bluuebunny/crossref_metadata_2025_split huggingface dataset:
In silico analysis of heme oxygenase structural homologues identifies group‐specific conservations
Authors: Irvin Joseph , Ropelewski Alexander J. , Perozich John 
Published: July 2017

Heme oxygenases (HO) catalyze the breakdown of heme, aiding the recycling of its components. Several other enzymes have homologous tertiary structures to HOs, while sharing little sequence homology. These homologues include thiaminases, the hydroxylase component of methane monooxygenases, and the R2 component of Class I ribonucleotide reductases (RNR). This study compared these structural homologues of HO, using a large number of protein sequences for each homologue. Alignment of a total of 472 sequences showed little sequence conservation, with no residues having conservation in more than 80% of aligned sequences and only five residues conserved in at least 60% of the sequences. Fourteen additional positions, most of which were critical for hydrophobic packing, displayed amino acid similarity of 60% or higher. Ten conserved sequence motifs were identified in HOs and RNRs. Phylogenetic analysis verified the existence of the four distinct groups of HO homologues, which were then analyzed by group entropy analysis to identify residues critical to the unique function of each enzyme. Other methods for determining functional residues were also performed. Several common index positions identified represent critical evolutionary changes that resulted in the unique function of each enzyme, suggesting potential targets for site‐directed mutagenesis. These positions included residues that coordinate ligands, form the active sites, and maintain enzyme structure.EnzymesHeme oxygenase (EC 1.14.14.18), methane monooxygenase (EC 1.14.13.25), ribonucleotide reductase (EC 1.17.4.1), thiaminase II (EC 3.5.99.2).
Mouse glutamate carboxypeptidase II (GCPII) has a similar enzyme activity and inhibition profile but a different tissue distribution to human GCPII
Authors: Knedlík Tomáš , Vorlová Barbora , Navrátil Václav , Tykvart Jan , Sedlák František , Vaculín Šimon , Franěk Miloslav , Šácha Pavel , Konvalinka Jan 
Published: July 2017

Glutamate carboxypeptidase II (GCPII), also known as prostate‐specific membrane antigen (PSMA) or folate hydrolase, is a metallopeptidase expressed predominantly in the human brain and prostate. GCPII expression is considerably increased in prostate carcinoma, and the enzyme also participates in glutamate excitotoxicity in the brain. Therefore, GCPII represents an important diagnostic marker of prostate cancer progression and a putative target for the treatment of both prostate cancer and neuronal disorders associated with glutamate excitotoxicity. For the development of novel therapeutics, mouse models are widely used. However, although mouse GCPII activity has been characterized, a detailed comparison of the enzymatic activity and tissue distribution of the mouse and human GCPII orthologs remains lacking. In this study, we prepared extracellular mouse GCPII and compared it with human GCPII. We found that mouse GCPII possesses lower catalytic efficiency but similar substrate specificity compared with the human protein. Using a panel of GCPII inhibitors, we discovered that inhibition constants are generally similar for mouse and human GCPII. Furthermore, we observed highest expression of GCPII protein in the mouse kidney, brain, and salivary glands. Importantly, we did not detect GCPII in the mouse prostate. Our data suggest that the differences in enzymatic activity and inhibition profile are rather small; therefore, mouse GCPII can approximate human GCPII in drug development and testing. On the other hand, significant differences in GCPII tissue expression must be taken into account when developing novel GCPII‐based anticancer and therapeutic methods, including targeted anticancer drug delivery systems, and when using mice as a model organism.
Quality assurance in proton beam therapy using a plastic scintillator and a commercially available digital camera
Authors: Almurayshid Mansour , Helo Yusuf , Kacperek Andrzej , Griffiths Jennifer , Hebden Jem , Gibson Adam 
Published: July 2017

AbstractPurposeIn this article, we evaluate a plastic scintillation detector system for quality assurance in proton therapy using a BC‐408 plastic scintillator, a commercial camera, and a computer.MethodsThe basic characteristics of the system were assessed in a series of proton irradiations. The reproducibility and response to changes of dose, dose‐rate, and proton energy were determined. Photographs of the scintillation light distributions were acquired, and compared with Geant4 Monte Carlo simulations and with depth‐dose curves measured with an ionization chamber. A quenching effect was observed at the Bragg peak of the 60 MeV proton beam where less light was produced than expected. We developed an approach using Birks equation to correct for this quenching. We simulated the linear energy transfer (LET) as a function of depth in Geant4 and found Birks constant by comparing the calculated LET and measured scintillation light distribution. We then used the derived value of Birks constant to correct the measured scintillation light distribution for quenching using Geant4.ResultsThe corrected light output from the scintillator increased linearly with dose. The system is stable and offers short‐term reproducibility to within 0.80%. No dose rate dependency was observed in this work.ConclusionsThis approach offers an effective way to correct for quenching, and could provide a method for rapid, convenient, routine quality assurance for clinical proton beams. Furthermore, the system has the advantage of providing 2D visualization of individual radiation fields, with potential application for quality assurance of complex, time‐varying fields.
Pnictogen (As, Sb, Bi) Nanosheets for Electrochemical Applications Are Produced by Shear Exfoliation Using Kitchen Blenders
Authors: Gusmão Rui , Sofer Zdeněk , Bouša Daniel , Pumera Martin 
Published: July 2017

AbstractLayered materials are of high importance because of their anisotropy and as a source of 2D materials. Whilst there is a plethora of multi‐elemental 2D materials, the number mono‐elemental 2D materials is rather limited. Herein, we demonstrate that aqueous shear exfoliation can be used to obtain As, Sb, and Bi exfoliated nanosheets. Morphological and chemical characterization of the exfoliated materials shows a decrease in thickness, sheet‐to‐nanosheet scale, and partial oxidation owing to a higher surface area. The electrochemical performance is tested in terms of inherent electrochemistry, electron transfer, and sensing applications as demonstrated with ascorbic acid. Potential energy‐related applications are evaluated in the hydrogen evolution reaction (HER), oxygen evolution reaction (OER), and oxygen reduction reaction (ORR), with shear‐exfoliated Sb having the best electrochemical performance overall. These findings will have a profound impact on the preparation and application of 2D mono‐elemental materials.
Metabolic engineering of isopropyl alcohol‐producing Escherichia coli strains with 13C‐metabolic flux analysis
Authors: Okahashi Nobuyuki , Matsuda Fumio , Yoshikawa Katsunori , Shirai Tomokazu , Matsumoto Yoshiko , Wada Mitsufumi , Shimizu Hiroshi 
Published: July 2017

AbstractMetabolic engineering of isopropyl alcohol (IPA)‐producing Escherichia coli strains was conducted along with 13C‐metabolic flux analysis (MFA). A metabolically engineered E. coli strain expressing the adc gene derived from Clostridium acetobutylicum and the IPADH gene from C. beijerinckii did not produce IPA during its exponential growth phase in the aerobic batch culture. 13C‐MFA was carried out, and revealed a deficiency in NADPH regeneration for IPA production in growth phase. Based on these findings, we used nitrogen‐starved culture conditions to reduce NADPH consumption for biomass synthesis. As a result, IPA yield was increased to 20% mol/mol glucose. 13C‐MFA revealed that the relative flux levels through the oxidative pentose phosphate (PP) pathway and the TCA cycle were elevated in nitrogen‐starved condition relative to glucose uptake rate. To prevent CO2 release in the 6‐phosphogluconate dehydrogenase (6PGDH) reaction, metabolism of this E. coli strain was further engineered to redirect glycolytic flux to the glucose 6‐phosphate dehydrogenase (G6PDH) and Entner‐Doudoroff (ED) pathway. IPA yield of 55% mol/mol glucose was achieved by combining the nitrogen‐starved culture condition with the metabolic redirection. The 13C‐MFA data and intracellular NADPH levels obtained under these IPA production conditions revealed linear correlations between the specific IPA production rate and NADPH concentration, as well as between IPA yield and the pyruvate dehydrogenase (PDH) flux. Our results showed that 13C‐MFA is a helpful tool for metabolic engineering studies, and that further improvement in IPA production by E. coli may be achieved by fine‐tuning the cofactor ratio and concentrations, as well as optimizing the metabolic pathways and culture conditions.
A novel keratin 13 variant in a four‐generation family with white sponge nevus
Authors: de Haseth Stephanie B. , Bakker Egbert , Vermeer Maarten H. , el Idrissi Hakima , Bosse Tjalling , Smit Vincent T.H.B.M. , Terron‐Kwiatkowski Anna , McLean W.H. Irwin , Peters Alexander A.W. , Hes Frederik J. 
Published: July 2017

Key Clinical MessageWe report a novel KRT13 germ line variant that causes white sponge nevus (WSN) with mucosal dysplasia. Genital, vaginal, and cervical WSN were observed in four female patients, of whom two had premalignant cervical lesions at young age. Two of the 12 patients with oral WSN developed oral squamous cell carcinoma.
Zeolitic Materials for DeNOx Selective Catalytic Reduction
Authors: Xin Ying , Li Qian , Zhang Zhaoliang 
Published: July 2017

AbstractSelective catalytic reduction (SCR) of NOx has been proven to be the most efficient technique for the removal of NOx (deNOx) from flue gas of stationary sources and diesel engine exhaust of mobile sources. Among various SCR catalysts, zeolites are considered as the most promising candidates for heavy‐duty trucks owing to their benign nature, very high NOx conversion and N2 selectivity, as well as excellent hydrothermal stability at high temperatures. In recent years, a tremendous number of research articles have reported on the evolution of zeolitic materials for deNOx, which makes a critical review timely to provide inspiration for future development. This paper first gives a chronological progress of zeolite catalysts specifically highlighting the CHA zeolites, the hotspot of present research and application, followed by a summary on the synthesis of CHA zeolites, the structure–activity relationships, as well as the reaction mechanisms and kinetics. Last but not least, a critical outlook is given together with expected research directions in developing zeolite‐based catalysts for deNOx.
Rhodium Pyrrolylphosphine Complexes as Highly Active and Selective Catalysts for Propene Hydroformylation: The Effect of Water and Aldehyde on the Reaction Regioselectivity
Authors: Mieczyńska Ewa , Grzybek Ryzard , Trzeciak Anna M. 
Published: July 2017

AbstractThe hydroformylation of propene catalyzed by Rh(acac)(CO)2 (acac=acetylacetonate) with a 13‐fold excess of N‐pyrrolylphosphine ligands PPyr3, PPh2Pyr, or PPh(Pyr)2 (Pyr=NC4H4) was investigated under a pressure of 15 bar (propene/H2/CO=5:5:5) at 80 °C. The N‐pyrrolylphosphine ligands facilitated an excellent regioselectivity towards n‐butanal aldehyde, significantly better than PPh3 and PCy3 under the same conditions. In the presence of the strongest π‐acceptor, PPyr3, the linear‐to‐branched aldehyde (l/b) ratio was 8.6, which increased to 27.1 if water was added to the system. The application of a pure aldehyde as a solvent instead of toluene caused a significant increase in the aldehyde yield but with a decreased l/b ratio (2.9–7.6). The regioselectivity parameter l/b increased to 19.3 after the introduction of water as a cosolvent.
α‐Oxo‐Ketenimines from Isocyanides and α‐Haloketones: Synthesis and Divergent Reactivity
Authors: Mamboury Mathias , Wang Qian , Zhu Jieping 
Published: July 2017

AbstractThe palladium‐catalyzed reaction of α‐haloketones with isocyanides afforded α‐oxo‐ketenimines through β‐hydride elimination of the β‐oxo‐imidoyl palladium intermediates. Reaction of these relatively stable α‐oxo‐ketenimines with nucleophiles such as hydrazines, hydrazoic acid, amines, and Grignard reagent afforded pyrazoles, tetrazole, β‐keto amidines, and enaminone, respectively, with high chemoselectivity. Whereas amines attack exclusively on the ketenimine functions, the formal [3+2] cycloaddition between N‐monosubstituted hydrazines and α‐oxo‐ketenimines was initiated by nucleophilic addition to the carbonyl group.
Evaluation of the use of Gossypium hirsutum oil and supercritical ethanol for the production of ethyl esters in non‐catalytic process
Authors: Azevêdo Saulo , Santos Ênio , Medeiros Aldo , Jesus Anderson , Oliveira Humberto , Sousa Elisa 
Published: July 2017

AbstractThe search for new sources of energy requires more and more interaction between the economical and technological viabilities associated with social development, increasing, in this manner, the interest in raw materials that generate regional development. Thus, this work analyzed the viability of ethyl esters production (biodiesel) from Gossypium hirsutum L. (cottonseed oil) without the use of a catalyst, in a continuous supercritical reactor. The reactions occurred at a tubular reactor, under 15 MPa and 20 MPa of pressure, reaction time (3.75–50 min), molar ratio of oil:alcohol (1:30–1:50), and temperature (250–400 °C). The maximum yield obtained was 75.05 % at 375 °C, under 20 or 15 MPa of pressure, molar ratio of oil:ethanol 1:40, and reaction times 30 and 40 min, respectively. A significant influence of the temperature on yield in esters was verified, but there was also thermal degradation under high temperatures, which caused a decrease in the ester's yield. The high content of polyunsaturated acids present in cotton oil possibly hampered the process of transesterification in long periods of reaction time and high temperatures.
The effect of synthesis parameters on the conductivity of PSf/PANI and PSf/PPy composite membranes
Authors: Sontakke Sharad M. , Awate Vedraj 
Published: July 2017

AbstractIn the present work, synthesis of PANI and PPy was carried out by chemical oxidative polymerization. The effect of synthesis parameters on the conductivity of the polymers was studied. The synthesized polymers, at optimized conditions of conductivity, were further characterized by XRD, SEM, FTIR, and TGA. Pure polysulphone membrane and its composite with the synthesized conductive membrane were carried out using immersion precipitation phase inversion. The synthesized membranes were characterized by FTIR, confocal microscopy, and TGA. The membranes were compared on the basis of various performance properties. It was observed that the pure water flux and water permeability increased in the order PSf < PSf/PANI < PSf/PPy. The composite membranes showed higher porosity, hydrophilicity, and better anti‐fouling characteristics compared to the pure PSf membrane.
Escaping introns in COI through cDNA barcoding of mushrooms: Pleurotus as a test case
Authors: Avin Farhat A. , Subha Bhassu , Tan Yee‐Shin , Braukmann Thomas W. A. , Vikineswary Sabaratnam , Hebert Paul D. N. 
Published: July 2017

AbstractDNA barcoding involves the use of one or more short, standardized DNA fragments for the rapid identification of species. A 648‐bp segment near the 5′ terminus of the mitochondrial cytochrome c oxidase subunit I (COI) gene has been adopted as the universal DNA barcode for members of the animal kingdom, but its utility in mushrooms is complicated by the frequent occurrence of large introns. As a consequence, ITS has been adopted as the standard DNA barcode marker for mushrooms despite several shortcomings. This study employed newly designed primers coupled with cDNA analysis to examine COI sequence diversity in six species of Pleurotus and compared these results with those for ITS. The ability of the COI gene to discriminate six species of Pleurotus, the commonly cultivated oyster mushroom, was examined by analysis of cDNA. The amplification success, sequence variation within and among species, and the ability to design effective primers was tested. We compared ITS sequences to their COI cDNA counterparts for all isolates. ITS discriminated between all six species, but some sequence results were uninterpretable, because of length variation among ITS copies. By comparison, a complete COI sequences were recovered from all but three individuals of Pleurotus giganteus where only the 5′ region was obtained. The COI sequences permitted the resolution of all species when partial data was excluded for P. giganteus. Our results suggest that COI can be a useful barcode marker for mushrooms when cDNA analysis is adopted, permitting identifications in cases where ITS cannot be recovered or where it offers higher resolution when fresh tissue is. The suitability of this approach remains to be confirmed for other mushrooms.
Spatial and temporal drivers of avian population dynamics across the annual cycle
Authors: Rushing Clark S. , Hostetler Jeffrey A. , Sillett T. Scott , Marra Peter P. , Rotenberg James A. , Ryder Thomas B. 
Published: July 2017

AbstractUntangling the spatial and temporal processes that influence population dynamics of migratory species is challenging, because changes in abundance are shaped by variation in vital rates across heterogeneous habitats and throughout the annual cycle. We developed a full‐annual‐cycle, integrated, population model and used demographic data collected between 2011 and 2014 in southern Indiana and Belize to estimate stage‐specific vital rates of a declining migratory songbird, the Wood Thrush (Hylocichla mustelina). Our primary objective was to understand how spatial and temporal variation in demography contributes to local and regional population growth. Our full‐annual‐cycle model allowed us to estimate (1) age‐specific, seasonal survival probabilities, including latent survival during both spring and autumn migration, and (2) how the relative contribution of vital rates to population growth differed among habitats. Wood Thrushes in our study populations experienced the lowest apparent survival rates during migration and apparent survival was lower during spring migration than during fall migration. Both mortality and high dispersal likely contributed to low apparent survival during spring migration. Population growth in high‐quality habitat was most sensitive to variation in fecundity and apparent survival of juveniles during spring migration, whereas population growth in low‐quality sites was most sensitive to adult apparent breeding‐season survival. These results elucidate how full‐annual‐cycle vital rates, particularly apparent survival during migration, interact with spatial variation in habitat quality to influence population dynamics in migratory species.
Seizures, electroencephalographic abnormalities, and outcome of ischemic stroke patients
Authors: Bentes Carla , Peralta Ana Rita , Martins Hugo , Casimiro Carlos , Morgado Carlos , Franco Ana Catarina , Viana Pedro , Fonseca Ana Catarina , Geraldes Ruth , Canhão Patrícia , Pinho e Melo Teresa , Paiva Teresa , Ferro José M. 
Published: July 2017

SummaryObjectiveSeizures and electroencephalographic (EEG) abnormalities have been associated with unfavorable stroke functional outcome. However, this association may depend on clinical and imaging stroke severity. We set out to analyze whether epileptic seizures and early EEG abnormalities are predictors of stroke outcome after adjustment for age and clinical/imaging infarct severity.MethodsA prospective study was made on consecutive and previously independent acute stroke patients with a National Institutes of Health Stroke Scale (NIHSS) score ≥ 4 on admission and an acute anterior circulation ischemic lesion on brain imaging. All patients underwent standardized clinical and diagnostic assessment during admission and after discharge, and were followed for 12 months. Video‐EEG (<60 min) was performed in the first 72 h. The Alberta Stroke Program Early CT Score quantified middle cerebral artery infarct size. The outcomes in this study were an unfavorable functional outcome (modified Rankin Scale [mRS] ≥ 3) and death (mRS = 6) at discharge and 12 months after stroke.ResultsUnfavorable outcome at discharge was independently associated with NIHSS score (p = 0.001), EEG background activity slowing (p < 0.001), and asymmetry (p < 0.001). Unfavorable outcome 1 year after stroke was independently associated with age (p = 0.001), NIHSS score (p < 0.001), remote symptomatic seizures (p = 0.046), EEG background activity slowing (p < 0.001), and asymmetry (p < 0.001). Death in the first year after stroke was independently associated with age (p = 0.028), NIHSS score (p = 0.001), acute symptomatic seizures (p = 0.015), and EEG suppression (p = 0.019).SignificanceAcute symptomatic seizures were independent predictors of vital outcome and remote symptomatic seizures of functional outcome in the first year after stroke. Therefore, their recognition and prevention strategies may be clinically relevant. Early EEG abnormalities were independent predictors and comparable to age and early clinical/imaging infarct severity in stroke functional outcome discrimination, reflecting the concept that EEG is a sensitive and robust method in the functional assessment of the brain.
An examination of the steady‐state assumption in soil development models with application to landscape evolution
Authors: Yu F. , Hunt A.G. 
Published: July 2017

AbstractSoil depth and soil production are highly complicated phenomena, generated from a complex interaction of physical, biological and chemical processes. It has, nevertheless, become increasingly clear that soil formation rates are closely related to chemical weathering rates. Somewhat paradoxically, it is likewise becoming apparent that such biogeochemical reactions as slowly transform rock to soil are limited by physical processes, such as flowing water and the formation of fractures. We have formulated a theoretical approach that relates soil formation rates to chemical weathering rates, and those, likewise, to solute transport rates. For such a theoretical framework to be relevant, the solute transport rates cannot equal those of the flowing water, as is the case in Gaussian solute transport. Rather, solute transport must be slowed in accordance with heavy‐tailed solute arrival time distributions. The inference is that the traditional advection–dispersion equation formulation for solute transport is inadequate in the typically heterogeneous geological media that weather to form soils. Here we examine the implications of this soil production model on the assumption of the approach to steady state. Particularly at slow erosion rates we find that many soil columns are not in equilibrium. This tendency may be accentuated in dry climates. Copyright © 2017 John Wiley & Sons, Ltd.