bluuebunny/crossref_metadata_2025_split huggingface dataset:
A QTAIM‐based energy partitioning for understanding the physical origin of conformational preferences: Application to the Z effect in O=C‐X‐R and related units
Authors: Ferro‐Costas David , Otero Nicolás , Graña Ana M. , Mosquera Ricardo A. 
Published: August 2012

AbstractA quantum theory of atoms in molecules‐based energy partitioning was carried out forZandEconformers of a series of O=C‐X‐R containing compounds. The results obtained for the simplest compound (formic acid) indicate that the attraction of the electron density within carbonyl oxygen by the nucleus of the acid hydrogen is the most important energy term forZpreference. This conclusion can be extended (mutatis mutandis) to larger carboxylic acids, esters, sulfur derivatives, secondary amides, and carbonyl isocyanates, and even explains the sequence of relative conformational energies in the HCXOH series (X = O, S, Se). In contrast, although the hyperconjugative model has been traditionally employed to explain this preference, we observe it is incompatible with: (i) relative values of diverse QTAIM atomic populations for theZ/Econformational equilibrium; (ii) conformational energies in the HCXOH series. © 2012 Wiley Periodicals, Inc.
Effect of atomic charge, solvation, entropy, and ligand protonation state on MM‐PB(GB)SA binding energies of HIV protease
Authors: Oehme Daniel P. , Brownlee Robert T. C. , Wilson David J. D. 
Published: August 2012

AbstractThe molecular mechanics‐Poisson‐Boltzmann surface area (MM‐PBSA) and MM‐generalized‐Born surface area (MM‐GBSA) approaches are commonly used in molecular modeling and drug design. Four critical aspects of these approaches have been investigated for their effect on calculated binding energies: (1) the atomic partial charge method used to parameterize the ligand force field, (2) the method used to calculate the solvation free energy, (3) inclusion of entropy estimates, and (4) the protonation state of the ligand. HIV protease has been used as a test case with six structurally different inhibitors covering a broad range of binding strength to assess the effect of these four parameters. Atomic charge methods are demonstrated to effect both the molecular dynamics (MD) simulation and MM‐PB(GB)SA binding energy calculation, with a greater effect on the MD simulation. Coefficients of determination and Spearman rank coefficients were used to quantify the performance of the MM‐PB(GB)SA methods relative to the experimental data. In general, better performance was achieved using (i) atomic charge models that produced smaller mean absolute atomic charges (Gasteiger, HF/STO‐3G and B3LYP/cc‐pVTZ), (ii) the MM‐GBSA approach over MM‐PBSA, while (iii) inclusion of entropy had a slightly positive effect on correlations with experiment. Accurate representation of the ligand protonation state was found to be important. It is demonstrated that these approaches can distinguish ligands according to binding strength, underlining the usefulness of these approaches in computer‐aided drug design. © 2012 Wiley Periodicals, Inc.
Efficient One‐pot Synthesis of Alkyl 3‐(alkyl)‐4‐methyl‐2‐thioxo‐2,3‐dihydrothiazole‐5‐carboxylates in a Multi Component Reaction
Authors: Iravani Nasir , Albadi Jalal , Varnaseri Somaieh , Jaberi Zahra , Karami Nahid , Khadamati Marzieh 
Published: August 2012

AbstractA simple and efficient one‐pot synthesis of alkyl 2‐(alkyl)‐4‐methyl‐2‐thioxo‐2,3‐dihydrothiazole‐5‐carboxylates from the reaction of primary alkylamines and carbon disulfide in the presence of 2‐chloro‐1,3‐dicarbonyl compounds is described. This new protocol has several advantages such as lack of necessity of the catalyst, good yields, mild conditions and short times for reaction.
Improved fat water separation with water selective inversion pulse for inversion recovery imaging in cardiac MRI
Authors: Havla Lukas , Basha Tamer , Rayatzadeh Hussein , Shaw Jaime L. , Manning Warren J. , Reeder Scott B. , Kozerke Sebastian , Nezafat Reza 
Published: August 2012

AbstractPurpose:To develop an improved chemical shift‐based water‐fat separation sequence using a water‐selective inversion pulse for inversion recovery 3D contrast‐enhanced cardiac magnetic resonance imaging (MRI).Materials and Methods:In inversion recovery sequences the fat signal is substantially reduced due to the application of a nonselective inversion pulse. Therefore, for simultaneous visualization of water, fat, and myocardial enhancement in inversion recovery‐based sequences such as late gadolinium enhancement imaging, two separate scans are used. To overcome this, the nonselective inversion pulse is replaced with a water‐selective inversion pulse. Imaging was performed in phantoms, nine healthy subjects, and nine patients with suspected arrhythmogenic right ventricular cardiomyopathy plus one patient for tumor/mass imaging. In patients, images with conventional turbo‐spin echo (TSE) with and without fat saturation were acquired prior to contrast injection for fat assessment. Subjective image scores (1 = poor, 4 = excellent) were used for image assessment.Results:Phantom experiments showed a fat signal‐to‐noise ratio (SNR) increase between 1.7 to 5.9 times for inversion times of 150 and 300 msec, respectively. The water‐selective inversion pulse retains the fat signal in contrast‐enhanced cardiac MR, allowing improved visualization of fat in the water‐fat separated images of healthy subjects with a score of 3.7 ± 0.6. Patient images acquired with the proposed sequence were scored higher when compared with a TSE sequence (3.5 ± 0.7 vs. 2.2 ± 0.5, P < 0.05).Conclusion:The water‐selective inversion pulse retains the fat signal in inversion recovery‐based contrast‐enhanced cardiac MR, allowing simultaneous visualization of water and fat. J. Magn. Reson. Imaging 2013;37:484–490. © 2012 Wiley Periodicals, Inc.
Automated truncation method for myocardial T2* measurement in thalassemia
Authors: He Taigang , Zhang Jun , Carpenter John‐Paul , Feng Yanqiu , Smith Gillian C. , Pennell Dudley J. , Firmin David N. 
Published: August 2012

AbstractPurpose:To propose an automated truncation method for myocardial T2* measurement and evaluate this method on a large population of patients with iron loading in the heart and scanned at multiple magnetic resonance imaging (MRI) centers.Materials and Methods:A total of 550 thalassemia patients were scanned at 20 international centers using a variety of MR scanners (Siemens, Philips, or GE). A single mid‐ventricular short axis slice was imaged. All patient data were anonymized before the T2* were measured by expert observers using standard techniques. These same datasets were then retrospectively processed using the proposed automated truncation method by another independent observer and the resulting T2* measurements were compared with those of expert readings.Results:The T2* measurements using the automated method showed good agreement with those measured by expert observers using standard techniques (P = 0.95) with a low coefficient of variation (1.6%).Conclusion:This study demonstrates feasibility and good reproducibility of a new automated truncation method for myocardial T2* measurement. This approach simplifies the overall analysis and can be easily incorporated into T2* analysis software to facilitate further development of a fully automated myocardial tissue iron quantification. J. Magn. Reson. Imaging 2013;37:479–483. © 2012 Wiley Periodicals, Inc.
A direct method to quadrature rules for a certain class of singular integrals with logarithmic, Cauchy, or Hadamard‐type singularities
Authors: Tsalamengas John L. 
Published: August 2012

SUMMARYSingular integrals of the form with logarithmic, Cauchy, or Hadamard‐type singularities in addition to endpoint algebraic singularities w(τ) = (1 − τ2)± 1/2 are frequently encountered in integral equation formulations of potential problems. Some of the existing quadratures for the evaluation of such integrals only apply to preassigned values of the external variable t. Other fairly general rules suffer from loss of accuracy when t is close to any of the nodes of the quadrature. Finally, derivation of the rules is in general multistage, and thus, considerable analytical preprocessing is required. In this paper, a straightforward direct method is presented, which demonstrates the derivation of numerical quadrature rules for Cauchy‐type and Hadamard‐type integrals from corresponding quadratures pertinent to logarithmically singular integrals. The proposed rules share the following characteristics: (1) their derivation, based on first principles, is remarkably simple; (2) the external variable t may be arbitrarily selected; and (3) in their framework, the loss of accuracy referred to earlier is fully remedied. Numerical examples and case studies illustrate the simplicity, flexibility, and high accuracy of the algorithms. Application to the solution of an integral equation associated with wave diffraction by a perfectly conducting strip is exemplified. Copyright © 2012 John Wiley & Sons, Ltd.
Biodegradation of phenol by using free and immobilized cells of Acinetobacter sp. BS8Y
Authors: Jiang Lichun , Ruan Qiping , Li Rulan , Li Tiandong 
Published: August 2012

AbstractStrain BS8Y with high biodegradation activity and high tolerance of phenol was isolated from activated sludge in an insulating material plant of China. This strain was capable of removing 99.2% of the initial 600 mg/l phenol in liquid minimal medium within 24 h and tolerating phenol at concentrations of up to 1200 mg/ml. DNA sequencing and homologous analysis of the 16S rRNA gene identified that the strain BS8Y belonged to an Acinetobacter species. Polyvinyl alcohol was used as gel matrix to immobilize the strain BS8Y. The factors affecting the phenol degradation by immobilized cells and the phenol removal efficiency of free and immobilized cells were investigated; the stability of the immobilized cells is also reported. The results show that the immobilized cells could tolerate a higher phenol level and protected the bacteria much more effectively against changes in temperature and pH. The phenol degradation efficiency was high at up to 96% within 30 h, with an initial concentration of 800 mg/l phenol, and the immobilized cells showed better performance than the suspended cells. Reusability tests revealed that the immobilized cells were stable enough even after reuse for ten times or storing at 4°C for 35 d. These results demonstrate that immobilized Acinetobacter sp. BS8Y possesses a good application potential in the treatment of phenol‐containing wastewater.
Decomposition of Microcystis blooms: Implications for the structure of the sediment bacterial community, as assessed by a mesocosm experiment in Lake Taihu, China
Authors: Shao Keqiang , Gao Guang , Chi Kexu , Qin Boqiang , Tang Xiangming , Yao Xin , Dai Jiangyu 
Published: August 2012

AbstractThe effect of decomposition of Microcystis blooms on the sediment bacterial communities was investigated in a 14‐day mesocosm experiments under dark and anoxic condition with three differing levels of Microcystis spp. biomass (from 20 to 2000 µg L−1) as measured by chlorophyll‐a (Chl‐a) concentration in the water column. Sediment samples were collected on days 0 and 14 for bacterial community composition (BCC) analysis, based on rapid decreases in the Chl‐a concentration of water column. The BCC was determined by denaturing gradient gel electrophoresis and sequencing of predominant bands. The results showed that after Microcystis decomposition (day 14), the bacterial phylotype diversity in the sediment increased in enclosures with added Microcystis, and the relative abundance of bacteria affiliated with Bacteroidetes and Verrucomicrobia strongly increased. Canonical correspondence analysis showed that organic matter and Chl‐a contributed significantly to the changes in sediment bacterial communities during Microcystis decomposition. The present results demonstrate Microcystis decomposition may directly and indirectly influence the BCC of the sediment.
Biosorption of aluminum, cobalt, and copper ions by Providencia rettgeri isolated from wastewater
Authors: Abo‐Amer Aly E. , Ramadan Abou Bakr , Abo‐State Mervat , Abu‐Gharbia Magdy A. , Ahmed Hamdy E. 
Published: August 2012

AbstractTwenty‐three bacterial isolates from polluted water and soil were screened for heavy metals resistance (i.e., Al3+, Co2+, and Cu2+). The most potent isolate was identified by morphological characteristics, biochemical tests and confirmed by API20E kits as Providencia rettgeri MAM‐4. Removal of Al3+ from aqueous solution by P. rettgeri is more efficient (∼fourfold) than that by B. cereus ATCC 11778 (a comparison strain) at concentration of 200 mg L−1 Al3+. P. rettgeri was able to remove Co2+ more than B. cereus ATCC 11778 at concentration of 50 mg L−1 Co2+. Inoculation of P. rettgeri into clay enhanced significantly the removal of Al3+, Co2+, and Cu2+. P. rettegri MI (mutant strain) was able to tolerate more Al3+ than that of the parent strain. P. rettgeri was resistant to 7 out of 15 antibiotics tested. P. rettgeri MAM‐4 isolated from wastewater had ability to remove Al3+, Co2+, and Cu2+ efficiently from aqueous media; and enhanced significantly metal biosporption by clay. This study has revealed that P. rettgeri could be employed as an effective and economic technology for the removal such metal elements from polluted environment.
Purification and characterization of an extracellular chitinase from antagonistic Streptomyces violaceusniger
Authors: Nagpure Anand , Gupta Rajinder K. 
Published: August 2012

AbstractThe actinomycetes Streptomyces violaceusniger showed strong antagonistic activity against various tested wood rotting fungi. An extracellular chitinase, produced by antagonistic S. violaceusniger MTCC 3959, was purified as follows: ammonium sulfate precipitation, chitin affinity and chromatographic separation of Q Sepharose. The molecular mass of the purified chitinase was estimated as 56.5 kDa by SDS‐PAGE. Chitinase was optimally active at pH of 5.0 and 50 °C. It retained almost 100% activity at pH 5.0 and also had high thermal tolerance at 50 °C. Enzyme activity was inhibited by Hg2+ and Ag+ cations, but was neither substantially inhibited by K+ cation nor by chelating agent EDTA. The apparent Km and Vmax at 37 °C were 0.1426 mM and 6.6 U/mg, respectively using pNP‐(GlcNAc)2 as substrate. The 56.5 kDa chitinase of strain MTCC 3959 represented an exo‐type activity. The purified chitinase was further identified by MALDI‐TOF. The results of peptide mass fingerprinting showed that 10 tryptic peptides of the chitinase were identical to the chitinase C from Streptomyces albus J1074 (GenBank Accession No. gi|239982330). The sequence of N‐terminal amino acid (AA) of the chitinase was determined to be G‐D‐G‐T‐G‐P‐G‐P‐G‐P.
Screening and identification of a Bacillus thuringiensis strain S1/4 with large and efficient insecticidal activities
Authors: Sellami Sameh , Zghal Taheni , Cherif Maroua , Zalila‐Kolsi Imen , Jaoua Samir , Jamoussi Kaïs 
Published: August 2012

AbstractThe bacterium Bacillus thuringiensis was recognized for its entomopathogenic activities related to Cry and Cyt proteins forming the δ‐endotoxins and some extracellular activities like the vegetative insecticidal proteins (VIP) and Cry1I. These activities may act specifically against diverse organisms and some of them typically characterize each strain. Here, we screened a set of 212 B. thuringiensis strains to search the higher insecticidal activities. These strains had bipyramidal and cubic crystal morphologies and 30% of them showed PCR amplification of vip3 internal region, from which five isolates (S1/4, S17, S122, S123, and S144) showed plasmid profile variability. These five strains contained the cry1I, cry1Aa and/or cry1Ac, cry1Ab and cry2 genes, and S1/4 harbored in addition the cry1C, vip1, and vip2 genes. They produced from 25 to 46 µg δ‐endotoxin per 107 spores. Their δ‐endotoxins displayed distinct lethal concentrations 50% against either Spodoptera littoralis or Ephestia kuehniella larvae with the lowest one for S1/4, which was also active against Tuta absoluta. Fortunately, the analysis of the culture supernatants revealed that S1/4 had the higher toxicity towards these lepidopteron but it did not show any toxicity against the Tribolium castaneum coleopteran larvae; additionally, S1/4 displayed an antibacterial activity. S1/4 is a good candidate for agricultural pest control, as it is more efficient than the reference strain HD1.
Biodegradation of BTEX mixture by Pseudomonas putidaYNS1 isolated from oil‐contaminated soil
Authors: You Youngnam , Shim Jaehong , Cho Choa‐Hyoung , Ryu Moon‐Hee , Shea Patrick J. , Kamala‐Kannan Seralathan , Chae Jong‐Chan , Oh Byung‐Taek 
Published: August 2012

AbstractThe presence of mixed contaminants, such as BTEX (benzene, toluene, ethylbenzene and xylene isomers) can affect the biodegradation, fate and environmental impacts of each compound. To understand the influence of interactions among BTEX compounds on their biodegradation, four bacteria were isolated from oil‐contaminated soil and assayed for BTEX biodegradation in vitro. The isolate exhibiting maximum biodegradation was identified as Pseudomonas putida based on the 16S rDNA sequence. The biodegradation of the BTEX compounds was greatly influenced by pH, temperature, and salinity. Substrate mixture studies (binary, tertiary and quaternary) revealed that the presence of toluene increased the biodegradation rate of benzene, ethylbenzene, and xylene.
Larger variability, better predictability?
Authors: Sun Bo , Wang Huijun 
Published: August 2012

AbstractThe statistical relationship between observed interannual variability and the corresponding predictability of June–July–August mean precipitation is computed and discussed, using hindcasts from the Development of a European Multimodel Ensemble System for Seasonal to Interanuual Prediction (DEMETER) project and reanalysis datasets of the Global Precipitation Climatology Project and Climatic Research Unit. It is found that there exists a globally positive correlation between the variability and predictability, being prominent in the low latitudes and less evident in the high latitudes. Although this correlation varies with modulated verification datasets, multi‐model ensembles and temporal periods, all of which are artificial factors, a significant positive correlation is found over East Asia, Australia, South America, Europe and Africa, while a negative correlation for North America, under most circumstances. Moreover, it is also found that different dynamical processes in the climate system seem to have made different contributions to building this ‘larger variability–better predictability’ relationship, possibly through enhancing the predictability over domains where there is a larger contribution to variability by the climate signals, while making an uncertain contribution to the predictability over domains that are less influenced by the signals.
SC‐1, a sorafenib derivative, shows anti‐tumor effects in osteogenic sarcoma cells
Authors: Wang Chen‐Ti , Lin Chen‐Si , Shiau Chung‐Wai , Chu Pei‐Yi , Hsiao Chung‐Ching , Chiang Yi‐Lun , Tai Wei‐Tien , Chen Kuen‐Feng 
Published: August 2012

AbstractDespite significant advances in the treatment of osteosarcoma (OS), overall survival rate of OS patients has remained relatively constant for over two decades and novel approaches are needed to further improve prognosis. Here, we report the anti‐tumor effect of SC‐1, a novel sorafenib derivative that closely resembles sorafenib structurally but is devoid of kinase inhibitory activity, on OS cells through mediation of signal transducer and activator of transcription 3 (STAT3). SC‐1 showed similar effects to sorafenib on growth inhibition and apoptosis, and downregulated phospho‐STAT3 (p‐STAT3) at tyrosine 705 in all tested OS cell lines (U2OS, HOS, and 143B). Expression of STAT3‐driven genes, including cylcin D1 and c‐myc, were also repressed by SC‐1. Ectopic expression of STAT3 in 143B cells abolished apoptosis in SC‐1‐treated cells. Inhibition of SHP‐1 decreased SC‐1‐induced apoptosis. SC‐1 upregulated the activity of SHP‐1 in tested OS cell lines in a dose‐dependent manner. Finally, SC‐1 reduced 143B tumor growth significantly in vivo, which was associated with downregulation of p‐STAT3 and upregulation of SHP‐1 activity. These data demonstrate that SC‐1 has clinical potential for the treatment of OS patients. © 2012 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 31: 335–342, 2013
Differential expression of basement membrane type IV collagen α2 and α6 chains as a prognostic factor in patients with extrahepatic bile duct carcinoma
Authors: Hirashima Kotaro , Iyama Ken‐Ichi , Baba Yoshifumi , Honda Yumi , Sado Yoshikazu , Ninomiya Yoshifumi , Watanabe Masayuki , Takamori Hiroshi , Beppu Toru , Baba Hideo 
Published: August 2012

AbstractBackgroundThe destruction of the basement membrane (BM) is the first step in cancer invasion and metastasis. Type IV collagen is a major component of the BM, and is composed of six genetically distinct α(IV) chains; α1(IV) to α6(IV). The loss of α5(IV) and α6(IV) chains from the epithelial BM at the early stage of cancer invasion has been reported in several types of cancers. However, the expression of α5(IV) and α6(IV) chains in extrahepatic bile duct carcinoma (EBDC) remains unclear.MethodsWe examined the expression of α(IV) chains by immunohistochemistry using 71 resected EBDC specimens. Prognostic significance of α(IV) chains was examined by Cox regression and Kaplan–Meier analyses.ResultsIn the invasive cancer, the expression of α6(IV) chain in the BM was lost partially or completely preceded by the loss of α2(IV) chain. The loss of α6(IV) chain in the BM of the invasive cancer was related to the tumor classification, TNM stages, and the expression of α2(IV) chain. The patients with α2(IV)‐negative and α6(IV)‐negative chains had significantly poorer prognosis than those with α2(IV)‐positive and α6(IV)‐positive/negative chains (P = 0.04).ConclusionsThe loss of α2(IV) and α6(IV) chains might be a useful prognostic factor in patients with EBDC. J. Surg. Oncol. 2013;107:402–407. © 2012 Wiley Periodicals, Inc.
Learning curve for cytoreductive surgery and hyperthermic intraperitoneal chemotherapy in peritoneal surface malignancies: Analysis of two centres
Authors: Kusamura Shigeki , Baratti Dario , Virzì Salvatore , Bonomi Serena , Iusco Domenico Rosario , Grassi Antonio , Hutanu Ionut , Deraco Marcello 
Published: August 2012

AbstractBackgroundWe assessed the learning curve (LC) of cytoreductive surgery (CRS) and hyperthermic intraperitoneal chemotherapy (HIPEC) in treating peritoneal surface malignancies (PSM) in two centers and evaluated in which extent surgical tutoring could abbreviate the learning process.MethodsSix hundred and forty‐one cases submitted to CRS using peritonectomy procedures and HIPEC were considered. After having overcome its own LC, the NCI of Milan has provided technical assistance to Bentivoglio's centre for the development of a new PSM program since 2003. The risk‐adjusted sequential probability ratio test (RA‐SPRT) was employed to assess the LC of the two centers. Outcomes were incomplete cytoreduction, G3‐5 morbidity (NCI‐CTCAE.v3) and procedure‐related mortality (PRM).ResultsRates of incomplete cytoreduction, G3‐5 morbidity, and PRM were 8.4%, 30.1%, and 3.9%, respectively, in the entire series. The breaking points of the LC concerning incomplete cytoreduction, G3‐5 morbidity, and PRM were achieved at 141, 158, and 144 cases, in the Milan's experience, and at 126, 134, and 60 cases in the Bentivoglio's experience.ConclusionsSurgical tutoring could substantially shorten the steep LC associated with CRS and HIPEC. Our data should be confirmed by further studies on LC focusing oncological outcomes. Other factors that could influence the length of learning process should be identified. J. Surg. Oncol. 2013;107:312–319. © 2012 Wiley Periodicals, Inc.