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Statistics is nowadays the customary language of functional imaging. It is common to express an experimental setting as a set of null hypotheses over complex models and to present results as maps of p-values derived from sophisticated probability distributions. However, the growing interest in the development of advanced statistical algorithms is not always paralleled by similar attention to how these techniques may regiment the ways in which users draw inferences from their data. This article investigates the logical bases of current statistical approaches in functional imaging and probes their suitability to inductive inference in neuroscience. The frequentist approach to statistical inference is reviewed with attention to its two main constituents: Fisherian "significance testing" and Neyman-Pearson "hypothesis testing". It is shown that these conceptual systems, which are similar in the univariate testing case, dissociate into two quite different methods of inference when applied to the multiple testing problem, the typical framework of functional imaging. This difference is explained with reference to specific issues, like small volume correction, which are most likely to generate confusion in the practitioner. Further insight into this problem is achieved by recasting the multiple comparison problem into a multivariate Bayesian formulation. This formulation introduces a new perspective where the inferential process is more clearly defined in two distinct steps. The first one, inductive in form, uses exploratory techniques to acquire preliminary notions on the spatial patterns and the signal and noise characteristics. The (smaller) set of likely spatial patterns generated is then tested with newer data and a more rigorous multiple hypothesis testing technique (deductive step).
Eur J Nucl Med Mol Imaging 2004 May
PMID:On the logic of hypothesis testing in functional imaging. 1473 Apr 2

Perhaps in keeping with their enigmatic name, 14-3-3 proteins offer a seemingly bewildering array of opportunities for interaction with signal transduction pathways. In each organism there are many isoforms that can form both homo- and heterodimers, and many biochemical activities have been attributed to the 14-3-3 group. The potential for diversity-and also confusion-is high. The mammalian literature on 14-3-3 proteins provides an appropriate context to appreciate the potential roles of 14-3-3s in plant signal transduction pathways. In addition, functional and structural themes emerge when 14-3-3s are examined and compiled in ways that draw attention to their participation in protein phosphorylation and protein-protein interactions. These themes allow examination of plant 14-3-3s from two perspectives: the ways in which plant 14-3- 3s contribute to and extend ideas already described in animals, and the ways that plant 14-3-3s present unique contributions to the field. The crystal structure of an animal 14-3- 3 has been solved. When considered with the evolutionary stability of large segments of the 14-3-3 protein, the structure illuminates several aspects of 14-3-3 function. However, diversity in other regions of the 14-3-3s and their presence as multigene families offer many opportunities for cell-specific specialization of individual functions.
Annu Rev Plant Physiol Plant Mol Biol 1996 Jun
PMID:14-3-3 PROTEINS AND SIGNAL TRANSDUCTION. 1501 82

Analysis of heat shock protein 65 (hsp65) gene restriction fragment length polymorphism (RFLP) is done frequently to identify non-tuberculous mycobacteria (NTM) on a genetic basis. Here we report the results of analysing the hsp65 patterns of some rarely isolated NTM for which patterns have not been published before (Mycobacterium bohemicum, Mycobacterium hassiacum, Mycobacterium heckeshornense, Mycobacterium monacense, and Mycobacterium triplex). Furthermore new hsp65-variants for Mycobacterium interjectum (type II), Mycobacterium mucogenicum (type V), Mycobacterium gordonae (type VIII) and Mycobacterium paraffinicum (perhaps synonymous to Mycobacterium scrofulaceum) are described. All species were characterised by hsp65-RFLP, sequencing a 441-bp fragment of the hsp65 gene and sequencing the hypervariable region of the 16S rDNA. Additional data for less frequently isolated mycobacteria are provided and the hitherto described data for the Mycobacterium gordonae complex are summarised. Although the hsp65-RFLP analysis turned out to be a useful method a number of restraints (lack of standardisation, slight variability in fragment length) limits its broader use. Reliable identification of NTM needs, however, more than one molecular method. Identification results obtained by applying different methods yielded conflicting results. Confusion may be caused by older data base entries which are not updated and not longer reflect the actual systematic and taxonomy of the genus Mycobacterium.
Mol Cell Probes 2004 Feb
PMID:Different molecular methods for the identification of rarely isolated non-tuberculous mycobacteria and description of new hsp65 restriction fragment length polymorphism patterns. 1503 71

Two acetylcholinesterase genes, Ace1 and Ace2, have been fully cloned and sequenced from both organophosphate-resistant and susceptible clones of cotton aphid. Comparison of both nucleic acid and deduced amino acid sequences revealed considerable nucleotide polymorphisms. Further study found that two mutations occurred consistently in all resistant aphids. The mutation F139L in Ace2 corresponding to F115S in Drosophila acetylcholinesterase might reduce the enzyme sensitivity and result in insecticide resistance. The other mutation A302S in Ace1 abutting the conserved catalytic triad might affect the activity and insecticide sensitivity of the enzyme. Phylogenetic analysis showed that insect acetylcholinesterases fall into two subgroups, of which Ace1 is the paralogous gene whereas Ace2 is the orthologous gene of Drosophila AChE. Both subgroups contain resistance-associated AChE genes. To avoid confusion in the future work, a nomenclature of insect AChE is also suggested in the paper.
Insect Biochem Mol Biol 2004 Apr
PMID:Mutations in acetylcholinesterase associated with insecticide resistance in the cotton aphid, Aphis gossypii Glover. 1504 Oct 23

Official nutrition committee reports in both North America and Europe now state that Vitamin D is more of a hormone than a nutrient. These statements are wrong, and do not reflect the definitions of either vitamin or hormone. Researchers often compound the problem by referring to calcitriol or other deltanoids as "Vitamin D". These things have serious consequences: (1) The literature is burdened by an ongoing confusion that presumes that the reader will somehow "know" what the writer refers to by "Vitamin D". (2) Medical practitioners not familiar with the ambiguities administer Vitamin D inappropriately when calcitriol or a deltanoid analog would be correct, or vice versa. (3) Attempts to promote Vitamin D nutrition are hindered by alarmist responses justifiably associated with the widespread administration of any hormone. Vitamin D is a vitamin in the truest sense of the word, because "insufficient amounts in the diet may cause deficiency diseases". The term, prohormone, is not relevant to the Vitamin D system, but 25-hydroxy-Vitamin D (calcidiol) is appropriately described as a prehormone, i.e. a glandular secretory product, having little or no inherent biologic potency, that is converted peripherally to an active hormone.
J Steroid Biochem Mol Biol 2004 May
PMID:Why "Vitamin D" is not a hormone, and not a synonym for 1,25-dihydroxy-vitamin D, its analogs or deltanoids. 1522 41

The evolutionary relationship of peculiar and poorly known Ganges River dolphin with extinct and extant cetaceans has been in the state of confusion for more than a century. The close resemblance of platanistidae with some of the extinct taxon viz., Dalpiaziniidae and Waipatiidae and their sister group relationship with many of the extant lineages of cetaceans has been reported but none of the alternative hypotheses provide an unambiguous placement for this species. The present study provides insights into the molecular relationships of Platanista with other cetaceans based on comprehensive analyses of the mitochondrial cytochrome b and nuclear interphotoreceptor retinoid-binding protein gene sequences, obtained from 15 specimens of Ganges dolphin from India and Bangladesh. The mean substitution distance analysis of phylogenetically informative characters in the cytochrome b sequences suggested that Platanista gangetica is significantly closer (P<0.001) to Mysticeti than to any other group of toothed whales. However, the conventional methods of phylogenetic reconstruction supported this finding with low to moderate (41-69%) bootstrap values.
Mol Phylogenet Evol 2004 Nov
PMID:Phylogenetic position of Platanista gangetica: insights from the mitochondrial cytochrome b and nuclear interphotoreceptor retinoid-binding protein gene sequences. 1533 63

Nitric oxide has emerged as one of the most important and diverse players in physiology. This small diatomic radical stunned researchers because of its existence and unique biological properties in human physiology. Over the last two decades it was found that NO often has fickle behavior in pathophysiological mechanisms. Where benefiting the host in one case yet inducing and augmenting injury in another. This has lead to confusion in is NO good or bad? Much of the answers to this dichotomy lies in the chemistry of NO and its related nitrogen oxide species. To help understand the complex chemistry with perspective to biology, a discussion on the chemical biology of NO is useful. The chemical biology defines the relevant chemical reaction of NO and nitrogen monoxide in the context of the biological conditions. We discuss in this article the chemistry of nitrogen oxide with different types of biological motifs. Reaction of NO with metal complexes and radicals require low concentration, where formation of reactive nitrogen oxide species require considerably higher amounts and generally are isolated to specific microenvironments in vivo. Though many reactive nitrogen oxide species are formed from chemical reactions with NO, there are several which appear to not require NO to be present, HNO and NO(2). These two species have unique physiological effects and represent additional complexity to this biological picture. From this discussion, a picture can be formed concerning the possible chemical dynamics, which can be plausible in different biological mechanisms.
Curr Mol Med 2004 Nov
PMID:The chemical dynamics of NO and reactive nitrogen oxides: a practical guide. 1557 20

Microsatellite genotyping errors will be present in all but the smallest data sets and have the potential to undermine the conclusions of most downstream analyses. Despite this, little rigorous effort has been made to quantify the size of the problem and to identify the commonest sources of error. Here, we use a large data set comprising almost 2000 Antarctic fur seals Arctocephalus gazella genotyped at nine hypervariable microsatellite loci to explore error detection methods, common sources of error and the consequences of errors on paternal exclusion. We found good concordance among a range of contrasting approaches to error-rate estimation, our range being 0.0013 to 0.0074 per single locus PCR (polymerase chain reaction). The best approach probably involves blind repeat-genotyping, but this is also the most labour-intensive. We show that several other approaches are also effective at detecting errors, although the most convenient alternative, namely mother-offspring comparisons, yielded the lowest estimate of the error rate. In total, we found 75 errors, emphasizing their ubiquitous presence. The most common errors involved the misinterpretation of allele banding patterns (n = 60, 80%) and of these, over a third (n = 22, 36.7%) were due to confusion between homozygote and adjacent allele heterozygote genotypes. A specific test for whether a data set contains the expected number of adjacent allele heterozygotes could provide a useful tool with which workers can assess the likely size of the problem. Error rates are also positively correlated with both locus polymorphism and product size, again indicating aspects where extra effort at error reduction should be directed. Finally, we conducted simulations to explore the potential impact of genotyping errors on paternity exclusion. Error rates as low as 0.01 per allele resulted in a rate of false paternity exclusion exceeding 20%. Errors also led to reduced estimates of male reproductive skew and increases in the numbers of pups that matched more than one candidate male. Because even modest error rates can be strongly influential, we recommend that error rates should be routinely published and that researchers make an attempt to calculate how robust their analyses are to errors.
Mol Ecol 2005 Feb
PMID:Microsatellite genotyping errors: detection approaches, common sources and consequences for paternal exclusion. 1566 Sep 49

The medicinal leech is the most famous representative of the Hirudinea. It is one of few invertebrates widely used in medicine and as a scientific model object. It has recently been given considerable conservation effort. Despite all attention there is confusion regarding the taxonomic status of different morphological forms, with many different species described in the past, but only two generally accepted at present. The results of the phylogenetic analysis of a nuclear (ITS2+5.8S rRNA) and two mitochondrial gene sequences (12S rRNA, COI) suggest that the genus Hirudo is monophyletic. It consists, apart form the type Hirudo medicinalis and the East Asian Hirudo nipponia, of three other, neglected species. All of them have already been described either as species or morphological variety, and can readily be identified by their coloration pattern. The type species is in weakly supported sister relation with Hirudo sp. n. (described as variety orientalis) from Transcaucasia and Iran. Sister to them stands Hirudo verbana from southeastern Europe and Turkey, which is nowadays predominantly bred in leech farms and used as 'medicinal leech.' The North African Hirudo troctina is the sister taxon to this group of Western Eurasian species, whereas the basal split is between H. nipponia and the Western Palaearctic clade.
Mol Phylogenet Evol 2005 Mar
PMID:Celebrity with a neglected taxonomy: molecular systematics of the medicinal leech (genus Hirudo). 1568 33

Usually, cotton laparotomy sponges are discarded when they become blood soaked. During bypass surgery, however, they are often wrung out into the pericardial sac and the contents of the sac are aspirated into the cardiopulmonary bypass (CPB) circuit. After cardiopulmonary bypass, many patients give evidence of mental confusion, excessive bleeding, and systemic inflammatory response syndrome (SIRS). We believe that a possible cause is reinfusion of blood that has been activated by contact with laparotomy sponges and contains fibrin microemboli and thrombin. Thrombin production, soluble fibrin (SF) development, and fibrinogen disappearance were measured, over time, in model systems composed of increasing amounts (0-10-20 microL) of tissue factor (TF) in 4 ml of anticoagulated blood distributed through the interstices of a 49-cm(2) laparotomy sponge. Clotting occurred in all of the sponges. Clotting was accelerated by the presence of TF. Without TF, clotting occurred in an average of 28 min (range 17-39). With 10 and 20 microl TF, clotting occurred in 20 (range 11-27) and 13 (range 10-16) min, respectively. Thrombin at a level of approximately 16 NIHU/ml whole blood was present in several donors for 10-20 min after clotting was complete. If 120 ml of blood was to be wrung from a full-sized laparotomy sponge at this point in time, it could contain as much as 2000 units of thrombin.
Blood Cells Mol Dis
PMID:Reinfusion of aspirated pericardial blood during CPB. Part II. Laparotomy sponges are hazardous parts of the CPB circuit? 1572 97


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