of CTD‐PAH.

Methods

Histologic analysis was performed on TNF‐Tg and wild‐type (WT) mice to characterize pulmonary vascular and right ventricular (RV) pathology (n = 40 [4–5 mice per group per time point]). Mice underwent right‐sided heart catheterization (n = 29) and micro–computed tomographic angiography (n = 8) to assess vascular disease. Bone marrow chimeric mice (n = 12), and anti‐TNF–treated mice versus placebo‐treated mice (n = 12), were assessed. RNA sequencing was performed on mouse lung tissue (n = 6).

Results

TNF‐Tg mice displayed a pulmonary vasculopathy marked by collagen deposition (P < 0.001) and vascular occlusion (P < 0.001) with associated RV hypertrophy (P < 0.001) and severely increased RV systolic pressure (mean ± SD 75.1 ± 19.3 mm Hg versus 26.7 ± 1.7 mm Hg in WT animals; P < 0.0001). TNF‐Tg mice had increased α‐smooth muscle actin (α‐SMA) staining, which corresponded to proliferation and loss of von Willebrand factor (vWF)–positive endothelial cells (P < 0.01). There was an increase in α‐SMA–positive, vWF‐positive cells (P < 0.01), implicating endothelial–mesenchymal transition. Bone marrow chimera experiments revealed that mesenchymal but not bone marrow–derived cells are necessary to drive this process. Treatment with anti‐TNF therapy halted the progression of disease. This pathology closely mimics human CTD‐PAH, in which patient lungs demonstrate increased TNF signaling and significant similarities in genomic pathway dysregulation.

Conclusion

The TNF‐Tg mouse represents a novel model of CTD‐PAH, recapitulates key disease features, and can serve as a valuable tool for discovery and assessment of therapeutics.
RuBisCO nano enzyme for mimicking CO2 conversion system in plants
Authors: Biçen Ünlüer Özlem , Say Rıdvan , Ersöz Arzu
Published: May 2020

In this study, carbon dioxide (CO2) capture and conversion systems based on the combination of biomimetic systems with nano enzymes have been developed. The effectiveness of the developed system has been investigated toward CO2 conversion. For this aim, nano ribulose bisphosphate carboxylase/oxygenase (RuBisCO) enzyme that plays role in the Calvin cycle in photosynthesis has been synthesized in 93 nm size according to AmiNoAcid (monomer) Decorated and Light Underpinning Conjugation Approach (ANADOLUCA) method. Enzymatic activity of synthesized nano RuBisCO enzyme has been spectrophotometrically determined by the formation of 3‐phosphoglycerate (3‐PGA) at the end of the reaction between CO2 and d‐ribulose‐1,5 biphosphate with the catalysis of RuBisCO enzyme at 340 nm. The effect of substrate concentration, pH, temperature, and Mg2+ ion concentration on the conversion reaction have investigated comparatively with nano and free RuBisCO enzyme. Besides this, the reusability feature of synthesized nano RuBisCO enzyme in conversion of CO2 reaction is indicated. When all data were evaluated, it has been seen that the nano RuBisCO enzyme is effective on the conversion of CO2 into 3‐PGA and can be used for CO2 capture and conversion systems repeatedly without any deformation in its structure.
Betaine‐assisted recombinase polymerase assay for rapid hepatitis B virus detection
Authors: Yi Ting‐ting , Zhang Han‐yun , Liang Hua , Gong Guo‐zhong , Cai Yan
Published: May 2020

Hepatitis B virus (HBV) is a worldwide epidemic pathogen that causes hepatitis B. On‐site screening the HBV infection is of critical importance for preventing and diagnosing HBV infection. In this paper, a simple, visual, and rapid method for on‐site detection of HBV‐DNA has been developed. This method is based on betaine‐assisted recombinase polymerase assay and followed with naked‐eye detection via lateral flow assay (BRPA‐LF). Result show that nonspecific amplification is prone to occur in recombinase polymerase amplification (RPA) if the assay was performed with serum sample without purification. This problem has been addressed by adding 0.8 M of betaine to the RPA reactions. It was demonstrated that BRPA‐LF can detect 1,000 copies of HBV‐DNA in 50 μL mixture, and achieved 90% sensitivity and 100% specificity for serum sample detection. These results demonstrated that BRPA‐LF can resist serum interference and has great potential for on‐site screening of HBV infection.
Sustainable production of ammonia fertilizers from biomass
Authors: Gençer Emre , Burniske Gary R. , Doering Otto C. , Tyner Wallace E. , Agrawal Rakesh , Delgass W. Nicholas , Ejeta Gebisa , McCann Maureen C. , Carpita Nicholas C.
Published: May 2020

Nitrogen is the most limiting plant nutrient. Inexpensive natural gas has substantially reduced costs of ammonia fertilizer for intensive agriculture in the developed world, but its excessive use negatively impacts downstream ecosystems. By contrast, the availability of ammonia fertilizer is a major economic bottleneck for agriculture in developing countries. A dedicated lignocellulosic biomass crop could supply sufficient substrate to generate optimal nitrogen fertilizer on less than 5% of a grower's food crop acreage. Reimagining ammonia generation using biomass could significantly enhance sustainable agricultural productivity in developing countries when combined with emerging catalytic technologies. © 2020 Society of Chemical Industry and John Wiley & Sons, Ltd
Photosynthetic Reduction of Xylose to Xylitol Using Cyanobacteria
Authors: Fan Eric S. , Lu Ken W. , Wen Rex C. , Shen Claire R.
Published: May 2020

Photosynthetic generation of reducing power makes cyanobacteria an attractive host for biochemical reduction compared to cell‐free and heterotrophic systems, which require burning of additional resources for the supply of reducing equivalent. Here, using xylitol synthesis as an example, efficient uptake and reduction of xylose photoautotrophically in Synechococcus elongatus PCC7942 are demonstrated upon introduction of an effective xylose transporter from Escherichia coli (Ec‐XylE) and the NADPH‐dependent xylose reductase from Candida boidinii (Cb‐XR). Simultaneous activation of xylose uptake and matching of cofactor specificity enabled an average xylitol yield of 0.9 g g−1 xylose and a maximum productivity of about 0.15 g L−1 day−1 OD−1 with increased level of xylose supply. While long‐term cellular maintenance still appears challenging, high‐density conversion of xylose to xylitol using concentrated resting cell further pushes the titer of xylitol formation to 33 g L−1 in six days with 85% of maximum theoretical yield. While the results show that the unknown dissipation of xylose can be minimized when coupled to a strong reaction outlet, it remains to be the major hurdle hampering the yield despite the reported inability of cyanobacteria to metabolize xylose.
Emerging Technologies for the Electrochemical Detection of Bacteria
Authors: McEachern Francis , Harvey Edward , Merle Geraldine
Published: May 2020

Infections are a huge economic liability to the health care system, although real‐time detection can allow early treatment protocols to avoid some of this cost and patient morbidity and mortality. Pseudomonas aeruginosa (PA) is a drug‐resistant gram‐negative bacterium found ubiquitously in clinical settings, accounting for up to 27% of hospital acquired infections. PA secretes a vast array of molecules, ranging from secondary metabolites to quorum sensing molecules, of which many can be exploited to monitor bacterial presence. In addition to electrochemical immunoassays to sense bacteria via antigen–antibody interactions, PA pertains a distinct redox‐active virulence factor called pyocyanin (PYO), allowing a direct electrochemical detection of the bacteria. There has been a surge of publications relating to the electrochemical tracing of PA via a myriad of novel biosensing techniques, materials, and methodologies. In addition to indirect methods, research approaches where PYO has been sensitively detected using surface modified electrodes are reviewed and compared with conventional PA‐sensing methodologies. This review aims at presenting indirect and direct electrochemical methods currently developed using various surface modified electrodes, materials, and electrochemical configurations on their electrocatalytic effects on sensing of PA and in particular PYO.
Evaluation of quenching methods for metabolite recovery in photoautotrophic Synechococcus sp. PCC 7002
Authors: Sake Cara L. , Newman Darrian M. , Boyle Nanette R.
Published: May 2020

The first step of many metabolomics studies is quenching, a technique vital for rapidly halting metabolism and ensuring that the metabolite profile remains unchanging during sample processing. The most widely used approach is to plunge the sample into prechilled cold methanol; however, this led to significant metabolite loss in Synecheococcus sp. PCC 7002. Here we describe our analysis of the impacts of cold methanol quenching on the model marine cyanobacterium Synechococcus sp. PCC 7002, as well as our brief investigation of alternative quenching methods. We tested several methods including cold methanol, cold saline, and two filtration approaches. Targeted central metabolites were extracted and metabolomic profiles were generated using liquid chromatography‐tandem mass spectrometry (LC‐MS/MS). The results indicate that cold methanol quenching induces dramatic metabolite leakage in Synechococcus, resulting in a majority of central metabolites being lost prior to extraction. Alternatively, usage of a chilled saline quenching solution mitigates metabolite leakage and improves sample recovery without sacrificing rapid quenching of cellular metabolism. Finally, we illustrate that metabolite leakage can be assessed, and subsequently accounted for, in order to determine absolute metabolite pool sizes; however, our results show that metabolite leakage is inconsistent across various metabolite pools and therefore must be determined for each individually measured metabolite.
William H. Pirkle: Stereochemistry pioneer
Authors: Welch Christopher J.
Published: May 2020

Professor William H. Pirkle (1934–2018) made a profound impact on modern chemistry by inventing and popularizing widely used techniques for the analysis and purification of enantiomers, contributions that paved the way for the subsequent advances in the discovery, development, and manufacture of enantiopure pharmaceuticals, agrochemicals, and specialty chemicals. Pirkle's pioneering 1966 demonstration of the use of chiral solvating agents for the nuclear magnetic resonance determination of enantiopurity led to a lifelong interest in understanding the supramolecular interactions responsible for enantiodifferentiation. Ongoing research into the chromatographic resolution of stereoisomers throughout the 1970s led in 1981 to the very first commercialization of a chiral stationary phase for the high‐performance liquid chromatography (HPLC) separation of enantiomers. The availability of this and subsequent “Pirkle columns” had a deep and lasting impact, becoming widely embraced by the chemical sciences research community worldwide and spearheading the wholesale changeover to HPLC as the preferred technique for measuring enantiopurity. Doc Pirkle was a highly creative, independent, and fun‐loving collaborator whose circle of friends extends around the globe. His research group at the University of Illinois, often referred to as The Pirkle Zoo, became a refuge for an interesting assembly of characters who flourished under his mentorship and guidance.
Visible Light Driven Copper(I) Catalyzed Oxyamination of Electron Deficient Alkenes†
Authors: Li Sanliang , Chen Qiaoyu , Li Wenbo , Gu Guangxin , Zhang Junliang
Published: May 2020

Summary of main observation and conclusion

A visible light driven Cu(I)‐catalyzed intermolecular oxyamination of electron‐deficient olefins has been achieved by using O‐benzoylhydroxylamines as donors both for amine and oxygen. The transformation properties afford mild conditions and a wide substrate scope, providing access to ester derivatives of β‐amino alcohols with good yields and high regioselectivity.
N‐Heterocyclic Carbene Organocatalysis: Activation Modes and Typical Reactive Intermediates
Authors: Chen Xingkuan , Wang Hongling , Jin Zhichao , Chi Yonggui Robin
Published: May 2020

N‐Heterocyclic carbene (NHC) organocatalysis has been developed as an important approach in modern organic synthesis. Versatile activation modes within NHC organocatalysis have been established with countless transformations being realized in both efficient and selective fashion. We would like to provide an overview on the key progresses achieved within this field in the past two decades. Since numerous excellent reviews have been documented within this area, we will mainly focus on the scientific development of this research field based on the basic reaction modes and typical reaction intermediates.
Safety of Candesartan, Amlodipine, and Atorvastatin in Combination: Interaction Study in Healthy Subjects
Authors: Gundlach Kristina , Wolf Katharina , Salem Isam , Randerath Olaf , Seiler Dan
Published: May 2020

For efficient cardiovascular risk protection antihypertensive treatment is often combined with cholesterol‐lowering treatment, although solid data of interaction and side effects are missing. This is a prospective, single‐center interaction study conducted in a fixed sequence design at steady state of candesartan, amlodipine, and atorvastatin. Five‐day monotherapy of candesartan 8 mg was followed by 5‐day atorvastatin 40 mg monotherapy and subsequently 9‐day amlodipine 5 mg monotherapy; each treatment separated by washout phases. Immediately after amlodipine monotherapy, all 3 drugs were administered concomitantly for 5 days. Pharmacokinetic parameters as well as safety were assessed. Eighteen healthy subjects enrolled and completed the study. No significant difference in the maximum concentration (Cmax) and the area the under plasma concentration–time curve (AUC) for amlodipine and AUC of atorvastatin was detected following combination versus monotherapy. Cmax of atorvastatin decreased slightly but clinically not relevantly when given in combination. A statistically significant but not below 0.80‐fold decrease between candesartan following combination vs monotherapy was detected for Cmax and AUC. In general, all treatments were well tolerated. Concluding, systemic exposure of candesartan, amlodipine, and atorvastatin is not clinically significantly changed upon coadministration. These data support a fixed‐dose combination of the 3 components for dual cardiovascular risk prevention.
Seismischer Nachweis von Mauerwerksbauten in deutschen Erdbebengebieten
Authors: Butenweg Christoph , Rosin Julia
Published: May 2020

Mit finanzieller Unterstützung der Deutschen Gesellschaft für Mauerwerks‐ und Wohnungsbau e.V. (DGfM) und des Deutschen Instituts für Bautechnik in Berlin (DIBt) wurden zwei aufeinander aufbauende Forschungsvorhaben zur Verbesserung der seismischen Nachweise von Mauerwerksbauten in deutschen Erdbebengebieten durchgeführt. Zunächst wurde das seismische Verhalten von drei modernen unbewehrten Mauerwerksgebäuden in der Region Emilia Romagna in Italien während der Erdbebenserie im Jahr 2012 in Kooperation mit der Universität Pavia eingehend untersucht. Aufbauend auf den Erkenntnissen dieser Untersuchungen wurde ein verbessertes seismisches Bemessungskonzept für unbewehrte Mauerwerksbauten erarbeitet. Der Beitrag stellt die wesentlichen Ergebnisse dieser Forschungsarbeiten und deren Eingang in die Normung vor.
Enhanced seed defenses potentially relax selection by seed predators against serotiny in lodgepole pine
Authors: Parker Anna L. , Benkman Craig W.
Published: May 2020

Serotiny, the retention of seeds in a canopy seed bank until high temperatures cause seeds to be released, is an important life history trait for many woody plants in fire‐prone habitats. Serotiny provides a competitive advantage after fire but increases vulnerability to predispersal seed predation, due to the seeds being retained in clusters in predictable locations for extended periods. This creates opposing selection pressures. Serotiny is favored in areas of high fire frequency, but is selected against by predispersal seed predators. However, predation also selects for cone traits associated with seed defense that could reduce predation on serotinous cones and thereby relax selection against serotiny. This helps explain the elevated defenses in highly serotinous species. However, whether such interactions drive variation in seed defenses within variably serotinous populations has been studied rarely. We investigated the effects of phenotypic selection exerted by red squirrel (Tamiasciurus hudsonicus) predation on Rocky Mountain lodgepole pine (Pinus contorta latifolia) seeds. Squirrels preferentially harvested cones with more and larger seeds, indicating a preference for a higher food reward. We found evidence for stronger selection on trees with serotinous cones, which presumably accounts for the elevated defenses of and lower predation on serotinous compared to non‐serotinous cones. Lower levels of predation on serotinous cones in turn lessen selection against serotiny by squirrels. This has important implications because the frequency of serotiny in lodgepole pine has profound consequences for post‐fire communities and ecosystems widespread in the Rocky Mountains.
Comment on van Netten, et al: Definitions and criteria for diabetic foot disease
Authors: Jarl Gustav , Rusaw David F. , Johannesson Anton
Published: May 2020

Objective

The International Working Group on the Diabetic Foot (IWGDF) recently published updated definitions for the diabetic foot field. However, the suggested definitions of lower limb amputations differ from the definitions of the International Organization of Standardization (ISO), which may create problems when implementing the definitions. This paper compares and discusses the amputation definitions of IWGDF and ISO.

Results

Despite many similarities, the IWGDF and ISO systems have some important differences. First, the IWGDF uses the term “minor amputation” which is value‐laden, arbitrary and has been defined in several different ways in the literature. Second, the IWGDF system lacks descriptions of amputations distal or through the ankle, which may increase the risk for misclassification. Third, hip disarticulations and transpelvic amputations are not included in the IWGDF system.

Conclusion

It is suggested that future updates of the IWGDF definitions should be aligned with those of ISO, to meet the goal of global consensus on terminology related to lower limb amputation.
Anti‐CD52 blocks EAE independent of PD‐1 signals and promotes repopulation dominated by double‐negative T cells and newly generated T and B cells
Authors: Haile Yohannes , Adegoke Adeolu , Laribi Bahareh , Lin Jiaxin , Anderson Colin C.
Published: May 2020

Lymphocyte depletion using anti‐CD52 antibody effectively reduces relapses of multiple sclerosis (MS). To begin to understand what mechanisms might control this outcome, we examined the effect of a murine‐CD52‐specific mAb on the depletion and repopulation of immune cells in mice with experimental autoimmune encephalomyelitis (EAE), a model of MS. We tested whether the tolerance‐promoting receptor programmed cell death protein‐1 (PD‐1) is required for disease remission post anti‐CD52, and found that PD‐1‐deficient mice with a more severe EAE were nevertheless effectively treated with anti‐CD52. Anti‐CD52 increased the proportions of newly generated T cells and double‐negative (DN) T cells while reducing newly generated B cells; the latter effect being associated with a higher expression of CD52 by these cells. In the longer term, anti‐CD52 caused substantial increases in the proportion of newly generated lymphocytes and DN T cells in mice with EAE. Thus, the rapid repopulation of lymphocytes from central lymphoid organs post anti‐CD52 may limit further disease. Furthermore, these data identify DN T cells, a subset with immunoregulatory potential, as a significant hyperrepopulating subset following CD52‐mediated depletion.
Pharmacological inhibition of RORC2 enhances human Th17‐Treg stability and function
Authors: Boardman Dominic A. , Garcia Rosa V. , Ivison Sabine M. , Bressler Brian , Dhar TG Murali , Zhao Qihong , Levings Megan K.
Published: May 2020

Inflammatory bowel diseases (IBD) are chronic conditions that result from uncontrolled intestinal inflammation. Pathogenic Th17 cells, characterized by production of IL‐17A in the absence of IL‐10, are thought to contribute to this inflammation, but in humans, antibody‐mediated blockade of IL‐17A is an ineffective IBD therapy whereas IL‐23 blockade is effective. Here, we investigated the effects of pharmacological inhibition of RORC2, the Th17 cell lineage‐defining transcription factor, on in vivo‐differentiated human Th17 cells and Th17‐like Tregs (Th17‐Tregs). BMS‐336, a small molecule RORC2 inverse agonist, inhibited expression of RORC2‐regulated genes in peripheral Th17 cells (CD4+CD25–CD127+CXCR3–CCR4+CCR6+) in a dose–dependent manner, with similar inhibitory effects on laminar propria mononuclear cells from IBD and non‐IBD subjects. Exposure of peripheral Th17‐Tregs (CD4+CD25hiCD127loCXCR3–CCR4+CCR6+) to BMS‐336 also inhibited IL‐17A production and prevented inflammatory cytokine‐induced destabilization, as evidenced by preserved FOXP3 expression and epigenetic status of the Treg‐specific demethylation region. In parallel, RORC2 inhibition increased the production of IL‐10 in Th17‐Tregs, resulting in enhanced suppression of inflammatory cytokines from myeloid cells. Thus, via its ability to simultaneously inhibit Th17 cells and enhance the stability and function of Th17‐Tregs, pharmacological inhibition of RORC2 is a promising approach to suppress inflammation and promote immune regulation in IBD.
A method of identifying the blood contributor in mixture stains through detecting blood‐specific mRNA polymorphism
Authors: Liu Zidong , Gao Zhe , Wang Jiaqi , Shi Jie , Liu Jinding , Chen Deqing , Li Wenyan , Guo Jiangling , Cheng Xiaojuan , Hao Ting , Li Zeqin , Li Yanhua , Yan Jiangwei , Zhang Gengqian
Published: May 2020

In the past decades, messenger RNA (mRNA) biomarkers have been employed to identify the origin of body fluids in forensic medicine. We hypothesized that the polymorphism of mRNA could be applied to identify individuals in mixture samples composed of two body fluids. In this study, we selected five blood‐specific mRNA biomarkers of venous blood (SPTB, CD3G, AMICA1, ANK1, and GYPA) that encompass 16 SNPs to identify the mixture contributor(s). Five specific gene markers for menstrual blood, semen, skin, saliva, and vaginal secretions were amplified and typed as body‐fluid positive controls. We established the system of multiplex PCR and single base extension (SBE) reaction followed by CE. The amplicon size was between 90bp and 294bp. The peripheral blood specificity was examined against other human body fluids, including saliva, semen, skin, menstrual blood, and vaginal secretion. The 16 SNPs were peripheral blood specific and could be successfully typed in homemade mixtures which are composed of different body fluids with 1 ng peripheral blood mRNA added. This system showed a supersensitivity (1:100) in detecting the trace amount of peripheral blood mixed in other body fluids and a combined discrimination power (CDP) of 0.99929 in Chinese population. It was the first time to establish a method for identifying the blood donors and deconvoluting mixtures through detecting mRNA polymorphism with SNaPshot assay. This peripheral blood specific SNP typing system showed high sensitivity to the typing of blood source specific markers regardless of other body fluids in the mixture.
A survey on subjecting electronic product code and non‐ID objects to IP identification
Authors: Imani Mehdi , Qiyasi Abolfazl , Zarif Nasrin , Ali Maaruf , Noshiri Omekolsoom , Faramarzi Kimia , Arabnia Hamid R. , Joudaki Majid
Published: May 2020

Over the last decade, both research on the Internet of Things (IoT) and real‐world IoT applications have grown exponentially. The IoT provides us with smarter cities, intelligent homes, and generally more comfortable lives. However, the introduction of these devices has led to several new challenges that must be addressed. One of the critical challenges facing interacting with IoT devices is to address billions of devices (things) around the world, including computers, tablets, smartphones, wearable devices, sensors, and embedded computers, and so on. This article provides a survey on subjecting Electronic Product Code and non‐ID objects to IP identification for IoT devices, including their advantages and disadvantages thereof. Different metrics are here proposed and used for evaluating these methods. In particular, the main methods are evaluated in terms of their: (i) computational overhead, (ii) scalability, (iii) adaptability, (iv) implementation cost, and (v) whether applicable to already ID‐based objects and presented in tabular format. Finally, the article proves that this field of research will still be ongoing, but any new technique must favorably offer the mentioned five evaluative parameters.
High spatio‐temporal resolution measurements of cohesive sediment erosion
Authors: Beckers Felix , Inskeep Caleb , Haun Stefan , Schmid Gerhard , Wieprecht Silke , Noack Markus
Published: May 2020

In this study, we present a novel approach to measure fundamental processes of cohesive sediment erosion. The experimental setup consists of a laboratory erosion flume (SETEG) and a photogrammetric method to detect sediment erosion (PHOTOSED). Detailed data are presented for three erosion experiments, which were conducted with a natural non‐cohesive/cohesive sediment mixture at increasing sediment depths (4, 8, 16 cm). In each experiment, the sediment was exposed to a set of incrementally increasing shear stresses and the erosion was measured dynamically, pixel‐based, and approximate to the process scale given the resolution of PHOTOSED. This enables us to distinguish between (i) individual emerging erosion spots caused by surface erosion and (ii) large holes torn open by detached aggregate chunks. Moreover, interrelated processes were observed, such as (iii) propagation of the erosion in the longitudinal and lateral direction leading to merging of disconnected erosion areas and (iv) progressive vertical erosion of already affected areas. By complementing the (bulk) erosion volume profiles with additional quantitative variables, which contain spatial information (erosion area, specific deepening, number of disconnected erosion areas), conclusions on the erosion behaviour (and the dominant processes) can be drawn without requiring qualitative information (such as visual observations). In addition, we provide figures indicating the spatio‐temporal erosion variability and the (bulk) erosion rates for selected time periods. We evaluate the variability by statistical quantities and show that significant erosion is mainly confined to only a few events during temporal progression, but then considerably exceeds the time‐averaged median of the erosion (factors between 7.0 and 16.0). Further, we point to uncertainties in using (bulk) erosion rates to assess cohesive sediment erosion and particularly the underlying processes. As a whole, the results emphasise the need to measure cohesive sediment erosion with high spatio‐temporal resolution to obtain reliable and robust information. © 2020 The Authors. Earth Surface Processes and Landforms published by John Wiley & Sons Ltd
Assessing paraglacial processes at Nexpayantla Gorge (Popocatépetl volcano, Central Mexico) using OSL and14C
Authors: Muñoz‐Salinas E. , Castillo M. , Franco‐Ramos O. , Arce J.L. , Sanderson D.C.W. , Cresswell A.C.
Published: May 2020

We evaluate the paraglacial activity in Nexpayantla, a subtropical mountainous gorge in Popocatépetl volcano (Central Mexico), fully deglaciated in the 20th century. Glacial advances are evidenced by the presence of moraines. Fluvio‐glacial terraces and an alluvial megafan resulted from the gorge deglaciation. Current reworking of the glacigenic material is done by landslides and debris flows produced on the moraines and terraces. To study the different phases of mobilization of glacigenic sediment, we used an approach based on the study of the optically stimulated luminescence (OSL) signals obtained from a portable OSL (POSL) reader in samples extracted from both glacigenic and paraglacial deposits. The luminescence (POSL) results obtained at moraines increase as altitude decreases, which is expected for deglaciated valleys where the oldest moraines are located at lower elevations. We evaluate the grade of luminescence signal reset of the glacigenic sediments during the proglacial stage, and the subsequent deglaciation phases. Our results indicate that there is a marked transition between glacial and fluvially dominated processes at Nexpayantla Gorge. We find that the grade of luminescence signal resetting in the paraglacial deposits is a good indicator to trace paraglacial stages and the beginning of exhaustion of the paraglacial activity in mountain areas. OSL ages confirm that the oldest fluvio‐glacial terraces found at the middle sector of Nexpayantla Gorge are ~2 ka, which is also supported by an AMS14C age. OSL dating was found challenging, since quartz grains have low sensitivity because of their volcanic origin; POSL signals, however, are in good agreement with the location and distribution of geomorphic markers. We propose that luminescence data obtained from the POSL unit can be useful to provide information about sediment mobilization in paraglacial environments during different climatic pulses – even for the case where mineral grains have low sensitivity, such as in volcanic sediments. © 2020 John Wiley & Sons, Ltd.
Quantitative reconstruction of Holocene sediment sources contributing to the central Jiangsu coast, China: New insights into source‐to‐sink processes
Authors: Yang Yang , Jia Jianjun , Zhou Liang , Gao Jianhua , Gao Wenhua , Shi Benwei , Li Zhanhai , Wang Ya Ping , Gao Shu
Published: May 2020

Coastal deltaic deposits are the primary locations for sediment storage on Earth, and quantifying their source contributions is a critical prerequisite for delineating S2S patterns in marginal seas. In most cases, quantification for the contribution by fine‐grained sediments (i.e. particle size < 63 μm) is considered to be representative to constrain the overall sediment supply. However, this approach may be inappropriate because large differences exist between the two quantities. Here we propose an approach to solve the problem, which is based on the maximum number of tracers from multiple sediment size fractions incorporating the content of all size fractions of sediment. Using this approach, absolute source contributions during the Holocene are reconstructed that provide a first‐order model for the S2S pattern of the central Jiangsu coast, China. The Huanghe River is the strongest driver for the Holocene sedimentation, with a mean contribution of ~72 ± 6% (1417 × 108 t). The absolute contributions from the Changjiang and offshore areas were of secondary importance, (i.e. ~17 ± 1% (330 × 108 t) and ~11 ± 5% (217 × 108 t), respectively). The results show that a large difference between the relative and absolute source contributions and the assumption that the relative contribution represents the absolute contribution is invalid in a coastal setting. The impact of the Huanghe is mainly based on episodic events, such as the event of 1128–1855 AD. The model also reveals that the offshore sediments are as important as the Changjiang sediments for the central Jiangsu coast during the Holocene. Thus, the model provides both the time series and overall quantities of sediment supply during the formation and evolution of the Holocene tidal flats on the Jiangsu coast. Our findings shed new light on quantitative analysis of sediment sources applicable to future S2S studies of marginal seas. © 2020 John Wiley & Sons, Ltd.
Monitoring coastal morphology: the potential of low‐cost fixed array action cameras for 3D reconstruction
Authors: Godfrey Samantha , Cooper James , Bezombes Frederic , Plater Andrew
Published: May 2020

The combination of structure‐from‐motion with multi‐view stereo (SfM‐MVS) photogrammetry has become an increasingly popular method for the monitoring and three‐dimensional (3D) reconstruction of coastal environments. Climate change is driving the potential for increased coastal landward retreat meaning geomorphological monitoring using methods such as SfM‐MVS has become essential for detecting and tracking impacts. SfM‐MVS has been well‐researched with a variety of platforms and spatial and temporal resolutions using mainly rectilinear digital cameras in coastal settings. However, there has been no assessment of the potential of fixed multi‐camera arrays to monitor landward retreat or on the significance of camera placement in relation to the scene. This study presents an innovative method of image acquisition using a purpose‐built camera grid and GoPro© action camera to evaluate the combined effects of camera height, obliqueness and overlap at a site of known landward retreat. This approach examines the effect of camera placement on scene reconstruction to aid the design of a multi‐camera array. SfM‐MVS dense point clouds display millimetre accuracy when compared to equivalent terrestrial laser scans and strong image network geometry with internal precision estimates of < 3 mm. Comparable point cloud reconstruction can be achieved with a small number of images stationed in appropriate positions. Initial results show as few as five images positioned at a cliff to camera ratio of 3:4.18 and camera obliqueness of 40° can provide reconstruction in the range of millimetres (mean error of 4.79 mm). These findings illustrate the importance of camera placement when using multiple cameras and aid the design of a low‐cost, fixed multi‐camera array for use at sites of small‐scale landward retreat. © 2020 The Authors. Earth Surface Processes and Landforms published by John Wiley & Sons Ltd
Thermo‐physical investigation of butyl stearate as potential phase change material for thermal energy storage in cooling application
Authors: Chinnasamy Veerakumar , Appukuttan Sreekumar
Published: May 2020

Phase change material (PCM) based energy storage technology is a promising solution to conserve thermal energy. This work involves studies on thermophysical properties of butyl stearate as PCM for thermal comfort application and its corrosion compatibility with commonly used heat exchanger construction materials. The thermophysical properties of butyl stearate is studied using differential scanning calorimetry and the result shows that the peak melting and freezing temperatures are 18.64°C and 13.28°C, respectively. The latent heat of melting and freezing are 120.59 Jg−1 and 120.70 Jg−1, respectively. The accelerated thermal cycling test reveals that butyl stearate is stable upto 1000 repeated thermal cycles. The thermogravimetric studies and Fourier transform infrared spectroscopy confirm that butyl stearate is thermally and chemically stable. The results of corrosion test provide information about selection of construction materials for heat exchanger and encapsulation in real‐time application. Butyl stearate is a potential PCM which can be used in thermal energy storage system for thermal comfort application.
Assessment of Transcriptomic and Apical Responses of Daphnia magna Exposed to a Polyethylene Microplastic in a 21-d Chronic Study
Authors: Coady Katherine K. , Burgoon Lyle , Doskey Claire , Davis John W.
Published: May 2020

There is global concern regarding the fate and effects of microplastics in the environment, particularly in aquatic systems. In the present study, ethylene acrylic acid copolymer particles were evaluated in a chronic toxicity study with the aquatic invertebrate Daphnia magna. The study design included a natural particle control treatment (silica) to differentiate any potential physical effects of a particle from the intrinsic toxicity of the test material. In addition to the standard endpoints of survival, growth, and reproduction, the transcriptomic profiles of control and ethylene acrylic acid copolymer-exposed D. magna were evaluated at the termination of the 21-d toxicity study. No significant effects on D. magna growth, survival, or reproduction were observed in comparison with both particle and untreated control groups. Significant transcriptomic alterations were induced at the highest treatment level of 2.3 × 1012 particles of the ethylene acrylic acid copolymer/L in key pathways linked to central metabolism and energy reserves, oxidative stress, and ovulation and molting, indicating a global transcriptomic response pattern. To put the results in perspective is challenging at this time, because, to date, microplastic environmental monitoring approaches have not been equipped to detect particles in the nanosize range. However, our results indicate that ethylene acrylic acid copolymer microplastics in the upper nanosize range are not expected to adversely affect D. magna growth, survival, or reproductive outcomes at concentrations of up to 1012 particles/L. Environ Toxicol Chem 2020;39:1578–1589. © 2020 SETAC
External Sources Inhibit Benthic Phosphorus Fluxes in the Lower Great Miami River, Southwest Ohio
Authors: Mullen Kortney R. , Hammerschmidt Chad R. , Ekberg Michael P. , McCarthy Mark J. , Newell Silvia E. , Agather Alison M.
Published: May 2020

Human activities have increased nutrient loadings to aquatic ecosystems, especially during the past century. During low river flow in late summer and early fall, elevated concentrations of phosphorus (P) and nitrogen are present in the temperate Lower Great Miami River and contribute to its eutrophication. Although wastewater treatment plants are suspected of being major sources of P to the river, riverbed sediment has not been examined as an additional potential source of P. Benthic P fluxes were measured at 11 representative locations along the Lower Great Miami River during 3 sampling campaigns in late summer and early fall of 2015. Benthic fluxes of filtered total P (range, −1.6−12 mg m−2 d−1) were related inversely to filtered total P concentrations in river water (p = 0.002, r = −0.60). This relationship suggests that elevated P in river water inhibits mobilization from sediment, likely by minimizing the concentration gradient between porewater and overlying water. To effectively mitigate long-term effects of legacy P stored in Lower Great Miami River sediments, external sources must continue to be managed and discharges reduced to allow legacy P to be mobilized and flushed from the system. Reducing nutrient loading will help protect water quality in the Lower Great Miami River, in other comparable rivers, and in downstream aquatic habitats. Environ Toxicol Chem 2020;39:1517–1525. © 2020 SETAC
Effects on Trout Alevins of Chronic Exposures to Chemically Dispersed Access Western Blend and Cold Lake Blend Diluted Bitumens
Authors: Adams Julie E. , Madison Barry N. , Charbonneau Kelli , Sereneo Marie , Baillon Lucie , Langlois Valerie S. , Brown R. Stephen , Hodson Peter V.
Published: May 2020

The present study assessed the chronic toxicity of 2 chemically enhanced water accommodated fractions (CEWAFs) of diluted bitumens (dilbits), Access Western Blend (AWB) and Cold Lake Blend (CLB), to rainbow trout alevins. Chemical dispersion was used to overcome the resistance to dispersion of dilbits and to generate test solutions that contained more and smaller oil droplets for increased partitioning of petroleum hydrocarbons into water. Test solutions were characterized by fluorescence spectroscopy, a rapid and inexpensive analytical tool to compare toxicity endpoints measured by fluorescence (total petroleum hydrocarbons measured by fluorescence [TPH-F]). Cumulative mortality and the prevalence and severity of malformations increased following exposure of alevins to dispersed dilbits. Toxicity curves overlapped for AWB and CLB when expressed as TPH-F and 22- to 24-d median lethal and effect concentrations ranged from 0.36 to 1.5 mg/L. Gene expression in alevins was also altered following exposure to dispersed dilbit, with relative cytochrome P450-1A mRNA levels increasing up to 170-fold for AWB and up to 240-fold for CLB. Access Western Blend and CLB caused similar toxicity to rainbow trout alevins as light to medium conventional crude oils, and rainbow trout alevins were more sensitive than yellow perch, Japanese medaka, and fathead minnow embryos exposed to dispersed AWB and CLB. The present study is the first to assess the embryotoxicity of dilbits to a Canadian freshwater salmonid species. Environ Toxicol Chem 2020;39:1620–1633. © 2020 SETAC

Abstract

The toxicity of chemically dispersed dilbit to rainbow trout alevins is similar to that of light to medium conventional crude oils. AWB = Access Western Blend; CEWAF = chemically enhanced water accommodated fraction; CLB = Cold Lake Blend; LC50 = median lethal concentration; TPH-F = total petroleum hydrocarbons measured by fluorescence.
Robust control volume finite element methods for numerical wave tanks using extreme adaptive anisotropic meshes
Authors: Via‐Estrem Lluis , Salinas Pablo , Xie Zhihua , Xiang Jiansheng , Latham John‐Paul , Douglas Steven , Nistor Ioan , Pain Christopher
Published: May 2020

Multiphase inertia‐dominated flow simulations, and free surface flow models in particular, continue to this day to present many challenges in terms of accuracy and computational cost to industry and research communities. Numerical wave tanks and their use for studying wave‐structure interactions are a good example. Finite element method (FEM) with anisotropic meshes combined with dynamic mesh algorithms has already shown the potential to significantly reduce the number of elements and simulation time with no accuracy loss. However, mesh anisotropy can lead to mesh quality‐related instabilities. This article presents a very robust FEM approach based on a control volume discretization of the pressure field for inertia dominated flows, which can overcome the typically encountered mesh quality limitations associated with extremely anisotropic elements. Highly compressive methods for the water‐air interface are used here. The combination of these methods is validated with multiphase free surface flow benchmark cases, showing very good agreement with experiments even for extremely anisotropic meshes, reducing by up to two orders of magnitude the required number of elements to obtain accurate solutions.
A highly accurate GPU Lattice Boltzmann method with directional interpolation for the probability distribution functions
Authors: Delgado‐Gutiérrez Arturo , Marzocca Pier , Cárdenas Diego , Probst Oliver
Published: May 2020

In this article, a highly accurate and graphics processing unit (GPU)‐accelerated Lattice Boltzmann Method (LBM) is presented. The methodology is derived from a combination of conventional and recent LBM algorithms, mainly focusing on reducing the computational time, memory allocation, and complexity of existing algorithms. The general implementation focuses on accelerating the overall methodology using GPGPU technology based on Compute Shaders from OpenGL and avoids the storage of the distribution function components to reduce the memory allocation size. Furthermore, an efficient spatial interpolation of the probability distribution function components is described, based on a directional interpolation, without unnecessary control points for the reconstruction of virtual nodes data. The present methodology, tested for spatial accuracy via two‐ and three‐dimensional Lid‐Driven Cavity benchmark cases, shows excellent agreement with the results reported in the literature. Additionally, time efficiency is analyzed by comparing different configurations for the construction of virtual streaming points.
Multi‐fidelity surrogate reduced‐order modeling of steady flow estimation
Authors: Wang Xu , Kou Jiaqing , Zhang Weiwei
Published: May 2020

A multi‐fidelity reduced‐order model (ROM), which incorporates low‐fidelity data to improve the prediction of high‐fidelity results, is proposed for the reconstruction of steady flow field at different conditions. The spatial basis functions of low‐fidelity and high‐fidelity data, which are generated for all training sets are extracted separately by proper orthogonal decomposition. Then a surrogate model is used to construct mappings between the mode coefficients obtained from low‐fidelity and the high‐fidelity data. In the online stage, both the low‐fidelity flow at the predicted state and the surrogate model are needed to predict the mode coefficients of the high‐fidelity flow, and the high‐fidelity flow field is subsequently reconstructed. This method differs from existing surrogate‐based reduced‐order modeling method because it allows the use of partial physical information for flow estimation, which is coming from the low‐fidelity data instead of adopting a black‐box mapping between system state and the projection coefficients. Numerical studies are presented for a lid‐driven cavity problem and transonic flow past a NACA0012 airfoil. Two low‐fidelity models, with either a coarse mesh or a lower numerical order, are considered respectively. Results show that the proposed multi‐fidelity ROM predicts the flow field accurately and outperforms the traditional methods in both interpolated and extrapolated conditions.