bluuebunny/crossref_metadata_2025 huggingface dataset:
Accurate Determination of Human CPR Conformational Equilibrium by smFRET Using Dual Orthogonal Noncanonical Amino Acid Labeling
Authors: Quast Robert B. , Fatemi Fataneh , Kranendonk Michel , Margeat Emmanuel , Truan Gilles
Published: November 2018

Conjugation of fluorescent dyes to proteins—a prerequisite for the study of conformational dynamics by single‐molecule (sm) FRET—can lead to substantial changes in a dye's photophysical properties, ultimately biasing the determination of inter‐dye distances. In particular, cyanine dyes and their derivatives, the most commonly used dyes in smFRET experiments, exhibit such behavior. To overcome this, we developed a general strategy to equip proteins site‐specifically with FRET pairs through chemoselective reactions with two distinct noncanonical amino acids simultaneously incorporated through genetic code expansion in Escherichia coli. Application of this technique to human NADPH‐cytochrome P450 reductase (CPR) demonstrated the importance of homogenously labeled samples for accurate determination of FRET efficiencies and unveiled the effect of NADP+ on the ionic‐strength‐dependent modulation of the conformational equilibrium of CPR. Thanks to its generality and accuracy, the presented methodology establishes a new benchmark for deciphering of complex molecular dynamics in single molecules.
Keep your eye on…
Authors: Knopf Alison
Published: November 2018

Free articles on ACEs from JAACAP

The need for pediatric readiness in the ED

The high level of daily marijuana use in young adults
Teen cannabis vaping and edible use increased in high‐density dispensary states
Authors: Knopf Alison
Published: November 2018

Legalizing cannabis has resulted in an increased use of vaping and edibles, which may be particularly appealing to young people. Whether these alternative methods of consumption magnify or mitigate the developmental harms of cannabis use is not known. Researchers wanted to find out whether legal cannabis laws, such as dispensary regulations, affect the way youth consume cannabis.
What's happening in the Texas ‘tent city’ for immigrant children
Authors: Knopf Alison
Published: November 2018

In October, the Department of Health and Human Services (HHS) went to Tornillo, Texas, to visit the temporary shelter it established for “unaccompanied alien children” (UAC) at the U.S. Customs and Border Protection (CBP) land port of entry (LPOE). The press referred to this shelter as a “tent city.”
Trauma‐informed health care: Its time is now
Authors: Paccione‐Dyszlewski Margaret
Published: November 2018

Those of us who work in health care are intimately familiar with trauma. Medical trauma routinely appears on our doorstep as the fractured pelvis, serious burn, or brain injury. But what of the other trauma — the one that is less visible, excruciatingly painful, and always present in health care settings: psychological trauma. There is hardly a patient or visitor who crosses the threshold of a health care facility who does not carry a reservoir of worry, fear, stress, or trauma.
Genotypic diversity of bran weight of whole grain rice and its relationship with grain physical traits
Authors: Chen Ming‐Hsuan , McClung Anna M.
Published: November 2018

Background and objectives

Rice bran, the outer most layer of the whole grain, is where nutrients, minerals, and bioactive compounds, except starch, are primarily deposited. Rice bran accounts for a small portion of the whole grain weight. Increasing the weight proportion of bran will enhance the health beneficial value of whole grain rice.

Findings

We determined the physical and bran traits of 135 rice genotypes grown in two years. More than a 2.3‐ and 2.5‐fold variation was found for bran weight per gram of whole grain and bran weight per surface area of the whole grain (BWS, representing bran thickness), respectively. Principle component analysis of the seven physical traits and two bran traits grouped the bran traits into PC3 and accounted for an average of 15.5% of the total variance, whereas kernel weight, width, thickness, and grain surface area were in PC1, and kernel length and length/width ratio were in PC2. Mean comparison among bran color classes showed that purple bran genotypes had the highest BWS, followed by red, white, light brown, and brown. BWS moderately correlated with kernel weight, width, and thickness.

Conclusions

This report demonstrates high bran weight genotypes can be selected to improve the nutritional value of whole grain rice.

Significance and novelty

Expressing bran weight based on grain surface area removed the confounding factor of differences in grain size and allowed identification of genotypes having high bran weight consistently across two years, suggesting this trait is genetically regulated and can be used in traditional breeding to improve bran weight proportion of whole grain rice leading to higher nutritional value of the rice.
Effect of Carbon Nanotubes and Carbon Nanotubes/Gold Nanoparticles Composite on the Photocatalytic Activity of TiO2 and TiO2‐SiO2
Authors: Chinh Vu Duc , Hung Le Xuan , Di Palma Luca , Hanh Vu Thi Hong , Vilardi Giorgio
Published: November 2018

A carbon nanotube (CNT)/gold nanoparticle (NP) nanocomposite was synthesized by simultaneously reducing the Au ions and depositing Au NPs on the surface of a CNT. The functional groups were investigated with Fourier transform infrared spectra. From the Raman spectra, the D‐band and G‐band of the CNT were identified. The deposition of nanometer‐sized Au NPs on the CNT sites was observed by transmission electron microscopy. The photodegradation of methylene blue (MB) in aqueous solutions was studied using various photocatalysts, including TiO2, TiO2‐SiO2, CNT/TiO2, CNT/TiO2‐SiO2, Au/TiO2, CNT‐Au/TiO2, and CNT‐Au/TiO2‐SiO2 composites. CNT addition leads to a synergic effect, improving the photoactivity of the catalysts. A possible physically based mechanism was proposed involving the reduction of electron‐hole recombination and fast electron‐transfer possibility.
Regional differences in gallbladder cancer pathogenesis: Insights from a multi‐institutional comparison of tumor mutations
Authors: Narayan Raja R. , Creasy John M. , Goldman Debra A. , Gönen Mithat , Kandoth Cyriac , Kundra Ritika , Solit David B. , Askan Gokce , Klimstra David S. , Basturk Olca , Allen Peter J. , Balachandran Vinod P. , D’Angelica Michael I. , DeMatteo Ronald P. , Drebin Jeffrey A. , Kingham T. Peter , Simpson Amber L. , Abou‐Alfa Ghassan K. , Harding James J. , O’Reilly Eileen M. , Butte Jean M. , Matsuyama Ryusei , Endo Itaru , Jarnagin William R.
Published: November 2018

Background

Although rare in the United States, gallbladder cancer (GBCA) is a common cause of cancer death in some parts of the world. To investigate regional differences in pathogenesis and outcomes for GBCA, tumor mutations were analyzed from a sampling of specimens.

Methods

Primary tumors from patients with GBCA who were treated in Chile, Japan, and the United States between 1999 and 2016 underwent targeted sequencing of known cancer‐associated genes. Fisher exact and Kruskal‐Wallis tests assessed differences in clinicopathologic and genetic factors. Kaplan‐Meier methods evaluated differences in overall survival from the time of surgery between mutations.

Results

A total of 81 patients were included. Japanese patients (11 patients) were older (median age, 72 years [range, 54‐81 years]) compared with patients from Chile (21 patients; median age, 59 years [range, 32‐73 years]) and the United States (49 patients; median age, 66 years [range, 46‐87 years]) (P = .002) and had more well‐differentiated tumors (46% vs 0% for Chile/United States; P < .001) and fewer gallstone‐associated cancers (36% vs 67% for Chile and 69% for the United States; P = .13). Japanese patients had a median mutation burden of 6 (range, 1‐23) compared with Chile (median mutation burden, 7 [range, 3‐20]) and the United States (median mutation burden, 4 [range, 0‐27]) (P = .006). Tumors from Japanese patients lacked AT‐rich interaction domain 1A (ARID1A) and phosphatidylinositol‐4,5‐bisphosphate 3‐kinase catalytic subunit alpha (PIK3CA) mutations, whereas Chilean tumors lacked Erb‐B2 receptor tyrosine kinase 3 (ERBB3) and AT‐rich interaction domain 2 (ARID2) mutations. SMAD family member 4 (SMAD4) was found to be mutated similarly across centers (38% in Chile, 36% in Japan, and 27% in the United States; P = .68) and was univariately associated with worse overall survival (median, 10 months vs 25 months; P = .039). At least one potentially actionable gene was found to be altered in 80% of tumors.

Conclusions

Differences in clinicopathologic variables suggest the possibility of distinct GBCA pathogenesis in Japanese patients, which may be supported by differences in mutation pattern. Among all centers, SMAD4 mutations were detected in approximately one‐third of patients and may represent a converging factor associated with worse survival. The majority of patients carried mutations in actionable gene targets, which may inform the design of future trials.
A monolithic fluid‐structure interaction framework applied to red blood cells
Authors: Cetin Ayse , Sahin Mehmet
Published: November 2018

A parallel fully coupled (monolithic) fluid‐structure interaction (FSI) algorithm has been applied to the deformation of red blood cells (RBCs) in capillaries, where cell deformability has significant effects on blood rheology. In the present FSI algorithm, fluid domain is discretized using the side‐centered unstructured finite volume method based on the Arbitrary Lagrangian‐Eulerian (ALE) formulation; meanwhile, solid domain is discretized with the classical Galerkin finite element formulation for the Saint Venant‐Kirchhoff material in a Lagrangian frame. In addition, the compatible kinematic boundary condition is enforced at the fluid‐solid interface in order to conserve the mass of cytoplasmic fluid within the red cell at machine precision. In order to solve the resulting large‐scale algebraic linear systems in a fully coupled manner, a new matrix factorization is introduced similar to that of the projection method, and the parallel algebraic multigrid solver BoomerAMG is used for the scaled discrete Laplacian provided by the HYPRE library, which we access through the PETSc library. Three important physical parameters for the blood flow are simulated and analyzed: (1) the effect of capillary diameter, (2) the effect of red cell membrane thickness, and (3) the effect of red cell spacing (hematocrit). The numerical calculations initially indicate a shape deformation in which biconcave discoid shape changes to a parachute‐like shape. Furthermore, the parachute‐like cell shape in small capillaries undergoes a cupcake‐shaped buckling instability, which has not been observed in the literature. The instability forms thin riblike features, and the red cell deformation is not axisymmetric but three‐dimensional.
Retracted: Complex image denoising framework with CNN‐wavelet under concurrency scenarios for informatics systems
Authors: Wang Liping , Huang Wenzhun , Zhang Shanwen , Liu Zhe
Published: November 2018

Image denoising based on convolutional neural networks and wavelet transform is a novel approach for the applications. In the image acquisition process, images are often contaminated by noise, which affects the image quality; therefore, it is necessary to eliminate noise before analyzing and using images. Wavelet analysis is a local analysis method with multi‐resolution characteristics, which is developed on the basis of short‐time Fourier transform. It can be used for the multi‐scale analysis of signals by means of expansion, translation and other operations, and extracting effective information from signals, which is a powerful tool for analyzing non‐stationary signals. Wavelet has good time‐frequency local characteristics, low entropy, and decorrelation. In this paper, we propose MRI image denoising framework based on convolutional neural networks and wavelet transform, and the experiment results show that the proposed method can keep the edge and curvature structure better while denoising. Compared with the other novel methodologies, the proposed algorithm can provide the higher robustness. In the future research, we will try the implementations of the methodologies.
Algorithms for in‐place matrix transposition
Authors: Gustavson Fred G. , Walker David W.
Published: November 2018

This paper presents implementations of in‐place algorithms for transposing rectangular matrices. One implementation is a swap‐based algorithm described by Tretyakov and Tyrtyshnikov,1 to which we have introduced a number of variations. In particular, we show how the original algorithm can be modified to require constant additional memory. A proof of correctness is also sketched. This algorithm is compared with cycle‐following approaches and with the swap‐based GCD Transpose algorithm that partitions the matrix into a hierarchy of square submatrices. The performance of parallel implementations on a multicore system is also investigated.
International Conference on Harmonization: Recent Reforms as a Driver of Global Regulatory Harmonization and Innovation in Medical Products
Authors: Lindström‐Gommers Lenita , Mullin Theresa
Published: November 2018

Eight years ago, this journal published “The Value and Benefits of the International Conference on Harmonization to Drug Regulatory Authorities: Advancing Harmonization for Better Public Health” to mark the 20th anniversary of the International Council on Harmonization (ICH). Much has happened since following the reform of ICH, which culminated in 2015 with the establishment of ICH as an international nonprofit association. This entailed a transformation of the collaboration between a limited number of parties in an informal setting into a formal international organization with its own legal entity. The reform was a time‐consuming exercise preceded by in‐depth and complex discussions, where different options had to be considered and different interests balanced while ICH continued its normal harmonization work within the existing framework. However, the mission of ICH remained unchanged: advancing harmonization for better health. This article describes what triggered the reform and the work that paved the way for reaching the end result.
Multiferroic Nature of Microwave‐Processed and Sol‐Gel Synthesized NanoPb1‐xCoxTiO3 (x = 0.2–0.8) Ceramics
Authors: Kumar Nagasamudram Suresh , Suvarna Reniguntla Padma , Naidu Kadiyala Chandra Babu
Published: November 2018

The lead cobalt titanate (PCT) nanoparticles are prepared through sol‐gel technique by changing the Co content from 0.2 to 0.8. Later, the prepared materials are microwave‐heated at 1023 K for ¾ h. The X‐ray diffraction analysis reveals the change of structure of PCT nanoparticles from tetragonal (T) to rhombohedral (R) phases at higher cobalt contents. In addition, the Williamson–Hall (W–H) plots are drawn to determine microstrain (ε′) and crystallite size (D′) values. The surface morphology is carried out using field emission scanning and transmission electron microscopes. Moreover, the room temperature multiferroic nature is described using polarization versus electric field (P–E) and magnetization versus applied magnetic field (M–H) curves. The magnetic hysteresis loop results indicate a transition from ferromagnetic to paramagnetic state.
Distribution of Yb3+ and Yb2+ Ions along YbF3‐Doped BaF2 Crystals
Authors: Stef Marius , Nicoara Irina , Vizman Daniel
Published: November 2018

BaF2 crystals doped with 0.05, 0.1, and 0.2 mol% YbF3 are grown using vertical Bridgman method. Transparent crystals, ≈5–6 cm in length, ≈10 mm in diameter, are obtained in vacuum using a shaped graphite furnace. The absorption spectra reveal the characteristic absorption bands of the Yb3+and Yb2+ ions in the as‐grown crystals. The distribution of ytterbium ions along the crystals and the effective segregation coefficient of the Yb3+ and Yb2+ ions in the BaF2 host are determined by using the optical absorption method. The crystals are cleaved from the bottom to the top into 10–17 slices of ≈2 mm thickness. The optical absorption spectrum of every slice is recorded. The dopant distribution along the crystal is estimated studying the absorption spectrum of every slice. Two well‐shaped and strong characteristic bands, 968 nm and 352 nm, respectively, are chosen. The Yb3+ and Yb2+ ions are not uniformly distributed along the BaF2 crystals. The calculated effective segregation coefficients of the Yb3+ range from 0.7 to 0.84 and from 0.66 to 0.82 for Yb2+ ions.
VyCAP's puncher technology for single cell identification, isolation, and analysis
Authors: Stevens Michiel , Oomens Lisa , Broekmaat Joska , Weersink Joris , Abali Fikri , Swennenhuis Joost , Tibbe Arjan
Published: November 2018

Here we present the Puncher technology for the isolation of single cells. This technology combines a silicon chip with microwells, fluorescence imaging, and a punching method to isolate and transfer the single cells to standard reaction tubes. The technology is compatible with commercially available downstream workflows and instrumentation. Here we focus on the isolation of CTC but the Puncher technology can be applied to isolate single cells from liquid biopsies and more general from cell suspensions. It is especially suited for cell suspensions that contain:

Cells of interest at a frequency of 1 per 10,000 or less

A low total number of cells ranging from 1 to 100,000, that are present in a volume of 0.01 to 50 mL.

The frequency of appearance of CTC in blood is in the order of the 1 per 106 leukocytes. To be able to isolate the single CTC with the Puncher technology, enrichment of the CTC by a 3 logs reduction of the leukocytes is required. Here we describe the use of Rosettesep and Parsortix as examples of pre‐enrichment methods that are compatible with the Puncher technology and further downstream applications. © 2018 International Society for Advancement of Cytometry
Identification of functionally primitive and immunophenotypically distinct subpopulations in secondary acute myeloid leukemia by mass cytometry
Authors: Bandyopadhyay Shovik , Fowles Jared S. , Yu Liyang , Fisher Daniel A.C. , Oh Stephen T.
Published: November 2018

Background

Background: Mass cytometry (CyTOF) is a powerful tool for analyzing cellular networks at the single cell level. Due to the high‐dimensional nature of this approach, analysis algorithms have been developed to visualize and interpret mass cytometry data. In this study, we applied these approaches to a cohort of patients with secondary acute myeloid leukemia (sAML).

Methods

We utilized mass cytometry to interrogate localization and intensity of thrombopoietin‐mediated intracellular signaling in sAML. Extracellular and intracellular phenotypes were dissected using SPADE, viSNE, and PhenoGraph.

Results

Healthy controls exhibited highly localized signaling responses largely restricted to the hematopoietic stem/progenitor cell (HSPC) compartment. In contrast, sAML samples contained subpopulations outside the HSPC compartment exhibiting thrombopoietin (TPO) sensitivity comparable to or greater than immunophenotypically defined HSPCs. We employed unsupervised clustering by PhenoGraph to elucidate distinct subpopulations within these heterogeneous samples. One metacluster composed almost exclusively of Lin− CD61+ CD34− CD38− CD45low cells was identified. This subpopulation was not readily identified by established manual gating approaches, and generally exhibited greater STAT phosphorylation in response to TPO stimulation than did Lin− CD61− CD34+ CD38− cells. Lin− CD61+ CD34− CD38− CD45low cells were identified in three additional sAML patients analyzed independently using a manual gating approach based upon PhenoGraph results. Each patient exhibited a similar TPO hypersensitivity to the PhenoGraph metacluster.

Conclusions

The identification of this cellular subpopulation highlights the limitations of manual gating in sAML. Our study demonstrates the potential for mass cytometry to elucidate rare subpopulations in highly heterogeneous tumors by utilizing unsupervised high dimensional analysis. © 2018 International Clinical Cytometry Society
An efficient resource allocation scheme in a dense RFID network based on cellular learning automata
Authors: Assarian Ali , Khademzadeh Ahmad , Hosseinzadeh Mehdi , Setayeshi Saeed
Published: November 2018

Radio‐frequency identification (RFID) is a wireless communication technology. Radio frequencies can cause interference in a dense RFID system, thus decreasing efficiency. In recent years, many protocols have been proposed to reduce reader collisions based on multiple‐access techniques. The main weakness of Time Division Multiple Access (TDMA)‐based schemes is the random selection of resources. Additionally, they do not consider the distance between the interfering readers. Therefore, the likelihood of interference in an RFID system will be increased. To address this problem, we propose a new scheme for allocating resources to readers using a learning technique. The proposed scheme takes into account the distance between interfering readers, and these readers acquire the necessary knowledge to select new resources based on the results of the previous selection of neighboring readers using cellular learning automata. This approach leads to reduced interference in an RFID system. The proposed scheme is fully distributed and operates without hardware redundancy. In this scheme, the readers select new resources without exchanging information with each other. The simulation results show that the percentage of kicked readers decreased by more than 20%, and the proposed scheme also provides higher throughput than do state‐of‐the‐art schemes for dense reader environments and leads to further recognition of tags.
End‐to‐end security‐reliability analysis of multi‐hop cognitive relaying protocol with TAS/SC‐based primary communication, total interference constraint and asymmetric fading channels
Authors: Nam Pham Minh , Duy Tran Trung , Ca Phan Van
Published: November 2018

In this paper, we analyze the tradeoff between outage probability (OP) and intercept probability (IP) for a multi‐hop relaying scheme in cognitive radio (CR) networks. In the proposed protocol, a multi‐antenna primary transmitter (PT) communicates with a multi‐antenna primary receiver (PR), using transmit antenna selection (TAS) / selection combining (SC) technique, while a secondary source attempts to transmit its data to a secondary destination via a multi‐hop approach in presence of a secondary eavesdropper. The secondary transmitters such as source and relays have to adjust their transmit power to satisfy total interference constraint given by PR. We consider an asymmetric fading channel model, where the secondary channels are Rician fading, while the remaining ones experience the Rayleigh fading. Moreover, an optimal interference allocation method is proposed to minimize OP of the primary network. For the secondary network, we derive exact expressions of end‐to‐end OP and IP which are verified by Monte Carlo simulations.
Development of an ultra‐high performance liquid chromatography–tandem mass spectrometry method for the determination of anabolic steroids currently available on the black market in the Czech Republic and Slovakia
Authors: Tircova Barbora , Bosakova Zuzana , Kozlik Petr
Published: November 2018

Over the past decade, the use of anabolic androgenic steroids (AAS) by recreational bodybuilders and regular gym members has been increasing exponentially. However, there is a lack of knowledge on AAS products sold in the Czech Republic and Slovakia. The aim of this study was to assess the quantity of active substances in AAS products obtained from AAS users in the Czech Republic and Slovakia. In addition, the study also examines the current trends in counterfeit AAS products used by recreational bodybuilders and regular gym members. For this purpose, the authors developed and validated a universal ultra‐high performance liquid chromatography with tandem mass spectrometry method to determine the most popular doping substances in different pharmaceutical formulations (oil‐based injectables, tablets, and capsules). This method was successfully utilized for the analysis of 358 AAS products. Our results showed that 58.9% AAS products analyzed contained the declared active substances at the declared concentrations, 15.9% contained no active substance, 16.8% were under‐concentrated, 4.5% contained active substances different from those declared on the label, and 3.6% products were over‐concentrated. Alarmingly, the results demonstrated that over 40% of the AAS analyzed failed to meet label claims and therefore may pose serious health risks to consumers. This study also highlighted that the availability of AAS should be more rigorously restricted and their quality closely monitored in order to protect AAS users. In conclusion, the authors have developed a precise, accurate, sensitive, selective, and robust method for the routine screening of products containing anabolic androgenic steroids.
Conventional versus real‐time quantitative PCR for rare species detection
Authors: Xia Zhiqiang , Johansson Mattias L. , Gao Yangchun , Zhang Lei , Haffner Gordon Douglas , MacIsaac Hugh J. , Zhan Aibin
Published: November 2018

Detection of species in nature at very low abundance requires innovative methods. Conventional PCR (cPCR) and real‐time quantitative PCR (qPCR) are two widely used approaches employed in environmental DNA (eDNA) detection, though lack of a comprehensive comparison of them impedes method selection. Here we test detection capacity and false negative rate of both approaches using samples with different expected complexities. We compared cPCR and qPCR to detect invasive, biofouling golden mussels (Limnoperna fortunei), in samples from laboratory aquaria and irrigation channels where this mussel was known to occur in central China. Where applicable, the limit of detection (LoD), limit of quantification (LoQ), detection rate, and false negative rate of each PCR method were tested. Quantitative PCR achieved a lower LoD than cPCR (1 × 10−7 vs. 10−6 ng/μl) and had a higher detection rate for both laboratory (100% vs. 87.9%) and field (68.6% vs. 47.1%) samples. Field water samples could only be quantified at a higher concentration than laboratory aquaria and total genomic DNA, indicating inhibition with environmental samples. The false negative rate was inversely related to the number of sample replicates. Target eDNA concentration was negatively related to distance from sampling sites to the water (and animal) source. Detection capacity difference between cPCR and qPCR for genomic DNA and laboratory aquaria can be translated to field water samples, and the latter should be prioritized in rare species detection. Field environmental samples may involve more complexities—such as inhibitors—than laboratory aquaria samples, requiring more target DNA. Extensive sampling is critical in field applications using either approach to reduce false negatives.
Maladaptive secondary sexual characteristics reduce the reproductive success of hybrids between native and non‐native salmonids
Authors: Fukui Sho , May‐McNally Shannan L. , Taylor Eric B. , Koizumi Itsuro
Published: November 2018

Human‐mediated hybridization between introduced and native species is one of the most serious threats to native taxa. Although field studies have attempted to quantify the relative fitness or reproductive success of parental species and their hybrids, only a few studies have unraveled the factors determining the fitness of hybrids. Here, we hypothesized that maladaptive secondary sexual characteristics may reduce fitness of hybrids between two fish species. To test this, we evaluated the reproductive success of introduced brook trout (BT: Salvelinus fontinalis), native white‐spotted charr (WSC: S. leucomaenis) and their hybrids in a natural stream in Hokkaido, Japan, where the two parental species show remarkably different male secondary sexual characteristics, such as elongated jaws and deeper bodies. We predicted that introgression from WSC is maladaptive for BT males because the BT male has more prominent secondary sexual characteristics. Our results suggest that both sexual selection and outbreeding depression in males and females significantly influence an individual's reproductive success. Our results also suggest that asymmetric introgression may increase the risks to persistence in the recipient species.
Biocrust research: A critical view on eight common hydrological‐related paradigms and dubious theses
Authors: Kidron Giora J.
Published: November 2018

Although being relatively young, research on biocrusts has already yielded numerous paradigms and/or dubious theses. The very existence of these “truths” may lead to erroneous conclusions and/or hinder research on these topics. In the current summary, eight paradigms and dubious theses are examined: (a) Biocrusts require physical crusts for establishment; (b) plant establishment is necessary for biocrust establishment on dunes; (c) developmental stages of biocrusts are often regarded as successional stages; (d) climate‐driven crust morphology determines crust hydrology; (e) infiltration (and subsequently run‐off) over biocrusts is determined by soil pores; (f) run‐off in dryland may stem from hydrophobicity; (g) exopolysaccharides trigger infiltration; and (h) mosses impede infiltration and subsequently the growth of perennial plants. During this summary, reasons that lie behind these paradigms and dubious theses are examined using data and/or rationale for a critical analysis. Experimental data, mostly gathered from the Nizzana research site of the Hallamish dune field (Negev Desert, Israel), and published material (mainly from the Tabernas and Tengger deserts) are used. It is argued that most of the paradigms were either based on improper techniques or never thoroughly investigated. The argument presented herein does not necessarily imply that none of the paradigms may take place under very specific conditions but that their acceptance as general “truth” is questionable.
An 11,000‐yr record of diatom assemblage responses to climate and terrestrial vegetation changes, southwestern Québec
Authors: Neil Karen , Gajewski Konrad
Published: November 2018

A high‐resolution diatom sequence was developed from continuously laminated lake sediments in southwestern Québec, which spanned the Holocene (~11,000 yr). General and species‐specific changes in the diatom record were synchronous with patterns of vegetation succession inferred from regional palynological studies, demonstrating significant influences of terrestrial ecosystems on lake water chemistry and aquatic biota. Principal components analysis was used to identify three major diatom biostratigraphic zones corresponding broadly to early, mid‐, and late Holocene climate intervals. Benthic alkaliphilus diatom taxa were abundant when the landscape was a Picea‐dominated woodland in the early Holocene (11.1–8.0 ka), and when climate conditions were inferred as relatively cool and dry. In the mid‐Holocene (8.0–3.6 ka), warmer temperatures resulted in a stabilization of soils and forests in the catchment area. Shade‐tolerant tree species (Tsuga, Fagus, and Betula) increased during this time, and planktonic diatom taxa (Discostella stelligera and Fragilaria tenera) were abundant in the lake. The well‐known decline in Tsuga across eastern North America between 6.0 and 5.0 ka corresponded to a shift toward more nutrient‐rich lake conditions for several centuries, indicated by an increase in benthic diatom taxa and a lower ratio of chrysophytes relative to diatoms. Neoglacial cooling in the late Holocene (3.6 ka to present) triggered an initial decline in D. stelligera, which later recovered as a result of nutrient inputs that were associated with increased abundances of hardwood, deciduous species (Betula and Alnus) in the catchment. In addition to providing a high‐resolution record of lake ontogeny for the region, the full Holocene record from this lake adds a new perspective on the spatial extent of regional aridity during the Medieval Warm Period (1.2–0.8 ka).
Patterns of dyspnoea onset in patients with acute heart failure: clinical and prognostic implications
Authors: Sokolska Justyna Maria , Sokolski Mateusz , Zymliński Robert , Biegus Jan , Siwołowski Paweł , Nawrocka‐Millward Sylwia , Jankowska Ewa Anita , Todd John , Banasiak Waldemar , Ponikowski Piotr
Published: November 2018

Aims

Despite attempts to improve the management of patients with acute heart failure (HF), virtually all therapeutic agents investigated in large clinical trials failed to show any consistent reduction in mortality and morbidity. Complexity of the clinical syndrome of acute HF seems to be likely an underlying explanation. Traditionally, clinical trials studied mixed patient populations with acute HF, and only recently, better clinical characterization of patients has been proposed. Dyspnoea is the most common presenting symptom related to hospital admission for acute HF. Whether in patients with acute HF, the pattern of symptoms onset preceding hospital admission is associated with clinical characteristics, and the outcomes have not yet been established.

Methods and results

We investigated 137 patients (mean age: 65 ± 13 years; 80% men) hospitalized due to acute HF with dyspnoea as major reported symptom, who were divided according to the time of its onset into those with acute (n = 98) vs. subacute (n = 39) onset (i.e. within 7 days vs. >7 days preceding hospital admission, respectively). On admission, the former group presented higher blood pressure (138 ± 33 vs. 121 ± 32 mmHg), more often moderate–severe pulmonary congestion (33 vs. 8%), and lower bilirubin level [1.07 (0.72–1.60) vs. 1.27 (0.87–2.06); P < 0.05 in all comparisons]. There were no other differences in baseline clinical characteristics and laboratory indices. Higher percentage of patients with an acute dyspnoea onset reported marked/moderate dyspnoea relief after 6 (18% vs. 7%), 24 (59% vs. 24%), and 48 h (80% vs. 46% assessed as an improvement of at least 5 points in self‐reported 10‐point Likert scale; P < 0.05 in all time points). In patients with an acute onset of dyspnoea after 48 h, a decrease of N‐terminal pro BNP was more frequently observed (83% vs. 65%), and the levels of endothelin‐1 were more reduced [−1.1 (−2.9–0.03) vs 0.4 (−2.2–1.4); all P < 0.05]. Patients with acute onset experienced less in‐hospital HF worsening (13% vs. 40%, P = 0.001), and 1 year cardiovascular mortality was significantly lower (20% vs. 41%, P = 0.01). On the multivariable analysis, subacute pattern of dyspnoea was independent predictor of 12 month cardiovascular mortality in patients with acute HF after adjusting for other prognostic factors: systolic blood pressure, urea, and HF de novo [hazard ratio (95% confidence interval): 2.32 (1.13–4.75), P = 0.02].

Conclusions

In patients with acute HF, the pattern of symptoms onset is associated with baseline differences in clinical characteristics, biomarker profile, response to standard treatment, and the long‐term outcomes. This is relevant information for planning future clinical trials.
STAT6 inhibitory peptide reduces dendritic cell migration to the lymph nodes to control Th2 adaptive immunity in the mouse lung
Authors: Lee Soojin , Shan Jichuan , Aldossary Haya , Gaudreault Véronique , Bazett Mark , Fixman Elizabeth D.
Published: November 2018

Type 2 immunity in the lung is promoted through the release of innate cytokines, including TSLP, from lung structural cells. These cytokines drive Type 2 immunity in part through upregulation of OX40L on dendritic cells (DCs). DCs expressing OX40L are potent inducers of Th2 differentiation. We have shown previously that STAT6 inhibitory peptide (STAT6‐IP), a cell penetrating peptide designed to inhibit the STAT6 transcription factor, reduces the induction of Th2 adaptive immunity in murine models of respiratory syncytial virus infection. Here we show that intranasal administration of STAT6‐IP at the time of antigen priming with ovalbumin (OVA), in conjunction with the Nod2 agonist, MDP, reduced frequencies of CD11b+ lung DCs expressing OX40L. Consistent with these reductions, fewer activated DCs were localized to the lung draining lymph nodes in STAT6‐IP‐treated mice. Upon OVA challenge four weeks later, mice treated with STAT6‐IP at the time of OVA/MDP priming did not develop airway hyperresponsiveness (AHR) and had reduced influx of eosinophils into the airways, mucus production, and serum OVA‐specific IgE levels. Our findings provide evidence that the long‐lasting inhibitory effects of STAT6‐IP are due in part to inhibition of DC responses that drive maladaptive Th2 adaptive immunity and allergic airways disease.
Innate and adaptive stimulation of murine diverse NKT cells result in distinct cellular responses
Authors: Tripathi Prabhanshu , Sedimbi Saikiran K. , Singh Avadhesh Kumar , Löfbom Linda , Issazadeh‐Navikas Shohreh , Weiss Siegfried , Förster Irmgard , Karlsson Mikael C. I. , Yrlid Ulf , Kadri Nadir , Cardell Susanna L.
Published: November 2018

Natural killer T (NKT) cells recognize glycolipids presented on CD1d. They share features of adaptive T lymphocytes and innate NK cells, and mediate immunoregulatory functions via rapid production of cytokines. Invariant (iNKT) and diverse (dNKT) NKT cell subsets are defined by their TCR. The immunological role of dNKT cells, that do not express the invariant TCRα‐chain used by iNKT cells, is less well explored than that of iNKT cells. Here, we investigated signals driving Toll‐like receptor (TLR) ligand activation of TCR‐transgenic murine dNKT cells. IFN‐γ production by dNKT cells required dendritic cells (DC), cell‐to‐cell contact and presence of TLR ligands. TLR‐stimulated DC activated dNKT cells to secrete IFN‐γ in a CD1d‐, CD80/86‐ and type I IFN‐independent manner. In contrast, a requirement for IL‐12p40, and a TLR ligand‐selective dependence on IL‐18 or IL‐15 was observed. TLR ligand/DC stimulation provoked early secretion of pro‐inflammatory cytokines by both CD62L+ and CD62L− dNKT cells. However, proliferation was limited. In contrast, TCR/co‐receptor‐mediated activation resulted in proliferation and delayed production of a broader cytokine spectrum preferentially in CD62L− dNKT cells. Thus, innate (TLR ligand/DC) and adaptive (TCR/co‐receptor) stimulation of dNKT cells resulted in distinct cellular responses that may contribute differently to the formation of immune memory.
Oxidative Ring‐Expansion of a Chitin‐Derived Platform Enables Access to Unexplored 2‐Amino Sugar Chemical Space
Authors: Pham Thuy Trang , Gözaydın Gökalp , Söhnel Tilo , Yan Ning , Sperry Jonathan
Published: November 2018

The chitin obtained from crustacean shell waste and other renewable resources may be used as a primary feedstock in the biorefineries of the future. Accordingly, the incorporation of chitin‐derived building blocks into new synthesis processes will accentuate the utility of this biopolymer, particularly in the production of bio‐based small molecules that contain one or more nitrogen atoms. Herein we report that enantioenriched 2‐amino sugars are readily accessible from the chitin‐derived platform 3‐acetamido‐5‐acetylfuran (3A5AF). Subjecting 3A5AF to a Noyori reduction–Achmatowicz rearrangement sequence gave N‐acetyl‐l‐rednose (RedNAc) in excellent yield and enantiopurity. Acetamide hydrolysis gave l‐rednose, a rare 2‐amino sugar found in natural anthracycline and angucycline antibiotics. RedNAc was subsequently shown to be a versatile platform from which a variety of stereochemically pure 2‐amino sugars are readily attainable. The synthesis of chiral, bio‐based N‐compounds from chitin emphasises the rapidly expanding utility of this biopolymer as a viable platform for fine chemical production.
Effects of astaxanthin on sensory‐motor function in a compression model of spinal cord injury: Involvement ofERKandAKTsignalling pathway
Authors: Fakhri Sajad , Dargahi Leila , Abbaszadeh Fatemeh , Jorjani Masoumeh
Published: November 2018

Background

Spinal cord injury (SCI) causes continuous neurological deficits and major sensory‐motor impairments. There is no effective treatment to enhance sensory‐motor function followingSCI. Thus, it is crucial to develop novel therapeutics for this particular patient population. Astaxanthin (AST) is a strong antioxidant, anti‐inflammatory and anti‐apoptotic agent. In the present study, it was tested in a severe compressionSCImodel with emphasis on sensory‐motor outcomes, signalling pathway, along with other complications.

Methods

A severeSCIwas induced by compression of the rat thoracic spinal cord with an aneurysm clip and treatment withASTor the vehicle was carried out, 30 min after injury. Behavioural tests including open field, von Frey, hot plate andBBBwere performed weekly to 28 days post‐injury. Rats were assigned to measure blood glucose, weight and auricle temperature. Western blot and histological analysis also were performed at the same time points.

Results

ASTdecreased mechanical and thermal pain and also improved motor function performance, reduced blood glucose and auricle temperature increases and attenuated weight loss inSCIrats. Western blot analysis showed decreased activation ofERK1/2 and increased activation ofAKTfollowingASTtreatment. The histology results revealed thatASTconsiderably preserved myelinated white matter and the number of motor neurons followingSCI.

Conclusion

Taken together, the beneficial effects ofASTto improve sensory‐motor outcomes, attenuate pathological tissue damage and modulateERKandAKTsignalling pathways followingSCI, suggest it as a strong therapeutic agent towards clinical applications.

Significance

Spinal cord injury (SCI) impairs sensory‐motor function and causes complications, which astaxanthin (AST) has the potential to be used as a treatment for. The present study investigates the effects ofASTin a compression model ofSCIwith emphasis on sensory‐motor outcomes alongside other complications, histopathological damage and also related signalling pathways.
A Gold–Palladium Nanoparticle Alloy Catalyst for CO Production from CO2 Electroreduction
Authors: Bellini Marco , Folliero Maria G. , Evangelisti Claudio , He Qinggang , Hu Yongfeng , Pagliaro Maria V. , Oberhauser Werner , Marchionni Andrea , Filippi Jonathan , Miller Hamish A. , Vizza Francesco
Published: November 2018

Electrochemical CO2 reduction reaction (CO2RR) is a promising technology for combining CO2 reutilization and renewable electricity storage. For economic feasibility, better catalysts are required to overcome current limitations such as high overpotentials, poor faradaic efficiencies (FEs), and low current densities. Herein, size‐ and composition‐controlled gold (Au)–palladium (Pd) bimetallic alloy nanoparticles prepared by a metal vapor synthesis technique together with the monometallic Au and Pd equivalent materials are investigated. X‐ray diffraction and high‐angle annular dark‐field scanning transmission electron microscopy energy‐dispersive X‐ray spectroscopy analyses confirm the Au–Pd alloy formation with an average atomic ratio of 76 Pd wt% and 24 Au wt%. These bimetallic and the monometallic catalysts are characterized and tested for the electroreduction of CO2 in electrochemical cells and also in a complete CO2 electrolysis cell. Analysis of the reduction products shows a 100% CO2RR selectivity for CO. The FE for CO with respect to H2 as high as 90% is obtained with Au–Pd/C by tuning the electrode structure. The Au/C and Pd/C catalysts also show a better selectivity for CO with no evidence of other CO2RR products. The Au–Pd alloy formation improves the FE of Pd for CO by suppressing the parasitic H2 evolution reaction.
Morphology and dynamics of the intertidal floodplain along the Amazon tidal river
Authors: Fricke Aaron T. , Nittrouer Charles A. , Ogston Andrea S. , Nowacki Daniel J. , Asp Nils E. , Souza Filho Pedro W. M.
Published: November 2018

Depositional environments along the tidal river downstream of Óbidos have been proposed as important sinks for up to one third of the sediment discharge from the Amazon River. However, the morphology of the intertidal floodplain and the dynamics of sediment exchange along this reach have yet to be described. River‐bank surveys in five regions along the Amazon tidal river reveal a distinct transition in bank morphology between the upper, central and lower reaches of the tidal river. The upper tidal‐river floodplain is defined by prominent natural levees that control the transfer of water and sediment between the mainstem Amazon River and its floodplain. Greater tidal influence in the central tidal river suppresses levee development, and tidal currents increase sediment transport into the distal parts of the floodplain. In the lower tidal river, the floodplain morphology closely resembles marine intertidal environments (e.g. mud flats, salt marshes), with dendritic tidal channels incising elevated vegetated flats. Theory, morphology and geochronology suggest that the dynamics of sediment delivery to the intertidal floodplain of the Amazon tidal river vary along its length due to the relative influence and coupling of fluvial and tidal dynamics. ©  2018 John Wiley & Sons, Ltd.
Formation of the oxidized flavor compounds at different heat treatment and changes in the oxidation stability of milk
Authors: Li Yan H. , Wang Wei J. , Zhang Fan , Shao Zhi Peng , Guo Liang
Published: November 2018

The oxidized flavor could affect the sensory acceptability of consumers. In this study, the oxidized flavor compound (OFC) in different heated milk was analyzed using the solid phase microextraction–gas chromatography–mass spectrometry (SPME–GC–MS). The concentration of OFC increased with increasing the intensity of heat treatment. The concentrations of heptanal, nonanal, 2‐heptanone, and 2‐nonanone in the heated milk samples were in the range of 1.88–5.51, 1.03–3.26, 6.89–88.04, and 1.46–12.78 μg/kg, respectively. The correlation coefficients between the OFC and the heat intensity were above 0.86. It was found that the intensity of heat treatment (below 80°C for 10 min) could not cause the significant changes in the distribution of fat globules. The contents of partial proteins in milk fat globule membrane gradually destructed with increasing the intensity of heat treatment. The DPPH˙ scavenging activity reduced by 23.15%, and the peroxide value (POV) increased by 37.23% as raw milk was heated at 90°C for 20 min. Values of thiobarbituric acid reactive substances (TBARS) had a tendency to increase as the heated time was operated for 20 min (p < 0.05). It indicated the heat treatment could change the oxidative environment of milk and influence the distribution of milk fat and the formation of oxidized flavor compounds.
How to Leverage Risk and Operational Discipline for Consistent, Predictable Performance
Authors: Bridle Peter V.
Published: November 2018

Do you really know what tomorrow will bring? Organizations must get operational risk firmly in their crosshairs before reliably predicting their futures.
After NAFTA: New Risks to North American Gas Trade?
Authors: Makholm Jeff D.
Published: November 2018

Just before a congressional deadline in September 2018, the Trump administration announced a new version of the 1994 North American Free Trade Agreement (NAFTA)—now called the United States–Mexico–Canada Agreement (USMCA). What does this mean for the robust and growing trade in gas and oil, shown in Figures 1 and 2, across the North American borders?
Few Workable Solutions for High Winter Spot Prices in Northeast
Authors: Smead Richard G.
Published: November 2018

Once again this winter, we are expecting a probable collision between New England gas‐fired power generation and unresolved gas‐supply issues. If last year is any guide, this may result in some very high prices in power and spot gas markets and in the extensive use of oil as an alternate fuel. Because we are now some 15 years into this phenomenon, it is worth revisiting why it exists and what some of the remedies might be.