bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thioesterases: A new perspective based on their primary and tertiary structures
Authors: Cantu David C. , Chen Yingfei , Reilly Peter J. 
Published: May 2010

AbstractThioesterases (TEs) are classified into EC 3.1.2.1 through EC 3.1.2.27 based on their activities on different substrates, with many remaining unclassified (EC 3.1.2.–). Analysis of primary and tertiary structures of known TEs casts a new light on this enzyme group. We used strong primary sequence conservation based on experimentally proved proteins as the main criterion, followed by verification with tertiary structure superpositions, mechanisms, and catalytic residue positions, to accurately define TE families. At present, TEs fall into 23 families almost completely unrelated to each other by primary structure. It is assumed that all members of the same family have essentially the same tertiary structure; however, TEs in different families can have markedly different folds and mechanisms. Conversely, the latter sometimes have very similar tertiary structures and catalytic mechanisms despite being only slightly or not at all related by primary structure, indicating that they have common distant ancestors and can be grouped into clans. At present, four clans encompass 12 TE families. The new constantly updated ThYme (Thioester‐active enzYmes) database contains TE primary and tertiary structures, classified into families and clans that are different from those currently found in the literature or in other databases. We review all types of TEs, including those cleaving CoA, ACP, glutathione, and other protein molecules, and we discuss their structures, functions, and mechanisms.
Modulation of polarization field by fluorine ions in AlGaN/GaN heterostructures revealed by positron annihilation spectroscopy
Authors: Wang Maojun , Cheng Chung Choi , Beling Chris D. , Fung Stevenson , Chen Kevin J. 
Published: May 2010

AbstractModulations of energy band and polarization field by fluorine ions in fluorine plasma treated AlGaN/GaN heterostructures were revealed by positron annihilation spectroscopy (PAS). It is found that the annihilation probability is mainly governed by the electric field in the AlGaN/GaN heterostructure, which could be modulated by charged ions, opposite to what was first expected from the large number of plasma‐induced defects such as Ga‐vacancies. The modulation of electric field is successfully observed through the opposite changes in the S parameters on the two sides of the hetero‐interface after fluorine plasma treatment due to the opposite E‐field directions. Fluorine is experimentally proved to be negatively charged in GaN related materials, which is consistent with the operation principle of enhancement‐mode AlGaN/GaN HEMT fabricated by fluorine plasma treatment. It is also suggested that PAS is a useful tool to probe the intrinsic electric field in AlGaN/GaN system.
Impact of n‐type doping on the terahertz surface emission from c‐plane InN
Authors: Polyakov V. M. , Cimalla V. , Lebedev V. , Schwierz F. 
Published: May 2010

AbstractWe theoretically investigate the influence of n‐type doping on the terahertz (THz) electric field emission from unbiased c‐plane InN surfaces using the ensemble Monte Carlo (MC) method. It is shown that the increase of n‐type doping has twofold effect on the THz surface emission. The detrimental effect of electron drift mobility decrease is compensated by doping‐derived electrons constructively contributing to the total dynamic dipole responsible for a generation of the THz electric field pulse emission from InN surface.
Determination of the valence band offsets at HfO2/InN(0001) and InN/In0.3Ga0.7N(0001) heterojunctions using X‐ray photoelectron spectroscopy
Authors: Eisenhardt Anja , Knübel Andreas , Schmidt Ralf , Himmerlich Marcel , Wagner Joachim , Schaefer Juergen A. , Krischok Stefan 
Published: May 2010

AbstractThe valence band offset (VBO) at a InN/In0.3Ga0.7N(0001) as well as HfO2/InN(0001) heterojunction is investigated by X‐ray photoelectron spectroscopy using monochromated AlKα radiation. The InN and In0.3Ga0.7N films were grown using plasma‐assisted molecular beam epitaxy, whereas HfO2 layers were deposited by plasma‐assisted electron beam evaporation. The VBOs were determined by analysing the core level binding energy and valence band maxima of bulk‐like films as well as of In0.3Ga0.7N and InN layers covered with 5 nm thick overlayers of InN and HfO2, respectively. The resulting VBO values are ∼0.5 eV for the InN/In0.3Ga0.7N heterojunction and ∼0.9 eV in the case of the HfO2/InN heterointerface.
MOVPE growth and optical characterization of InGaAsN T‐shaped quantum wires lattice‐matched to GaAs
Authors: Klangtakai Pawinee , Sanorpim Sakuntam , Katayama Ryuji , Onabe Kentaro 
Published: May 2010

AbstractInGaAsN T‐shaped quantum wire (T‐QWR) lattice‐matched to GaAs was grown by metal organic vapour‐phase epitaxy (MOVPE) and its optical property was investigated. The InGaAsN T‐QWR was observed at the intersection of two InGaAsN quantum wells (QWs) on (001) and (110) surfaces, namely QW1 and QW2, respectively. In, N contents and well‐thickness in QW1 and QW2 were determined by high resolution X‐ray diffraction (HRXRD). Photoluminescence (PL) was taken to obtain excitonic states in the one‐dimensional T‐QWR as well as QW1 and QW2. High PL intensity reveals an achievement of high quality T‐QWR. At low‐temperature, InGaAsN T‐QWR exhibits an emission at around 1.141 eV with a large lateral confinement of about 61 and 99 meV for QW1 and QW2, respectively. This method for producing InGaAsN T‐QWR may be useful for optical or electronic device applications.
Stress relaxed nanoepitaxy GaN for growth of phosphor‐free indium‐rich nanostructures incorporated in apple‐white LEDs
Authors: Soh C. B. , Liu W. , Chua S. J. , Ang N. S. S. , Yong A. M. , Lai S. C. , Teng J. H. 
Published: May 2010

AbstractPhosphor‐free apple‐white light emitting diodes (LEDs) have been fabricated using dual stacked InGaN/GaN multiple quantum wells (MQWs) comprising a lower set of long wavelength emitting indium rich nanostructures incorporated in MQWs with an upper set of cyan‐green emitting MQWs. The LEDs were grown on nano‐epitaxial lateral overgrown (ELO) GaN template formed by regrowth of GaN over SiO2 film patterned using an anodic alumina oxide mask with holes of ∼125 nm diameter and a period of 250 nm. The MQWs grown on the nano‐ELO GaN templates show stronger photoluminescence intensity and a higher activation energy for their peak emission. A minimal shift in the electroluminescence (EL) spectra with higher injection current applied for LEDs grown on ELO‐GaN compared to conventional GaN template, suggests a reduction in strain of the quantum well layers on the nano‐ELO GaN template. An enhancement in the light extraction efficiency is also achieved with multiple scattering via the embedded SiO2 mask.
Various misfit dislocations in green and yellow GaInN/GaN light emitting diodes
Authors: Zhu Mingwei , You Shi , Detchprohm Theeradetch , Paskova Tanya , Preble Edward A. , Wetzel Christian 
Published: May 2010

AbstractWe report the growth and structural characteristics of green and yellow (529–576 nm) GaInN/GaN light emitting diodes (LEDs) grown on two types of c‐plane substrates – bulk GaN and sapphire. In this longer wavelength range, depending on the substrate, we find different strain relaxation mechanisms within the GaInN/GaN quantum well (QW) region. In optimized epitaxy, structures on sapphire that contain a low density of threading dislocations (TDs) within the n‐GaN show virtually no generation of additional misfit dislocations (MDs) (<108 cm−2) or V‐defects within the QW region for emission wavelengths up to 571 nm. On bulk GaN substrate, however, where much fewer TDs reach the QWs, strain relaxation is observed by inclined dislocation pairs in green emitters and a high density of edge‐type MDs in yellow emitters. The electroluminescence line width, as well as the efficiency droop, was found to increase with dislocation density in the QWs.
A novel Gymnema sylvestre extract stimulates insulin secretion from human islets in vivo and in vitro
Authors: Al‐Romaiyan A. , Liu B. , Asare‐Anane H. , Maity C. R. , Chatterjee S. K. , Koley N. , Biswas T. , Chatterji A. K. , Huang G‐C. , Amiel S. A. , Persaud S. J. , Jones P. M. 
Published: May 2010

AbstractMany plant‐based products have been suggested as potential antidiabetic agents, but few have been shown to be effective in treating the symptoms of Type 2 diabetes mellitus (T2DM) in human studies, and little is known of their mechanisms of action. Extracts of Gymnema sylvestre (GS) have been used for the treatment of T2DM in India for centuries. The effects of a novel high molecular weight GS extract, Om Santal Adivasi, (OSA®) on plasma insulin, C‐peptide and glucose in a small cohort of patients with T2DM are reported here. Oral administration of OSA® (1 g/day, 60 days) induced significant increases in circulating insulin and C‐peptide, which were associated with significant reductions in fasting and post‐prandial blood glucose. In vitro measurements using isolated human islets of Langerhans demonstrated direct stimulatory effects of OSA® on insulin secretion from human ?‐cells, consistent with an in vivo mode of action through enhancing insulin secretion. These in vivo and in vitro observations suggest that OSA® may provide a potential alternative therapy for the hyperglycemia associated with T2DM. Copyright © 2010 John Wiley & Sons, Ltd.
High‐throughput metabolic stability studies in drug discovery by orthogonal acceleration time‐of‐flight (OATOF) with analogue‐to‐digital signal capture (ADC)
Authors: Temesi David G. , Martin Scott , Smith Robin , Jones Christopher , Middleton Brian 
Published: May 2010

AbstractScreening assays capable of performing quantitative analysis on hundreds of compounds per week are used to measure metabolic stability during early drug discovery. Modern orthogonal acceleration time‐of‐flight (OATOF) mass spectrometers equipped with analogue‐to‐digital signal capture (ADC) now offer performance levels suitable for many applications normally supported by triple quadruple instruments operated in multiple reaction monitoring (MRM) mode. Herein the merits of MRM and OATOF with ADC detection are compared for more than 1000 compounds screened in rat and/or cryopreserved human hepatocytes over a period of 3 months. Statistical comparison of a structurally diverse subset indicated good agreement for the two detection methods. The overall success rate was higher using OATOF detection and data acquisition time was reduced by around 20%. Targeted metabolites of diazepam were detected in samples from a CLint determination performed at 1 µM. Data acquisition by positive and negative ion mode switching can be achieved on high‐performance liquid chromatography (HPLC) peak widths as narrow as 0.2 min (at base), thus enabling a more comprehensive first pass analysis with fast HPLC gradients. Unfortunately, most existing OATOF instruments lack the software tools necessary to rapidly convert the huge amounts of raw data into quantified results. Software with functionality similar to open access triple quadrupole systems is needed for OATOF to truly compete in a high‐throughput screening environment. Copyright © 2010 John Wiley & Sons, Ltd.
Thin‐layer chromatography and mass spectrometry coupled using proximal probe thermal desorption with electrospray or atmospheric pressure chemical ionization
Authors: Ovchinnikova Olga S. , Van Berkel Gary J. 
Published: May 2010

AbstractAn atmospheric pressure proximal probe thermal desorption sampling method coupled with secondary ionization by electrospray or atmospheric pressure chemical ionization was demonstrated for the mass spectrometric analysis of a diverse set of compounds (dyestuffs, pharmaceuticals, explosives and pesticides) separated on various high‐performance thin‐layer chromatography plates. Line scans along or through development lanes on the plates were carried out by moving the plate relative to a stationary heated probe positioned close to or just touching the stationary phase surface. Vapors of the compounds thermally desorbed from the surface were drawn into the ionization region of a combined electrospray ionization/atmospheric pressure chemical ionization source where they merged with reagent ions and/or charged droplets from a corona discharge or an electrospray emitter and were ionized. The ionized components were then drawn through the atmospheric pressure sampling orifice into the vacuum region of a triple quadrupole mass spectrometer and detected using full scan, single ion monitoring, or selected reaction monitoring mode. Studies of variable parameters and performance metrics including the proximal probe temperature, gas flow rate into the ionization region, surface scan speed, read‐out resolution, detection limits, and surface type are discussed. Published in 2010 by John Wiley & Sons, Ltd.
Comparison of analytical approaches for liquid chromatography/mass spectrometry determination of the alcohol biomarker ethyl glucuronide in urine
Authors: Helander Anders , Kenan Naama , Beck Olof 
Published: May 2010

AbstractOfficial guidelines originating from a European Union directive regulate requirements for analytical methods used to identify chemical compounds in biological matrices. This study compared different liquid chromatography/electropray ionization mass spectrometry (LC/ESI‐MS) and tandem mass spectrometry (LC/ESI‐MS/MS) procedures for accurate determination of the conjugated ethanol metabolite and alcohol biomarker ethyl glucuronide (EtG) in urine, and the value of combined EtG and ethyl sulfate (EtS) measurement. Analysis was carried out on 482 urines following solid‐phase extraction (SPE) sample cleanup or using direct injection of a diluted sample. SPE combined with LC/MS/MS was demonstrated to be the most selective and sensitive method and was chosen as reference method. The EtG results by different methods showed good correlation (r = 0.96–0.98). When comparing five reporting limits for EtG in the range 0.10–1.00 mg/L, the overall agreement with the reference method (frequency of true positives plus true negatives) was 82–97% for direct‐injection LC/MS/MS, 90–97% for SPE‐LC/MS, 86–98% for direct‐injection LC/MS, and 86–98% for direct‐injection LC/MS analysis of EtG and EtS. Most deviations were attributable to uncertainty in quantitation, when the value was close to a cutoff but the respective results were slightly above and below, or vice versa, the critical limit. However, for direct‐injection LC/MS/MS, despite earning 4 identification points, equally many negative results were due to a product ion ratio outside the ±20% deviation accepted by the guidelines. These results indicate that the likelihood of different analytical methods to provide reliable analytical results depends on the reporting limit applied. Copyright © 2010 John Wiley & Sons, Ltd.
Testing the use of septum‐capped vials for 13C‐isotope abundance analysis of carbon dioxide
Authors: Hardie S. M. L. , Garnett M. H. , Fallick A. E. , Stott A. W. , Rowland A. P. , Ostle N. J. 
Published: May 2010

AbstractStudying ecosystem processes in the context of carbon cycling and climate change has never been more important. Stable carbon isotope studies of gas exchange within terrestrial ecosystems are commonly undertaken to determine sources and rates of carbon cycling. To this end, septum‐capped vials (‘Exetainers’) are often used to store samples of CO2 prior to mass spectrometric analysis. To evaluate the performance of such vials for preserving the isotopic integrity (δ13C) and concentration of stored CO2 we performed a rigorous suite of tests. Septum‐capped vials were filled with standard gases of varying CO2 concentrations (∼700 to 4000 ppm), δ13C values (approx. −26.5 to +1.8‰V‐PDB) and pressures (33 and 67% above ambient), and analysed after a storage period of between 7 and 28 days. The vials performed well, with the vast majority of both isotope and CO2 concentration results falling within the analytical uncertainty of chamber standard gas values. Although the study supports the use of septum‐capped vials for storing samples prior to mass spectrometric analysis, it does highlight the need to ensure that sampling chamber construction is robust (air‐tight). Copyright © 2010 John Wiley & Sons, Ltd.
Isomer differentiation via collision‐induced dissociation: The case of protonated α‐, β2‐ and β3‐phenylalanines and their derivatives
Authors: Lam Adrian K. Y. , O'Hair Richard A. J. 
Published: May 2010

AbstractA combination of electrospray ionisation (ESI), multistage and high‐resolution mass spectrometry experiments is used to examine the gas‐phase fragmentation reactions of the three isomeric phenylalanine derivatives, α‐phenylalanine, β2‐phenylalanine and β3‐phenylalanine. Under collision‐induced dissociation (CID) conditions, each of the protonated phenylalanine isomers fragmented differently, allowing for differentiation. For example, protonated β3‐phenylalanine fragments almost exclusively via the loss of NH3, only β2‐phenylalanine via the loss of H2O, while α‐ and β2‐phenylalanine fragment mainly via the combined losses of H2O + CO. Density functional theory (DFT) calculations were performed to examine the competition between NH3 loss and the combined losses of H2O and CO for each of the protonated phenylalanine isomers. Three potential NH3 loss pathways were studied: (i) an aryl‐assisted neighbouring group; (ii) 1,2 hydride migration; and (iii) neighbouring group participation by the carboxyl group. Finally, we have shown that isomer differentiation is also possible when CID is performed on the protonated methyl ester and methyl amide derivatives of α‐, β2‐ and β3‐phenylalanines. Copyright © 2010 John Wiley & Sons, Ltd.
Bayesian learning theory applied to human cognition
Authors: Jacobs Robert A. , Kruschke John K. 
Published: May 2010

AbstractProbabilistic models based on Bayes' rule are an increasingly popular approach to understanding human cognition. Bayesian models allow immense representational latitude and complexity. Because they use normative Bayesian mathematics to process those representations, they define optimal performance on a given task. This article focuses on key mechanisms of Bayesian information processing, and provides numerous examples illustrating Bayesian approaches to the study of human cognition. We start by providing an overview of Bayesian modeling and Bayesian networks. We then describe three types of information processing operations—inference, parameter learning, and structure learning—in both Bayesian networks and human cognition. This is followed by a discussion of the important roles of prior knowledge and of active learning. We conclude by outlining some challenges for Bayesian models of human cognition that will need to be addressed by future research.WIREs Cogn Sci2011 2 8–21 DOI: 10.1002/wcs.80This article is categorized under:Computer Science > Artificial IntelligencePsychology > Learning
The Surgical Strategy and the Molecular Analysis of Patients with Parathyroid Cancer
Authors: Enomoto Keisuke , Uchino Shinya , Ito Akiko , Watanabe Shin , Shibuya Hiroshi , Enomoto Yukie , Noguchi Shiro 
Published: May 2010

AbstractBackgroundParathyroid cancer is a rare endocrine tumor, and the prognostic factors for this cancer remain unclear. The standard therapy is en bloc resection of the primary tumor at the time of the initial operation. However, the clinical significance of prophylactic neck dissection (PND) in the management of parathyroid cancer has not yet been established. In this study, we investigated its clinical significance in patients with parathyroid cancer and the association of gene mutations with tumor progression.MethodsA total of 12 patients with parathyroid cancer were treated and have been followed at Noguchi Thyroid Clinic and Hospital Foundation since 1977. In all, 11 patients were treated with the initial surgery for the cancer, and 1 patient underwent surgery for a metastatic lung lesion. Somatic and germ‐line mutations of the HRPT2 and MEN1 were examined by polymerase chain reaction and automated DNA sequencing.ResultsEn bloc resections of thyroid tissue were performed in 10 patients, and 1 patient underwent only parathyroidectomy with limited resection of the thyroid gland. PND was performed in eight patients, and no lymph node metastases were found in the histological specimens. Six of the eight patients had no evidence of the disease, and two had recurring disease (neck lymph node and lung in one patient and local, lung, and brain in another). PND was not performed in three patients, two of whom had no evidence of the disease and one with recurrence at the site of a regional lymph node. There were no significant differences in disease‐free survival and cause‐specific survival between the patients who underwent PND and the patients who did not (P = 0.98 and P = 0.32, respectively). Among the 12 patients with parathyroid cancer, 1 had a germ‐line mutation of the HRPT2 at exon 7, codon 234, CGA (Arg) to TGA (Stop), and 1 patient had a tumor‐specific mutation at exon 1, nucleotide 34–37 delAACA. Two of the four patients with recurrent disease had an HRPT2 gene mutation. MEN1 gene analysis revealed one somatic missense mutation at exon 2, codon 121, GTC (Val) to GAC (Asp) in one patient.ConclusionsPND for patients with parathyroid cancer resulted in no evidence of lymph node metastasis and does not improve the prognosis. HRPT2 gene mutation may be associated with tumor recurrence.
Aminoacylase 1 deficiency associated with autistic behavior
Authors: Tylki‐Szymanska Anna , Gradowska Wanda , Sommer Anke , Heer Angelina , Walter Melanie , Reinhard Christina , Omran Heymut , Sass Jörn Oliver , Jurecka Agnieszka 
Published: May 2010

AbstractAminoacylase 1 (ACY1) deficiency is a recently described inborn error of metabolism. Most of the patients reported so far have presented with rather heterogeneous neurologic symptoms. At this moment, it is not clear whether ACY1 deficiency represents a true metabolic disease with a causal relationship between the enzyme defect and the clinical phenotype or merely a biochemical abnormality. Here we present a patient identified in the course of selective screening for inborn errors of metabolism (IEM). The patient was diagnosed with autistic syndrome and admitted to the Children's Memorial Health Institute (CMHI) for metabolic evaluation. Organic acid analysis using gas chromatography–mass spectrometry (GC‐MS) revealed increased urinary excretion of several N‐acetylated amino acids, including the derivatives of methionine, glutamic acid, alanine, glycine, leucine, isoleucine, and valine. In Epstein‐Barr virus (EBV)‐transformed lymphoblasts, ACY1 activity was deficient. The mutation analysis showed a homozygous c.1057C>T transition, predicting a p.Arg353Cys substitution. Both parents were heterozygous for the mutation and had normal results in the organic acid analysis using GC‐MS. This article reports the findings of an ACY1‐deficient patient presenting with autistic features.