Molecular transistors based on BDT-type molecular bridges.

In this work we study the effect of electron correlations in molecular transistors with molecular bridges based on 1,4-benzene-dithiol (BDT) and 2-nitro-1,4-benzene-dithiol (nitro-BDT) by using ab initio electron propagator calculations. We find that there is no gate field effect for the BDT based transistor in accordance with the experimental data. After verifying the computational method on the BDT molecule, we consider a transistor with a nitro-BDT molecular bridge. From the electron propagator calculations, we predict strong negative differential resistance at small positive and negative values of source-drain voltages. The explanation of the peak and the minimum in the current is given in terms of the molecular orbital picture and switch-on (-off) properties due to the voltage dependencies of the Dyson poles (ionization potentials). When the current is off, the electronic states on both electrodes are populated resulting in the vanishing tunneling probability due to the Pauli principle. Besides the minimum and the maximum in the I-V characteristics, we find a strong gate field effect in the conductance where the peak at V(sd) = 0.15 eV and E(g) = 4x10(-3) a.u. switches to the minimum at E(g) = -4x10(-3) a.u. A similar behavior is discovered at the negative V(sd). Such a feature can be used for fast current modulation by changing the polarity of a gate field.

Probability that a two-stage genome-wide association study will detect a disease-associated snp and implications for multistage designs.

Large two-stage genome-wide association studies (GWASs) have been shown to reduce required genotyping with little loss of power, compared to a one-stage design, provided a substantial fraction of cases and controls, pi(sample), is included in stage 1. However, a number of recent GWASs have used pi(sample) < 0.2. Moreover, standard power calculations are not applicable because SNPs are selected in stage 1 by ranking their p-values, rather than comparing each SNP's statistic to a fixed critical value. We define the detection probability (DP) of a two-stage design as the probability that a given disease-associated SNP will have a p-value among the lowest ranks of p-values at stage 1, and, among those SNPs selected at stage 1, at stage 2. For 8000 cases and 8000 controls available for study and for odds ratios per allele in the range 1.1-1.3, we show that DP is substantially reduced for designs with pi(sample)

New discoveries of skeletal elements of Hadropithecus stenognathus from Andrahomana Cave, southeastern Madagascar.

Remains of what appears to be a single, subadult Hadropithecus stenognathus were recovered from a previously unexcavated site at Andrahomana Cave (southeastern Madagascar). Specimens found comprise isolated teeth and cranial fragments (including the frontal processes of the orbits), as well as a partial postcranial skeleton. They include the first associated fore- and hind-limb bones, confirming the hind-limb attributions made by Godfrey and co-workers in 1997, and refuting earlier attributions by Lamberton in 1937/1938. Of particular interest here are the previously unknown elements, including a sacrum, other vertebrae and ribs, some hand bones, and the distal epiphysis of a femur. We briefly discuss the functional implications of previously unknown elements. Hadropithecus displayed a combination of characters reminiscent of lemurids, others more like those of the larger-bodied Old World monkeys, and still others more like those of African apes. Yet other characteristics appear unique. Lemurid-like postcranial characteristics may be primitive for the Archaeolemuridae. Hadropithecus diverges from the Lemuridae in the direction of Archaeolemur, but more extremely so. Thus, for example, it exhibits a stronger reduction in the size of the hamulus of the hamate, greater anteroposterior compression of the femoral shaft, and greater asymmetry of the femoral condyles. Nothing in its postcranial anatomy signals a close relationship to either the Indriidae or the Palaeopropithecidae.

Localization of opioid receptor antagonist [3H]-LY255582 binding sites in mouse brain: comparison with the distribution of mu, delta and kappa binding sites.

Agonist stimulation of opioid receptors increases feeding in rodents, while opioid antagonists inhibit food intake. The pan-opioid antagonist, LY255582, produces a sustained reduction in food intake and body weight in rodent models of obesity. However, the specific receptor subtype(s) responsible for this activity is unknown. To better characterize the pharmacology of LY255582, we examined the binding of a radiolabeled version of the molecule, [(3)H]-LY255582, in mouse brain using autoradiography. In mouse brain homogenates, the K(d) and B(max) for [(3)H]-LY255582 were 0.156 +/- 0.07 nM and 249 +/- 14 fmol/mg protein, respectively. [(3)H]-LY255582 bound to slide mounted sections of mouse brain with high affinity and low non-specific binding. High levels of binding were seen in areas consistent with the known localization of opioid receptors. These areas included the caudate putamen, nucleus accumbens, claustrum, medial habenula, dorsal endopiriform nucleus, basolateral nucleus of the amygdala, hypothalamus, thalamus and ventral tegmental area. We compared the binding distribution of [(3)H]-LY255582 to the opioid receptor antagonist radioligands [(3)H]-naloxone (mu), [(3)H]-naltrindole (delta) and [(3)H]-norBNI (kappa). The overall distribution of [(3)H]-LY255582 binding sites was similar to that of the other ligands. No specific [(3)H]-LY255582 binding was noted in sections of mu-, delta- and kappa-receptor combinatorial knockout mice. Therefore, it is likely that LY255582 produces its effects on feeding and body weight gain through a combination of mu-, delta- and kappa-receptor activity.

The removal of uranium from mining waste water using algal/microbial biomass.

We describe a three step process for the removal of uranium (U) from dilute waste waters. Step one involves the sequestration of U on, in, and around aquatic plants such as algae. Cell wall ligands efficiently remove U(VI) from waste water. Growing algae continuously renew the cellular surface area. Step 2 is the removal of U-algal particulates from the water column to the sediments. Step 3 involves reducing U(VI) to U(IV) and transforming the ions into stable precipitates in the sediments. The algal cells provide organic carbon and other nutrients to heterotrophic microbial consortia to maintain the low E(H), within which the U is transformed. Among the microorganisms, algae are of predominant interest for the ecological engineer because of their ability to sequester U and because some algae can live under many extreme environments, often in abundance. Algae grow in a wide spectrum of water qualities, from alkaline environments (Chara, Nitella) to acidic mine drainage waste waters (Mougeotia, Ulothrix). If they could be induced to grow in waste waters, they would provide a simple, long-term means to remove U and other radionuclides from U mining effluents. This paper reviews the literature on algal and microbial adsorption, reduction, and transformation of U in waste streams, wetlands, lakes and oceans.

Synthesis and biological activity of some known and putative duloxetine metabolites.

Several putative phase I duloxetine metabolites, 4-hydroxy-, 5-hydroxy-, 6-hydroxy-, 5-hydroxy-6-methoxy-, 6-hydroxy-5-methoxy-, 5,6-dihydroxy-, and 4,6-dihydroxyduloxetine were synthesized, and their phase II metabolite as glucuronide or sulfate conjugates were also synthesized. Their in vitro binding activities were compared to that of parent compound duloxetine.

Preclinical characterization of 2-[3-[3-[(5-ethyl-4'-fluoro-2-hydroxy[1,1'-biphenyl]-4-yl)oxy]propoxy]-2-propylphenoxy]benzoic acid metabolism: in vitro species comparison and in vivo disposition in rats.

Assessment of the pharmacokinetics of [14C]2-[3-[3-[(5-ethyl-4'-fluoro-2-hydroxy[1,1'-biphenyl]-4-yl)oxy]propoxy]-2-propylphenoxy-]benzoic acid ([14C]LY293111), an experimental anti-cancer agent, suggested long-lived circulating metabolites in rats. In vivo metabolites of LY293111 were examined in plasma, bile, urine, and feces of Fischer 344 (F344) rats after oral administration of [14C]LY293111. Metabolites were profiled by high-performance liquid chromatography-radiochromatography, and identified by liquid chromatography (LC)/mass spectrometry and LC/NMR. The major in vivo metabolites of LY293111 identified in rats were phenolic (ether), acyl, and bisglucuronides of LY293111. Measurement of radioactivity in rat plasma confirmed that a fraction of LY293111-derived material was irreversibly bound to plasma protein and that this bound fraction increased over time. This was consistent with the observed disparity in half-lives between LY293111 and total radioactivity in rats and monkeys, and is likely due to covalent modification of proteins by the acyl glucuronide. In vitro metabolism of [14C]LY293111 in liver slices from CD-1 mice, F344 rats, rhesus and cynomolgus monkeys, and humans indicates that glucuronidation was the primary metabolic pathway in all species. The acyl glucuronide was the most prevalent radioactive peak (16% of total 14C) produced by F344 rat slices, whereas the ether glucuronide was the major metabolite in all other species (26-36% of total 14C). Several minor hydroxylated metabolites were detected in F344 rat slice extracts but were not observed in other species. The data presented suggest that covalent modification of proteins by LY293111 acyl glucuronide is possible in multiple species, although the relative reactivity of this metabolite appears to be low compared with those known to cause adverse drug reactions.

Arthropod phylogeny based on eight molecular loci and morphology.

The interrelationships of major clades within the Arthropoda remain one of the most contentious issues in systematics, which has traditionally been the domain of morphologists. A growing body of DNA sequences and other types of molecular data has revitalized study of arthropod phylogeny and has inspired new considerations of character evolution. Novel hypotheses such as a crustacean-hexapod affinity were based on analyses of single or few genes and limited taxon sampling, but have received recent support from mitochondrial gene order, and eye and brain ultrastructure and neurogenesis. Here we assess relationships within Arthropoda based on a synthesis of all well sampled molecular loci together with a comprehensive data set of morphological, developmental, ultrastructural and gene-order characters. The molecular data include sequences of three nuclear ribosomal genes, three nuclear protein-coding genes, and two mitochondrial genes (one protein coding, one ribosomal). We devised new optimization procedures and constructed a parallel computer cluster with 256 central processing units to analyse molecular data on a scale not previously possible. The optimal 'total evidence' cladogram supports the crustacean-hexapod clade, recognizes pycnogonids as sister to other euarthropods, and indicates monophyly of Myriapoda and Mandibulata.

[3H]LY341495 binding to group II metabotropic glutamate receptors in rat brain.

[3H]LY341495 is a highly potent and selective antagonist for group II metabotropic glutamate (mGlu) receptors (mGlu2 and mGlu3), which has been used to label these receptors in cells expressing recombinant receptor subtypes. In this study, we characterized the kinetics, pharmacology, and distribution of [3H]LY341495 binding to mGlu receptors in rat brain tissue. Equilibrium experiments in the rat forebrain demonstrated binding to a single site that was saturable, reversible, and of high affinity (Bmax, 3.9 +/- 0.65 pmol/mg of protein, Kd, 0.84 +/- 0.11 nM). The relative order of potencies for displacement of [3H]LY341495 by mGlu receptor ligands was LY341495 >> L-glutamic acid > LY354740 > (2S,1'S,2'S)-2-(carboxycyclopropyl)glycine > 4-(2R,4R)-aminopyrrolidine-2,4-dicarboxylate > (1S,3R)-1-aminocyclopentane-1,3-dicarboxylic acid > (R,S)-alpha-methyl-4-phosphonophenylglycine > (R,S)3,5-dihydroxyphenylglycine > L-(+)-2-amino-4-phosphonobutyric acid. [3H]LY341495 was not displaced by the selective ionotropic glutamate receptor agonists N-methyl-D-aspartic acid, (R,S)-alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid, or kainate at concentrations up to 1 mM. Comparison of [3H]LY341495 binding in rat brain with recombinant mGlu receptor subtypes demonstrated a very high correlation with mGlu3 receptor binding (r2 = 0.957), a significant, but lower, correlation with mGlu2 receptor binding (r2 = 0.869), but no significant correlation to mGlu8 receptor binding (r2 = 0.284). Regional studies using autoradiography showed a similar distribution of [3H]LY341495 binding to that for group II mGlu receptors previously reported by others using immunocytochemical techniques. These studies indicate that [3H]LY341495 selectively labels group II (mGlu2/3) receptors, but under the conditions used, [3H]LY341495 may bind predominately to mGlu3 receptor populations in the rat forebrain.

Binding of an AMPA receptor potentiator ([3H]LY395153) to native and recombinant AMPA receptors.

LY395153 is a member of a newly described class of arylpropylsulfonamide AMPA receptor potentiators. Here, we characterize and compare [(3)H]LY395153 binding to native AMPA receptors from rat cerebral cortex and recombinant human GluR4(flip) receptors expressed in HEK293 cells. L-Glutamate and AMPA increased [(3)H]LY395153 binding to both native and recombinant AMPA receptors in a concentration dependent and stereoselective manner; this effect of AMPA receptor agonists reflects an apparent increase in ligand affinity. In the presence of L-glutamate (500 microM), [(3)H]LY395153 binding is saturable; the affinity of this radioligand is slightly, albeit statistically significantly higher at human GluR4(flip) (K(d)=55.6+/-5.3nM) than rat cortical receptors (K(d)=110+/-15.1nM). NBQX competitively inhibited L-glutamate-induced increases in [(3)H]LY395153 binding in both native and recombinant receptors, whilst LY303070 (the active isomer of GYKI53655) noncompetitively inhibited this effect in native, but not recombinant receptors. The prototypic AMPA receptor potentiator cyclothiazide competitively inhibited [(3)H]LY395153 binding with a potency (K(i) approximately 7 microM) comparable to EC(50) values reported in electrophysiological studies. In contrast, the structurally unrelated AMPA receptor potentiator CX 516 did not inhibit [(3)H]LY395153 binding at concentrations of up to 600 microM. Further, at concentrations reported to facilitate AMPA receptor desensitization, thiocyanate acts as a competitive inhibitor of [(3)H]LY395153 binding. [(3)H]LY395153 binding was unaffected by a variety of structurally (and mechanistically) diverse compounds tested at a concentration of 10 microM. These data indicate [(3)H]LY395153 is a useful probe for labeling a unique modulatory site on both native and recombinant AMPA receptors.

Management of acute pulmonary hemorrhage in children.

OBJECTIVE: Acute pulmonary hemorrhage can result from a variety of causes. This report offers a diagnosis and treatment plan for children with acute, life-threatening pulmonary hemorrhage resulting from a variety of causes. METHODS: Retrospective review of children with acute pulmonary hemorrhage cared for at a tertiary care children's hospital during from January 1, 1993 to September 1, 1999. PATIENTS: Fourteen children were identified with life-threatening pulmonary hemorrhage during the study period. INTERVENTIONS: Bronchoscopy was the keystone to diagnosis of pulmonary hemorrhage in this series. All of the children underwent multiple procedures to stabilize the airway and control blood loss. These interventions included CO2 laser bronchoscopy, Nd-YAG laser bronchoscopy, endoscopic balloon occlusion of a lobe or main bronchus, topical airway vasoconstrictors, endoscopic tumor excision, transcatheter embolization of bronchial vessels, and lobectomy. OUTCOMES: Three children died and 11 survived without neurological sequelae. CONCLUSIONS: Control of acute pulmonary hemorrhage is a difficult problem and often requires multiple procedures. Endoscopic control is usually required for palliation until more definitive therapy can be undertaken.

Homology and the optimization of DNA sequence data.

Three methods of nucleotide character analysis are discussed. Their implications for molecular sequence homology and phylogenetic analysis are compared. The criterion of inter-data set congruence, both character based and topological, are applied to two data sets to elucidate and potentially discriminate among these parsimony-based ideas.

Efficiency of parallel direct optimization.

Tremendous progress has been made at the level of sequential computation in phylogenetics. However, little attention has been paid to parallel computation. Parallel computing is particularly suited to phylogenetics because of the many ways large computational problems can be broken into parts that can be analyzed concurrently. In this paper, we investigate the scaling factors and efficiency of random addition and tree refinement strategies using the direct optimization software, POY, on a small (10 slave processors) and a large (256 slave processors) cluster of networked PCs running LINUX. These algorithms were tested on several data sets composed of DNA and morphology ranging from 40 to 500 taxa. Various algorithms in POY show fundamentally different properties within and between clusters. All algorithms are efficient on the small cluster for the 40-taxon data set. On the large cluster, multibuilding exhibits excellent parallel efficiency, whereas parallel building is inefficient. These results are independent of data set size. Branch swapping in parallel shows excellent speed-up for 16 slave processors on the large cluster. However, there is no appreciable speed-up for branch swapping with the further addition of slave processors (>16). This result is independent of data set size. Ratcheting in parallel is efficient with the addition of up to 32 processors in the large cluster. This result is independent of data set size.

Multiple sequence alignment in phylogenetic analysis.

Multiple sequence alignment is discussed in light of homology assessments in phylogenetic research. Pairwise and multiple alignment methods are reviewed as exact and heuristic procedures. Since the object of alignment is to create the most efficient statement of initial homology, methods that minimize nonhomology are to be favored. Therefore, among all possible alignments, the one that satisfies the phylogenetic optimality criterion the best should be considered the best alignment. Since all homology statements are subject to testing and explanation this way, consistency of optimality criteria is desirable. This consistency is based on the treatment of alignment gaps as character information and the consistent use of a cost function (e.g., insertion-deletion, transversion, and transition) through analysis from alignment to phylogeny reconstruction. Cost functions are not subject to testing via inspection; hence the assumptions they make should be examined by varying the assumed values in a sensitivity analysis context to test for the robustness of results. Agreement among data may be used to choose an optimal solution set from all of those examined through parameter variation. This idea of consistency between assumption and analysis through alignment and cladogram reconstruction is not limited to parsimony analysis and could and should be applied to other forms of analysis such as maximum likelihood.

Potential to prevent carbon dioxide rebreathing of commercial products marketed to reduce sudden infant death syndrome risk.

OBJECTIVE: Rebreathing of exhaled air is one proposed mechanism for the increased risk for sudden infant death syndrome among prone sleeping infants. We evaluated how carbon dioxide (CO(2)) dispersal was affected by a conventional crib mattress and 5 products recently marketed to prevent prone rebreathing. SETTING: Infant pulmonary laboratory. EQUIPMENT: An infant mannequin with its nares connected via tubing to an 100-mL reservoir filled with 5% CO(2). The sleep surfaces studied included: firm mattress covered by a sheet, Bumpa Bed, Breathe Easy, Kid Safe/Baby Air, Halo Sleep System, and Sleep Guardian. The mannequin was positioned prone face-down or near-face-down. The sleep surfaces were studied with the covering sheet taut, covering sheet wrinkled, and with the mannequin arm positioned up, near the face. MEASUREMENTS: . We measured the fall in percentage end-tidal CO(2) as the reservoir was ventilated with the piston pump. The half-time for CO(2) dispersal (t(1/2)) is an index of the ability to cause or prevent rebreathing. RESULTS: Compared with the face-to-side control, 5 of 6 surfaces allowed a significant increase in t(1/2) in all 3 prone scenarios. The firm mattress and 4 of the 5 surfaces designed to prevent rebreathing consistently allowed t(1/2) above thresholds for the onset of CO(2) retention and lethal rebreathing in an animal model (J Appl Physiol. 1995;78:740). CONCLUSIONS: With very few exceptions, infants should be placed supine for sleep. For infants placed prone or rolling to the prone position, significant rebreathing of exhaled air would be likely on all surfaces studied, except one.

Binding of [3H](2S,1'S,2'S)-2-(9-xanthylmethyl)-2-(2'-carboxycyclopropyl) glycine ([3H]LY341495) to cell membranes expressing recombinant human group III metabotropic glutamate receptor subtypes.

LY341495 is a highly potent and selective antagonist for group II mGlu receptors (mGlu2 and mGlu3). High affinity binding of [3H]LY341495 to recombinant human group II mGlu receptors (mGlu2 and mGlu3), and in rat brain homogenates (Kd approximately 1 nM), has been previously described. Although LY341495 is a very selective nM-potent antagonist for group II mGlu receptors, it is also a relatively potent antagonist for group III mGlu receptors at high nanomolar to low micromolar concentrations. In this study we examined and characterized the binding of [3H]LY341495 to membranes of cells expressing recombinant human group III mGlu receptors. Using up to 100 nM of [3H]LY341495, the level of specific binding in human mGlu4a receptor-expressing cell membranes was not appreciable and binding to this site was not examined further. In contrast, we demonstrated sufficient specific binding of [3H]LY341495 to human mGlu6, mGlu7a and mGlu8a receptor-expressing cell membranes to allow for further characterizations. [3H]LY341495 binding was saturable and rapidly reversible. [3H]LY341495 bound to a single site in each cell line, with Kd and Bmax values of 31.6+/-6.8 nM and 3.3+/-0.7 pmol/mg protein (mGlu6), 72.7+/-22.0 nM and 3.7+/-0.4 pmol/mg protein (mGlu7a), and 14.0+/-1.1 nM and 3.0+/-0.2 pmol/mg protein (mGlu8a). [3H]LY341495 binding to mGlu6, 7a and 8a was displaceable by compounds which interact functionally with group III mGlu receptors. For example, L-AP4 displaced [3H]LY341495 with Ki values of 6.8+/-3.1 microM (mGlu6), 211+/-43 microM (mGlu7a) and 1.6+/-0.3 microM (mGlu8a). With L-glutamate, we obtained Ki values of 12.3+/-3.5, 869+/-154 and 4.5+/-0.83 microM, for mGlu6, mGlu7a and mGlu8a, respectively. Ki values for unlabelled LY341495 were 0.058+/-0.008, 0.22+/-0.05 and 0.029+/-0.008 microM, respectively. These studies demonstrated that [3H]LY341495 is a useful radioligand for studying the pharmacology and expression of recombinant mGlu6, 7a and 8a receptors in cell lines.

Triploblastic relationships with emphasis on the acoelomates and the position of Gnathostomulida, Cycliophora, Plathelminthes, and Chaetognatha: a combined approach of 18S rDNA sequences and morphology.

Triploblastic relationships were examined in the light of molecular and morphological evidence. Representatives for all triploblastic "phyla" (except Loricifera) were represented by both sources of phylogenetic data. The 18S ribosomal (rDNA) sequence data for 145 terminal taxa and 276 morphological characters coded for 36 supraspecific taxa were combined in a total evidence regime to determine the most consistent picture of triploblastic relationships for these data. Only triploblastic taxa are used to avoid rooting with distant outgroups, which seems to happen because of the extreme distance that separates diploblastic from triploblastic taxa according to the 18S rDNA data. Multiple phylogenetic analyses performed with variable analysis parameters yield largely inconsistent results for certain groups such as Chaetognatha, Acoela, and Nemertodermatida. A normalized incongruence length metric is used to assay the relative merit of the multiple analyses. The combined analysis having the least character incongruence yields the following scheme of relationships of four main clades: (1) Deuterostomia [((Echinodermata + Enteropneusta) (Cephalochordata (Urochordata + Vertebrata)))]; (2) Ecdysozoa [(((Priapulida + Kinorhyncha) (Nematoda + Nematomorpha)) ((Onychophora + Tardigrada) Arthropoda))]; (3) Trochozoa [((Phoronida + Brachiopoda) (Entoprocta (Nemertea (Sipuncula (Mollusca (Pogonophora (Echiura + Annelida)))))))]; and (4) Platyzoa [((Gnathostomulida (Cycliophora + Syndermata)) (Gastrotricha + Plathelminthes))]. Chaetognatha, Nemertodermatida, and Bryozoa cannot be assigned to any one of these four groups. For the first time, a data analysis recognizes a clade of acoelomates, the Platyzoa (sensu Cavalier-Smith, Biol. Rev. 73:203-266, 1998). Other relationships that corroborate some morphological analyses are the existence of a clade that groups Gnathostomulida + Syndermata (= Gnathifera), which is expanded to include the enigmatic phylum Cycliophora, as sister group to Syndermata.

Transformationalism, taxism, and developmental biology in systematics.

Issues concerning transformational and taxic comparisons are central to understanding the impact of the recent proliferation of molecular developmental data on evolutionary biology. More importantly, an understanding of taxism and transformationalism in comparative biology is critical to assessing the impact of the recent developmental data on systematic theory and practice. We examine the philosophical and practical aspects of the transformational approach and the relevance of this approach to recent molecular-based developmental data. We also examine the theoretical basis of the taxic approach to molecular developmental data and suggest that developmental data are perfectly amenable to the taxic approach. Two recent examples from the molecular developmental biology literature--the evolution of insect wings and the evolution of dorsal ventral inversion in vertebrates and invertebrates--are used to compare the taxic and transformational approaches. We conclude that the transformational approach is entirely appropriate for ontogenetic studies and furthermore can serve as an excellent source of hypotheses about the evolution of characters. However, the taxic approach is the ultimate arbiter of these hypotheses.