Efficient model chemistries for peptides. I. Split-valence Gaussian basis sets and the heterolevel approximation in RHF and MP2

We present an exhaustive study of more than 250 ab initio potential energy surfaces (PESs) of the model dipeptide HCO-L-Ala-NH2. The model chemistries (MCs) used are constructed as homo- and heterolevels involving possibly different RHF and MP2 calculations for the geometry and the energy. The basis sets used belong to a sample of 39 selected representants from Pople's split-valence families, ranging from the small 3-21G to the large 6-311++G(2df,2pd). The reference PES to which the rest are compared is the MP2/6-311++G(2df,2pd) homolevel, which, as far as we are aware, is the more accurate PES of a dipeptide in the literature. The aim of the study presented is twofold: On the one hand, the evaluation of the influence of polarization and diffuse functions in the basis set, distinguishing between those placed at 1st-row atoms and those placed at hydrogens, as well as the effect of different contraction and valence splitting schemes. On the other hand, the investigation of the heterolevel assumption, which is defined here to be that which states that heterolevel MCs are more efficient than homolevel MCs. The heterolevel approximation is very commonly used in the literature, but it is seldom checked. As far as we know, the only tests for peptides or related systems, have been performed using a small number of conformers, and this is the first time that this potentially very economical approximation is tested in full PESs. In order to achieve these goals, all data sets have been compared and analyzed in a way which captures the nearness concept in the space of MCs.Comment: 54 pages, 16 figures, LaTeX, AMSTeX, Submitted to J. Comp. Che

Reconstructed spatial resolution and contrast recovery with Bayesian penalized likelihood reconstruction (Q.Clear) for FDG-PET compared to time-of-flight (TOF) with point spread function (PSF)

BACKGROUND: Bayesian penalized likelihood reconstruction for PET (e.g., GE Q.Clear) aims at improving convergence of lesion activity while ensuring sufficient signal-to-noise ratio (SNR). This study evaluated reconstructed spatial resolution, maximum/peak contrast recovery (CRmax/CRpeak) and SNR of Q.Clear compared to time-of-flight (TOF) OSEM with and without point spread function (PSF) modeling. METHODS: The NEMA IEC Body phantom was scanned five times (3 min scan duration, 30 min between scans, background, 1.5-3.9 kBq/ml F18) with a GE Discovery MI PET/CT (3-ring detector) with spheres filled with 8-, 4-, or 2-fold the background activity concentration (SBR 8:1, 4:1, 2:1). Reconstruction included Q.Clear (beta, 150/300/450), "PSF+TOF4/16" (iterations, 4; subsets, 16; in-plane filter, 2.0 mm), "OSEM+TOF4/16" (identical parameters), "PSF+TOF2/17" (2 it, 17 ss, 2.0 mm filter), "OSEM+TOF2/17" (identical), "PSF+TOF4/8" (4 it, 8 ss, 6.4 mm), and "OSEM+TOF2/8" (2 it, 8 ss, 6.4 mm). Spatial resolution was derived from 3D sphere activity profiles. RC as (sphere activity concentration [AC]/true AC). SNR as (background mean AC/background AC standard deviation). RESULTS: Spatial resolution of Q.Clear150 was significantly better than all conventional algorithms at SBR 8:1 and 4:1 (Wilcoxon, each p < 0.05). At SBR 4:1 and 2:1, the spatial resolution of Q.Clear300/450 was similar or inferior to PSF+TOF4/16 and OSEM+TOF4/16. Small sphere CRpeak generally underestimated true AC, and it was similar for Q.Clear150/300/450 as with PSF+TOF4/16 or PSF+TOF2/17 (i.e., relative differences < 10%). Q.Clear provided similar or higher CRpeak as OSEM+TOF4/16 and OSEM+TOF2/17 resulting in a consistently better tradeoff between CRpeak and SNR with Q.Clear. Compared to PSF+TOF4/8/OSEM+TOF2/8, Q.Clear150/300/450 showed lower SNR but higher CRpeak. CONCLUSIONS: Q.Clear consistently improved reconstructed spatial resolution at high and medium SBR compared to PSF+TOF and OSEM+TOF, but only with beta = 150. However, this is at the cost of inferior SNR with Q.Clear150 compared to Q.Clear300/450 and PSF+TOF4/16/PSF+TOF2/17 while CRpeak for the small spheres did not improve considerably. This suggests that Q.Clear300/450 may be advantageous for the 3-ring detector configuration because the tradeoff between CR and SNR with Q.Clear300/450 was superior to PSF+TOF4/16, OSEM+TOF4/16, and OSEM+TOF2/17. However, it requires validation by systematic evaluation in patients at different activity and acquisition protocols

Qualitative and Semiquantitative Assessment of Exposure to Engineered Nanomaterials within the French EpiNano Program: Inter- and Intramethod Reliability Study

The relatively recent development of industries working with nanomaterials has created challenges for exposure assessment. In this article, we propose a relatively simple approach to assessing nanomaterial exposures for the purposes of epidemiological studies of workers in these industries. This method consists of an onsite industrial hygiene visit of facilities carried out individually and a description of workstations where nano-objects and their agglomerates and aggregates (NOAA) are present using a standardized tool, the Onsite technical logbook. To assess its reliability, we implemented this approach for assessing exposure to NOAA in workplaces at seven workstations which synthesize and functionalize carbon nanotubes. The prediction of exposure to NOAA using this method exhibited substantial agreement with that of the reference method, the latter being based on an onsite group visit, an expert’s report and exposure measurements (Cohen kappa = 0.70, sensitivity = 0.88, specificity = 0.92). Intramethod comparison of results for exposure prediction showed moderate agreement between the three evaluators (two program team evaluators and one external evaluator) (weighted Fleiss kappa = 0.60, P = 0.003). Interevaluator reliability of the semiquantitative exposure characterization results was excellent between the two evaluators from the program team (Spearman rho = 0.93, P = 0.03) and fair when these two evaluators’ results were compared with the external evaluator’s results. The project was undertaken within the framework of the French epidemiological surveillance program EpiNano. This study allowed a first reliability assessment of the EpiNano method. However, to further validate this method a comparison with robust quantitative exposure measurement data is necessary

Left ventricular function assessment by free-breathing magnetic resonance sequence with multiple excitations

OBJECTIVE: To evaluate the efficacy of free-breathing magnetic resonance sequence with three excitations in the determination of ventricular volumes and masses in individuals without breathholding. MATERIALS AND METHODS: Left ventricular volumes and masses determined in 32 healthy volunteers through two cine magnetic resonance imaging sequences were compared: the first sequence, traditionally utilized and considered as a standard, performed under apnea, with a single excitation, and the second one, with free-breathing and three excitations. Three observers at different levels of experience evaluated the agreement and reproducibility. Intraclass correlation coefficient, paired t-test, Bland-Altman plots and sign test were utilized for statistical analysis. RESULTS: According to the two most experienced observers, intraclass correlation coefficients were > 0.913, the paired t-test demonstrated P values > 0.05, Bland-Altman plots had differences randomly distributed around zero and the sign test descriptive levels were > 0.05. CONCLUSION: The sequence evaluated presents an excellent agreement and reproducibility as compared with the standard sequence, and can be utilized in patients with respiratory limitations.OBJETIVO: Avaliar a eficácia da sequência de ressonância magnética com três excitações, para obtenção de volumes e massas ventriculares, em indivíduos com respiração livre, sem apneia. MATERIAIS E MÉTODOS: Em 32 voluntários sadios, foram comparados os volumes e massas do ventrículo esquerdo, obtidos por meio de duas sequências de ressonância magnética em modo cine. A primeira, tradicionalmente utilizada e considerada padrão, em apneia e com excitação única, e a segunda, em respiração livre e com três excitações. Três leitores, com diferentes níveis de experiência, testaram a concordância e a reprodutibilidade. Para a análise estatística foram utilizados o coeficiente de correlação intraclasse, o teste t-pareado, os gráficos de Bland-Altman e o teste do sinal. RESULTADOS: Para os dois observadores mais experientes, os coeficientes de correlação intraclasse foram superiores a 0,913, assim como os níveis descritivos do teste t-pareado acima de 0,05, os gráficos de Bland-Altman com as diferenças distribuídas aleatoriamente em torno do zero e o teste do sinal com seu nível descritivo superior a 0,05. CONCLUSÃO: A sequência testada apresenta ótima concordância e reprodutibilidade em relação à sequência padrão, podendo ser aplicada em indivíduos com limitações respiratórias.Universidade Federal de São Paulo (UNIFESP) Escola Paulista de MedicinaColégio Brasileiro de Radiologia e Diagnóstico por ImagemUNIFESP, EPMSciEL

Biometric analysis of uterine cervix during pregnancy using transvaginal ultrasonography and magnetic resonance imaging

OBJECTIVE: To evaluate the uterine cervix length with magnetic resonance imaging in comparison with findings at transvaginal ultrasonography. MATERIALS AND METHODS: Twenty pregnant women between the 19th and 30th gestational weeks underwent magnetic resonance imaging and transvaginal ultrasonography for evaluation of their uterine cervix. Measurements by means of magnetic resonance imaging were performed by two specialists in imaging diagnosis for calculating the interobserver variability of the method. RESULTS: Calculation of the Pearson's correlation coefficient between measurements of the cervical length demonstrated a significant correlation between the results of both methods (r=0.628; p<0.01). The paired t test demonstrated no statistically significant difference between measurements obtained by transvaginal ultrasonography and magnetic resonance imaging (p=0.068). Interobserver agreement in cervical measurements by magnetic resonance imaging was high (a=0.96), demonstrating the reliability of the method. CONCLUSION: The comparison between both imaging methods in the evaluation of cervical biometry showed no statistically significant difference thus reinforcing the utilization of ultrasonography. However, in some cases where transvaginal ultrasonography is contraindicated, magnetic resonance imaging can be alternatively utilized for measurement of the cervical length.OBJETIVO: Avaliar o comprimento do colo uterino por meio da ressonância magnética e comparar aos achados da ultra-sonografia transvaginal. MATERIAIS E MÉTODOS: Foram realizados exames ultra-sonográficos e de ressonância magnética do colo uterino em 20 pacientes com idade gestacional entre 19 e 30 semanas. As medidas do colo obtidas pelo exame de ressonância magnética foram aferidas por dois especialistas em diagnóstico por imagem, para calcular a variabilidade interobservador do método. RESULTADOS: O cálculo do coeficiente de correlação de Pearson entre as medidas do comprimento cervical indicou correlação significante entre os métodos (r=0,628; p<0,01). A aplicação do teste t pareado não evidenciou diferença significativa entre as medidas aferidas pela ultra-sonografia transvaginal e ressonância magnética (p=0,068). A análise da variabilidade interobservador das medidas do colo obtidas pela ressonância magnética demonstrou alta confiabilidade do método (a=0,96). CONCLUSÃO: A comparação entre os dois métodos de imagem na avaliação da biometria cervical não apresentou diferença estatística, o que reforça a aplicação do exame ultra-sonográfico. Entretanto, em situações nas quais a ultra-sonografia transvaginal apresenta contra-indicações, o exame de ressonância magnética poderá apresentar-se como segunda opção para a avaliação do comprimento cervical.Centro de Diagnóstico por ImagemCentro de Treinamento de Ultra-SonografiaUniversidade Federal de São Paulo (UNIFESP) Escola Paulista de Medicina Departamento de ObstetríciaUniversidade Federal de São Paulo (UNIFESP) Escola Paulista de Medicina Programa de Pós-GraduaçãoUNIFESP, EPM, Depto. de ObstetríciaUNIFESP, EPM, Programa de Pós-GraduaçãoSciEL

Sustainable housing - a case study of heritage building in Hangzhou China

Surrounded by high-rise buildings, some two-storey buildings with black roofs are sited along the Xiaohe (Little River) in the north of Hangzhou, China. The buildings were originally built in the late Qing Dynasty (late 19th century) and restored in 2007 by the Hangzhou municipal government. The architectural materials used in the buildings are mainly concrete for the ground floor and timber to the first floor. Three buildings located at Xiaohe Historical Street were investigated to establish whether traditional buildings performed as well as modern buildings. Hourly temperature and humidity readings from September 2009 to August 2010 were recorded for the selected houses. It was concluded through comparisons that the restored heritage buildings provided similar thermal comfort and conditions to modern buildings

Comparison of the Automated Oscillometric Method With the Gold Standard Doppler Ultrasound Method to Access the Ankle-Brachial Pressure Index

Objective: Despite its screening interest, the ankle-brachial pressure index (ABPI) remains uncommon in general practice, because it needs training and specific devices as Doppler. Easier methods such as the use of automated oscillometric devices may facilitate the peripheral arterial diseases (PADs) screening. We wanted to assess the reliability of the automated oscillometric measurement of the ABPI, compared with the gold standard Doppler ultrasound measurement. Patients and Method: In 287 patients aged 65 years or older without diagnosed PAD, we performed ABPI measurements with oscillometric and Doppler devices. Reproducibility was assessed by the intraclass correlation coefficient of agreement (R) and the Bland and Altman method. Results: The intermethod reliability was bad (R = .346, 95% CI = (0.268-0.420)), with a large confidence interval of the individual differences between the 2 methods: 95% CI = (—0.183-0.346). Conclusion: Automatic oscillometric devices cannot be recommended as reliable methods for ABPI measurement

Observer variability of absolute and relative thrombus density measurements in patients with acute ischemic stroke

Introduction: Thrombus density may be a predictor for acute ischemic stroke treatment success. However, only limited data on observer variability for thrombus density measurements exist. This study assesses the variability and bias of four common thrombus density measurement methods by expert and non-expert observers. Methods: For 132 consecutive patients with acute ischemic stroke, three experts and two trained observers determined thrombus density by placing three standardized regions of interest (ROIs) in the thrombus and corresponding contralateral arterial segment. Subsequently, absolute and relative thrombus densities were determined using either one or three ROIs. Intraclass correlation coefficient (ICC) was determined, and Bland–Altman analysis was performed to evaluate interobserver and intermethod agreement. Accuracy of the trained observer was evaluated with a reference expert observer using the same statistical analysis. Results: The highest interobserver agreement was obtained for absolute thrombus measurements using three ROIs (ICCs ranging from 0.54 to 0.91). In general, interobserver agreement was lower for relative measurements, and for using one instead of three ROIs. Interobserver agreement of trained non-experts and experts was similar. Accuracy of the trained observer measurements was comparable to the expert interobserver agreement and was better for absolute measurements and with three ROIs. The agreement between the one ROI and three ROI methods was good. Conclusion: Absolute thrombus density measurement has superior interobserver agreement compared to relative density measurement. Interobserver variation is smaller when multiple ROIs are used. Trained non-expert observers can accurately and reproducibly assess absolute thrombus densities using three ROIs

Relationship of promising methods in the detection of anthracycline-induced cardiotoxicity in breast cancer patients

Purpose\ud It remains challenging to identify patients at risk of anthracycline-induced cardiotoxicity. To better understand the different risk-stratifying approaches, we evaluated 123I-metaiodobenzylguanidine (123I-mIBG) scintigraphy and its interrelationship with conventional echocardiography, 2D strain imaging and several biomarkers.\ud \ud Methods\ud We performed 123I-mIBG scintigraphy, conventional and strain echocardiography and biomarker (NT-proBNP, TNF-α, galectin-3, IL-6, troponin I, ST-2 and sFlt-1) assessment in 59 breast cancer survivors 1 year after anthracycline treatment. Interobserver and intermethod variability was calculated on planar and SPECT 123I-mIBG scintigraphy, using the heart/mediastinum (H/M) ratio and washout (WO). Pearson’s r and multivariate analyses were performed to identify correlations and independent predictors of 123I-mIBG scintigraphy results.\ud \ud Results\ud Delayed planar anterior whole-heart ROI (WH) H/M ratios and WO were the most robust 123I-mIBG parameters. Significant correlations were observed between 123I-mIBG parameters and several conventional echo parameters, global longitudinal and radial strain (GLS and GRS) and galectin-3. The highest Pearson’s r was observed between delayed H/M ratio and GRS (Pearson’s r 0.36, p = 0.01). Multivariate analysis showed that GRS was the only independent predictor of the delayed WH H/M ratio (p = 0.023).\ud \ud Conclusion\ud The delayed planar H/M ratio is the most robust 123I-mIBG parameter. It correlates with several conventional echocardiographic parameters, GLS, GRS and galectin-3. Of these, only GRS predicts the H/M ratio