bluuebunny/crossref_metadata_2025 huggingface dataset:
Iron overload induced death of osteoblasts in vitro: involvement of the mitochondrial apoptotic pathway
Authors: Tian Qing , Wu Shilei , Dai Zhipeng , Yang Jingjing , Zheng Jin , Zheng Qixin , Liu Yong
Published: November 2016

Background

Iron overload is recognized as a new pathogenfor osteoporosis. Various studies demonstrated that iron overload could induce apoptosis in osteoblasts and osteoporosis in vivo. However, the exact molecular mechanisms involved in the iron overload-mediated induction of apoptosis in osteoblasts has not been explored.

Purpose

In this study, we attempted to determine whether the mitochondrial apoptotic pathway is involved in iron-induced osteoblastic cell death and to investigate the beneficial effect of N-acetyl-cysteine (NAC) in iron-induced cytotoxicity.

Methods

The MC3T3-E1 osteoblastic cell line was treated with various concentrations of ferric ion in the absence or presence of NAC, and intracellular iron, cell viability, reactive oxygen species, functionand morphology changes of mitochondria and mitochondrial apoptosis related key indicators were detected by commercial kits. In addition, to further explain potential mechanisms underlying iron overload-related osteoporosis, we also assessed cell viability, apoptosis, and osteogenic differentiation potential in bone marrow-derived mesenchymal stemcells(MSCs) by commercial kits.

Results

Ferric ion demonstrated concentration-dependent cytotoxic effects on osteoblasts. After incubation with iron, an elevation of intracelluar labile iron levels and a concomitant over-generation of reactive oxygen species (ROS) were detected by flow cytometry in osteoblasts. Nox4 (NADPH oxidase 4), an important ROS producer, was also evaluated by western blot. Apoptosis, which was evaluated by Annexin V/propidium iodide staining, Hoechst 33258 staining, and the activation of caspase-3, was detected after exposure to iron. Iron contributed to the permeabilizatio of mitochondria, leading to the release of cytochrome C (cyto C), which, in turn, induced mitochondrial apoptosis in osteoblasts via activation of Caspase-3, up-regulation of Bax, and down-regulation of Bcl-2. NAC could reverse iron-mediated mitochondrial dysfunction and blocked the apoptotic events through inhibit the generation of ROS. In addition, iron could significantly promote apoptosis and suppress osteogenic differentiation and mineralization in bone marrow-derived MSCs.

Conclusions

These findings firstly demonstrate that the mitochondrial apoptotic pathway involved in iron-induced osteoblast apoptosis. NAC could relieved the oxidative stress and shielded osteoblasts from apoptosis casused by iron-overload. We also reveal that iron overload in bone marrow-derived MSCs results in increased apoptosis and the impairment of osteogenesis and mineralization.
Yangtze River, an insignificant genetic boundary in tufted deer (Elaphodus cephalophus): the evidence from a first population genetics study
Authors: Sun Zhonglou , Pan Tao , Wang Hui , Pang Mujia , Zhang Baowei
Published: November 2016

Great rivers were generally looked at as the geographical barrier to gene flow for many taxonomic groups. The Yangtze River is the third largest river in the world, and flows across South China and into the East China Sea. Up until now, few studies have been carried out to evaluate its effect as a geographical barrier. In this study, we attempted to determine the barrier effect of the Yangtze River on the tufted deer (Elaphodus cephalophus) using the molecular ecology approach. Using mitochondrial DNA control region (CR) sequences and 13 nuclear microsatellite loci, we explored the genetic structure and gene flow in two adjacent tufted deer populations (Dabashan and Wulingshan populations), which are separated by the Yangtze River. Results indicated that there are high genetic diversity levels in the two populations, but no distinguishable haplotype group or potential genetic cluster was detected which corresponded to specific geographical population. At the same time, high gene flow was observed between Wulingshan and Dabashan populations. The tufted deer populations experienced population decrease from 0.3 to 0.09 Ma BP, then followed by a distinct population increase. A strong signal of recent population decline (T= 4,396 years) was detected in the Wulingshan population by a Markov-Switching Vector Autoregressions(MSVAR) process population demography analysis. The results indicated that the Yangtze River may not act as an effective barrier to gene flow in the tufted deer. Finally, we surmised that the population demography of the tufted deer was likely affected by Pleistocene climate fluctuations and ancient human activities.
Deconvoluting simulated metagenomes: the performance of hard- and soft- clustering algorithms applied to metagenomic chromosome conformation capture (3C)
Authors: DeMaere Matthew Z. , Darling Aaron E.
Published: November 2016

Background

Chromosome conformation capture, coupled with high throughput DNA sequencing in protocols like Hi-C and 3C-seq, has been proposed as a viable means of generating data to resolve the genomes of microorganisms living in naturally occuring environments. Metagenomic Hi-C and 3C-seq datasets have begun to emerge, but the feasibility of resolving genomes when closely related organisms (strain-level diversity) are present in the sample has not yet been systematically characterised.

Methods

We developed a computational simulation pipeline for metagenomic 3C and Hi-C sequencing to evaluate the accuracy of genomic reconstructions at, above, and below an operationally defined species boundary. We simulated datasets and measured accuracy over a wide range of parameters. Five clustering algorithms were evaluated (2 hard, 3 soft) using an adaptation of the extended B-cubed validation measure.

Results

When all genomes in a sample are below 95% sequence identity, all of the tested clustering algorithms performed well. When sequence data contains genomes above 95% identity (our operational definition of strain-level diversity), a naive soft-clustering extension of the Louvain method achieves the highest performance.

Discussion

Previously, only hard-clustering algorithms have been applied to metagenomic 3C and Hi-C data, yet none of these perform well when strain-level diversity exists in a metagenomic sample. Our simple extension of the Louvain method performed the best in these scenarios, however, accuracy remained well below the levels observed for samples without strain-level diversity. Strain resolution is also highly dependent on the amount of available 3C sequence data, suggesting that depth of sequencing must be carefully considered during experimental design. Finally, there appears to be great scope to improve the accuracy of strain resolution through further algorithm development.
Antioxidant nutrition in Atlantic salmon (Salmo salar) parr and post-smolt, fed diets with high inclusion of plant ingredients and graded levels of micronutrients and selected amino acids
Authors: Hamre Kristin , Sissener Nini H. , Lock Erik-Jan , Olsvik Pål A. , Espe Marit , Torstensen Bente E. , Silva Joana , Johansen Johan , Waagbø Rune , Hemre Gro-Ingunn
Published: November 2016

The shift from marine to plant-based ingredients in fish feeds affects the dietary concentrations and bioavailability of micronutrients, amino acids and lipids and consequently warrants a re-evaluation of dietary nutrient recommendations. In the present study, an Atlantic salmon diet high in plant ingredients was supplemented with graded levels of nutrient premix (NP), containing selected amino acids, taurine, cholesterol, vitamins and minerals. This article presents the results on the antioxidant nutrients vitamin C, E and selenium (Se), and effects on tissue redox status. The feed ingredients appeared to contain sufficient levels of vitamin E and Se to cover the requirements to prevent clinical deficiency symptoms. The body levels of α-tocopherol (TOH) in parr and that of Se in parr and post-smolt showed a linear relationship with dietary concentration, while α-TOH in post-smolt seemed to be saturable with a breakpoint near 140 mg kg−1. Ascorbic acid (Asc) concentration in the basal feed was below the expected minimum requirement, but the experimental period was probably too short for the fish to develop visible deficiency symptoms. Asc was saturable in both parr and post-smolt whole body at dietary concentrations of 190 and 63–89 mg kg−1, respectively. Maximum whole body Asc concentration was approximately 40 mg kg−1in parr and 14 mg kg−1in post-smolt. Retention ranged from 41 to 10% in parr and from −206 to 12% in post-smolt with increasing NP supplementation. This indicates that the post-smolts had an extraordinarily high consumption of Asc. Analyses of glutathione (GSH) and glutathione disulphide (GSSG) concentrations and the calculated GSH based redox potentials in liver and muscle tissue, indicated only minor effects of diets on redox regulation. However, the post-smolt were more oxidized than the parr. This was supported by the high consumption of Asc and high expression of gpx1 and gpx3 in liver. Based on the present trials, the recommendations for supplementation of vitamin C and E in diets for Atlantic salmon are similar to current practices, e.g. 150 mg kg−1of α-TOH and 190 mg kg−1Asc which was the saturating concentration in parr. Higher concentrations than what would prevent clinical deficiency symptoms are necessary to protect fish against incidents of oxidative stress and to improve immune and stress responses. There were no indications that the Se requirement exceeded the current recommendation of 0.3 mg kg−1.
A Responsive Website: Development and Traffic Analysis
Authors: Guidang Excel Philip
Published: November 2016

Internet Access is now more mobile than ever because of the introduction of internet enabled devices such as Smart-watch, Smartphones, Tablets, Phablets in addition to the Laptops and Palmtops. The study developed a responsive website and provided a website traffic analysis. It employed the descriptive and applied methods of research. Documentary analysis was used to determine the Transparency Seal requirements. The Enidus web application development model was used to develop a responsive website. Google Analytics was used to describe the website traffic. The study found out that the Transparency Seal requirements were divided into seven (7) categories namely: a) Agency's Mandate, Vision, Mission, and List of Officials; b) Annual Financial Reports; c) DBM Approved Budget and Targets; d) Projects, Programs, and Activities, Beneficiaries, and Status of Implementation; e) Annual Procurement Plan 2015; f) System of Ranking Delivery Units and Individuals; and g) Quality Management System certified by international certifying body or Agency Operations Manual. The Enidus model provides a clear perspective regarding the life-cycle of a website. Google Analytics is an excellent tool for Website Administrators to monitor website traffic for it provides data not only on the visitors' sessions, but also to the devices used.
Can the Myocardial Performance Index Be Used as a New Predictive Factor for a Poor Prognosis in Fetuses With Idiopathic Polyhydramnios?
Authors: Gezer Cenk , Ekin Atalay , Ozeren Mehmet , Taner Cuneyt Eftal , Mat Emre , Solmaz Ulas
Published: November 2016

Objectives

The purpose of this study was to determine whether there are any changes in cardiac function in fetuses with idiopathic polyhydramnios and also to evaluate the value of the myocardial performance index for prediction of adverse perinatal outcomes.

Methods

A prospective case‐control study was conducted with a total of 134 fetuses between 24 and 40 weeks' gestation. Polyhydramnios was defined as an amniotic fluid index of greater than 24 cm. Seventy‐three fetuses of healthy mothers were assigned as the control group whereas 36 fetuses with an amniotic fluid index of 24 to 34 cm constituted the nonsevere polyhydramnios group, and 31 fetuses with an amniotic fluid index of 35 cm or greater constituted the severe polyhydramnios group. Fetal echocardiography was performed to compare cardiac function parameters among groups. To determine which perinatal outcomes were independently associated with an increased myocardial performance index, a multivariate logistic regression analysis was performed.

Results

The myocardial performance index was significantly higher in polyhydramnios groups compared with controls (P < .001). Among fetuses with polyhydramnios, the myocardial performance index was significantly higher in severe polyhydramnios compared with nonsevere polyhydramnios (P = .003). An increased myocardial performance index in polyhydramnios was independently associated with nonreassuring fetal status (odds ratio, 2.12; 95% confidence interval, 1.41–4.53; P = .005), emergency cesarean delivery (odds ratio, 1.54; 95% confidence interval, 1.12–2.37; P= .025), and respiratory distress syndrome (odds ratio, 1.79; 95% confidence interval, 1.21–3.87; P = .012).

Conclusions

An increased myocardial performance index is an early indicator of adverse perinatal outcomes in pregnancies complicated by idiopathic polyhydramnios.
Potential and Actual impacts of deforestation and afforestation on land surface temperature
Authors: Li Yan , Zhao Maosheng , Mildrexler David J. , Motesharrei Safa , Mu Qiaozhen , Kalnay Eugenia , Zhao Fang , Li Shuangcheng , Wang Kaicun
Published: November 2016

Forests are undergoing significant changes throughout the globe. These changes can modify water, energy, and carbon balance of the land surface, which can ultimately affect climate. We utilize satellite data to quantify the potential and actual impacts of forest change on land surface temperature (LST) from 2003 to 2013. The potential effect of forest change on temperature is calculated by the LST difference between forest and nearby nonforest land, whereas the actual impact on temperature is quantified by the LST trend difference between deforested (afforested) and nearby unchanged forest (nonforest land) over several years. The good agreement found between potential and actual impacts both at annual and seasonal levels indicates that forest change can have detectable impacts on surface temperature trends. That impact, however, is different for maximum and minimum temperatures. Overall, deforestation caused a significant warming up to 0.28 K/decade on average temperature trends in tropical regions, a cooling up to −0.55 K/decade in boreal regions, a weak impact in the northern temperate regions, and strong warming (up to 0.32 K/decade) in the southern temperate regions. Afforestation induced an opposite impact on temperature trends. The magnitude of the estimated temperature impacts depends on both the threshold and the data set (Moderate Resolution Imaging Spectroradiometer and Landsat) by which forest cover change is defined. Such a latitudinal pattern in temperature impact is mainly caused by the competing effects of albedo and evapotranspiration on temperature. The methodology developed here can be used to evaluate the temperature change induced by forest cover change around the globe.
Detrital zircon U‐Pb ages and Hf isotopic constraints on the terrigenous sediments of the Western Alps and their paleogeographic implications
Authors: Chu Yang , Lin Wei , Faure Michel , Wang Qingchen
Published: November 2016

Detrital zircons from Cretaceous micaschist, late Eocene‐earliest Oligocene sandstone and early Oligocene siltstone of the Western Alps fall into three main separable age clusters at 610–540 Ma, 490–430 Ma, and 340–280 Ma that correspond to the Cadomian (Neoproterozoic), Ordovician, and Variscan (Carboniferous) events widespread in western and central Europe. Hf isotopic results indicate that these three magmatic and tectonic episodes did not give rise to significant production of juvenile crust. A distinguishable group of Triassic zircons, around 250–200 Ma which is considered to derive from the Southern Alps, has been detected in the early Oligocene “Schistes à Blocs” formation and the Briançonnais “Flysch Noir”. In contrast, this age group is absent in late Eocene to earliest Oligocene sandstones. In agreement with sedimentological studies, our results show that the main source areas of the Eocene sandstone were probably located in the European continent. The arrival of detritus from the Internal Zone occurred in early Oligocene, coeval with the tectonic rotation from northwestward to westward in the propagation of allochthonous units. Based on previous studies and our new data, we argue that the Briançonnais Zone was likely a paleorelief since the middle Eocene that accounts for the lack of detritus from the Adriatic units. Contemporary sediments were accumulated in the foredeep of the Adriatic plate. From Oligocene time onward, the blockage was cut through after a regional uplifting, and thus, the Internal Zone started to provide detritus into the western flexural basins.
Panel regressions to estimate low‐flow response to rainfall variability in ungaged basins
Authors: Bassiouni Maoya , Vogel Richard M. , Archfield Stacey A.
Published: November 2016

Multicollinearity and omitted‐variable bias are major limitations to developing multiple linear regression models to estimate streamflow characteristics in ungaged areas and varying rainfall conditions. Panel regression is used to overcome limitations of traditional regression methods, and obtain reliable model coefficients, in particular to understand the elasticity of streamflow to rainfall. Using annual rainfall and selected basin characteristics at 86 gaged streams in the Hawaiian Islands, regional regression models for three stream classes were developed to estimate the annual low‐flow duration discharges. Three panel‐regression structures (random effects, fixed effects, and pooled) were compared to traditional regression methods, in which space is substituted for time. Results indicated that panel regression generally was able to reproduce the temporal behavior of streamflow and reduce the standard errors of model coefficients compared to traditional regression, even for models in which the unobserved heterogeneity between streams is significant and the variance inflation factor for rainfall is much greater than 10. This is because both spatial and temporal variability were better characterized in panel regression. In a case study, regional rainfall elasticities estimated from panel regressions were applied to ungaged basins on Maui, using available rainfall projections to estimate plausible changes in surface‐water availability and usable stream habitat for native species. The presented panel‐regression framework is shown to offer benefits over existing traditional hydrologic regression methods for developing robust regional relations to investigate streamflow response in a changing climate.
A comparative study of the degradation of yeast cyclins Cln1 and Cln2
Authors: Quilis Inma , Igual J. Carlos
Published: November 2016

The yeast cyclins Cln1 and Cln2 are very similar in both sequence and function, but some differences in their functionality and localization have been recently described. The control of Cln1 and Cln2 cellular levels is crucial for proper cell cycle initiation. In this work, we analyzed the degradation patterns of Cln1 and Cln2 in order to further investigate the possible differences between them. Both cyclins show the same half‐life but, while Cln2 degradation depends on ubiquitin ligases SCFGrr1 and SCFCdc4, Cln1 is affected only by SCFGrr1. Degradation analysis of chimeric cyclins, constructed by combining fragments from Cln1 and Cln2, identifies the N‐terminal sequence of the proteins as responsible of the cyclin degradation pattern. In particular, the N‐terminal region of Cln2 is required to mediate degradation by SCFCdc4. This region is involved in nuclear import of Cln1 and Cln2, which suggests that differences in degradation may be due to differences in localization. Moreover, a comparison of the cyclins that differ only in the presence of the Cln2 nuclear export signal indicates a greater instability of exported cyclins, thus reinforcing the idea that cyclin stability is influenced by their localization.
Peptide‐Enhanced Selective Surface Deposition of Polymer‐Based Fragrance Delivery Systems
Authors: Günay Kemal Arda , Benczédi Daniel , Herrmann Andreas , Klok Harm‐Anton
Published: November 2016

Surface deposition is a critical step in the application of fragrance‐containing products. This contribution presents a novel strategy to enhance the deposition of polymer‐based fragrance delivery systems onto cotton substrates from the application medium using phage display identified peptides. Following the identification of cotton binding peptide ligands under fabric softening conditions via phage display, the strongest binding peptide ligand is incorporated into two model polymer‐based fragrance delivery systems, viz., polymer profragrances and polymer nanoparticles. The model polymer profragrance used is a linear, water soluble poly(N‐(2‐hydroxypropyl)methacrylamide) conjugate, while poly(styrene‐co‐acrylic acid) (PS‐co‐PAA) nanoparticles prepared via miniemulsion polymerization are chosen as the second model system. The incorporation of the cotton binding peptide ligand into these fragrance delivery systems enhances their surface deposition two‐ to three‐fold, as evidenced by fluorescence intensity measurements. In the case of the fragrance‐containing PS‐co‐PAA nanoparticles, the enhanced surface deposition also translates into an increased fragrance release from the cotton surface according to dynamic headspace sampling measurements.
Irradiation Sterilized Gelatin–Water–Glycerol Ternary Gel as an Injectable Carrier for Bone Tissue Engineering
Authors: Zhao Yantao , Han Liwei , Yan Jun , Li Zhonghai , Wang Fuli , Xia Yang , Hou Shuxun , Zhong Hongbin , Zhang Feimin , Gu Ning
Published: November 2016

Injectable gelatin gels offer an attractive option for filling bone defects. The challenge is to fabricate gelatin gels with optimal gelation properties, which can be irradiation sterilized. Here, a gelatin–water–glycerol (GWG) gel is reported for use as a broad‐spectrum injectable carrier. This ternary gel is high in glycerol and low in water, and remains stable after gamma irradiation at doses (25 kGy). As an injectable gel, it remains a viscous solution at gelatin concentrations ≤2.0%, at room temperature. Its storage modulus increases dramatically and eventually exceeds the loss modulus around 46–50 °C, indicating a transition from a liquid‐like state to an elastic gel‐like state. This ternary gel ranges significantly in terms of storage modulus (12–1700 Pa) while demonstrating a narrow pH range (5.58–5.66), depending on the gelatin concentration. Therefore, it can be loaded with a variety of materials. It is highly cytocompatible compared with saline in vivo and culture media in vitro. When loaded with demineralized bone matrix, the composites show favorable injectability, and excellent osteogenesis performance, after irradiation. These features can be attributed to high hydrophilicity and fast degradability. These findings justify that this ternary gel is promising as an irradiation‐sterilized and universal injectable delivery system.
Turbulent mixing in the confined swirling flow of a multi‐inlet vortex reactor
Authors: Liu Zhenping , Hitimana Emmanuel , Olsen Michael G. , Hill James C. , Fox Rodney O.
Published: November 2016

Turbulent mixing in the confined swirling flow of a multi‐inlet vortex reactor (MIVR) was investigated using planar laser induced fluorescence (PLIF). The investigated Reynolds numbers based on the bulk inlet velocity ranged from 3290 to 8225, and the Schmidt number of the passive scalar was 1250. Measurements were taken in the MIVR at three different heights (¼, ½, and ¾ planes). The mixing characteristics and performance of the MIVR were investigated using instantaneous PLIF fields and pointwise statistics such as mixture fraction mean, variance, and one‐point concentration probability density function. It was found that the scalar is stretched along velocity streamlines, forming a spiral mixing pattern in the free‐vortex region. In the forced‐vortex region, mixing intensifies as the turbulent fluctuations increase significantly there. The mixing mechanisms in the MIVR were revealed by identifying specific segregation zones. At Re = 8225 the mixing in the free‐vortex region was dominated by both large‐scale structures and turbulent diffusion, while in the forced‐vortex region mixing is dominated by turbulent diffusion. © 2016 American Institute of Chemical Engineers AIChE J, 63: 2409–2419, 2017
Catalytic oxidation of solid carbon and carbon monoxide over cerium‐zirconium mixed oxides
Authors: Yin Kehua , Davis Robert J. , Mahamulkar Shilpa , Jones Christopher W. , Agrawal Pradeep , Shibata Hirokazu , Malek Andrzej
Published: November 2016

A series of cerium‐zirconium mixed oxides was prepared and evaluated in the catalytic oxidation of solid coke with 10 vol % O2 in He at 673 K using a thermogravimetric analyzer. The measured first order rate constant for coke oxidation was proportional to the catalyst loading when the mass ratio of catalyst to coke was low, which enabled the calculation of a surface area specific reaction rate. The validity of the normalization method was confirmed by performing CO oxidation over the cerium‐zirconium mixed oxides in a fixed bed reactor at 573 K. Although there was no correlation between the coke oxidation rate and the oxygen storage capacity or the reducibility of the catalysts, there was an excellent correlation to the CO oxidation rate. Kinetic studies of both coke and CO oxidation suggested an important role of surface lattice oxygen from the catalyst in the two reactions. © 2016 American Institute of Chemical Engineers AIChE J, 63: 725–738, 2017
Angelman syndrome: Current and emerging therapies in 2016
Authors: Tan Wen‐Hann , Bird Lynne M.
Published: November 2016

Angelman syndrome (AS) is a severe neurodevelopmental disorder caused by a loss of the maternally‐inherited UBE3A; the paternal UBE3A is silenced in neurons by a mechanism involving an antisense transcript (UBE3A‐AS) at the unmethylated paternal locus. We reviewed all published information on the clinical trials that have been completed as well as the publicly available information on ongoing trials of therapies in AS. To date, all clinical trials that strove to improve neurodevelopment in AS have been unsuccessful. Attempts at hypermethylating the maternal locus through dietary compounds were ineffective. The results of an 8‐week open‐label trial using minocycline as a matrix metalloproteinase‐9 inhibitor were inconclusive, while a subsequent randomized placebo‐controlled trial suggested that treatment with minocycline for 8 weeks did not result in any neurodevelopmental gains. A 1‐year randomized placebo‐controlled trial using levodopa to alter the phosphorylation of calcium/calmodulin‐dependent kinase II did not lead to any improvement in neurodevelopment. Topoisomerase inhibitors and antisense oligonucleotides are being developed to directly inhibit UBE3A‐AS. Artificial transcription factors are being developed to “super activate” UBE3A or inhibit UBE3A‐AS. Other strategies targeting specific pathways are briefly discussed. We also reviewed the medications that are currently used to treat seizures and sleep disturbances, which are two of the more common complications of AS. © 2016 Wiley Periodicals, Inc.
Deriving Structural Information from Experimentally Measured Data on Biomolecules
Authors: van Gunsteren Wilfred F. , Allison Jane R. , Daura Xavier , Dolenc Jožica , Hansen Niels , Mark Alan E. , Oostenbrink Chris , Rusu Victor H. , Smith Lorna J.
Published: November 2016

During the past half century, the number and accuracy of experimental techniques that can deliver values of observables for biomolecular systems have been steadily increasing. The conversion of a measured value Qexpof an observable quantity Q into structural information is, however, a task beset with theoretical and practical problems: 1) insufficient or inaccurate values of Qexp, 2) inaccuracies in the functionused to relate the quantity Q to structure, 3) how to account for the averaging inherent in the measurement of Qexp, 4) how to handle the possible multiple‐valuedness of the inverseof the function, to mention a few. These apply to a variety of observable quantities Q and measurement techniques such as X‐ray and neutron diffraction, small‐angle and wide‐angle X‐ray scattering, free‐electron laser imaging, cryo‐electron microscopy, nuclear magnetic resonance, electron paramagnetic resonance, infrared and Raman spectroscopy, circular dichroism, Förster resonance energy transfer, atomic force microscopy and ion‐mobility mass spectrometry. The process of deriving structural information from measured data is reviewed with an eye to non‐experts and newcomers in the field using examples from the literature of the effect of the various choices and approximations involved in the process. A list of choices to be avoided is provided.
Sulfur and Its Role In Modern Materials Science
Authors: Boyd Darryl A.
Published: November 2016

Although well‐known and studied for centuries, sulfur continues to be at the center of an extensive array of scientific research topics. As one of the most abundant elements in the Universe, a major by‐product of oil refinery processes, and as a common reaction site within biological systems, research involving sulfur is both broad in scope and incredibly important to our daily lives. Indeed, there has been renewed interest in sulfur‐based reactions in just the past ten years. Sulfur research spans the spectrum of topics within the physical sciences including research on improving energy efficiency, environmentally friendly uses for oil refinery waste products, development of polymers with unique optical and mechanical properties, and materials produced for biological applications. This Review focuses on some of the latest exciting ways in which sulfur and sulfur‐based reactions are being utilized to produce materials for application in energy, environmental, and other practical areas.
Metal Fluorides as Analogues for Studies on Phosphoryl Transfer Enzymes
Authors: Jin Yi , Richards Nigel G. , Waltho Jonathan P. , Blackburn G. Michael
Published: November 2016

The 1994 structure of a transition‐state analogue with AlF4− and GDP complexed to G1α, a small G protein, heralded a new field of research into the structure and mechanism of enzymes that manipulate the transfer of phosphoryl (PO3−) groups. The number of enzyme structures in the PDB containing metal fluorides (MFx) as ligands that imitate either a phosphoryl or a phosphate group was 357 at the end of 2016. They fall into three distinct geometrical classes: 1) Tetrahedral complexes based on BeF3− that mimic ground‐state phosphates; 2) octahedral complexes, primarily based on AlF4−, which mimic “in‐line” anionic transition states for phosphoryl transfer; and 3) trigonal bipyramidal complexes, represented by MgF3− and putative AlF30 moieties, which mimic the geometry of the transition state. The interpretation of these structures provides a deeper mechanistic understanding into the behavior and manipulation of phosphate monoesters in molecular biology. This Review provides a comprehensive overview of these structures, their uses, and their computational development.
Preparation and characterization of the ethylene‐vinyl acetate copolymer partially hydrolyzed assisted by microwave radiation
Authors: Paradinha Matheus Moresco , Gonzalez Dias Fernanda Trindade , Wanke Cesar Henrique , de Lima Novello Júnia Capua , Tondo Eduardo Cesar , De Nardi Martins Johnny , Bianchi Otávio
Published: November 2016

Ethylene‐vinyl acetate copolymer (EVA) was modified by hydrolysis using dielectric heating. The modified EVA was characterized by Fourier transform infrared spectroscopy, differential scanning calorimetry, thermogravimetric analysis (TG), 1H Nuclear magnetic resonance (NMR), gel permeation chromatography, and small‐angle X‐ray scattering. The results showed that the EVA was hydrolyzed with degree between 36.1 and 42.6% according to 1H NMR and TG results. The relative reaction rate for the sample prepared in the oil bath was ∼9%/h, while in the dielectric was ∼150%/h for 15 min. This significant improvement was due to the specific effect of microwave‐assisted reactions through dipole rotation and ionic polarization contributions. The hydrolysis reaction promoted a reduction of the pendent group size of EVA backbone. This change directly contributed to increasing melt temperature, crystallization temperature, melt and crystallization enthalpies. Also, decreased the long period, increased the volume crystallinity, and caused reductions amorphous/crystalline interface and two‐phase model deviations. © 2016 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2017, 134, 44558.
RA‐dimer B, a New Dimeric RA‐series Cyclopeptide Incorporating Two Different Types of Cycloisodityrosine Units, from Rubia cordifolia L.
Authors: Hitotsuyanagi Yukio , Tsuchiya Takayuki , Ohata Masako , Yoshida Ayaka , Fukaya Haruhiko , Park Hyun Sun , Takeya Koichi , Kawahara Nobuo
Published: November 2016

RA‐dimer B, a new cytotoxic RA‐series peptide, was isolated from the roots of Rubia cordifolia L. Its structure was elucidated on the basis of spectroscopic analysis to be a dimeric cyclopeptide composed of deoxybouvardin and allo‐RA‐V. Those two cyclopeptide units are connected by an ether linkage between the phenolic oxygen atom of deoxybouvardin and the ϵa carbon atom of Tyr‐6 of allo‐RA‐V. RA‐dimer B was synthesized by the coupling reaction of deoxybouvardin with the boronic acid derivative of allo‐RA‐V, and subsequent deprotection, confirming the relative stereochemistry and establishing the absolute configuration of this peptide. RA‐dimer B showed cytotoxic activity against human promyelocytic leukaemia HL‐60, human colonic carcinoma HCT‐116, and human renal cell carcinoma ACHN cells with IC50 values of 0.59, 0.54, and 0.74 μm, respectively.
Molecular basis and potential activity of HIV‐1 reverse transcriptase toward trimethylamine‐based compounds
Authors: Padariya Monikaben , Kalathiya Umesh , Baginski Maciej
Published: November 2016

Reverse transcriptase (RT) inhibitors are currently used to treat human immunodeficiency virus (HIV)‐1 infections. In this work, novel triethylamine derivatives were designed and studied by rigid and flexible docking and molecular dynamics (MD) approaches. An apo form of HIV‐1 RT was also studied by MD simulation to analyze comparative response of protein in ligand‐bound and ligand‐unbound forms. Among newly designed HIV‐1 RT inhibitors, compound HIV104 was the most potent inhibitor considering different docking results. Molecular docking results were further validated by MD simulations of an HIV‐1 RT/HIV104 complex using two independent software (Discovery Studio Client 3.1 and GROMACS) to perform comparative analysis. Results suggest that hydroxyl and carboxyl groups present at –R1 position in compounds favored strong H‐bond contacts as well as good interaction energy profile. Our MD results are consistent with the observations that conformational dynamics between the thumb and finger subdomains of HIV‐1 RT controls its dynamics on substrate binding and subsequent activity. MD studies of HIV‐1 RT/HIV104 provide insight into interrelatedness of residue scale interactions and global conformational change and also hint at the complex nature of allosteric inhibition. Thus, the results obtained from this study facilitate the design of potent HIV‐1 RT inhibitors.
A physical mechanism of magnetoreception: Extension and analysis
Authors: Binhi Vladimir N. , Prato Frank S.
Published: November 2016

Proposed is a general physical mechanism of magnetoreception of weak magnetic fields (MFs). The mechanism is based on classical precessional dynamics of a magnetic moment in a thermally disturbed environment and includes a minimum of necessary parameters—the gyromagnetic ratio, thermal relaxation time, and rate of downstream events generated by changes in the state of the magnetic moment. The mechanism imposes general restrictions on the probability of initial biophysical magnetic transduction event before the involvement of specific biophysical and biochemical mechanisms—i.e., regardless of the nature of an MF target and the subsequent cascade of events. It is shown that biological effects of weak MFs have, in certain cases, nonlinear and frequency selective properties. The observation of these characteristics provides information not only on the target's gyromagnetic ratio, but also on the parameters of its interaction with the immediate environment. This enables one to develop experimental strategies for identifying the biophysical mechanisms of magnetoreception including the specific case of effects of a near‐zero MF exposure. The mechanism is universally applicable to magnetic moments of different nature, in particular, of electron and proton orbital motion and of spins. Experimental exposure conditions are derived which would lead to validation of the proposed mechanism. Bioelectromagnetics. 38:41–52, 2017. © 2016 Wiley Periodicals, Inc.
Hinweise für den Ansatz der Betonzugfestigkeit beim Nachweis der Mindestbewehrung für frühen Zwang gemäß Eurocode 2‐2 (DIN EN 1992‐2/NA)
Authors: Haveresch Karlheinz , Maurer Reinhard , Tauscher Franka
Published: November 2016

Im Dezember 2015 wurde die A1‐Änderung [1] zum deutschen Nationalen Anhang [2] von DIN EN 1992‐1‐1 veröffentlicht. Die Änderungen betreffen u. a. den Ansatz der wirksamen Betonzugfestigkeit bei der Ermittlung der Mindestbewehrung zur Begrenzung der Rissbreiten bei frühem Zwang. Der nachfolgende Beitrag erläutert die Hintergründe, warum eine entsprechende A1‐Änderung zu DIN EN 1992‐2/NA nicht erfolgt. Als Begründung für diese unterschiedliche Vorgehensweise werden die wesentlichen Unterschiede zwischen dem Hochbau und dem Brückenbau dargestellt.
UPLC‐MS/MS method for the determination of tobacco‐specific biomarker NNAL, tamoxifen and its main metabolites in rat plasma
Authors: Xiong Wei , Zhao Jiajia , Wang Ling , Jiang Xuehua
Published: November 2016

Cigarette smoke is known to interact with tamoxifen‐metabolizing enzymes and transporters and potentially affect its treatment outcome. 4‐(N‐nitrosomethylamino)‐1‐(3‐pyridyl)‐1‐butanol (NNAL) is an important metabolite of 4‐(methylnitro‐samino)‐1‐(3‐pyridyl)‐1‐butanone (NNK) because it is frequently used as a biomarker to assess human smoke exposure. In order to study the potential pharmacokinetic interaction between cigarette smoke and tamoxifen in rats a UPLC‐MS/MS method for the simultaneous determination of NNAL and tamoxifen along with its metabolites in rat plasma has been developed and validated. Analytes were extracted with methanol and separated on a HSS T3 column by a gradient elution with the mobile phase consisting of acetonitrile and water. The lower limits of quantitation ranged from 0.05 to 0.62 ng/mL. Precisions showed RSD <15.8% and accuracy in the range 80.6–116.0%. Mean analyte recoveries ranged from 76.9 to 108.4%. The method was successfully applied to study the effects of cigarette smoke condensate (CSC), NNK and benzo(a)pyrene pre‐treatment on the pharmacokinetics of tamoxifen and its metabolites in rats. Significant effects of CSC, NNK, benzo(a)pyrene were observed on pharmacokinetics of tamoxifen and its metabolites. We also found that plasma NNAL levels are statistically significant correlated with plasma 4‐hydroxy‐tamoxifen and endoxifen.
Promoting Effect of Bismuth Oxide on Palladium for Low‐Temperature Carbon Monoxide Oxidation
Authors: Ma Dong‐Dong , Ding Ding , Huang Jun‐Jie , Zhang Hong , Zheng Yan‐Ping , Chen Ming‐Shu , Wan Hui‐Lin
Published: November 2016

By using a modified coimpregnation method, a multicomponent Pd&Bi(1.4)/TiO2‐N catalyst with hierarchical metal–metal oxide interfaces was prepared that showed a better activity and stability for low‐temperature CO oxidation than Pd/TiO2‐N and Pd/P25. The structural characterization and catalytic activity results proved that an appropriate amount of Bi species has a clear promoting effect on the Pd‐based catalyst. Particularly, the catalyst can be mass‐produced conveniently, which may be beneficial for versatile reactions and practical applications.
Selective Hydrogenation of 2‐Methylfuran and 2,5‐Dimethylfuran over Atomic Layer Deposited Platinum Catalysts on Multiwalled Carbon Nanotube and Alumina Supports
Authors: Kang Jungshik , Liang Xinhua , Guliants Vadim V.
Published: November 2016

2‐Methylfuran (2MF) and 2,5‐dimethylfuran (DMF) were hydrogenated in the vapor phase to the corresponding tetrahydrofurans, linear 2‐ketones, and alcohols over Pt nanoparticles supported on multiwalled carbon nanotubes (MWCNTs) and alumina by atomic layer deposition. The hydrogenation behavior of sub‐nanometer Pt deposited on alumina was influenced by the acidity of the support. Relative to a commercial Pt/C catalyst, the Pt/MWCNT catalyst was found to contain similarly sized Pt nanoparticles that display a broader size distribution and significantly more n‐alkanes than oxygenates during hydrogenation of these alkyl‐substituted furans.
Wilkinson‐Type Immobilized Catalyst on Diamond Nanoparticles for Alkene Reduction
Authors: Queffélec Clémence , Schlindwein Simon H. , Gudat Dietrich , Silvestre Virginie , Rodriguez‐Zubiri Mireia , Fayon Franck , Bujoli Bruno , Wang Qi , Boukherroub Rabah , Szunerits Sabine
Published: November 2016

The immobilization of heterogeneous catalysts on solid support materials is an important task of current catalytic and materials science research. We report here the development of a diamond nanoparticles‐based Wilkinson's type catalyst for the reduction of olefins to saturated hydrocarbons. The strategy is based on the formation of rhodium(I)‐modified nanodiamonds (NDs–Rh) using a surface‐immobilized catechol phosphane ligand, to which rhodium metal centers can be coordinated. The resulting material was characterized by solid‐state NMR spectroscopy, X‐ray photoelectron spectroscopy, thermogravimetry, and TEM before testing the catalytic efficiency of the catalyst. Excellent hydrogenation efficiency with yields in the range of 85–99 % could be obtained with these new NDs–Rh catalysts, which showed in addition good recyclability without loss of activity.
Furan‐ and Thiophene‐Based Auxochromes Red‐shift Chlorin Absorptions and Enable Oxidative Chlorin Polymerizations
Authors: Xiong Ruisheng , Bornhof Anna‐Bea , Arkhypchuk Anna I. , Orthaber Andreas , Borbas K. Eszter
Published: November 2016

The de novo syntheses of chemically stable chlorins with five‐membered heterocyclic (furane, thiophene, formylfurane and formylthiophene) substituents in selected meso‐ and β‐positions are reported. Heterocycle incorporation in the 3‐ and 13‐positions shifted the chlorin absorption and emission to the red (up to λem=680 nm), thus these readily incorporated substituents function analogously to auxochromes present in chlorophylls, for example, formyl and vinyl groups. Photophysical, theoretical and X‐ray crystallographic experiments revealed small but significant differences between the behavior of the furan‐ and the thiophene‐based auxochromes. Four regioisomeric bis‐thienylchlorins (3,10; 3,13, 3,15 and 10,15) were oxidatively electropolymerized; the chlorin monomer geometry had a profound impact on the polymerization efficiency and the electrochemical properties of the resulting material. Chemical co‐polymerization of 3,13‐bis‐thienylchlorin with 3‐hexylthiophene yielded an organic‐soluble red‐emitting polymer.
Fine‐Tuning the Fluorescence Gain of FRET‐Type (Bodipy)(Bodipy′)‐NHC‐Iridium Complexes for CO Detection with a Large Virtual Stokes Shift
Authors: Halter Oliver , Fernández Israel , Plenio Herbert
Published: November 2016

Complexes of the general formula [IrCl(cod)(bdp‐NHC‐bdp′)] and [IrCl(cod)(bdp‐NHC)] (bdp=bodipy=4,4‐difluoro‐4‐bora‐3a,4a‐diaza‐s‐indacene, cod=1,5‐cyclooctadiene) were synthesized. The substitution reaction of cod with two molecules of CO converts weakly fluorescent into strongly fluorescent complexes [IrCl(CO)2(bdp‐NHC‐bdp′)] and [IrCl(CO)2(bdp‐NHC)]. Bdp and bdp“ form a fluorescence resonance energy transfer (FRET) pair and the excitation of bdp leads to a strong emission from bdp” with a virtual Stokes shift of 98 nm. The fluorescence gain (IFl[Ir(CO)2]]/IFl[Ir(cod)]=1.7) upon reaction with CO in this complex is modest. To increase the fluorescence gain, the quenching capacity of the transition metal was improved by increasing the electron density at iridium. This was achieved by substituting the metal‐bound chloride with an electron‐rich thiolate RC6H4S. Depending on the nature of the R substituent in [Ir(SC6H4R)(cod)(bdp‐NHC‐bdp′)], an improved fluorescence gain in the cod/CO substitution reaction of up to 4.3 was observed and up to 26 (from gain=5) in [Ir(SC6H4R)(cod)(bdp‐NHC)]. DFT calculations on closely related [Ir(SC6H4R)(cod)(bdp‐NHC)] complexes indicate that a photoinduced electron transfer mechanism is the dominant quenching pathway for the iridium thiolates with R=COMe, CF3, Cl, H, Me, tBu, OMe, NEt2. The CO‐responsive FRET complex was immobilized on paper, displaying a red fluorescent color upon exposure to CO.
Water‐Resistant and Transparent Plastic Films from Functionalizable Organic Polymers: Coordination Polymers as Templates for Solid‐State [2+2]‐Photopolymerization
Authors: Garai Mousumi , Biradha Kumar
Published: November 2016

An organic polymer containing cyclobutanes and amides as backbones and pyridyl groups as sidearms was synthesized by single‐crystal‐to‐single‐crystal (SCSC) [2+2]‐photopolymerization in the coordination polymers (CPs) of diene. The diene molecule was photo‐inactive in its crystals and formed a triply intertwined 1D‐helical CP with Cd(NO3)2 and Cu(NO3)2 salts. The 1D‐CP was transformed into a coordination polymer of organic polymers containing threefold interpenetrated 3D‐networks of CdSO4 topology through a [2+2]‐reaction in SCSC manner upon irradiation. The organic polymer was separated from its CPs and found to have an unusually high degree of polymerization for this type of reaction. Furthermore, the organic polymer was amenable for N‐alkylation reactions such as methylation, propylation, and decylation. The formate salts of the organic polymer and the methylated polymer were shown to form plastic films with a combination of properties such as high transparency, tensile strengths, gas permeability, thermal stability, water‐resistance, and resistance to other organic solvents. The methylated polymer was also able to capture chromate ions and anionic dyes from aqueous solutions.
Preparation of Polyfunctional Organozinc Halides by an InX3‐ and LiCl‐Catalyzed Zinc Insertion to Aryl and Heteroaryl Iodides and Bromides
Authors: Benischke Andreas D. , Le Corre Grégoire , Knochel Paul
Published: November 2016

A catalytic system consisting of InCl3 (3 mol %) and LiCl (30 mol %) allows a convenient preparation of polyfunctional arylzinc halides via the insertion of zinc powder to various aryl iodides in THF at 50 °C in up to 95 % yield. The use of a THF/DMPU (1:1) mixture shortens the reaction rates and allows the preparation of keto‐substituted arylzinc reagents. In the presence of In(acac)3 (3 mol %) and LiCl (150 mol %), the zinc insertion to various aryl and heteroaryl bromides proceeds smoothly (50 °C, 2–18 h). Alkyl bromides are also converted to the corresponding zinc reagents in the presence of In(acac)3 (10 mol %) and LiCl (150 mol %) in 70–80 % yield.