The combined use of self-organizing maps and Andrews' Curves

The use of self-organizing maps to analyze data often depends on finding effective methods to visualize the SOM's structure. In this paper we propose a new way to perform that visualization using a variant of Andrews' Curves. Also we show that the interaction between these two methods allows us to find sub-clusters within identified clusters. Perhaps more importantly, using the SOM to pre-process data by identifying gross features enables us to use Andrews' Curves on data sets which would have previously been too large for the methodology. Finally we show how a three way interaction between the human user and these two methods can be a valuable exploratory data analysis tool.     

First report of an intraerythrocytic small piroplasm in wild Iberian lynx (Lynx pardinus)

A wild injured Iberian lynx (Lynx pardinus) was taken from the Sierra Morena population. During the health check small intraerythrocytic piroplasms, morphologically indistinguishable from other feline piroplasms, were observed in Wright-Giemsa-stained blood films. Amplification by polymerase chain reaction of a portion of the 18S nuclear small subunit (NSS) rRNA gene and sequencing revealed similarity of the unknown organism with sequences obtained from Pallas's cat from Mongolia and from a domestic cat in Spain. In a retrospective (1993-2003) study of 50 Iberian lynx tissue samples, no amplifications of the 18S NSS rRNA gene of the organism were obtained. This is the first report of a naturally occurring erythroparasitemia in the Iberian lynx and the first documented case of naturally occurring piroplasm infection in a free-ranging felid from Europe.     

Boar sperm velocity and motility patterns under capacitating and non-capacitating incubation conditions

This study compares the velocity and motility of boar sperm under capacitating and non-capacitating incubation conditions. Aliquots of pooled, washed boar sperm were incubated in either Tyrode's complete medium (TCM; a capacitating medium), Ca2+-free TCM (TCM-Ca2+), or Ca2+ and NaHCO3-free TCM (Tyrode's basal medium [TBM]; a non-capacitating medium). Motility patterns were determined every hour over a 3h period of incubation at 38 degrees C. Capacitation status was assessed by the chlortetracycline assay after 1 and 3h of incubation. Experiments were repeated five times. Compared to the TBM control, a significant increase was seen in the percentage of capacitated sperm after 1h of incubation in TCM: the kinematics of these sperm cells were favorably modified. However, the motility patterns of sperm cells incubated in TCM and TCM-Ca2+ were very similar. Under capacitating conditions (TCM), the coefficients of linearity (LIN) and straightness (STR) significantly increased over time (LIN values were significantly different after 3h of incubation, while STR values were significantly different after only 2 h). Significant correlations were seen between LIN and the percentage of cells showing the B pattern (r = 0.334, P < 0.05) and the number of acrosome reacted spermatozoa (r = 0.301, P < 0.05). This suggests that capacitated boar spermatozoa may have a species-specific motility pattern.     

Allelic variation of polymorphic locus lytB, encoding a choline-binding protein, from streptococci of the mitis group

The choline-binding protein LytB, an N-acetylglucosaminidase of Streptococcus pneumoniae, is the key enzyme for daughter cell separation and is believed to play a critical pathogenic role, facilitating bacterial spreading during infection. Because of these peculiarities LytB is a putative vaccine target. To determine the extent of LytB polymorphism, the lytB alleles from seven typical, clinical pneumococcal isolates of various serotypes and from 13 additional streptococci of the mitis group (12 atypical pneumococci and the Streptococcus mitis type strain) were sequenced. Sequence alignment showed that the main differences among alleles were differences in the number of repeats (range, 12 to 18) characteristic of choline-binding proteins. These differences were located in the region corresponding to repeats 11 to 17. Typical pneumococcal strains contained either 14, 16, or 18 repeats, whereas all of the atypical isolates except strains 1283 and 782 (which had 14 and 16 repeats, respectively) and the S. mitis type strain had only 12 repeats; atypical isolate 10546 turned out to be a DeltalytB mutant. We also found that there are two major types of alternating repeats in lytB, which encode 21 and 23 amino acids. Choline-binding proteins are linked to the choline-containing cell wall substrate through choline residues at the interface of two consecutive choline-binding repeats that create a choline-binding site. The observation that all strains contained an even number of repeats suggests that the duplication events that gave rise to the choline-binding repeats of LytB involved two repeats simultaneously, an observation that is in keeping with previous crystallographic data. Typical pneumococcal isolates usually grew as diplococci, indicating that an active LytB enzyme was present. In contrast, most atypical isolates formed long chains of cells that did not disperse after addition of purified LytB, suggesting that in these strains chains were produced through mechanisms unrelated to LytB.     

Synthesis, characterization and antiproliferative behavior of tricarbonyl complexes of rhenium(I) with some 6-amino-5-nitrosouracil derivatives: crystal structure of fac-[ReCl(CO)3(DANU-N5,O4)] (DANU=6-amino-1,3-dimethyl-5-nitrosouracil)

New complexes of rhenium(I) with some 5-nitrosopyrimidines with general formula [ReCl(CO)3L] have been prepared and characterized by elemental analysis, conductivity measurements, IR and 1H, 13C and 15N NMR spectroscopic methods. The complexes appear to be monomeric and the pyrimidine ligands act in a neutral form. The structure of [ReCl(CO)3(DANU)].CH3CN has been solved by X-ray diffraction. The coordination environment around the Re(I) may be described as a distorted octahedron in which the ligand behaves in a bidentate fashion through N5 and O4 atoms, making a five-membered chelate ring. The coordination sphere is completed with three carbonyl groups in fac-arrangement and one chlorine atom. The evaluation of the antiproliferative behavior against five human tumor cell lines (human breast cancer MCF-7 and EVSA-T, human neuroblastoma NB69, human glioma H4 and human bladder carcinoma cell line ECV) suggested a modulator behavior of cell growth at low concentrations due to their estrogenic-like characteristics.     

Finite element prediction of proximal femoral fracture patterns under different loads

The main purpose of this work is to discuss the ability of finite element analyses, together with an appropriate anisotropic fracture criterion, to predict the ultimate load and type of fracture in bones and more specifically in the proximal femur. We show here that the use of a three-dimensional anisotropic criterion provides better results than other well-known isotropic criteria. The criterion parameters and the anisotropic elastic properties were defined in terms of the bone tissue microstructure, quantified by the apparent density and the so-called "fabric tensor", whose spatial distributions were obtained by means of an anisotropic remodeling model able to capture the main features of the internal structure of long bones. In order to check the validity of the results obtained, they have been compared with those of an experimental work that analyzes different types of fractures induced in the proximal femur by a static overload.     

Allelochemicals from Stauranthus perforatus, a Rutaceous tree of the Yucatan Peninsula, Mexico

Aqueous leachates and a CHCl3-MeOH (1:1) extract of roots of Stauranthus perforatus showed a significant phytotoxic effect on Amaranthus hypochondriacus and Echinochloa crus-galli. Bioassay-directed fractionation of the active organic extract led to the isolation and characterization of ten secondary metabolites, which included two pyranocoumarins [xanthyletin (1) and 3-(1',1'-dimethylallyl)-xanthyletin (2)], four furanocoumarins [chalepensin (3), ammirin (4), chalepin (5) and 2'-isopropyl-psoralene (6)], two lignans [asarinin (7) and fargesin (8)], one sesquiterpene [4,5-epoxi-beta-caryophyllene (9)], and one alkamide [pellitorine (10)]. From these compounds, 2'-isopropyl-psoralene (6) or anhydromarmesin, is reported for the first time as a natural product, whereas compounds 4-10 are now reported as being present in S. perforatus. Metabolites 1, 3-5 and 10 caused significant inhibition of radicle growth of A. hypochondriacus and E. crus-galli. Furthermore, in a greenhouse experiment the decomposition of the leaves and roots in the soil had a significant inhibitory effect on the growth of weeds. The allelopathic action of the decomposition of roots was evident up to the sixth week of the experiment. The effect of leaves was comparable to that of DPCA (dimethyl tetrachloroterephthalate), a commercial herbicide. Finally different concentrations of Stauranthus root powder were combined with maize kernels and used to feed corn weevil. The treatments resulted in high mortality of this insect.     

Potato tuber isoapyrases: substrate specificity, affinity labeling, and proteolytic susceptibility

Apyrase/ATP-diphosphohydrolase hydrolyzes di- and triphosphorylated nucleosides in the presence of a bivalent ion with sequential release of orthophosphate. We performed studies of substrate specificity on homogeneous isoapyrases from two potato tuber clonal varieties: Desiree (low ATPase/ADPase ratio) and Pimpernel (high ATPase/ADPase ratio) by measuring the kinetic parameters K(m) and k(cat) on deoxyribonucleotides and fluorescent analogues of ATP and ADP. Both isoapyrases showed a broad specificity towards dATP, dGTP, dTTP, dCTP, thio-dATP, fluorescent nucleotides (MANT-; TNP-; ethene-derivatives of ATP and ADP). The hydrolytic activity on the triphosphorylated compounds was always higher for the Pimpernel apyrase. Modifications either on the base or the ribose moieties did not increase K(m) values, suggesting that the introduction of large groups (MANT- and TNP-) in the ribose does not produce steric hindrance on substrate binding. However, the presence of these bulky groups caused, in general, a reduction in k(cat), indicating an important effect on the catalytic step. Substantial differences were observed between potato apyrases and enzymes from various animal tissues, concerning affinity labeling with azido-nucleotides and FSBA (5'-p-fluorosulfonylbenzoyl adenosine). PLP-nucleotide derivatives were unable to produce inactivation of potato apyrase. The lack of sensitivity of both potato enzymes towards these nucleotide analogues rules out the proximity or adequate orientation of sulfhydryl, hydroxyl or amino-groups to the modifying groups. Both apyrases were different in the proteolytic susceptibility towards trypsin, chymotrypsin and Glu-C.