bluuebunny/crossref_metadata_2025_split huggingface dataset:
A semiempirical approach to ligand‐binding affinities: Dependence on the Hamiltonian and corrections
Authors: Mikulskis Paulius , Genheden Samuel , Wichmann Karin , Ryde Ulf 
Published: March 2012

AbstractWe present a combination of semiempirical quantum‐mechanical (SQM) calculations in the conductor‐like screening model with the MM/GBSA (molecular‐mechanics with generalized Born and surface‐area solvation) method for ligand‐binding affinity calculations. We test three SQM Hamiltonians, AM1, RM1, and PM6, as well as hydrogen‐bond corrections and two different dispersion corrections. As test cases, we use the binding of seven biotin analogues to avidin, nine inhibitors to factor Xa, and nine phenol‐derivatives to ferritin. The results vary somewhat for the three test cases, but a dispersion correction is mandatory to reproduce experimental estimates. On average, AM1 with the DH2 hydrogen‐bond and dispersion corrections gives the best results, which are similar to those of standard MM/GBSA calculations for the same systems. The total time consumption is only 1.3–1.6 times larger than for MM/GBSA. © 2012 Wiley Periodicals, Inc.
Beta‐decomposition for the volume and area of the union of three‐dimensional balls and their offsets
Authors: Kim Deok‐Soo , Ryu Joonghyun , Shin Hayong , Cho Youngsong 
Published: March 2012

AbstractGiven a set of spherical balls, called atoms, in three‐dimensional space, its mass properties such as the volume and the boundary area of the union of the atoms are important for many disciplines, particularly for computational chemistry/biology and structural molecular biology. Despite many previous studies, this seemingly easy problem of computing mass properties has not been well‐solved. If the mass properties of the union of the offset of the atoms are to be computed as well, the problem gets even harder. In this article, we propose algorithms that compute the mass properties of both the union of atoms and their offsets both correctly and efficiently. The proposed algorithms employ an approach, called the Beta‐decomposition, based on the recent theory of the beta‐complex. Given the beta‐complex of an atom set, these algorithms decompose the target mass property into a set of primitives using the simplexes of the beta‐complex. Then, the molecular mass property is computed by appropriately summing up the mass property corresponding to each simplex. The time complexity of the proposed algorithm is O(m) in the worst case where m is the number of simplexes in the beta‐complex that can be efficiently computed from the Voronoi diagram of the atoms. It is known in ℝ3 that m = O(n) on average for biomolecules and m = O(n2) in the worst case for general spheres where n is the number of atoms. The theory is first introduced in ℝ2 and extended to ℝ3. The proposed algorithms were implemented into the software BetaMass and thoroughly tested using molecular structures available in the Protein Data Bank. BetaMass is freely available at the Voronoi Diagram Research Center web site. © 2012 Wiley Periodicals, Inc.
Concise Synthesis of Yashabushidiol A and (±)‐Diospongin A
Authors: Ho Tse‐Lok , Tang Bin , Ma Guohua , Xu Pengfei 
Published: March 2012

AbstractSynthesis of (±)‐diospongin A has been achieved from the (2SR,4RS)‐pentane‐1,2,4,5‐tetraol in six steps. An intermediate has also been converted into yashabushidiol A. This work features a desymmetric cyclization and reduction of a meso‐1,7‐diarylheptanoid precursor to furnish the desired cis‐2,6‐disubstituted tetrahydropyran.
A novel MRI‐compatible brain ventricle phantom for validation of segmentation and volumetry methods
Authors: Khan Amanda F. , Drozd John J. , Moreland Robert K. , Ta Robert M. , Borrie Michael J. , Bartha Robert ,   and the Alzheimer's Disease Neuroimaging Initiative
Published: March 2012

AbstractPurpose:To create a standardized, MRI‐compatible, life‐sized phantom of the brain ventricles to evaluate ventricle segmentation methods using T1‐weighted MRI. An objective phantom is needed to test the many different segmentation programs currently used to measure ventricle volumes in patients with Alzheimer's disease.Materials and Methods:A ventricle model was constructed from polycarbonate using a digital mesh of the ventricles created from the 3 Tesla (T) MRI of a subject with Alzheimer's disease. The ventricle was placed in a brain mold and surrounded with material composed of 2% agar in water, 0.01% NaCl and 0.0375 mM gadopentetate dimeglumine to match the signal intensity properties of brain tissue in 3T T1‐weighted MRI. The 3T T1‐weighted images of the phantom were acquired and ventricle segmentation software was used to measure ventricle volume.Results:The images acquired of the phantom successfully replicated in vivo signal intensity differences between the ventricle and surrounding tissue in T1‐weighted images and were robust to segmentation. The ventricle volume was quantified to 99% accuracy at 1‐mm voxel size.Conclusion:The phantom represents a simple, realistic and objective method to test the accuracy of lateral ventricle segmentation methods and we project it can be extended to other anatomical structures. J. Magn. Reson. Imaging 2012;36:476–482. © 2012 Wiley Periodicals, Inc.
Uniaxial compression of SiO2 glass cylinders: Analysis using stress‐dependent material coefficients
Authors: Richter F. , Hoffmann H.‐J. 
Published: March 2012

AbstractThe present publication extends the prior analysis and discussion of data from the uniaxial compression (upsetting) of hot glass cylinders of vitreous silica that clearly revealed nonlinearity in viscoelastic parameters, i. e., Young's modulus and viscosity. While the simple Maxwell model is retained, the assumption of constant material coefficients in the course of an experiment is dropped. Two approaches, supported by both numerical integration and FEM simulations are applied to unravel the stress dependence of Young's modulus and the viscosity. Thus, nonlinearities are manifested by a non‐Hookean elasticity and a non‐Newtonian viscosity. The stress relaxation behaviour has also been analyzed disregarding any particular model. The relaxation ability is characterized by thermorheological simplicity depending on both the temperature and the stress attained.
Magnetotransport in organic Dirac fermion system at the quantum limit: Interlayer Hall effect and surface transport via helical edge states
Authors: Osada Toshihito 
Published: March 2012

AbstractWe discuss two anomalous features of interlayer magnetotransport observed in α‐(BEDT‐TTF)2I3 in terms of massless Dirac fermions: the interlayer Hall effect and high‐field interlayer magnetoresistance (MR). The former is the anomalous Hall effect, which does not depend on magnetic field strength. It depends only on field orientation showing cotθ‐type angle dependence. We have derived the lowest order contribution of interlayer coupling to conductivity and successfully reproduced the interlayer Hall effect as a transport phenomenon in the massless Dirac fermion system at the quantum limit. The latter is an exponential increase of interlayer MR and its follow‐on saturation in higher magnetic fields. The exponential increase is evidence of the existence of a mobility gap at the Fermi level. It strongly suggests that the ν = 0 quantum Hall state is realized by spin splitting. In this case, two edge states with opposite spin and chirality are formed on the edge surface. The surface transport via edge states becomes dominant in interlayer transport in high enough fields, where bulk transport becomes exponentially small. The observed saturation of interlayer MR is well explained with this scenario.
High‐temperature thermoelectric properties of Cu2In4Te7
Authors: Plirdpring Theerayuth , Kurosaki Ken , Kosuga Atsuko , Ishimaru Manabu , Ohishi Yuji , Muta Hiroaki , Yamanaka Shinsuke 
Published: March 2012

AbstractCu2Ga4Te7 has recently been reported to have a relatively high thermoelectric (TE) figure of merit (ZT). However, the TE properties of Cu2In4Te7, which has the same defect zinc‐blende structure as Cu2Ga4Te7, have been hardly investigated. Here, we demonstrate that Cu2In4Te7 has relatively high ZT values that are similar to those of Cu2Ga4Te7. High‐density polycrystalline bulk samples of Cu2In4Te7 were prepared and their electrical resistivity (ϱ), Seebeck coefficient (S), and thermal conductivity (κ) were measured. Cu2In4Te7 has a maximum ZT of 0.3 at 700 K, with ϱ, S, and κ values of 62.1 × 10–5 Ω m, 394 μV K–1, and 0.61 W m–1 K–1, respectively. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Stable isotope switching (SIS): a new stable isotope probing (SIP) approach to determine carbon flow in the soil food web and dynamics in organic matter pools
Authors: Maxfield P. J. , Dildar N. , Hornibrook E. R. C. , Stott A. W. , Evershed R. P. 
Published: March 2012

RATIONALERecent advances in stable isotope probing (SIP) have allowed direct linkage of microbial population structure and function. This paper details a new development of SIP, Stable Isotope Switching (SIS), which allows the simultaneous assessment of carbon (C) uptake, turnover and decay, and the elucidation of soil food webs within complex soils or sedimentary matrices.METHODSSIS utilises a stable isotope labelling approach whereby the 13C‐labelled substrate is switched part way through the incubation to a natural abundance substrate. A 13CH4 SIS study of landfill cover soils from Odcombe (Somerset, UK) was conducted. Carbon assimilation and dissimilation processes were monitored through bulk elemental analysis isotope ratio mass spectrometry and compound‐specific gas chromatography/combustion/isotope ratio mass spectrometry, targeting a wide range of biomolecular components including: lipids, proteins and carbohydrates.RESULTSCarbon assimilation by primary consumers (methanotrophs) and sequential assimilation into secondary (Gram‐negative and ‐positive bacteria) and tertiary consumers (Eukaryotes) was observed. Up to 45% of the bacterial membrane lipid C was determined to be directly derived from CH4 and at the conclusion of the experiment ca. 50% of the bulk soil C derived directly from CH4 was retained within the soil.CONCLUSIONSThis is the first estimate of soil organic carbon derived from CH4 and it is comparable with levels observed in lakes that have high levels of benthic methanogenesis. SIS opens the way for a new generation of SIP studies aimed at elucidating total C dynamics (incorporation, turnover and decay) at the molecular level in a wide range of complex environmental and biological matrices. Copyright © 2012 John Wiley & Sons, Ltd.
The ongoing pursuit of a prophylactic HSV vaccine
Authors: Chung Erin , Sen Jonathan 
Published: March 2012

SUMMARYHSV is among the most common human pathogens in the world. It is known to cause painful, persistent skin lesions, while also being the most common cause of fatal non‐epidemic encephalitis as well as the leading cause of corneal blindness. The development of prophylactic vaccines could substantially reduce global health problems associated with HSV. So far, HSV vaccine strategies have shown noticeable efficacy in early development during preclinical phases but remained unsuccessful or unproven in human trials. New understanding of how the immune system mounts a defence against HSV offers practical strategies for vaccine development. A number of promising vaccine candidates are currently awaiting clinical development or already undergoing clinical testing. Therefore, this is a suitable time to assess the progress of HSV vaccine development and consider existing challenges and future improvements needed to achieve an effective prophylactic HSV vaccine. Copyright © 2012 John Wiley & Sons, Ltd.
Combining qualitative information and semi‐quantitative data for guaranteed invalidation of biochemical network models
Authors: Rumschinski Philipp , Streif Stefan , Findeisen Rolf 
Published: March 2012

SUMMARYMathematical models of complex biological networks are valuable to make predictions on system properties and to identify therapeutic targets. However, development, validation and analysis of predictive models is often hampered as absolute and quantitative measurement data are rarely available. Instead, the data are typically uncertain with respect to the measured variable or time, relational due to normalization, or data are given as conditional if‐then observations. Many common approaches for model development and validation cannot deal with such semi‐quantitative data and qualitative information. We present a framework for the guaranteed invalidation and parameter estimation of dynamical models using such data. For this purpose, the data are formally expressed by sets of equalities and inequalities containing binary variables. Then a mixed‐integer nonlinear feasibility problem is constructed, which is subsequently relaxed into a mixed‐integer linear program that can be solved efficiently. A model can be proved inconsistent, that is, invalid with the uncertain and semi‐quantitative/qualitative data, if the solution set of the mixed‐integer linear program is empty. To exemplify the approach, we analyze different models whether they can show adaptation to a step‐input. First, we invalidate all but one model and, second, derive outer‐bounds for those regions in the parameter space of the non‐invalidated model that contain parameterizations for which it is consistent with the data. Copyright © 2012 John Wiley & Sons, Ltd.
The effective method of database server forensics on the enterprise environment
Authors: Son Namheun , Lee Keungi , Jeon SangJun , Lee Sangjin , Lee Changhoon 
Published: March 2012

ABSTRACTWhen a forensic investigation is carried out in the enterprise environment, most of the important data are stored in database servers, and data stored in them are very important elements for a forensic investigation. As for database servers with such data stored, there are over 10 various kinds, such as SQL Server and Oracle. All the methods of investigating a database system are important, but this study suggests a single methodology likely to investigate all the database systems while considering the unique characteristics of each database system. A method of detecting a server and acquiring and investigating data in the server can be effectively used for such an investigation on the enterprise environment. For the existing investigation on server systems, severs should be shut down, and disc imaging should be conducted first. However, such a method may inflict great losses on the company in some cases. That is why we need a method to acquire data of a server in on‐line state, and this study discusses this method. Besides, on the basis of methodology, this study attempts to determine a possibility that this new forensic investigation method can be practically used by directly applying this method to SQL Server and MySQL databases. Copyright © 2012 John Wiley & Sons, Ltd.
Virtual autopsy by computed tomographic angiography of the fetal heart: a feasibility study
Authors: Votino C. , Cannie M. , Segers V. , Dobrescu O. , Dessy H. , Gallo V. , Cos T. , Damry N. , Jani J. 
Published: March 2012

AbstractObjectiveTo determine the feasibility of postmortem computed tomographic (pm‐CT) angiography for fetal heart evaluation.MethodsFollowing termination of pregnancy (TOP) or intrauterine fetal death (IUFD) beyond 18 weeks' gestation, 33 fetuses were examined by pm‐CT; in eight contrast medium was injected through the umbilical cord and in 25 contrast medium was injected directly into the heart. Logistic regression analysis was used to investigate the effect on the ability to visualize cardiac structures on pm‐CT angiography of gestational age at TOP or delivery following IUFD, the time delay between fetal death and examination, the technique used for contrast‐medium injection, the presence of cardiac abnormalities and whether or not there was IUFD. The diagnostic accuracy of pm‐CT angiography for the evaluation of fetal cardiac structures was also evaluated.ResultsCardiac anatomy including heart situs, the four‐chamber view and great vessels could be visualized on pm‐CT angiography in 29 out of 33 fetuses (87.9%). Logistic regression analysis showed that the ability to visualize cardiac structures on pm‐CT angiography was positively correlated only with contrast medium injected directly into the heart. Twenty‐five out of the 33 fetuses underwent conventional autopsy. There were five cases with suspected major cardiac abnormality at prenatal ultrasound and one with a minor cardiac abnormality. In one of these cases, severe leakage into the pleural cavity did not allow for visualization of any heart structure on pm‐CT angiography and in another invasive autopsy was declined. In two of the remaining four cases, the findings on pm‐CT angiography and invasive autopsy were in agreement, while in two a ventricular septal defect was found on invasive autopsy but not on pm‐CT. None of the 27 cases with normal hearts was falsely classified as abnormal using pm‐CT angiography.ConclusionPm‐CT angiography by direct injection into the heart seems to be a feasible method for its evaluation. The extent to which such a technique could be used for the evaluation of congenital heart disease as an alternative to classical postmortem autopsy remains to be determined. Copyright © 2012 ISUOG. Published by John Wiley & Sons, Ltd.
Impact of concomitant anterior vaginal reconstructive surgery on transobturator suburethral tape procedures
Authors: Huang W.‐C. , Yang S.‐H. , Yang J.‐M. , Tzeng C.‐R. 
Published: March 2012

AbstractObjectiveTo explore the functional and morphological impact of concomitant anterior vaginal reconstructive surgery on outcome of transobturator suburethral tape (TOT) procedures.MethodsThis was a retrospective review and analysis of data from 196 women who had undergone a TOT procedure with or without concomitant anterior vaginal reconstructive surgery during a 30‐month period. Retrieved data included clinical information and ultrasound findings. Ultrasound examinations assessed the tape location and tape tension at rest, on straining and during coughing. Ultrasound parameters representing tape location comprised the sagittal tape–symphysis pubis distance, sagittal tape–symphysis pubis angle and tape percentile (an indication of tape position along the urethra with respect to urethral length); those representing tape tension included urethral encroachment, sagittal tape–urethra distances at the upper end, central point and lower end of the tape and axial urethral central echolucent area at the center of the tape.ResultsOf the 196 women, 117 had undergone a TOT procedure without concomitant anterior vaginal surgery (Group 1), 44 had undergone TOT placement with anterior colporrhaphy (Group 2) and 35 had undergone TOT placement with a transobturator vaginal mesh procedure (Group 3). At the 3‐month follow‐up, functional outcomes as well as resting and dynamic ultrasound findings were similar between women following TOT procedures without (Group 1) and with (Groups 2 and 3) concomitant anterior vaginal surgery. However, a significantly higher rate of urethral encroachment at rest was noted in Group 2.ConclusionsConcomitant anterior vaginal reconstructive surgery neither aggravates the functional outcome nor affects the ultrasound findings of TOT procedures.
Improvement of FISH–FCM enumeration performance in filamentous yeast species in activated sludge by snailase partial digestion
Authors: Cui Cancan , Zhang Yanyan , Han Hui , Zheng Shaokui 
Published: March 2012

AbstractThis paper developed a novel strategy to improve the fluorescence in situ hybridization–flow cytometry (FISH–FCM) enumeration performance in filamentous yeast species in activated sludge by snailase partial digestion to fully disaggregate filamentous yeast chains into single cells. A 2 h 2% snailase partial digestion liberated more rod‐shaped yeast single cells from intertwined filamentous yeast samples than did sonication disaggregation, based on an optical microscopic observation and the forward‐light‐scatter frequency histogram of FCM analysis. However, adding snailase resulted in a fluorescence‐quenching phenomenon of the hybridized filamentous yeast cells, which was minimized by lowering the snailase concentration. An approximately 3 h 0.5% snailase partial digestion conducted between sonication and hybridization significantly improved the FISH–FCM enumeration performance for filamentous yeast species by 37%. The results presented here will facilitate the rapid detection, identification and exact enumeration of specific filamentous fungal species in environmental samples. Copyright © 2012 John Wiley & Sons, Ltd.
Dinuclear Five‐Coordinate Copper(II) Complexes with Chelating Diphosphonic Acid Ligands: Hydrothermal Synthesis, Structure, and Thermal Properties
Authors: Dehghanpour Saeed , Asadizadeh Saeedeh , Assoud Jalil 
Published: March 2012

AbstractThe synthesis of two new diphosphonic acid ligands,[ethane‐1, 2‐diylbis(azanediyl)]bis[(4‐chlorophenyl)methylene]diphosphonic acid (L1P), [ethane‐1, 2‐diylbis(azanediyl)]bis[(4‐bromophenyl)methylene]diphosphonic acid (L2P), and their corresponding copper complexes, Cu2(L1P)2 (1) and Cu2(L2P)2 (2) are described herein. Complex 2 was structurally characterized with X‐ray single crystal diffraction. The structure of 2 consists of five‐coordinatecopper(II) ions with a distorted square pyramidal arrangement doubly bridged by OPO from phosphonate groups. The Cu–Cu distance is 4.7810(2) Å. The crystal packing is determined by interdinuclear hydrogen bonds, which lead to one‐dimensional chains. The results of thermogravimetric investigations (TG‐DTA), UV/Vis diffuse reflectance, infrared and (1H and 13C) NMR spectroscopy, as well as elemental analyses of compounds 1 and 2 are also presented.
New Borate‐citrate: Synthesis, Structure, and Properties of Sr[B(C6H5O7)2](H2O)4·3H2O
Authors: Wu Hongping , Pan Shilie , Jia Dianzeng , Yu Hongwei , Chen Zhaohui 
Published: March 2012

AbstractSingle crystals of Sr[B(C6H5O7)2](H2O)4·3H2O, a new borate‐citrate material, were grown with sizes up to 8 × 6 × 2 mm by slow evaporation of water at room temperature. The structure of Sr[B(C6H5O7)2](H2O)4·3H2O was determined by single‐crystal X‐ray diffraction. It crystallizes in the monoclinic space group P21/c, with a = 11.363(3) Å, b = 18.829(4) Å, c = 11.976(3) Å, β = 110.736(3)°, and Z = 4. The SrO8 dodecahedra, BO4 tetrahedra and citrate groups are linked together to form chains. The compound was characterized by IR and UV/Vis/NIR transmittance spectroscopy as well as thermal analysis.