bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sequence fingerprint and structural analysis of the SCOR enzyme A3DFK9 from Clostridium thermocellum
Authors: Huether Robert , Liu Zhi‐Jie , Xu Hao , Wang Bi‐Cheng , Pletnev Vladimir Z. , Mao Qilong , Duax William L. , Umland Timothy C. 
Published: August 2009

AbstractWe have identified a highly conserved fingerprint of 40 residues in the TGYK subfamily of the short‐chain oxidoreductase enzymes. The TGYK subfamily is defined by the presence of an N‐terminal TGxxxGxG motif and a catalytic YxxxK motif. This subfamily contains more than 12,000 members, with individual members displaying unique substrate specificities. The 40 fingerprint residues are critical to catalysis, cofactor binding, protein folding, and oligomerization but are substrate independent. Their conservation provides critical insight into evolution of the folding and function of TGYK enzymes. Substrate specificity is determined by distinct combinations of residues in three flexible loops that make up the substrate‐binding pocket. Here, we report the structure determinations of the TGYK enzyme A3DFK9 from Clostridium thermocellum in its apo form and with bound NAD+ cofactor. The function of this protein is unknown, but our analysis of the substrate‐binding loops putatively identifies A3DFK9 as a carbohydrate or polyalcohol metabolizing enzyme. C. thermocellum has potential commercial applications because of its ability to convert biomaterial into ethanol. A3DFK9 contains 31 of the 40 TGYK subfamily fingerprint residues. The most significant variations are the substitution of a cysteine (Cys84) for a highly conserved glycine within a characteristic VNNAG motif, and the substitution of a glycine (Gly106) for a highly conserved asparagine residue at a helical kink. Both of these variations occur at positions typically participating in the formation of a catalytically important proton transfer network. An alternate means of stabilizing this proton wire was observed in the A3DFK9 crystal structures. Proteins 2010. © 2009 Wiley‐Liss, Inc.
Substrate uptake and protein stability relationship in mammalian histidine decarboxylase
Authors: Pino‐Ángeles A. , Morreale A. , Negri A. , Sánchez‐Jiménez F. , Moya‐García A. A. 
Published: August 2009

AbstractThere is some evidence linking the substrate entrance in the active site of mammalian histidine decarboxylase and an increased stability against proteolytic degradation. In this work, we study the basis of this relationship by means of protein structure network analysis and molecular dynamics simulations. We find that the substrate binding to the active site influences the conformation of a flexible region sensible to proteolytic degradation and observe how formation of the Michaelis–Menten complex increases stability in the conformation of this region. Proteins 2010. © 2009 Wiley‐Liss, Inc.
I‐TASSER: Fully automated protein structure prediction in CASP8
Authors: Zhang Yang 
Published: August 2009

AbstractThe I‐TASSER algorithm for 3D protein structure prediction was tested in CASP8, with the procedure fully automated in both the Server and Human sections. The quality of the server models is close to that of human ones but the human predictions incorporate more diverse templates from other servers which improve the human predictions in some of the distant homology targets. For the first time, the sequence‐based contact predictions from machine learning techniques are found helpful for both template‐based modeling (TBM) and template‐free modeling (FM). In TBM, although the accuracy of the sequence based contact predictions is on average lower than that from template‐based ones, the novel contacts in the sequence‐based predictions, which are complementary to the threading templates in the weakly or unaligned regions, are important to improve the global and local packing in these regions. Moreover, the newly developed atomic structural refinement algorithm was tested in CASP8 and found to improve the hydrogen‐bonding networks and the overall TM‐score, which is mainly due to its ability of removing steric clashes so that the models can be generated from cluster centroids. Nevertheless, one of the major issues of the I‐TASSER pipeline is the model selection where the best models could not be appropriately recognized when the correct templates are detected only by the minority of the threading algorithms. There are also problems related with domain‐splitting and mirror image recognition which mainly influences the performance of I‐TASSER modeling in the FM‐based structure predictions. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Assessment of CASP8 structure predictions for template free targets
Authors: Ben‐David Moshe , Noivirt‐Brik Orly , Paz Aviv , Prilusky Jaime , Sussman Joel L. , Levy Yaakov 
Published: August 2009

AbstractThe biennial CASP experiment is a crucial way to evaluate, in an unbiased way, the progress in predicting novel 3D protein structures. In this article, we assess the quality of prediction of template free models, that is, ab initio prediction of 3D structures of proteins based solely on the amino acid sequences, that is, proteins that did not have significant sequence identity to any protein in the Protein Data Bank. There were 13 targets in this category and 102 groups submitted predictions. Analysis was based on the GDT_TS analysis, which has been used in previous CASP experiments, together with a newly developed method, the OK_Rank, as well as by visual inspection. There is no doubt that in recent years many obstacles have been removed on the long and elusive way to deciphering the protein‐folding problem. Out of the 13 targets, six were predicted well by a number of groups. On the other hand, it must be stressed that for four targets, none of the models were judged to be satisfactory. Thus, for template free model prediction, as evaluated in this CASP, successes have been achieved for most targets; however, a great deal of research is still required, both in improving the existing methods and in development of new approaches. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Silicon nanocluster aggregation in SiO2:Si layers
Authors: Fitting H.‐J. , Kourkoutis L. Fitting , Salh Roushdey , Zamoryanskaya M. V. , Schmidt B. 
Published: August 2009

AbstractEnergy‐filtered transmission electron microscopy (EFTEM) in combination with electron energy loss spectroscopy (EELS) and cathodoluminescence (CL) have been used to investigate Si+‐implanted amorphous silicon dioxide layers and the formation of Si nanoclusters. Therefore, amorphous, thermally grown SiO2 layers on Si substrate were implanted by Si+ ions with an energy of 150 keV and a dose of 5 × 1016 ions/cm2 leading to an atomic dopant fraction of about 4 at%. Afterwards a post‐implantation thermal annealing has been performed at temperatures Ta = 700–1300 °C, for 60 min in vacuum. This thermal annealing leads to Si cluster formation and a change of the SiOx matrix from about x = 1.923 to 1.929 connected with additional visible luminescence bands in the green‐yellow region. CL spectra in the near infrared (NIR) region indicate such Si aggregation by appearance of an additional band in extension of the common NBOHC band at 1.9 eV towards the NIR region. This band shifts with increasing annealing temperatures of the implanted sample to lower energies, probably, due to cluster growth and quantum confinement effects.
Influence of hydrogen on nanocrystalline diamond surfaces investigated with HREELS and XPS
Authors: Haensel Thomas , Uhlig Jens , Koch Roland J. , Ahmed Syed Imad‐Uddin , Garrido José A. , Steinmüller‐Nethl Doris , Stutzmann Martin , Schaefer Juergen A. 
Published: August 2009

AbstractNanocrystalline diamond (NCD) films are of great importance for many applications. They can be implemented as transparent protective coatings or for the use in electronic devices, sensor systems, and bioelectronic systems. In many applications the surface properties dictate the eventual performance of the device and, therefore, need to be thoroughly understood. This paper is devoted to investigating the changes occurring in the vibrational structure and surface chemical composition of hydrogen‐containing NCD films as a function of annealing treatments as well as exposure to atomic hydrogen. High resolution electron energy loss spectroscopy (HREELS) as a surface sensitive method was utilized to analyze the temperature‐correlated desorption of hydrogen and graphitization of the surface. These measurements were correlated with X‐ray‐induced photoelectron spectroscopy (XPS) measurements to study the chemical composition. Results indicate that water and graphitic‐like contaminations are removed from the sample surface after annealing up to about 350 °C. Annealing the sample up to 950 °C decreases the hydrogen content drastically. At temperatures up to 1050 °C the CH stretching and bending modes are not detectable, indicating that the hydrogen is totally removed from the surface. Analysis of the C 1s XPS spectra revealed that a graphitic‐like phase is formed. An atomic hydrogen treatment was applied to get further information about the surface composition. Additionally, from our HREELS and XPS data we are able to determine the sp2/sp3 ratio for the different surface treatments.
Dynamic fatigue studies of ZnO nanowires by in‐situ transmission electron microscopy
Authors: Gao Zhiyuan , Ding Yong , Lin Shisheng , Hao Yue , Wang Zhong Lin 
Published: August 2009

AbstractThe fatigue behavior of ceramic ZnO nanowires (NWs) has been investigated under resonance cyclic loading conditions using in‐situ transmission electron microscopy (TEM). After mechanical deformation at the resonance frequency at a vibration angle of 5.2° for 35 billion cycles, no failure or any defect generations have been found. We believe that the dislocation‐free nature of NWs and the large surface‐to‐volume ratio contribute to the NWs' ability to undergo deformation without fatigue or fracture, proving their durability and toughness for nanogenerators and nanopiezotronics.magnified image(© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Identification of plant extracts with potential antidiabetic properties: effect on human peroxisome proliferator‐activated receptor (PPAR), adipocyte differentiation and insulin‐stimulated glucose uptake
Authors: Christensen Kathrine B. , Minet Ariane , Svenstrup Henrik , Grevsen Kai , Zhang Hongbin , Schrader Eva , Rimbach Gerald , Wein Silvia , Wolffram Siegfried , Kristiansen Karsten , Christensen Lars P. 
Published: August 2009

AbstractThiazolidinediones (TZDs) are insulin sensitizing drugs used to treat type 2 diabetes. The primary target of the TZDs is the peroxisome proliferator‐activated receptor (PPAR) γ, a key regulator of adipogenesis and glucose homeostasis. Currently prescribed TZDs are full PPARγ agonists, and their use is associated with several side effects. Partial PPARγ agonists appear to be associated with fewer side effects but may still confer the desired insulin sensitizing action. Extracts from common medicinal/food plants were tested in a screening platform comprising a series of bioassays, including tests for PPARγ, α and δ transactivation, adipocyte differentiation and insulin‐stimulated glucose uptake, allowing identification of plants containing potentially interesting PPAR agonists. Twenty‐two plant extracts out of 133 were found to increase insulin‐stimulated glucose uptake and 18 extracts were found to activate PPARγ, 3 to activate PPARα and γ, 6 to activate PPARδ and γ, and 9 to activate PPARγ, α and δ. Among the 24 different plant species tested in the platform, 50% were shown to contain compounds capable of activating PPARγ and stimulating insulin‐dependent glucose uptake with no or little effect on adipocyte differentiation warranting further studies and characterization. Copyright © 2009 John Wiley & Sons, Ltd.
A theoretical study on the LaF3 molecule embedded in argon matrix
Authors: Lanza Giuseppe 
Published: August 2009

AbstractThe LaF3·Arn (n = 1–21) clusters have been proposed as models to account for the matrix effects on the molecular properties of the LaF3 molecule isolated in argon solid matrix at cryogenic temperature. Because of the strong Lewis acid character of the LaF3 molecule, there is a substantial electron‐density transfer from the argon atoms to the molecule that induces important geometrical changes in the structure and vibrational frequencies. The present bottom‐up approach reveals the formation of two sets of structures close in energy having the D3h‐LaF3 and the C3v‐LaF3. The D3h‐LaF3 structures are more compact with respect to the C3v series. The largest investigated cluster of the D3h series, the LaF3·Ar21 resembles an hcp structure with the LaF3 occupying the central substitutional site that it is expected to be energetically preferred. The C3v‐LaF3 structures are more stable for lighter clusters and their high formation rates in the gas‐phase, immediately before matrix incorporation, could explain experimental IR/Raman results that point to a pyramidal shape for the molecule in argon matrix. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Multi‐residue analysis of eight thioamphetamine designer drugs in human urine by liquid chromatography/tandem mass spectrometry
Authors: Nieddu Maria , Boatto Gianpiero , Pirisi Maria Antonietta , Baralla Elena 
Published: August 2009

AbstractAn analytical procedure for the simultaneous determination in human urine of several thioamphetamine designer drugs (2C‐T and ALEPH series) is reported. The quantitative analysis was performed by liquid chromatography/tandem mass spectrometry and has been fully validated. The mass spectrometer was operated in positive‐ion, selected reaction monitoring (SRM) mode. In order to minimize interferences with matrix components and to preconcentrate target analytes, solid‐phase extraction was introduced in the method as a clean‐up step. The entire method was validated for selectivity, linearity, precision and accuracy. The method turned out to be specific, sensitive, and reliable for the analysis of amphetamine derivatives in urine samples. The calibration curves were linear over the concentration range of 1 to 100 ng mL−1 for all drugs with correlation coefficients that exceeded 0.996. The lower limits of detection (LODs) and quantification (LOQs) ranged from 1.2 to 4.9 ng mL−1 and from 3.2 to 9.6 ng mL−1, respectively. Copyright © 2009 John Wiley & Sons, Ltd.
In search of a mental model‐like concept for group‐level modeling
Authors: Kim Hyunjung 
Published: August 2009

AbstractIn system dynamics, we care about mental models, because it is what we attempt to describe, understand, and improve using qualitative maps and computer simulation models. But if we are developing maps and models from a group of individuals, can we still call what we are trying to study a mental model? The main difference between individual and group‐level phenomena is that in a group setting interaction and communication among individuals shape what is represented in maps and models. This paper attempts to clarify the object of our group‐level modeling by surveying existing literature searching for concepts similar to “mental model” at the group level. The survey leads to an insight that what we attempt to represent with our maps and models varies widely by our selection of modeling methods, and how we define our object will draw attention to a different set of theoretical literature. Copyright © 2009 John Wiley & Sons, Ltd.
Sustainable green catalysis by supported metal nanoparticles
Authors: Fukuoka Atsushi , Dhepe Paresh L. 
Published: August 2009

AbstractThe recent progress of sustainable green catalysis by supported metal nanoparticles is described. The template synthesis of metal nanoparticles in ordered porous materials is studied for the rational design of heterogeneous catalysts capable of high activity and selectivity. The application of these materials in green catalytic processes results in a unique activity and selectivity arising from the concerted effect of metal nanoparticles and supports. The high catalytic performances of Pt nanoparticles in mesoporous silica is reported. Supported metal catalysts have also been applied to biomass conversion by heterogeneous catalysis. Additionally, the degradation of cellulose by supported metal catalysts, in which bifunctional catalysis of acid and metal plays the key role for the hydrolysis and reduction of cellulose, is also reported. © 2009 The Japan Chemical Journal Forum and Wiley Periodicals, Inc. Chem Rec 9: 224–235; 2009: Published online in Wiley InterScience (www.interscience.wiley.com) DOI 10.1002/tcr.200900004
Early intervention in management of very preterm growth‐restricted fetuses: 2‐year outcome of infants delivered on fetal indication before 30 gestational weeks
Authors: Brodszki J. , Morsing E. , Malcus P. , Thuring A. , Ley D. , Maršál K. 
Published: August 2009

AbstractObjectivesTo describe the outcome of growth‐restricted fetuses with absent or reversed end‐diastolic flow (ARED) in the umbilical artery delivered on fetal indication before 30 gestational weeks.MethodsBetween 1998 and 2004, 42 fetuses with intrauterine growth restriction (IUGR) and ARED in the umbilical artery were delivered liveborn by Cesarean section on fetal indication before 30 gestational weeks. The median gestational age at delivery was 27 + 1 (range, 24 + 4 to 29 + 5) weeks. An additional four fetuses died in utero at a median gestational age of 24 + 2 (range, 23 + 5 to 25 + 4) weeks. Neonatal morbidity, infant mortality and major neurological morbidity of liveborn infants were compared with those in two control groups: all 371 liveborn infants delivered at < 30 weeks during the corresponding time period (Group A) and a subset of these, 42 matched infants without IUGR (Group B).ResultsThirty‐two fetuses (7%) were delivered within 48 h of the occurrence of ARED (25 absent, seven reversed end‐diastolic flow). The remaining 10 fetuses (five absent, five reversed end‐diastolic flow) were monitored for a median of 6.5 (range, 3–18) days before delivery. One infant died in the neonatal period and three during the first year of postnatal life (2‐year survival 90%). The incidence of chronic lung disease was higher in the ARED Group than in Control Groups A and B (P = 0.001 and P = 0.03, respectively). There were no differences between the groups in the occurrence of necrotizing enterocolitis, cerebral hemorrhage or retinopathy of prematurity. Cerebral palsy was diagnosed in 14% of the index group compared with 11% and 17% of Control Groups A and B (P > 0.05).ConclusionsVery preterm growth‐restricted fetuses with umbilical artery ARED delivered on fetal indication, in most cases before the occurrence of severe changes in the ductus venosus velocity waveforms and/or fetal heart rate tracings, showed high 2‐year survival and low morbidity. Copyright © 2009 ISUOG. Published by John Wiley & Sons, Ltd.
Assessment of intracranial translucency (IT) in the detection of spina bifida at the 11–13‐week scan
Authors: Chaoui R. , Benoit B. , Mitkowska‐Wozniak H. , Heling K. S. , Nicolaides K. H. 
Published: August 2009

AbstractObjectivePrenatal diagnosis of open spina bifida is carried out by ultrasound examination in the second trimester of pregnancy. The diagnosis is suspected by the presence of a ‘lemon‐shaped’ head and a ‘banana‐shaped’ cerebellum, thought to be consequences of caudal displacement of the hindbrain. The aim of the study was to determine whether in fetuses with spina bifida this displacement of the brain is evident from the first trimester of pregnancy.MethodsIn women undergoing routine ultrasound examination at 11–13 weeks' gestation as part of screening for chromosomal abnormalities, a mid‐sagittal view of the fetal face was obtained to measure nuchal translucency thickness and assess the nasal bone. In this view the fourth ventricle, which presents as an intracranial translucency (IT) between the brain stem and choroid plexus, is easily visible. We measured the anteroposterior diameter of the fourth ventricle in 200 normal fetuses and in four fetuses with spina bifida.ResultsIn the normal fetuses the fourth ventricle was always visible and the median anteroposterior diameter increased from 1.5 mm at a crown–rump length (CRL) of 45 mm to 2.5 mm at a CRL of 84 mm. In the four fetuses with spina bifida the ventricle was compressed by the caudally displaced hindbrain and no IT could be seen.ConclusionThe mid‐sagittal view of the face as routinely used in screening for chromosomal defects can also be used for early detection of open spina bifida. Copyright © 2009 ISUOG. Published by John Wiley & Sons, Ltd.
Performance analysis of DSRC priority mechanism for road safety applications in vehicular networks
Authors: He Jianhua , Tang Zuoyin , O'Farrell Tim , Chen Thomas M. 
Published: August 2009

AbstractDedicated short range communications (DSRC) has been regarded as one of the most promising technologies to provide robust communications for large scale vehicle networks. It is designed to support both road safety and commercial applications. Road safety applications will require reliable and timely wireless communications. However, as the medium access control (MAC) layer of DSRC is based on the IEEE 802.11 distributed coordination function (DCF), it is well known that the random channel access based MAC cannot provide guaranteed quality of services (QoS). It is very important to understand the quantitative performance of DSRC, in order to make better decisions on its adoption, control, adaptation, and improvement. In this paper, we propose an analytic model to evaluate the DSRC‐based inter‐vehicle communication. We investigate the impacts of the channel access parameters associated with the different services including arbitration inter‐frame space (AIFS) and contention window (CW). Based on the proposed model, we analyze the successful message delivery ratio and channel service delay for broadcast messages. The proposed analytical model can provide a convenient tool to evaluate the inter‐vehicle safety applications and analyze the suitability of DSRC for road safety applications. Copyright © 2009 John Wiley & Sons, Ltd.
Load balancing and its performance evaluation for layer 3 and IEEE 802.21 frameworks in PMIPv6‐based wireless networks
Authors: Kim Mun‐Suk , Lee SuKyoung 
Published: August 2009

AbstractMobile IP (MIP) requires mobile nodes (MNs) to register with the home agents (HAs) whenever the MNs change their point of attachment (PoA: access point (AP) or base station (BS)) in different subnets. Thus, such registrations cause excessive signaling overhead and long service delay. To solve this problem, proxy mobile IPv6 (PMIPv6) has been proposed by the IETF NETLMM working group. In PMIPv6, a new entity called mobile access gateway (MAG) performs the mobility‐related signaling with the local mobility anchor (LMA) on behalf of the MN and establishes a tunnel with the LMA. However, a number of MNs must be associated with an MAG, which means that the MAG can be easily overloaded. Therefore, in this paper, we propose a load balancing mechanism among the MAGs in the PMIPv6 network. The PMIPv6 handover signaling procedure is extended to support the proposed load balancing mechanism. We also discuss using IEEE 802.21 Media Independent Handover (MIH) protocol for load balancing to determine the load status at the candidate PoAs, in addition to the load status at the candidate MAGs. To evaluate the performance, we analyze the average waiting time in the queue at the MAG. Through simulations and numerical analysis, we show that the proposed load balancing mechanism can produce less queueing delay at the MAG and a higher data transmission rate at the PoA than when a load balancing operation is not performed in the PMIPv6 network. Copyright © 2009 John Wiley & Sons, Ltd.