Assisted Diagnosis of Cervical Intraepithelial Neoplasia (CIN)

This paper introduces an automated computer- assisted system for the diagnosis of cervical intraepithelial neoplasia (CIN) using ultra-large cervical histological digital slides. The system contains two parts: the segmentation of squamous epithelium and the diagnosis of CIN. For the segmentation, to reduce processing time, a multiresolution method is developed. The squamous epithelium layer is first segmented at a low (2X) resolution. The boundaries are further fine tuned at a higher (20X) resolution. The block-based segmentation method uses robust texture feature vectors in combination with support vector machines (SVMs) to perform classification. Medical rules are finally applied. In testing, segmentation using 31 digital slides achieves 94.25% accuracy. For the diagnosis of CIN, changes in nuclei structure and morphology along lines perpendicular to the main axis of the squamous epithelium are quantified and classified. Using multi-category SVM, perpendicular lines are classified into Normal, CIN I, CIN II, and CIN III. The robustness of the system in term of regional diagnosis is measured against pathologists' diagnoses and inter-observer variability between two pathologists is considered. Initial results suggest that the system has potential as a tool both to assist in pathologists' diagnoses, and in training.

Breit-Pauli R-matrix calculation of fine-structure effective collision strengths for the electron impact excitation of Mg V

Context. Electron-impact excitation collision strengths are required for the analysis and interpretation of stellar observations.
Aims. This calculation aims to provide effective collision strengths for the Mg V ion for a larger number of transitions and for a greater temperature range than previously available, using collision strength data that include contributions from resonances.
Methods. A 19-state Breit-Pauli R-matrix calculation was performed. The target states are represented by configuration interaction wavefunctions and consist of the 19 lowest LS states, having configurations 2s22p4, 2s2p5, 2p6, 2s22p33s, and 2s22p33p. These target states give rise to 37 fine-structure levels and 666 possible transitions. The effective collision strengths were calculated by averaging the electron collision strengths over a Maxwellian distribution of electron velocities.
Results. The non-zero effective collision strengths for transitions between the fine-structure levels are given for electron temperatures in the range = 3.0 - 7.0. Data for transitions among the 5 fine-structure levels arising from the 2s22p4 ground state configurations, seen in the UV range, are discussed in the paper, along with transitions in the EUV range – transitions from the ground state 3P levels to 2s2p5?3P levels. The 2s22p4?1D–2s2p5?1P transition is also noted. Data for the remaining transitions are available at the CDS.

Electron-impact excitation of Fe II: Effective collision strengths for optically allowed fine-structure transitions

In this paper. we present collision strengths and Maxwellian averaged effective collision strengths for the electron-impact excitation of Fe II. We consider specifically the optically allowed lines for transitions from the 3d(6)4s and 3d(7) even parity configuration states to the 3d(6)4p odd parity configuration levels. The parallel suite of Breit-Pauli codes are utilized to compute the collision cross-sections where relativistic effects are included explicitly in both the target and the scattering approximation. A total of 100 LS or 262-jj levels formed from the basis configurations 3d(6)4s, 3d(7) and 3d(6)4p were included in the wave-function representation of the target, including all doublet. quartet and sextet terms. The Maxwellian averaged effective collision strengths are computed across a wide range of electron temperatures from 100 to 100,000 K, temperatures of importance in astrophysical and plasma applications. A detailed comparison is made with previous works and significant differences were found to occur for some of the transitions considered. We conclude that in order to obtain converged collision strengths and effective collision strengths for these allowed transitions it is necessary to include contributions from partial waves up to L = 50 explicitly in the calculation, and in addition, account for contributions from even higher partial waves through a "top up" procedure.

Effective collision strengths for electron-impact excitation of S X

Effective collision strengths computed by the R-matrix method are presented for the electron-impact excitation of nitrogen-like S X. The total wave function used in the expansion includes the lowest 11 eigenstates of S X which arise from the 2s(2)2p(3), 2s2p(4), 2p(5) and 2s(2)2p(2)3s configurations. These 11 LS target states correspond to 22 fine-structure levels, giving 231 possible transitions. All the effective collision strengths for these transitions are tabulated in the range log T(K) = 4.6 to log T(K) = 6.7. The energy level values and oscillator strengths for allowed transitions are also tabulated. The effective collision strengths were calculated by averaging the electron collision strengths over a Maxwellian distribution of velocities. The present effective collision strengths are the only results currently available for these fine-structure transition rates. (C) 2000 Academic Press.

Partial agonism, neutral antagonism, and inverse agonism at the human wild-type and constitutively active cholecystokinin-2 receptors

Cholecystokinin receptor-2 (CCK2R) is a G protein receptor that regulates a number of physiological functions. Activation of CCK2R and/or expression of a constitutively active CCK2R variant may contribute to human diseases, including digestive cancers. Search for antagonists of the CCK2R has been an important challenge during the last few years, leading to discovery of a set of chemically distinct compounds. However, several early-discovered antagonists turned out to be partial agonists. In this context, we carried out pharmacological characterization of six CCK2R antagonists using COS-7 cells expressing the human CCK2R or a CCK2R mutant having a robust constitutive activity on inositol phosphates production, and we investigated the molecular mechanisms which, at a CCK2R binding site, account for these features. Results indicated that three compounds, 3R(+)-N-(2,3-dihydro-1-methyl-2-oxo-5-phenyl-1H-1,4-benzodiazepin-3- yl)-N'-(3-methylphenyl)urea (L365,260), 4-{[2-[[3-(lH-indol-3-yl)-2- methyl-1-oxo-2-[[[1.7.7-trimethyl-bicyclo[2.2.1]hept-2-yl)-oxy]carbonyl]amino] propyl]amino]-1-phenylethyl]amino-4-oxo-[lS-la.2[S*(S*)]4a]} -butanoate N-methyl-D-glucamine (PD135, 158), and (R)-1-naphthalenepropanoic acid, b-[2-[[2-(8-azaspiro-[4.5]dec-8-ylcarbonyl)-4,6-dimethylphenyl]amino]-2- oxoethyl] (CR2945), were partial agonists; one molecule, 1-[(R)-2,3-dihydro-1- (2,3-dihydro-1-(2-methylphenacyl)-2-oxo-5-phenyl-1H-1,4-benzodiazepin-3-yl] -3-(3-methylphenyl)urea (YM022), was a neutral antagonist; and two compounds, N-(+)-[1-(adamant-1-ylmethyl)-2,4-dioxo-5-phenyl2,3,4,5-tetrahydro-1H-1, 5-benzodiazepin-3-yl]-N'-phenylurea (GV150,013X) and ([(N-[methoxy-3 phenyl] N-[N-methyl N-phenyl carbamoylmethyl], carbomoylmethyl)-3 ureido]-3-phenyl)2-propionic acid (RPR101,048), were inverse agonists. Furthermore, target- and pharmacophore-based docking of ligands followed by molecular dynamic simulation experiments resulted in consistent motion of aromatic residues belonging to a network presumably important for activation, thus providing the first structural explanations for the different pharmacological profiles of tested compounds. This study confirms that several referenced so-called antagonists are in fact partial agonists, and because of this undesired activity, we suggest that newly generated molecules should be preferred to efficiently block CCK2R-related physiological effects. Furthermore, data on the structural basis for the different pharmacological features of CCK2R ligands will serve to further clarify CCK2R mechanism of activation. Copyright © 2006 The American Society for Pharmacology and Experimental Therapeutics.

Electron-impact excitation of Ni II: Effective collision strengths for optically allowed fine-structure transitions

In this paper, we present collision strengths and Maxwellian averaged effective collision strengths for the electron-impact excitation of Ni II. Attention is expressly concentrated on the optically allowed fine-structure transitions between the 3d 9, 3d 84s, and 3d 74s 2 even parity levels and the 3d 84p and 3d 74s 4p odd parity levels. The parallel RMATRXII R-matrix package has been recently extended to allow for the inclusion of relativistic fine-structure effects. This suite of codes has been utilized in conjunction with the parallel PSTGF and PSTGICF programs in order to compute converged total collision strengths for the allowed transitions with which this study is concerned. All 113 LS terms identified with the 3d 9, 3d 84s, 3d 74s 2, 3d 84p, and 3d 74s 4p basis configurations were included in the target wavefunction representation, giving rise to a sophisticated 295 jj-level, 1930 coupled channel scattering complex. Maxwellian averaged effective collision strengths have been computed at 30 individual electron temperatures ranging from 30 to 1,000,000 K. This range comfortably encompasses all temperatures significant to astrophysical and plasma applications. The convergence of the collision strengths is exhaustively investigated and comparisons are made with previous theoretical works, where significant discrepancies exist for the majority of transitions. We conclude that intrinsic in achieving converged collision strengths and thus effective collision strengths for the allowed transitions is the combined inclusion of contributions from the (N + 1) partial waves extending to a total angular momentum value of L = 50 and further contributions from even higher partial waves accomplished by employing a "top-up" procedure.

An efficient feature selection method for mobile devices with application to activity recognition

This paper presents a feature selection method for data classification, which combines a model-based variable selection technique and a fast two-stage subset selection algorithm. The relationship between a specified (and complete) set of candidate features and the class label is modelled using a non-linear full regression model which is linear-in-the-parameters. The performance of a sub-model measured by the sum of the squared-errors (SSE) is used to score the informativeness of the subset of features involved in the sub-model. The two-stage subset selection algorithm approaches a solution sub-model with the SSE being locally minimized. The features involved in the solution sub-model are selected as inputs to support vector machines (SVMs) for classification. The memory requirement of this algorithm is independent of the number of training patterns. This property makes this method suitable for applications executed in mobile devices where physical RAM memory is very limited. An application was developed for activity recognition, which implements the proposed feature selection algorithm and an SVM training procedure. Experiments are carried out with the application running on a PDA for human activity recognition using accelerometer data. A comparison with an information gain based feature selection method demonstrates the effectiveness and efficiency of the proposed algorithm.

Structural and kinetic studies of spin crossover in an Iron(II) complex with a novel tripodal ligand

Configurational and ligand conformational influences on the kinetics of (1)A(1) reversible arrow T-5(2) spin crossover in the Fe(II) complex with the novel tripodal ligand, 1,1,1-tris((N-(2-pyridylmethyl)-N-methylamino)methyl)ethane (tptMetame), have been explored. Despite having six chelate rings and three chiral nitrogen atoms, only one enantiomeric pair of isomers, Delta, SSS, and Lambda, RRR, of the complex ion is observed. The conformation of the three rings forming the upper ''cap'' of the complex structure can be assigned delta or lambda with respect to the 3-fold molecular axis. X-ray data at 300 and 153 K, above and below the critical temperature for the spin transition, show that the conformation of the ligand ''cap'' is the same as the absolute configuration of the complex, with the same Lambda lambda(CAP)(or Delta delta(CAP)) combination prevailing for both the LS ((1)A(1)) and HS (T-5(2)) isomers. Molecular mechanics calculations further show that the ligand energy remains lowest for this Lambda lambda(CAP) (or Delta delta(CAP)) combination at all Fe-N distances over the range spanning the LS and HS isomers. Measurements of the spin crossover relaxation time have been carried out in solution over the temperature range 293-170 K. The observed monophasic relaxation traces are also consistent with the absolute configuration of the complex remaining unaltered during the spin crossover.

Electron-impact excitation of CrII: A theoretical calculation of effective collision strengths for optically allowed transitions.

In this paper, we present electron-impact excitation collision strengths and Maxwellian averaged effective collision strengths for the complicated iron-peak ion Cr II. We consider specifically the allowed lines for transitions from the 3d(5) and 3d(4)4s even parity configuration states to the 3d(4)4p odd parity configuration levels. The parallel suite of R-Matrix packages, RMATRX II, which have recently been extended to allow for the inclusion of relativistic effects, were used to compute the collision cross sections. A total of 108 LS pi/280 J pi levels from the basis configurations 3d(5), 3d(4)4s, and 3d(4)4p were included in the wavefunction representation of the target including all doublet, quartet, and sextet terms. Configuration interaction and correlation effects were carefully considered by the inclusion of seven more configurations and a pseudo-corrector (4d) over bar type orbital. The 10 configurations incorporated into the Cr II model thus listed are 3d(5), 3d(4)4s, 3d(4)4p, 3d(3)4s(2), 3d(3)4p(2), 3d(3)4s4p, 3d(4)(4d) over bar, 3d(3)4s (4d) over bar, 3d(3)4p (4d) over bar, and 3d(3)(4d) over bar (2), constituting the largest Cr II target model considered to date in a scattering calculation. The Maxwellian averaged effective collision strengths are computed for a wide range of electron temperatures 2000-100,000 K which are astrophysically significant. Care has been taken to ensure that the partial wave contributions to the collision strengths for these allowed lines have converged with "top-up" from the Burgess-Tully sum rule incorporated. Comparisons are made with the results of Bautista et al. and significant differences are found for some of the optically allowed lines considered.

Spin-orbit effects on photoionization-produced alignment of the Ar+ 3p(4)(P-3)4p levels

We have determined photoionization spectra of Ar with excitation of the 3p(4)(P-3)4p states emphasizing the effects of two different classes of Ar+ spin-orbit interactions. The spin-orbit splitting of each Ar+ state adequately describes the resonant excitation of the quartet states of Ar+, and gives Ar photoionization cross sections with excitation of the 3p4(3P)4p P-2(3/2)o and P-4(5/2)o levels of Ar+ in sufficiently good agreement with experiment to identify the observed resonances and to estimate the excitation strengths. In addition, we demonstrate the importance of spin-orbit induced mixing of different Ar+ LS-coupled states for observables such as the alignment of the 3p(4)(P-3)4p P-4(5/2)o level and the excitation of Rydberg series converging to the 3p(4)(P-3)4p S-2(o) and S-4(o) thresholds.

Electron-impact excitation of Fe II

We report in this paper the computation of accurate total collision strengths and effective collision strengths for electron-impact excitation of FeII, using the parallel R-matrix program PRMAT. Target states corresponding to the 3d(6)4s, 3d(7), 3d(6)4p and 3d(5)4s4s basis configurations were included in the calculations giving rise to a 113 LS state 354 coupled channel problem. Following a detailed systematic study of correlation effects in both the target state and collision wavefunctions, it was found that an additional 21 configuration functions needed to be included in the Configuration Interaction expansion to obtain significantly more accurate target states and collision wavefunctions. This much improved 26-configuration model has been used to calculate converged total effective collision strengths for all sextet to quartet transitions among these levels with total spin S=2, giving a total of 1785 lines. These calculations have laid the foundation for an approach which may be adopted in the study of electron collisions with the low ionization stages of other iron peak elements. The work has been further extended with the commencement of a Breit-Pauli relativistic calculation for one of the smaller models and includes 262 fine-structure levels and over 1800 coupled channels. At the same time the PRMAT parallel R-matrix package is being extended to include relativistic effects which will allow us to attempt the more sophisticated 26-configuration model and produce for the first time the amount and quality of atomic data required to perform a meaningful synthesis of the Fe II spectrum.

Excitation of the 3p^4(4s,3d,4p) Ar^+ states during Ar photoionization:Intensity, alignment, and orientation

Ar photoionization is studied using the R-matrix formalism with emphasis on the simultaneous excitation of the residual A^r+ ion. Cross sections have been obtained for excitation of the 3p^4(3d,4s,4p) states. A comparison with experiments having a resolution of 70 meV shows reasonable agreement for the position and shape of resonance structures. The relative magnitude of the resonances proves to be more elusive. The partial cross section for excitation of the 3p^4(3Pe)4p(2P_3/2^o) and (2D_3/2^o) levels is treated in more detail. A comparison of LS-coupling calculations with high-resolution experimental results shows good agreement for both the excitation cross sections and the polarization of the fluorescence. We also predict the orientation for both levels. We demonstrate that the polarization of the fluorescence originating from the (2D_3/2^o) level can be employed to study spin-orbit effects in Ar photoionization.

Predicting organic acid concentration from UV/vis spectrometry measurements - A comparison of machine learning techniques

The concentration of organic acids in anaerobic digesters is one of the most critical parameters for monitoring and advanced control of anaerobic digestion processes. Thus, a reliable online-measurement system is absolutely necessary. A novel approach to obtaining these measurements indirectly and online using UV/vis spectroscopic probes, in conjunction with powerful pattern recognition methods, is presented in this paper. An UV/vis spectroscopic probe from S::CAN is used in combination with a custom-built dilution system to monitor the absorption of fully fermented sludge at a spectrum from 200 to 750 nm. Advanced pattern recognition methods are then used to map the non-linear relationship between measured absorption spectra to laboratory measurements of organic acid concentrations. Linear discriminant analysis, generalized discriminant analysis (GerDA), support vector machines (SVM), relevance vector machines, random forest and neural networks are investigated for this purpose and their performance compared. To validate the approach, online measurements have been taken at a full-scale 1.3-MW industrial biogas plant. Results show that whereas some of the methods considered do not yield satisfactory results, accurate prediction of organic acid concentration ranges can be obtained with both GerDA and SVM-based classifiers, with classification rates in excess of 87% achieved on test data.

Characterising cement-superplasticiser interaction using zeta potential measurements

The zeta potential generated at the interface between cement particle surfaces adsorbed with superplasticisers have been studied using electroacoustic technique, which is capable of measuring zeta potential at high concentrated suspensions. The study has been undertaken to examine the differences in the magnitude of the zeta potential for ordinary Portland cement (OPC) and Portland pozzolanic (fly ash) cement (PPC) pastes along with the differential impacts of different types of superplasticisers on both the varieties of cement pastes. In the latter context, the effects of three different types of superplasticisers namely Ligno Sulphonate (LS), Sulphonated Melamine Formaldehyde (SMF) and Sulphonated Naphthalene Formaldehyde (SNF) have been specifically studied. The results show that the cement pastes with PPC shows better dispersion when compared with the OPC. The paper also endeavors to unfold the relationship and significance of cement interaction with three different superplasticisers.

A sequential algorithm for sparse support vector classifiers

Support vector machines (SVMs), though accurate, are not preferred in applications requiring high classification speed or when deployed in systems of limited computational resources, due to the large number of support vectors involved in the model. To overcome this problem we have devised a primal SVM method with the following properties: (1) it solves for the SVM representation without the need to invoke the representer theorem, (2) forward and backward selections are combined to approach the final globally optimal solution, and (3) a criterion is introduced for identification of support vectors leading to a much reduced support vector set. In addition to introducing this method the paper analyzes the complexity of the algorithm and presents test results on three public benchmark problems and a human activity recognition application. These applications demonstrate the effectiveness and efficiency of the proposed algorithm.


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