A benchmark calculation for the fuzzy c-means clustering algorithm: initial memberships

We report a benchmark calculation for the fuzzy c-means clustering algorithm that can be used as a reference in theoretical and practical studies related to classification methodologies. A full exploration of the hard-initialization space is done for all possible different groupings on a simple fifteen-pattern system to describe their stationary points. Numerical problems associated with the stopping criteria are discussed in relation with the calculation of some validity indexes. All necessary information to assure an easy reproduction of the obtained results is clearly reported.     

Single-fiber diffuse optical time-of-flight spectroscopy

We demonstrate interstitial diffuse optical time-of-fight spectroscopy based on a single fiber for both light delivery and detection. Detector saturation due to the massive short-time reflection is avoided by ultrafast gating of a single photon avalanche diode. We show that the effects of scattering and absorption are separable and that absorption can be assessed independently of scattering. Measurements on calibrated liquid phantoms and subsequent Monte Carlo-based evaluation illustrate that absorption coefficients can be accurately assessed over a wide range of medically relevant optical properties. Our findings pave the way to simplified and less invasive interstitial in vivo spectroscopy.     

Investigating the spectrum of biological activity of substituted quinoline-2-carboxamides and their isosteres

In this study, a series of thirty-five substituted quinoline-2-carboxamides and thirty-three substituted naphthalene-2-carboxamides were prepared and characterized. They were tested for their activity related to the inhibition of photosynthetic electron transport (PET) in spinach (Spinacia oleracea L.) chloroplasts. Primary in vitro screening of the synthesized compounds was also performed against four mycobacterial species. N-Cycloheptylquinoline-2-carboxamide, N-cyclohexylquinoline-2-carboxamide and N-(2-phenylethyl)quinoline-2-carboxamide showed higher activity against M. tuberculosis than the standards isoniazid or pyrazinamide and 2-(pyrrolidin-1-ylcarbonyl)quinoline and 1-(2-naphthoyl)pyrrolidine expressed higher activity against M. kansasii and M. avium paratuberculosis than the standards isoniazid or pyrazinamide. The most effective antimycobacterial compounds demonstrated insignificant toxicity against the human monocytic leukemia THP-1 cell line. The PET-inhibiting activity expressed by IC(50) value of the most active compound N-benzyl-2-naphthamide was 7.5 μmol/L. For all compounds, the structure-activity relationships are discussed.     

Investigation on the protective effects of cranberry against the DNA damage induced by benzo[a]pyrene

There are few reports that demonstrate the antigenotoxic potential of cranberries. Although the types of berry fruits consumed worldwide are many, this paper focuses on cranberries that are commonly consumed in Mexico (Vaccinium macrocarpon species). The purpose of the present study is to determine whether cranberry ethanolic extract (CEE) can prevent the DNA damage produced by benzo[a]pyrene (B[a]P) using an in vivo mouse peripheral blood micronucleus assay. The experimental groups were organized as follows: a negative control group (without treatment), a positive group treated with B[a]P (200 mg/kg), a group administered with 800 mg/kg of CEE, and three groups treated with B[a]P and CEE (200, 400, and 800 mg/kg) respectively. The CEE and benzo[a]pyrene were administered orally for a week, on a daily basis. During this period the body weight, the feed intake, and the determination of antigenotoxic potential were quantified. At the end of this period, we continued with the same determinations for one week more (recovery period) but anymore administration of the substances. The animals treated with B[a]P showed a weight increase after the first week of administration. The same phenomenon was observed in the lots combined with B[a]P and CEE (low and medium doses). The dose of 800 mg/kg of CEE showed similar values to the control group at the end of the treatment period. In the second part of the assay, when the substances were not administered, these experimental groups regained their normal weight. The dose of CEE (800 mg/kg) was not genotoxic nor cytotoxic. On the contrary, the B[a]P increases the frequency of micronucleated normochromatic erythrocytes (MNNE) and reduces the rate of polychromatic erythrocytes (PE) at the end of the treatment period. With respect to the combined lots, a significant decrease in the MN rate was observed from the sixth to the eighth day of treatment with the two high doses applied; the highest protection (60%) was obtained with 800 mg/kg of CEE. The same dose showed an anticytotoxic effect which corresponded to an improvement of 62.5% in relation to the animals administered with the B[a]P. In the second period, all groups reached values that have been seen in the control group animals. Our results suggest that the inhibition of clastogenicity of the cranberry ethanolic extract against B[a]P is related to the antioxidant capacity of the combination of phytochemicals present in its chemical composition.     

Nuclear magnetic relaxation induced by exchange-mediated orientational randomization: Longitudinal relaxation dispersion for spin I = 1

The frequency dependence of the longitudinal relaxation rate, known as the magnetic relaxation dispersion (MRD), can provide a frequency-resolved characterization of molecular motions in complex biological and colloidal systems on time scales ranging from 1 ns to 100 μs. The conformational dynamics of immobilized proteins and other biopolymers can thus be probed in vitro or in vivo by exploiting internal water molecules or labile hydrogens that exchange with a dominant bulk water pool. Numerous water (1)H and (2)H MRD studies of such systems have been reported, but the widely different theoretical models currently used to analyze the MRD data have resulted in divergent views of the underlying molecular motions. We have argued that the essential mechanism responsible for the main dispersion is the exchange-mediated orientational randomization (EMOR) of anisotropic nuclear (electric quadrupole or magnetic dipole) couplings when internal water molecules or labile hydrogens escape from orientationally confining macromolecular sites. In the EMOR model, the exchange process is thus not just a means of mixing spin populations but it is also the direct cause of spin relaxation. Although the EMOR theory has been used in several studies to analyze water (2)H MRD data from immobilized biopolymers, the fully developed theory has not been described. Here, we present a comprehensive account of a generalized version of the EMOR theory for spin I = 1 nuclides like (2)H. As compared to a previously described version of the EMOR theory, the present version incorporates three generalizations that are all essential in applications to experimental data: (i) a biaxial (residual) electric field gradient tensor, (ii) direct and indirect effects of internal motions, and (iii) multiple sites with different exchange rates. In addition, we describe and assess different approximations to the exact EMOR theory that are useful in various regimes. In particular, we consider the experimentally important dilute regime, for which approximate analytical results are derived. As shown by the analytical expressions, and confirmed by exact numerical calculations, the dispersion is governed by the pure nuclear quadrupole resonance frequencies in the ultraslow-motion regime, where the relaxation rate also exhibits a much stronger dependence on the electric field gradient asymmetry than in the motional-narrowing regime.     

Immunoextraction of zinc proteins from human plasma using chicken yolk antibodies immobilized onto paramagnetic particles and their electrophoretic analysis

Zinc(II) as the only transition metal lacking redox activity is an essential part of approximately 10% proteins as a cofactor of these proteins. Considering the fact that there are numerous zinc(II) containing proteins, proteomics and metallomics studies aimed on them require accurate methods for preparation of real biological samples prior to their subsequent analysis using 2DE and MS. For this purpose, we suggested a new method based on chicken anti-zinc antibodies and magnetizable particles. Antibodies were covalently immobilized to the surface of paramagnetic beads activated with tosyl group. Binding of the antibody to the beads was confirmed by secondary anti-chicken antibody conjugated with horseradish peroxidase. The immunoextraction conditions, such as concentration of the beads (6-18 μg/mL of the sample), time of immunoextraction (6-34 min), pH and composition of the elution buffer, and time of extraction (48-300 s) were optimized. Subsequently, zinc proteins were extracted from human plasma and total concentration of zinc was monitored by electrochemical detection in the extracts. Under optimal conditions it was possible to monitor the proteins and zinc removal from the sample by chip CE, SDS-PAGE, and indirectly using electrochemistry.     

The effect of human agent in project management

The article deals with the effect of a human agent on the activity realization in a project. It does so from the perspective of the Theory of Constraints where the weakest point is the deadline of partial activity. Every existing activity in any project is, to a higher or lower extent, determined by the effect of the human agent. The inefficiency of a number of projects in practice is largely caused by an unsuccessful realization of partial activities. The effect of the human agent is in this respect fundamental. The human agent, as an allocated resource in the activity, is liable to a number of non-specified impacts and stimuli, and as such s/he is rather versatile in his/her behaviour. The versatility of the human agent in projects can be described by the “Student Syndrome” phenomenon and by the first “Parkinson’s law”. Both these qualitative phenomena create a starting point for the introduced theoretical and quantitative research. The findings in this article are based on the set of real data of work effort of the students of daily study programme on one university in the Czech Republic. The article presents, as the authors’ own theoretical contribution, a mathematical model for the “Student Syndrome” phenomenon with a practical use in quantitative methods of project management. This model was derived analytically from a performed data analysis and we can assume that it will be useful for further theoretical development of quantitative methods in project management. In the article we deduce the theoretical differentiation of the “Student Syndrome” phenomenon in work effort into three terminable phases during three different types of resource work allocation. We can regard this original viewpoint as suggestive for the area of human resources management in projects. Its contribution lies in delimitation of time-targeted resource stimulation, which may lead to lower project costs, besides higher work efficiency and compliance with time-targeted deadlines of activity termination. The article brings the quantification of qualitative features of the human agent in project management.     

Recent Progress with the SMILETRAP Penning Mass Spectrometer

The Penning trap mass spectrometer SMILETRAP has been considerably improved during the last two years. The helium pressure has been carefully stabilized and is now independent of irregular air pressure. The temperature of the hyperboloidal precision trap is stabilized to ±0.03°C. Remaining temperature instabilities are compensated by changes in the current of a warm coil surrounding the precision trap. The frequency synthesizer is now locked to GPS. This means that it is much easier to accurately measure resonances during several days. The improvements have demonstrated that in mass doublet measurements with an excitation time of 1 s it is possible to determine the mass of ions with q/A=1/2 at an uncertainty to a few times of 0.1 ppb, using selected rather than cooled ions. In routine measurements lasting for one day it is possible to reach a mass uncertainty of 1 ppb. The masses of the following particles and atoms have been measured with uncertainties in the region 0.3–2 ppb: p, ³H, ³He, ⁴He, ²²Ne, ²⁸Si, ³⁶Ar, ⁷⁶Ge, ⁷⁶Se, ⁸⁶Kr and ¹³³Cs. It has also been shown that though we are using a warm bore the trap pressure is sufficiently low to prevent electron capture from the rest gas for excitation times of 3 s and for ion charges as high as 50+. This revised version was published online in July 2006 with corrections to the Cover Date.