bluuebunny/crossref_metadata_2025 huggingface dataset:
Metalloproteinases secretion from cultured cells: Differentiation by detergents
Authors: Seredyński Rafał , Hotowy Katarzyna , Czapińska Elżbieta , Nowak Nicole , Terlecka Ewa , Kustrzeba-Wójcicka Irena , Gamian Andrzej , Terlecki Grzegorz , Gutowicz Jan
Published: January 2019

Aim: Matrix metalloproteinases, particularly MMP-2 and MMP-9, are the active factors influencing the structure and properties of the extracellular matrix. This effect is enhanced in metastasis. Hence, it is necessary to enrich the knowledge of the relation between the accumulation and distribution of the enzymes in cells and the intensity of their secretion.
Material/Methods: The study was conducted on three cell lines of dermal origin: normal line of human dermal fibroblasts (NHDF) and two melanoma lines (BM and B16F10). The results were obtained with substrate zymography, immunofluorescence microscopy and detergent-complemented fluorimetric assay.
Results: All the studied cell lines revealed relatively rich content of MMP-2 (latent and active) with random intracellular localization. Nevertheless, the enzyme secretion was differentiated in various types of cells. The most intensive proMMP-2 secretion was obtained for NHDF, relatively lower for BM, and the lowest for B16F10 line. Zymographic detection of the active form of MMP-2 was restricted to NHDF and BM cell lines. On the other hand, differentiating usage of detergents Brij 35P and Triton X-100 evidenced an active fraction of MMP-2 present in cells of all studied lines. Triton X-100-generated lysis of cells of high MMP-2 secretion (NHDF, BM) revealed the presence of intracellular inhibitors.
Conclusions: From the obtained results it can be concluded that the active form of MMP-2 is localized pericellularly in studied cells, being a minor fraction of a total amount of cellular MMP-2. The rest of the enzyme content is located deeper in cell cytoplasm in a latent form. The activity of the pericellular fraction of the enzyme can be measured with detergent-complemented fluorimetric assay, constituting a potentially useful tool for evaluating the enzyme distribution.
Incidence of Respiratory Syncytial Virus Infection Among Young Children of Bandar Abbas, Southern Iran
Authors: Rajaei Shahrokh , Rahmati Mohammad Bagher , Zare Shahram , Attarzadeh Yazdi Ghassem
Published: January 2019

Background: Respiratory syncytial virus (RSV) is a lower respiratory tract infection in infants and children younger than five years old. This disease is an important factor for hospitalization during the winter months. Methods: To determine the percentage of RSV infection in infants younger than 60 months old in different seasons, the current study was performed during 12 months in 2014 in Bandar Abbas, southern Iran. Overall, 182 children aged less than five years with clinical symptoms of tachydyspnea, fever, cold/cough, sore throat, and aches (examined by one specialist pediatrician) were consecutively selected from inpatient or outdoor patients of the children’s hospital in Bandar Abbas, Iran. Children’s throat swabs were collected and RSV infection was detected by real time-polymerase chain reaction (RT-PCR). Results: In total, 57.14% of all children were male and 42.86% were female. Respiratory syncytial virus infection was found in 46 out of 182 patients (25.3%). Among the 46 children with RSV infection, 22 patients (47.83%) were male and 24 patients (52.17%) were female with no significant difference between males and females. Most RSV infections were found in infants younger than 36 months old. There were significant differences between RSV positivity in winter and summer as 86.96% of positive RSV was during winter and 13.04% was during summer. Conclusions: This study indicates that RSV is an important cause of respiratory tract infection in winter time in infants less than 36 months old in Bandar Abbas.
A matter of timing
Authors: Perry Michael W , Desplan Claude
Published: January 2019

A genetic pathway that times development works together with the sex-determination pathway to control the timing of sexually dimorphic neural development in C. elegans.
Timing mechanism of sexually dimorphic nervous system differentiation
Authors: Pereira Laura , Aeschimann Florian , Wang Chen , Lawson Hannah , Serrano-Saiz Esther , Portman Douglas S , Großhans Helge , Hobert Oliver
Published: January 2019

The molecular mechanisms that control the timing of sexual differentiation in the brain are poorly understood. We found that the timing of sexually dimorphic differentiation of postmitotic, sex-shared neurons in the nervous system of the Caenorhabditis elegans male is controlled by the temporally regulated miRNA let-7 and its target lin-41, a translational regulator. lin-41 acts through lin-29a, an isoform of a conserved Zn finger transcription factor, expressed in a subset of sex-shared neurons only in the male. Ectopic lin-29a is sufficient to impose male-specific features at earlier stages of development and in the opposite sex. The temporal, sexual and spatial specificity of lin-29a expression is controlled intersectionally through the lin-28/let-7/lin-41 heterochronic pathway, sex chromosome configuration and neuron-type-specific terminal selector transcription factors. Two Doublesex-like transcription factors represent additional sex- and neuron-type specific targets of LIN-41 and are regulated in a similar intersectional manner.
Building making scholarship
Authors: Nielsen Liv Merete
Published: January 2019

Artikkelen beskriver hvordan forskning innen skapende profesjonsfag har blitt drevet fram av professor Halina Dunin-Woyseth. Med bakgrunn som arkitekt har hun hatt et innsideperspektiv på de utfordringene de skapende profesjonsfagene sto overfor. Som en av de få arkitekter som også hadde doktorgrad fikk hun ansvar for utviklingen av doktorgradsprogrammet på Arkitektur- og designhøgskolen i Oslo (AHO). Hun utviklet kunnskapskonseptene ‘the making professions’ og ‘the making disciplines’ for å synliggjøre og håndtere de skapende profesjonenes utfordringer som selvstendige forskbare (researchable) fagfelt i møte med etablerte akademiske disipliner. I 1995 sto hun sentralt i avgjørelsen om å åpne doktorprogrammet på AHO for designere og designdidaktikere, noe som har spilt en avgjørende rolle for framveksten av et designdidaktisk forskningsfelt i Norge. Innsatsen til Dunin-Woyseth går langt ut over det å være én persons innsats, den eksemplifiserer hvordan utdanning og forskning med et innsideperspektiv på kunnskapsutvikling har avgjørende betydning for et demokrati der også representanter for praktiske profesjoner må kunne artikulere sin innsidekunnskap med akademisk troverdighet. Framhevingen av et innsideperspektiv (Ryle, 1945) og viktigheten av aktive fagmiljøer (Becher & Trowler, 2001) setter også Halina Dunin-Woyseths innsats inn i et større perspektiv. Hun har høstet internasjonal anerkjennelse både som teoretiker og feltbygger.
Bokanmeldelse: Boka om kunst og håndverk i barnehagen
Authors: Bråten Ingvard
Published: January 2019

Boka om kunst og håndverk i barnehagen har vokst fram ved kunst og håndverksmiljøet ved Dronning Mauds Minne Høgskole for barnehagelærerutdanning (DMMH) i Trondheim. Dette er en grunnbok som skal gi en kunst og håndverksfaglig kunnskapsbase til studenter i kunnskaps­området Kunst, kultur og kreativitet i barnehagelærerutdanningen. Videre henvender boka seg til ansatte i barnehagen. Ved siden av de tre redaktørene, Frisch, Letnes og Moe, har Vigdis Dagsdatter Øien skrevet ett kapittel.
Generation of mesothelial progenitor‐like cells from mouse‐induced pluripotent stem cells
Authors: Inagaki Natsuko F. , Inagaki Fuyuki F. , Kokudo Norihiro , Miyajima Atsushi
Published: January 2019

Mesothelial cells, which cover the surface of visceral organs and serous cavities in mammals, play a crucial role in preventing adhesion. We previously reported that primary mesothelial progenitor cells (MPCs) can not only prevent postoperative adhesion but also promote liver regeneration after hepatectomy. Induced pluripotent stem cells (iPSCs) have the potential to be used for regenerative medicine. Here, we have established a differentiation protocol for mouse iPSC‐derived MPCs (miMPCs) via the exposure to defined factors, as well as purification using MPC‐specific cell surface antigens. Furthermore, the miMPCs had the ability to suppress postoperative adhesion and facilitate liver regeneration. This is the first report highlighting the generation of functional miMPCs, which may offer potential for de novo cell therapy.
Suitability of Raman Spectroscopy for Assessing Anisotropic Strain in Thin Films of Doped Ceria
Authors: Kraynis Olga , Makagon Evgeniy , Mishuk Eran , Hartstein Michal , Wachtel Ellen , Lubomirsky Igor , Livneh Tsachi
Published: January 2019

A protocol for characterizing relaxation of anisotropic strain in thin films of 10 mol% Eu‐ or Sm‐doped ceria is described. The method is based on comparison of Raman spectra and X‐ray diffraction patterns from substrate‐supported films, displaying in‐plane compressive strain (initial state), with analogous data from 2 mm diameter self‐supported films (i.e., membranes), prepared by partial substrate removal (final state). These membranes are found to be relaxed, i.e., approximately unstrained, but with increased unit cell volume. The effective (i.e., 2‐state) Grüneisen parameter of the F2g Raman active mode for these films is calculated to be 0.4 ± 0.1, which is ≈30% of the literature value for the corresponding ceramics under isostatic pressure. On this basis, it is found that the observed red‐shift of the F2g mode frequency following isothermal strain relaxation of the doped ceria thin films cannot be determined solely by the increase in average unit cell volume. The study presented here may shed light on the suitability of Raman spectroscopy as a technique for characterizing strain in lanthanide‐doped ceria thin films.
In Situ Microwave‐Assisted Fabrication of Hierarchically Arranged Metal Sulfide Counter Electrodes to Boost Stability and Efficiency of Quantum Dot‐Sensitized Solar Cells
Authors: Tsai Jia‐Shan , Dehvari Khalilalrahman , Ho Wei‐Chuan , Waki Keiko , Chang Jia‐Yaw
Published: January 2019

This study describes preparation of metal sulfide counter electrodes (CEs) through one‐pot microwave‐assisted route to improve power conversion efficiency (PCE) of quantum dot‐sensitized solar cells at a lower cost. The CuS nanorods, Ni0.96S nanoparticles, and PbS nanocubes are synthesized and deposited in situ on fluorine‐doped tin oxide substrate to serve as CEs without further post‐treatment. Effects of several reaction parameters including sulfur precursor (Na2S, C2H5NS, CH4N2S), Cu concentration, reaction time, and choice of cation (Cu, Ni, Pb) on the CEs morphology, electrochemical characteristics, and PCE are studied. Furthermore, nanostructure formation and thin film growth are studied and correlated with PCE, from which morphology‐ and composition‐performance relationships can be inferred. Hierarchically assembled nanorod CuS CEs exhibit higher electrochemical stability in the S2–/Sn2– redox reaction. Together with the efficient charge transfer and higher diffusion coefficient of polysulfide redox at the electrode/electrolyte interface, deduced from electrochemical impedance spectroscopy and Tafel analyses, a PCE of 8.32% is achieved for the CuS CE. The enhanced photovoltaic performance is ascribed to the 1D CuS nanorods forming a diffusive structure which decreases charge transfer impedance and facilitates regeneration of polysulfide redox leading to a higher short‐circuit current density and fill factor.
Multifunctional and Tunable Surfaces Based on Pyrene Functionalized Nanoparticles
Authors: Wittmann Judith E. , Stiegler Lisa M. S. , Henkel Christian , Träg Johannes , Götz Klaus , Unruh Tobias , Zahn Dirk , Hirsch Andreas , Guldi Dirk , Halik Marcus
Published: January 2019

The tuning of the optical properties of pyrene, immobilized on alumina nanoparticle surfaces, is demonstrated. To this end, phosphonic acid functionalized pyrene derivatives are shown to self‐assemble into stoichiometrically mixed monolayers featuring hydrophilic, hydrophobic, or fluorophilic phosphonic acid ligands and to form defined core–shell hybrids depending on the molecular mixing ratio and the nature of the ligand monomer, excimer, or mutual emission of both evolved. The spectroscopic observations are explained by the respective mobility of the dye molecules with respect to their fixed, specific anchor points and the resulting probability to form excimers and are supported by molecular dynamic simulations, X‐ray reflectivity measurements, and temperature‐dependent steady‐state fluorescence assays. In terms of an additional tuning of the emission color change and/or the on‐off switching of the fluorescence, the formation of core–shell–shell system is carried out by applying amphiphiles. The general concept is fully transferable to demobilized films of nanoparticles, thereby enabling a switchable solid‐state surface.
Benchmarking the Activity, Stability, and Inherent Electrochemistry of Amorphous Molybdenum Sulfide for Hydrogen Production
Authors: Escalera‐López Daniel , Lou Zhiheng , Rees Neil V.
Published: January 2019

Anodically electrodeposited amorphous molybdenum sulfide (AE‐MoSx) has attracted significant attention as a non‐noble metal electrocatalyst for its high activity toward the hydrogen evolution reaction (HER). The [Mo3S13]2− polymer‐based structure confers a high density of exposed sulfur moieties, widely regarded as the HER active sites. However, their intrinsic complexity conceals full understanding of their exact role in HER catalysis, hampering their full potential for water splitting applications. In this report, a unifying approach is adopted accounting for modifications in the inherent electrochemistry (EC), HER mechanism, and surface species to maximize the AE‐MoSx electroactivity over a broad pH region (0–10). Dramatic enhancements in HER performance by selective electrochemical cycling within reductive (overpotential shift, ηHER ≈ −350 mV) and electro‐oxidative windows (ηHER ≈ −290 mV) are accompanied by highly stable performance in mildly acidic electrolytes. Joint analysis of X‐ray photoelectron spectroscopy, Raman, and EC experiments corroborate the key role of bridging and terminal S ligands as active site generators at low pH, and reveal molybdenum oxysulfides (Mo5+OxSy) to be the most active HER moiety in AE‐MoSx in mildly acidic‐to‐neutral environments. These findings will be extremely beneficial for future tailoring of MoSx materials and their implementation in commercial electrolyzer technologies.
Simultaneously tuning dense skin and porous substrate of asymmetric hollow fiber membranes for efficient purification of aggressive natural gas
Authors: Liu Gongping , Labreche Ying , Li Nanwen , Liu Yang , Zhang Chen , Miller Stephen J. , Babu Vinod P. , Bhuwania Nitesh , Koros William J.
Published: January 2019

Highly permeable, selective, and stable asymmetric membranes are required to replace the traditional separation approaches for natural gas purification with higher energy efficiency and smaller footprints. Herein, we report on the design and engineering of defect‐free asymmetric hollow fiber membranes with a thin dense skin and highly porous substrate to effectively deal with aggressive natural gas. A crosslinkable polymer with rigid molecular structure and high molecular weight was synthesized for developing spinning dope with desirable solution properties. Phase separation behavior of the polymer was carefully controlled by systematic formulation of the dope composition and optimizing spinning conditions, thereby realizing simultaneously tuning dense skins and porous substrates of the spun asymmetric hollow fiber membranes. The crosslinked hollow fiber membrane, with well‐preserved delicate asymmetric nanostructures, exhibited unprecedentedly high and stable separation performance for long‐term processing extremely aggressive CO2/CH4 mixtures (with pressure up to 820 psi containing C6+ hydrocarbons), thereby showing great potential for practical application of natural gas purification. This work offers a new platform to create hollow fiber membranes with both high permeance and plasticization resistance in natural gas service. © 2019 American Institute of Chemical Engineers AIChE J, 65: 1269–1280, 2019
In Vitro Reconstitution of Bacterial DMSP Biosynthesis
Authors: Liao Cangsong , Seebeck Florian P.
Published: January 2019

Dimethylsulfoniopropionate (DMSP) is one of the most abundant sulfur metabolites in marine environments. The biosynthesis of DMSP and its degradation to dimethylsulfide are important links in the planetary sulfur cycle. Herein, the first complete description of a DMSP biosynthetic pathway is provided by the in vitro reconstitution of four enzymes from Streptomyces mobaraensis. The isolation of DMSP from S. mobaraensis cells grown at high salinity confirmed that this actinobacterium is indeed is a DMSP‐producing organism. The described DMSP biosynthesis follows the same route as that previously described for angiosperm plants. Despite this chemical congruence, limited sequence similarity between plant and bacterial enzymes suggests that the two biosynthetic activities emerged by convergent evolution.
In Situ Generation of an N‐Heterocyclic Carbene Functionalized Metal–Organic Framework by Postsynthetic Ligand Exchange: Efficient and Selective Hydrosilylation of CO2
Authors: Zhang Xu , Sun Jiao , Wei Guangfeng , Liu Zhipan , Yang Huimin , Wang Kaimin , Fei Honghan
Published: January 2019

The reported metal–organic framework (MOF) catalyst realizes CO2 to methanol transformation under ambient conditions. The MOF is one rare example containing metal‐free N‐heterocyclic carbene (NHC) moieties, which are installed using an in situ generation strategy involving the incorporation of an imidazolium bromide based linker into the MOF by postsynthetic ligand exchange. Importantly, the resultant NHC‐functionalized MOF is the first catalyst capable of performing quantitative hydrogen transfer from silanes to CO2, thus achieving quantitative (>99 %) methanol yield. Density‐functional theory calculations indicate the high catalytic activity of the NHC sites in MOFs are attributed to the decreased reaction barrier of a reaction route involving the formation of an NHC‐silane adduct. In addition, the MOF‐immobilized NHC catalyst shows enhanced stability for up to eight cycles without base activation, as well as high selectivity towards the desired silyl methoxide product.
Economic, social, and environmental cost optimization of biomass transportation: a regional model for transportation analysis in plant location process
Authors: Ko Sangpil , Lautala Pasi , Fan Jiqing , Shonnard David R.
Published: January 2019

The need to build an efficient procurement system has been recognized as one of the main obstacles to the extension of the bioenergy industry. Transportation is a key component of that system, as it accounts for a significant portion of the delivered cost. One of the most critical factors affecting transportation cost is the interrelationship between feedstock sources and facility locations, including plant and off‐plant transfer / storage facilities. At the same time, biomass energy sustainability is sensitive to the performance of each component in the entire process. The main goal of this study is to build a mixed integer linear programming (MILP) model that uses region‐specific data to minimize sustainable transportation costs. This consists of economic, environmental, and societal factors. The upstream air emissions as a result of residues collection at the forest, transloading, and transportation by truck or multimodally (truck and rail), which include greenhouse gases (GHG), particulate matter (PM), and nitrogen oxides (NOx), are calculated and included in the analysis. The model was tested on a case study that evaluated transportation costs for nine alternative plant locations in the state of Wisconsin. The results revealed that when equally weighed, external (social and environmental) costs accounted for a considerable portion of total transportation cost (approximately 26–37%). The study also shows that total upstream GHG and air emissions increased as the plant capacity increased, due to the longer transportation distances, but per unit emissions decreased. © 2019 Society of Chemical Industry and John Wiley & Sons, Ltd
Further evaluation of treatments for vocal stereotypy: Response interruption and redirection and response cost
Authors: McNamara Kiersty , Cividini‐Motta Catia
Published: January 2019

The purpose of this study was to expand on research on treatments for stereotypy by evaluating the effects of response interruption and redirection (RIRD) and response cost (RC) alone and as a treatment package on vocal stereotypy. Treatment phases included RIRD, RC, and response interruption and redirection plus response cost (RIRD + RC). The efficacy of these treatments was determined by measuring duration of stereotypy in session and during treatment intervals. Vocal stereotypy decreased in all three treatment conditions; however, when data analysis included stereotypy occurring during treatment intervals, stereotypy during the RC condition occurred at similar levels as baseline for one treatment evaluation phase for Karl and both treatment evaluations phases for Jon. We discuss implications of these findings, limitations of the current study, and areas for future research.
IMSSAP: After‐school interactive mobile learning student support application
Authors: Khachan Ahmad M. , Özmen Ahmet
Published: January 2019

Traditional methods intended for education are no longer suitable for it, since they are unable to meet the students’ learning needs. M‐learning is becoming a global interest. Various studies were conducted in many countries such as South Korea, Taiwan, UK, Malaysia, Serbia, European Union, and Saudi Arabia investigating student's readiness to adopt M‐learning. Our study aims to introduce a new mobile bite‐sized learning tool and to explore student's readiness to adopt M‐learning and to investigate the motivational and acceptance factors related to it. We introduced our learning tool (IMSSAP), after‐school interactive M‐learning student support Application, to university students from different majors in Turkey. Analysis of the questionnaire data revealed that an easy to use tool with social media collaboration and sharing capabilities appears to be the vital factors that will motivate students to adopt M‐learning. An improvement in the relation between the students, the teachers and the academic institution was obvious. Student's performance got much better added to better analytical and critical skills advancement. We have compared IMSSAP with another learning tool in the same class for clarity and reliability of the results.

Highlights: A cloud‐based mobile application built with Google‐Firebase platform in the model of Backend as a Service (BaaS). Bite‐sized learning methodology used to fulfill student's needs in a social circle era. Lightweight learning tool created for knowledge sharing and a learning process monitoring facility.
Do doctors who order more routine medical tests diagnose more cancers? A population‐based study from Ontario Canada
Authors: Hall Stephen F. , Webber Colleen , Groome Patti A. , Booth Christopher M. , Nguyen Paul , DeWit Yvonne
Published: January 2019

Background

The overuse of medical tests leads to higher costs, wasting of resources, and the potential for overdiagnosis of disease. This study was designed to determine whether the patients of family doctors who order more routine medical tests are diagnosed with more cancers.

Method

A retrospective population‐based cross‐sectional study using administrative health care data in Ontario Canada. We investigated the ordering of 23 routine laboratories and imaging tests 2008‐20012 by 6849 Ontario family physicians on their 4.9 million rostered adult patients. We compared physicians’ test utilization and calculated case‐mix adjusted observed to expected (O:E) utilization ratios to categorize physicians as Typical, Higher or Lower testers. Age‐sex standardized rates (cases/10 000 patient years) and Rate Ratios were determined for cancers of the thyroid, prostate, breast, lymphoma, kidney, melanoma, uterus, ovary, lung, esophagus, and pancreas for each tester group.

Results

There was wide variation in the use of the 23 tests by Ontario physicians. 26% and 24% of physicians were deemed Higher Testers for laboratory and imaging tests, while 41% and 38% were Typical Testers. The patients of higher test users were diagnosed with more cancers of thyroid (laboratory [RR 1.61, 95% CI 1.39‐1.87] and imaging [RR 2.08, 95% CI 0.88‐2.30]) and prostate (laboratory [RR 1.10, 95% CI 1.03‐1.18] and imaging [RR 1.05, 95% CI 1.00‐1.10]).

Conclusion

There is a wide variation in the ordering of routine and common medical tests among Ontario family doctors. The patients of higher testers were diagnosed with more thyroid and prostate cancers.
Phytochemical Analysis and Total Antioxidant Capacity of Rhizome, Above‐Ground Vegetative Parts and Flower of Three Iris Species
Authors: Kostić Aleksandar Ž. , Gašić Uroš M. , Pešić Mirjana B. , Stanojević Sladjana P. , Barać Miroljub B. , Mačukanović‐Jocić Marina P. , Avramov Stevan N. , Tešić Živoslav Lj.
Published: January 2019

This study was aimed at investigating the phytochemical composition and antioxidant capacity of rhizomes, above‐ground vegetative parts and flowers of three Iris species: Iris humilis Georgi, Iris pumila L. and Iris variegata L. UHPLC‐Orbitrap MS analysis was used for determination of phytochemical profile. Total pigments, phenolics, flavonoids, soluble sugars and starch content as well as ABTS antioxidant capacity were also determined. In total, 52 phenolics compounds were identified with 9 compounds (derivatives of iriflophenone, apigenin C‐glycosides, luteolin O‐glycoside, isoflavones derivatives of iristectorigenin, dichotomitin, nigracin and irilone) never reported before in Iris spp. Differences in phenolic composition profile, pigments, soluble sugar, starch, total phenolics and flavonoids content and total antioxidant capacity were found among Iris species and different part of plants. Significant correlation between total phenolic content and antioxidant capacity was determined. The obtained results are comparable with those obtained for medical plants. These findings could be useful for fingerprinting characterization of Iris species and estimation of possible use in pharmaceutical industries.
A Fluorogenic AggTag Method Based on Halo‐ and SNAP‐Tags to Simultaneously Detect Aggregation of Two Proteins in Live Cells
Authors: Jung Kwan Ho , Kim Sojung F. , Liu Yu , Zhang Xin
Published: January 2019

Protein aggregation involves the assembly of partially misfolded proteins into oligomeric and higher‐order structures that have been associated with several neurodegenerative diseases. However, numerous questions relating to protein aggregation remain unanswered due to the lack of available tools for visualization of these species in living cells. We recently developed a fluorogenic method named aggregation tag (AggTag), and presented the AggTag probe P1, based on a Halo‐tag ligand, to report on the aggregation of a protein of interest (POI) in live cells. However, the Halo‐tag‐based AggTag method only detects the aggregation of one specific POI at a time. In this study, we have expanded the AggTag method by using SNAP‐tag technology to enable fluorogenic and biorthogonal detection of the aggregation of two different POIs simultaneously in live cells. A new AggTag probe—P2, based on a SNAP‐tag ligand bearing a green solvatochromic fluorophore—was synthesized for this purpose. Using confocal imaging and chemical crosslinking experiments, we confirmed that P2 can also report both on soluble oligomers and on insoluble aggregates of a POI fused with SNAP‐tag in live cells. Ultimately, we showed that the orthogonal fluorescence of P1 and P2 allows for simultaneous visualization of two different pathogenic protein aggregates in the same cell.
Enhanced Bio‐Electrochemical Reduction of Carbon Dioxide by Using Neutral Red as a Redox Mediator
Authors: Seelajaroen Hathaichanok , Haberbauer Marianne , Hemmelmair Christine , Aljabour Abdalaziz , Dumitru Liviu Mihai , Hassel Achim Walter , Sariciftci Niyazi Serdar
Published: January 2019

Microbial electrosynthetic cells containing Methylobacterium extorquens were studied for the reduction of CO2 to formate by direct electron injection and redox mediator‐assisted approaches, with CO2 as the sole carbon source. The formation of a biofilm on a carbon felt (CF) electrode was achieved while applying a constant potential of −0.75 V versus Ag/AgCl under CO2‐saturated conditions. During the biofilm growth period, continuous H2 evolution was observed. The long‐term performance for CO2 reduction of the biofilm with and without neutral red as a redox mediator was studied by an applied potential of −0.75 V versus Ag/AgCl. The neutral red was introduced into the systems in two different ways: homogeneous (dissolved in solution) and heterogeneous (electropolymerized onto the working electrode). The heterogeneous approach was investigated in the microbial system, for the first time, where the CF working electrode was coated with poly(neutral red) by the oxidative electropolymerization thereof. The formation of poly(neutral red) was characterized by spectroscopic techniques. During long‐term electrolysis up to 17 weeks, the formation of formate was observed continuously with an average Faradaic efficiency of 4 %. With the contribution of neutral red, higher formate accumulation was observed. Moreover, the microbial electrosynthetic cell was characterized by means of electrochemical impedance spectroscopy to obtain more information on the CO2 reduction mechanism.
Fe−N3/C Active Catalytic Sites for the Oxygen Reduction Reaction Prepared with Molecular‐Level Geometry Control through the Covalent Immobilization of an Iron−Terpyridine Motif onto Carbon
Authors: Fruehwald Holly M. , Ebralidze Iraklii I. , Zenkina Olena V. , Easton E. Bradley
Published: January 2019

A model for a non‐precious metal catalyst for the oxygen reduction reaction (ORR) in aqueous media has been prepared by functionalizing a commercial Vulcan XC‐72 carbon support with a terpyridine‐based nitrogenous ligand. The terpyridine ligand geometry allows the formation of active catalytic sites by selectively embedding a N3/C structural motif into the carbon support confirmed by using thermogravimetric analysis (TGA) and X‐ray photoelectron spectroscopy (XPS) measurements. Room‐temperature metal–ligand coordination results in the desired Fe−N3/C moieties on the surface. This model system was used to demonstrate the catalytic activity of the surfaces containing mainly Fe−N3 sites for the ORR in acidic and basic media. Importantly, we demonstrate that the system could be prepared under mild reaction conditions, does not require high‐ temperature treatments, and shows catalytic activity for the ORR. Interestingly, when the system was pyrolyzed in an N2 atmosphere at 700 °C the resulting activity declined. The non‐heat‐treated Fe−N3/C surface demonstrates comparable activity in acidic electrolyte medium when compared to most literature catalysts that are typically heat treated to produce four nitrogen atoms coordinated to one iron center (Fe−N2+2/C). Interestingly, despite the fact that many systems reported so far in the literature exhibit enhanced activity after heat treatment, our system showed an increase in activity when the material was not pyrolyzed.
Solid‐Phase Synthesis and Purification of Protein–DNA Origami Nanostructures
Authors: Burgahn Teresa , Garrecht Ruben , Rabe Kersten S. , Niemeyer Christof M.
Published: January 2019

We present a facile method for the combined synthesis and purification of protein‐decorated DNA origami nanostructures (DONs). DONs bearing reductively cleavable biotin groups in addition to ligands for ligation of recombinant proteins are bound to magnetic beads. Protein immobilization is conducted with a large protein excess to achieve high ligation yields. Subsequent to cleavage from the solid support, pure sample solutions are obtained which are suitable for direct AFM analysis of occupation patterns. We demonstrate the method's utility using three different orthogonal ligation methods, the “halo‐based oligonucleotide binder” (HOB), a variant of Halo‐tag, the “SpyTag/SpyCatcher” (ST/SC) system, and the enzymatic “ybbR tag” coupling. We find surprisingly low efficiency for ST/SC ligation, presumably due to electrostatic repulsion and steric hindrance, whereas the ybbR method, despite its ternary nature, shows good ligation yields. Our method is particularly useful for the development of novel ligation methods and the synthesis of mechanically fragile DONs that present protein patterns for surface‐based cell assays.
Total Synthesis of Spirotryprostatins through Organomediated Intramolecular Umpolung Cyclization
Authors: Xi Yong‐Kai , Zhang Hongbin , Li Rui‐Xi , Kang Shi‐Yuan , Li Jin , Li Yan
Published: January 2019

Cyclodipeptide 2,5‐diketopiperazines (DKP) are privileged structural units present in drugs and natural alkaloids. This work reports a new method for the synthesis of biologically important DKP scaffolds based on an intramolecular nucleophilic α‐addition of general amides towards an alkynamide system. The utility of this umpolung cyclization mediated by trimethyl phosphine and l‐glutamic acid is highlighted by its application to the concise total syntheses of 6‐methoxyspirotryprostatin B (the first total synthesis), spirotryprostatin A, and spirotryprostatin B.
Atomically Precise Bimetallic Nanoclusters as Photosensitizers in Photoelectrochemical Cells
Authors: Wang Yu , Liu Xiao‐He , Kovalenko Sergey A. , Chen Qing‐Yun , Pinna Nicola
Published: January 2019

The atomically precise bimetallic nanocluster (NC), Au24Ag20(PhCC)20(SPy)4Cl2 (1) (Py=pyridine), was employed for the first time as a stable photosensitizer for photoelectrochemical applications. The sensitization of TiO2 nanotube arrays (TNA) with 1 greatly enhances the light‐harvesting ability of the composite because 1 shows a high molar extinction coefficient (ϵ) in the UV/Vis region. Compared to a more standard Au25(SG)18‐TNA (2‐TNA; SG=glutathione) composite, 1‐TNA shows a much better stability under illumination in both neutral and basic conditions. The precise composition of the photosensitizers enables a direct comparison of the sensitization ability between 1 and 2. With the same cluster loading, the photocurrent produced by 1‐TNA is 15 times larger than that of 2‐TNA. The superior performance of 1‐TNA over 2‐TNA is attributed not only to the higher light absorption ability of 1 but also to the higher charge‐separation efficiency. Besides, a ligand effect on the stability of the photoelectrode and charge‐transfer between the NCs and the semiconductor is revealed. This work paves the way to study the role of metal nanoclusters as photosensitizers at the atomic level, which is essential for the design of better material for light energy conversion.
Evaluation of the enantioselectivity of capillary electrokinetic chromatography using ethanediamine‐bonded poly (glycidyl methacrylate) microspheres as the pseudostationary phases
Authors: Sun Xiaodong , Yu Tao , Xu Guangfu , Du Yingxiang , Chen Jiaquan , Li Xiaoqi
Published: January 2019

In this work, a new capillary electrokinetic chromatography (EKC) approach using ethanediamine‐bonded poly (glycidyl methacrylate) (Ami‐PGMA) microspheres as pseudostationary phases (PSPs) for enantioseparation with a polysaccharide, chondroitin sulfate E (CSE), as the chiral selector. The CSE@Ami‐PGMA EKC system was applied to enantioseparate basic drugs, and distinct improved separations of tested enantiomers were obtained while comparing with the single CSE system (the resolution increased from 0.41 to 1.26 for nefopam, from 1.24 to 2.15 for laudanosine, and from 0.92 to 2.36 for amlodipine). The Ami‐PGMA microspheres were fully characterized by scanning electron microscopy (SEM) and Fourier Transform Infrared (FT‐IR) spectroscopy, and the results showed Ami‐PGMA microspheres were uniform and spherical in size (1 μm). Several principal parameters were systematically investigated, and the optimal chiral separations were obtained with Tris/H3PO4 (20 mM, pH 2.4, and 3.4 for NEF) containing 2.5% (w/v) CSE and 20‐μg Ami‐PGMA microspheres in 20°C. Subsequently, the concentrations of Ami‐PGMA microspheres and CSE were proved to be the dominant factors for the separation in the CSE@Ami‐PGMA EKC system by Statistical Product and Service Solutions (SPSS).
An approach to chance constrained problems using weighted empirical distribution and differential evolution with application to flood control planning
Authors: Tagawa Kiyoharu , Miyanaga Shun
Published: January 2019

This paper proposes a new approach to solve chance constrained problems (CCPs) efficiently. Specifically, the probabilistic constraint in CCP can be evaluated directly if the cumulative distribution function (CDF) of uncertain function value is known. Therefore, the CDF is approximated by using weighted empirical CDF (W ECDF). Then a powerful evolutionary algorithm, namely differential evolution, combined with W ECDF is used to solve CCP. In order to demonstrate the performance of the proposed method, it is applied to flood control planning problems.
An indicator‐based decision framework for the northern California red abalone fishery
Authors: Harford William J. , Dowling Natalie A. , Prince Jeremy D. , Hurd Frank , Bellquist Lyall , Likins Jack , Wilson Jono R.
Published: January 2019

Among abalone species that were once harvested along the California coastline, red abalone (Haliotis rufescens) supports the remaining recreational fishery. To support development of a red abalone fishery management plan, non‐governmental organizations have initiated expanded data collection and developed fishery management strategies. The latter is the subject of this study, as we present a management strategy evaluation (MSE) of a multi‐indicator decision tree. The decision tree relies on landings from each of 56 fishing sites and length frequency information collected during fishery‐independent diver surveys at a subset of sites. The decision tree was designed to cope with existing data limitations and to ensure that localized meta‐population dynamics were adequately considered in decision‐making. It was also necessary to balance the potential for localized abundance changes with the practical issue of implementing fishery regulations at larger spatial scales. The MSE demonstrated that undesirably low stock sizes could be avoided while also continuing to maintain a viable fishery, even under environmental conditions that are detrimental to abalone populations. Under less‐severe environmental conditions, stock size was maintained, on average, above the biomass associated with production of maximum sustainable yield. Our discussion centers on steps that were taken to refine the decision tree and to incorporate feedback from scientists and stakeholders and to facilitate transparent evaluation of management options.
River‐valley morphology, basin size, and flow‐event magnitude interact to produce wide variation in flooding dynamics
Authors: Van Appledorn Molly , Baker Matthew E. , Miller Andrew J.
Published: January 2019

Inundation dynamics are a key driver of ecosystem form and function in river‐valley bottoms. Inundation itself is an outcome of multi‐scalar interactions and can vary strongly within and among river reaches. As a result, establishing to what degree and how inundation dynamics vary spatially both within and among river reaches can be challenging. The objective of this study was to understand how river‐valley morphology, basin size, and flow‐event magnitude interact to affect inundation dynamics in river‐valley bottoms. We used 2D hydraulic models to simulate inundation in four river reaches from Maryland's Piedmont physiographic province, and qualitatively and quantitatively summarized within‐ and among‐reach patterns of inundation extent, duration, depth, shear stress, and wetting frequencies. On average, reaches from confined valley settings experienced less extensive flooding, shorter durations and shallower depths, stronger gradients of maximum shear stress, and relatively infrequent wetting compared to reaches from unconfined settings. These patterns were generally consistent across flow‐event magnitudes. Patterns of within‐reach flooding across event magnitudes revealed complex interactions between hydrology and surface topography. We concluded that valley morphology had a greater impact on flooding patterns than basin size: Inundation patterns were more consistent across reaches of similar morphology than similar basin size, but absolute values of inundation characteristics varied between large and small basins. Our results showed that the manifestation of out‐of‐bank flows in valley floors can vary widely depending on geomorphic context, even within a single physiographic province, which suggests that hydrologic and hydraulic conditions experienced on the valley floor may not be well represented by existing hydrologic metrics derived from discharge data alone. We thus support the notion that 2D hydraulic models can be useful hydrometric tools for cross‐scale investigations of floodplain ecosystems.
Intermittent flooding of organic‐rich soil promotes the formation of denitrification hot moments and hot spots
Authors: Tomasek Abigail A. , Hondzo Miki , Kozarek Jessica L. , Staley Christopher , Wang Ping , Lurndahl Nicole , Sadowsky Michael J.
Published: January 2019

Anthropogenic activities have altered the nitrogen cycle, necessitating management on the landscape level. Isolated time periods and areas, termed hot moments and hot spots, respectively, frequently account for a large percentage of nitrate removal in aquatic ecosystems. A series of experiments were conducted to determine the effect of hydrologic connectivity on denitrification rates, gene abundances, and nitrous oxide fluxes. Experimental areas were divided into flooded (always inundated), floodzone (intermittently inundated), and nonfloodzone (not inundated) locations in low‐organic and organic‐rich soil. Our results demonstrate that intermittent flood events enhance denitrification rates from days to weeks after flooding, depending on the inundation period. Microbial analysis demonstrated that short‐term flood events did not lead to increases in denitrifying gene abundances. Enhanced denitrification rates did not have a corresponding increase in the ratio of incomplete to complete denitrification. Incomplete to complete denitrification ratios were high in always‐inundated low‐organic sandy soil, peaking at 40%. Our results suggest that management strategies that promote hydrologic connectivity and intermittent flooding of organic‐rich floodplain soils promote the formation of denitrification hot moments and hot spots, with relatively low incomplete denitrification (<3% of the total denitrification rates).
A new flux‐limiting approach–based kinetic scheme for the Euler equations of gas dynamics
Authors: Kumar Raushan , Dass Anoop K.
Published: January 2019

This paper proposes a new kinetic‐theory‐based high‐resolution scheme for the Euler equations of gas dynamics. The scheme uses the well‐known connection that the Euler equations are suitable moments of the collisionless Boltzmann equation of kinetic theory. The collisionless Boltzmann equation is discretized using Sweby's flux‐limited method and the moment of this Boltzmann level formulation gives a Euler level scheme. It is demonstrated how conventional limiters and an extremum‐preserving limiter can be adapted for use in the scheme to achieve a desired effect. A simple total variation diminishing criteria relaxing parameter results in improving the resolution of the discontinuities in a significant way. A 1D scheme is formulated first and an extension to 2D on Cartesian meshes is carried out next. Accuracy analysis suggests that the scheme achieves between first‐ and second‐order accuracy as is expected for any second‐order flux‐limited method. The simplicity and the explicit form of the conservative numerical fluxes add to the efficiency of the scheme. Several standard 1D and 2D test problems are solved to demonstrate the robustness and accuracy.
Chemical‐petrographic and isotopic characterization of the volcanic pavement along the ancient Appia route at the Aurunci Mountain Pass, Italy: Insights on possible provenance
Authors: Di Luzio Emiliano , Arienzo Ilenia , Boccuti Simona , De Meo Anna , Sottili Gianluca
Published: January 2019

The ancient Appia route was built across central‐southern Italy between the fourth and second century before the common era (B.C.E.). At the Aurunci Mountain Pass, the route crosses carbonate ridges that provided the raw material used to pave the road in the first century C.E. This material was replaced with lava blocks of unknown origin in the third century C.E. The study area is at least 50 km from the main volcanic centers along the peri‐Tyrrhenian side of Italy, such as the Colli Albani, Roccamonfina, and Middle Latin Valley volcanoes. The main objective of this research was the chemical–petrographic and isotopic characterization of rock samples from the Appia flagstones to unravel their possible provenance. The analytical procedure included scanning electron microscope and electron microprobe analyses and 87Sr/86Sr–143Nd/144Nd isotopic measurements. Samples taken from unknown quarries found in the Middle Latin Valley volcanic field underwent the same analyses. After comparing the analysis results with data from the literature, the most likely source area was identified with the Roccamonfina precaldera ultrapotassic sequence. The availability and use of volcanic resources for the construction and maintenance of the ancient Appia route in the investigated territories are only outlined in this work and deserve further study.
A comparison of popular TDT‐generalizations for family‐based association analysis
Authors: Hecker Julian , Laird Nan , Lange Christoph
Published: January 2019

The transmission disequilibrium test (TDT) is the gold standard for testing the association between a genetic variant and disease in samples consisting of affected individuals and their parents. In practice, more complex pedigree structures, that is siblings with no parents, or three‐generational pedigrees with possibly missing genotypes, are common. There are several generalizations of the TDT that are suitable for use with arbitrary pedigree structures. We consider three such frequently used generalizations, family‐based association test, pedigree disequilibrium test, and generalized disequilibrium test, that have accompanying software and compare them regarding validity and power in the single variant setting. We use simulations to study the effects of population admixture, populations whose genotypes are not in Hardy–Weinberg equilibrium (HWE), different pedigree structures, and the presence of linkage. Whereas our results show that some TDT generalizations can have a substantially increased Type 1 error, these tests are often used in substantive research without caveats about the validity of their Type 1 error. For the association analysis of rare variants in sequencing studies, region‐based extensions of the TDT generalizations, that rely on the postulated robustness of the single variant tests, have been proposed. We discuss the implications of our results for these region‐based extensions.