bluuebunny/crossref_metadata_2025_split huggingface dataset:
The pKa Cooperative: A collaborative effort to advance structure‐based calculations of pKa values and electrostatic effects in proteins
Authors: Nielsen Jens E. , Gunner M. R. , García‐Moreno E. Bertrand 
Published: September 2011

AbstractThe pKa Cooperative (http://www.pkacoop.org) was organized to advance development of accurate and useful computational methods for structure‐based calculation of pKa values and electrostatic energies in proteins. The Cooperative brings together laboratories with expertise and interest in theoretical, computational, and experimental studies of protein electrostatics. To improve structure‐based energy calculations, it is necessary to better understand the physical character and molecular determinants of electrostatic effects. Thus, the Cooperative intends to foment experimental research into fundamental aspects of proteins that depend on electrostatic interactions. It will maintain a depository for experimental data useful for critical assessment of methods for structure‐based electrostatics calculations. To help guide the development of computational methods, the Cooperative will organize blind prediction exercises. As a first step, computational laboratories were invited to reproduce an unpublished set of experimental pKa values of acidic and basic residues introduced in the interior of staphylococcal nuclease by site‐directed mutagenesis. The pKa values of these groups are unique and challenging to simulate owing to the large magnitude of their shifts relative to normal pKa values in water. Many computational methods were tested in this first Blind Prediction Challenge and critical assessment exercise. A workshop was organized in the Telluride Science Research Center to objectively assess the performance of many computational methods tested on this one extensive data set. This volume of Proteins: Structure, Function, and Bioinformatics introduces the pKa Cooperative, presents reports submitted by participants in the Blind Prediction Challenge, and highlights some of the problems in structure‐based calculations identified during this exercise. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Electrical transport in strained MgxZn1−xO:P thin films grown by pulsed laser deposition on ZnO(000‐1)
Authors: Brandt Matthias , Bonholzer Michael , Stölzel Marko , Benndorf Gabriele , Spemann Daniel , Lorenz Michael , Grundmann Marius 
Published: September 2011

AbstractPhosphorus‐doped MgxZn1−xO thin films with various Mg content (0.07 ≤ x ≤ 0.28) and up to 0.7 at% P were grown on ZnO(000‐1) single crystals by pulsed laser deposition (PLD). In dependence on the dopant concentrations, tensile or compressively strained, in‐plane lattice matched, i.e., pseudomorphic growth of the MgZnO:P films was confirmed by high‐resolution X‐ray diffraction (HR‐XRD). All investigated, high‐quality MgZnO:P films are n‐type, also after post‐growth annealing at 850 °C. From the Hall analysis the activation energy of the dominating donors was derived, yielding values of up to 345 meV for high oxygen partial pressure during growth, and shallow donors with an activation energy of about 30 meV for low oxygen pressure. The Hall‐mobility of the MgxZn1−xO:P films at a temperature of 65 K was as high as 740 cm2/Vs, and reached values up to 190 cm2/Vs at room temperature, close to the best values reported for bulk ZnO.
Flow‐dependent background‐error covariances for a convective‐scale data assimilation system
Authors: Brousseau Pierre , Berre Loïk , Bouttier François , Desroziers Gérald 
Published: September 2011

AbstractAROME‐France is a convective‐scale numerical weather prediction system which has been running operationally at Météo‐France since the end of 2008. It uses a 3D‐Var assimilation scheme in order to determine its initial conditions. Static background‐error covariances are calculated for the 3D‐Var using differences between AROME forecasts from an ensemble data assimilation. In this study, the covariance calculation is generalized in order to estimate time‐dependent background‐error covariances. A six‐member ensemble is shown to provide robust covariance estimates in the context of the considered homogeneous covariance formulation. There is significant day‐to‐day variability in the variances, autocorrelations, and cross‐correlations of background errors. This variability is linked to the meteorological conditions over the AROME‐France model domain. The benefits of using flow‐dependent background‐error covariances, instead of static ones, are shown using assimilation diagnostics and measures of forecast performance. Copyright © 2011 Royal Meteorological Society
Ensemble prediction and parameter estimation system: the concept
Authors: Järvinen Heikki , Laine Marko , Solonen Antti , Haario Heikki 
Published: September 2011

AbstractThis paper discusses algorithmic estimation of numerical weather prediction (NWP) model closure parameters which appear in physical parametrizations of sub‐grid scale processes. Currently, these parameters are specified manually. Our hypothesis is that the NWP model forecast skill is sensitive to the specified parameter values. Therefore some parameter value combinations score better than others, but it is very demanding to manually specify the optimal combination. First, we approximate the number of test forecasts that would be needed to estimate the posterior probability densities of a limited number of closure parameters, in a spirit of the Bayesian parameter estimation approach. Second, we discuss various options to accommodate the related huge computational task; we end up proposing that operational ensemble prediction might be a potential host. Third, we analyse the ensemble prediction system characteristics from the parameter estimation point of view. We rule out various standard parameter estimation methods; instead we suggest an estimation concept that can be on‐line coupled with existing ensemble prediction systems to utilize the operational ensemble simulations. Thus practically no additional computations are introduced. Such a method, the ensemble prediction and parameter estimation system (EPPES), is developed here and demonstrated in low‐order numerical tests in the companion paper (Laine M, Solonen A, Haario H, Järvinen H. 2011. Q. J. R. Meteorol. Soc. DOI: 10.1002/qj.922). Copyright © 2011 Royal Meteorological Society
Quantitative analysis of remedial approaches, costs, and time required to remediate dry cleaner sites
Authors: Luis Steven J. , King Stacey L. , Zandipour Nazgol , Koenigsberg Stephen S. 
Published: September 2011

AbstractThis article presents an analysis of remedial approaches, costs, and time required to remediate dry cleaner sites in the United States based on data compiled by the State Coalition for the Remediation of Dry Cleaners (SCRD). Trends in soil and groundwater remedy selection are identified and discussed. Median costs and the time required to remediate dry cleaner sites are presented. In addition, median costs and the duration of soil and groundwater remediation for the most widely used remedial approaches are reported. The analysis is intended to serve the needs of stakeholders, including responsible parties, consultants, regulators, and litigants, as well as real estate developers, banks, and other holders of portfolios of impacted dry cleaner sites by providing quantitative results useful for planning and transactional analysis. © 2011 Wiley Periodicals, Inc.
Field‐scale uranium (VI) bioimmobilization monitored by lipid biomarkers and 13C‐acetate incorporation
Authors: Peacock Aaron D. , Hedrick David B. , Long Philip E. , Nevin Kelly P. , Resch Charles T. , Lovley Derek R. , White David C. 
Published: September 2011

AbstractAt the Old Rifle uranium mill‐tailing site in eastern Colorado, a test of subsurface amendment with acetate to stimulate the reductive immobilization of uranium was monitored by using lipid biomarker analysis and incorporation of 13C‐labeled acetate into lipid biomarkers. Both sediment and groundwater samples were analyzed. Within 7 days of acetate addition, groundwater microbial biomass increased by a factor of 5, and remained higher than control values in most samples for the 28 days sampled. At 29 days after the beginning of acetate amendment, 4 of 12 sediment samples had microbial biomass greater than the 95 percent confidence interval of controls. The mole percents of the phospholipid fatty acids 16:1ω7c and 16:1ω5c increased over control values upon acetate amendment, and incorporated high levels of 13C from labeled acetate in groundwater and sediment samples. 16:1ω7c is a biomarker for Geobacter, and evidence is provided that 16:1ω5c represents an unidentified iron‐reducing bacterium, probably a member of the Desulfobulbaceae. Biomarkers for organisms other than iron‐reducing bacteria, iso‐ and anteiso‐branched fatty acids and 18:1ω9c, decreased upon acetate amendment, and had their highest stable isotope incorporation at least 4 days after labeled acetate amendment ended, evidence for carbon‐sharing between iron‐reducers and other microorganisms. © 2011 Wiley Periodicals, Inc.
Monte Carlo simulation of secondary electron images for real sample structures in scanning electron microscopy
Authors: Zhang P. , Wang H. Y. , Li Y. G. , Mao S. F. , Ding Z. J. 
Published: September 2011

AbstractMonte Carlo simulation methods for the study of electron beam interaction with solids have been mostly concerned with specimens of simple geometry. In this article, we propose a simulation algorithm for treating arbitrary complex structures in a real sample. The method is based on a finite element triangular mesh modeling of sample geometry and a space subdivision for accelerating simulation. Simulation of secondary electron image in scanning electron microscopy has been performed for gold particles on a carbon substrate. Comparison of the simulation result with an experiment image confirms that this method is effective to model complex morphology of a real sample. SCANNING 34: 145–150, 2012. © 2011 Wiley Periodicals, Inc.
Cellular Uptake and Cytotoxic Impact of Chemically Functionalized and Polymer‐Coated Carbon Nanotubes
Authors: Ali‐Boucetta Hanene , Al‐Jamal Khuloud T. , Müller Karin H. , Li Shouping , Porter Alexandra E. , Eddaoudi Ayad , Prato Maurizio , Bianco Alberto , Kostarelos Kostas 
Published: September 2011

AbstractThe impact of nanomaterials such as carbon nanotubes on biological matter is a topic of increasing interest and concern and requires a multifaceted approach to be resolved. A modified cytotoxic (lactate dehydrogenase (LDH)) assay is developed in an attempt to offer a valid and reliable methodology for screening carbon nanotube toxicity in vitro. Two of the most widely used types of surface‐modified multiwalled carbon nanotubes (MWNTs) are tested: ammonium‐functionalized MWNTs (MWNT‐NH3+) and Pluronic F127 coated MWNTs (MWNT:F127). Chemically functionalized MWNTs show significantly greater cellular uptake into lung epithelial A549 cells compared to the non‐covalently Pluronic F127‐coated MWNTs. In spite of this, MWNT:F127 exhibit enhanced cytotoxicity according to the modified LDH assay. The validity of the modified LDH assay is further validated by direct comparison with other less reliable or accurate cytotoxicity assays. These findings indicate the reliability of the modified LDH assay as a screening tool to assess carbon nanotube cytotoxicity and illustrate that high levels of carbon nanotube cellular internalization do not necessarily lead to adverse responses.
Effect of Nitrogen and Niobium on the Structure and Secondary Hardening of Super Hard High Speed Tool Steel
Authors: Halfa Hossam , Eissa Mamdouh , El‐Fawakhry Kamal , Mattar Taha 
Published: September 2011

AbstractHigh‐speed steels have been used mostly for multi‐point cutting tools and for plastic working tools. High speed steels are ferrous based alloys of the Fe‐C‐X multi‐component system where X represents a group of alloying elements comprising mainly Cr, W or Mo, V, and Co. The properties of these steels can be improved by modifying their chemical composition or the technology of their production. One of the new trends in modifying the tool steels chemical composition consists in the addition of niobium and nitrogen. In this work, the effects of niobium and nitrogen on morphology of carbides and secondary hardening temperature of investigated high speed tool steels were studied. This experimental work shows that, the conventional ingots have many types of carbides of different shapes and sizes precipitate on the boundary together with thick needle like carbides. On the contrary, for nitrogen steel, the nitrogen alloying leads to form dense, fine and well distributed microstructure. While, on the case of niobium alloying, single carbide (MC), and different types of eutectic carbides were precipitated which have a major effect on the secondary hardening temperature.
Correlation of tape location and tension with surgical outcome after transobturator suburethral tape procedures
Authors: Yang J.‐M. , Yang S.‐H. , Huang W.‐C. , Tzeng C.‐R. 
Published: September 2011

AbstractObjectiveTo explore, using 4D ultrasound, the importance of location and tension of transobturator sub‐ urethral tape (TOT) with respect to surgical outcome.MethodsEnrolled into the study were 56 women who had undergone TOT placement in the treatment of urodynamic stress incontinence. Tape location and tension were assessed by 4D ultrasound with the women at rest, during straining and during coughing. Ultrasound parameters representing tape location included the sagittal tape–symphysis pubis distance (sTSD), sagittal tape–symphysis pubis angle (sTSA) and tape percentile (an indication of tape position along the urethra with respect to urethral length), while those representing tape tension included urethral encroachment, sagittal tape–urethra distances at the upper end (sTUDu), center (sTUDc) and lower end (sTUDl) of the tape and axial urethral central echolucent area at the tape center (aUCEAc).ResultsIn women in whom the tape procedure had been successful, during increased intra‐abdominal pressure sTSA and the incidence of urethral encroachment increased, while sTUDu, sTUDc, sTUDl and aUCEAc decreased. Compared with those reporting no stress urinary incontinence (SUI) symptoms, women who reported SUI postoperatively had lower tape percentile. Women with SUI postoperatively demonstrated no manifestation on ultrasound of urethral encroachment at rest or during increased intra‐abdominal pressure. Women with postoperative overactive bladder (OAB) symptoms had shorter resting sTSD and larger resting sTSA than did women without OAB symptoms. Women reporting postoperative de novo or worsening voiding difficulty had larger resting sTSA and higher incidence of urethral encroachment at rest than did women without this difficulty.ConclusionsBoth tape location and tape tension are associated with surgical outcome of TOT procedures. Assessment of tape location and tension can be achieved using 4D ultrasound. Copyright © 2012 ISUOG. Published by John Wiley & Sons, Ltd.
Adenoma malignum of the uterine cervix: ultrasonographic findings in 11 patients
Authors: Park S. B. , Moon M. H. , Hong S. R. , Lee M. S. , Cho H. C. , Han B. H. , Lim K. T. 
Published: September 2011

AbstractObjectiveTo evaluate the ultrasonographic features of adenoma malignum, a minimal deviation adenocarcinoma of the uterine cervix.MethodsEighteen consecutive patients with pathologically confirmed adenoma malignum were enrolled in this study at two institutions. Preoperative ultrasound examination was performed and the results were available in 11 patients. We analyzed retrospectively the gray‐scale ultrasound findings for the following morphologic characteristics: cervical enlargement, as well as size, location and ultrasonographic characteristics of lesions. In five patients we also evaluated Doppler features with regard to intralesional vascularity.ResultsThe cervix was enlarged in 73% (8/11) of cases. The mean greatest tumor diameter was 4.2 (range, 2.5–6.8) cm. In five (45%) cases, the cervix was completely infiltrated by the tumor. At gray‐scale ultrasound examination, three (27%) tumors were multilocular lesions, four (36%) were multilocular lesions with solid components and four (36%) were solid lesions. In the multilocular lesions with or without a solid component, locules tended to be 1 cm or less in average diameter (86%, 6/7 cases) and there tended to be 11–20 in number (57%, 4/7 cases). In most (57%, 4/7) cases the locular fluid was homogeneously hypoechoic. Most (75%, 3/4) solid lesions manifested heterogeneous echogenicity. The five (100%) tumors examined with Doppler manifested moderate or abundant color content on color or power Doppler.ConclusionsAdenoma malignum can appear sonographically as solid, multilocular and multilocular solid cervical lesions. Awareness of its clinical and ultrasonographic features might improve diagnosis before surgery. Copyright © 2011 ISUOG. Published by John Wiley & Sons, Ltd.
Comparison of the Survival Difference Between AJCC 6th and 7th Editions for Gastric Cancer Patients
Authors: Fang Wen‐Liang , Huang Kuo‐Hung , Chen Jen‐Hao , Lo Su‐Shin , Hsieh Mao‐Chih , Shen King‐Han , Li Anna Fen‐Yau , Niu Dau‐Ming , Chiou Shih‐Hwa , Wu Chew‐Wun 
Published: September 2011

AbstractBackgroundThe AJCC 7th edition changes the classification of T‐ and N‐factors and the TNM stage of gastric cancer. We evaluated its prognostic impact.MethodsFrom December 1987 to December 2006, a total of 1,380 patients underwent curative surgery for gastric cancer at the Department of Surgery, Taipei Veterans General Hospital, with a retrieved lymph node number ≥15. Survival was compared for disease classified according to the AJCC 6th and 7th editions.ResultsThere is a significant difference in 5‐year survival between T2 and T3 gastric cancer classified according to the AJCC 7th edition (75.2 vs. 54.9%, p < 0.001), as well as between N1 and N2 (71.4 vs. 44.1%, p < 0.001). Although patients with N3a had a better 5‐year survival than did those with N3b (27.6 vs. 11.3%, p < 0.001), the N3 categories were combined and not applied in the TNM stage in the 7th edition. Multivariate analysis using Cox’s proportional hazards model with a forward logistics regression stepwise procedure demonstrates that age, N category of 6th edition, and T and N categories of 7th edition are independent prognostic factors; however, T category of 6th edition is no longer significant. Furthermore, the discriminative power of survival difference between each TNM stage seems to be comparable between the 6th and 7th editions.ConclusionsThe AJCC 7th edition provides a more stratified survival difference in staging of gastric cancer. Future division of N3a and N3b in the classification of the TNM stage is recommended.
A prospective, multicentre, open-label study to evaluate the effectiveness of aripiprazole in the treatment of a broad range of patients with schizophrenia
Authors: Peuskens J. , Bervoets C. , Kok F. , Delatte B. , Touquet G. , Gillain B. , de Patoul A. , Halkin V. , Loze J.-Y. , Vansteelandt K. , Constant E. 
Published: September 2011

AbstractPurposeThe aim of this study is to evaluate the effectiveness of 12-week treatment with aripiprazole in a broad range of patients suffering from schizophrenia by using a variety of physicians, caregivers and patients scales.Subjects and methodsA total of 361 in- or outpatients who met Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition (DSM-IV) criteria for schizophrenia received open-label aripiprazole (10–30mg per day) in this 12-week, prospective, multicentre, uncontrolled study. The primary endpoint was the Clinical Global Impression-Improvement (CGI-I) scale which measured effectiveness of study medication, including efficacy, safety and tolerability. A variety of physician-, patient- and caregiver-rated parameters were measured to gain a complete view of the effectiveness of aripiprazole.ResultsThe effectiveness of aripiprazole treatment was demonstrated in a broad range of schizophrenia patients (CGI-I score of 3.0; 95% confidence interval: 2.8, 3.2: last observation carried forward [LOCF]) as the upper bound of the 95% CI was less than 4 (score of “no change”). Both patient and caregiver PGI-I scores (LOCF: 95% CI: 2.79, 3.09 and, 95% CI: 2.74, 3.17, respectively) corroborate this finding. Aripiprazole had a positive effect on disease severity by study end, as assessed by an increase of the (physician-rated) CGI-S scores, with 57.3% of patients having improved disease, one-third maintaining their condition (30.8%) and 11.3% with worsening symptoms (LOCF). The Investigator Assessment Questionnaire (IAQ) showed a great improvement (>50% of patients). Patients reported significantly improved quality of life and overall, 71% of patients and 67% of caregivers preferred aripiprazole to their previous antipsychotic medication (LOCF; P<0.0001 over time).ConclusionAripiprazole was effective in a broad range of patients with schizophrenia.
Characteristics of Subjects With Schizophrenia Spectrum Disorder With and Without Antipsychotic Medication – a 10-Year Follow-Up of the Northern Finland 1966 Birth Cohort Study
Authors: Moilanen J. , Haapea M. , Miettunen J. , Jääskeläinen E. , Veijola J. , Isohanni M. , Koponen H. 
Published: September 2011

AbstractObjectiveTo estimate the prevalence of non-medicated subjects having schizophrenia spectrum disorder and to study how they differ from medicated subjects in terms of sociodemographic and illness-related variables. We also aim to find the predictors for successful antipsychotic withdrawal.MethodsData of 70 subjects with schizophrenic psychoses (mean duration of illness 10.4 years) from the Northern Finland 1966 Birth Cohort were gathered by interview at the age of 34 and from hospital records. The stability of remission was assessed by comparing hospitalization rates between non-medicated and medicated subjects over an 8.7-year additional follow-up period.ResultsTwenty-four (34%) subjects were currently not receiving medication. They were more often males, less often on a disability pension, more often in remission, and had better clinical outcomes. Relapses during the follow-up were equally frequent between non-medicated and medicated subjects (47% vs. 56%). Not having been hospitalised during previous 5 years before the interview predicted long-term successful antipsychotic withdrawal without relapse.ConclusionsDespite a lack of precise predictors, there might be subgroup of schizophrenia spectrum subjects who do not need permanent antipsychotic medication, and a fewer previous psychiatric treatments may indicate such a subgroup.