bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantification of stratum corneum ceramides and lipid envelope ceramides in the hereditary ichthyoses
Authors: PAIGE D.G. , MORSE-FISHER N. , HARPER J.I.
Published: July 2006

Ceramides (sphingolipids) are the main polar lipids of the stratum corneum and play an important role in skin barrier function, cell adhesion and epidermal differentiation. In view of the function of ceramides in normal skin, this study aimed to assess their levels in patients with various types of hereditary ichthyosis, in which epidermal homeostasis is markedly abnormal. Stratum corneum samples were collected from 80 patients and 23 normal controls, and the intercellular and lipid envelope ceramides were analysed by high-performance thin-layer chromatography. The covalently bound ceramides (ceramides A and B) of the lipid envelope were present in all patients studied, and showed no significant differences from control samples. Total ceramides (ceramides 1–6) were decreased in bullous ichthyosiform erythroderma, which is presumably a secondary phenomenon similar to that seen in patients with atopic dermatitis. Patients with non-erythrodermic lamellar ichthyosis showed a marked decrease in levels of the important acylceramide, ceramide 1, whereas those with other types of autosomal recessive ichthyosis (limited lamellar ichthyosis and non-bullous ichthyosiform erythroderma) had mean levels similar to the controls. Ceramide 1 deficiency may therefore define a subgroup within the autosomal recessive ichthyoses. Sjögren-Larsson syndrome (SLS) shows a deficiency of both acyl-ceramides (ceramides 1 and 6), which would seem likely to disrupt the normal skin barrier function. Furthermore, glucosyl-ceramides (cerebrosides) are known to be deficient in the neural tissue of patients with SLS. The relationship of these ceramide abnormalities to the underlying fatty alcohol oxidoreductase defect remains uncertain, but they may provide an interesting link between the nerve damage and cutaneous abnormalities seen in this rare neurodermatosis.
bcl-2 expression reliably distinguishes trichoepitheliomas from basal cell carcinomas
Authors: SMOLLER B.R. , VAN DE RIJN M. , LEBRUN D. , WARNKE R.A.
Published: July 2006

Trichoepitheliomas (TE) are benign follicular neoplasms which are frequently confused with basal cell carcinomas (BCC). It is important to distinguish these entities precisely, as the treatments and prognoses are different. To this end, we stained a series of formalin-fixed, paraffin-embedded specimens of unequivocal TE and BCC with antibodies directed against bcl-2, an oncogene associated with programmed cell death, and known to be overexpressed in some malignant tumours. The TE showed staining of tumour cells limited to the outermost layer of the proliferation. The BCC tumour cells demonstrated diffuse staining throughout the tumour nodules. This difference in staining pattern was then applied to more equivocal cases, and seemed clearly to separate the entities. The observed findings may prove to be of diagnostic help in distinguishing borderline cases, and also offer some possible explanations for the biological differences between these neoplasms.
Childhood Jessner's lymphocytic infiltrate of the skin
Authors: HIGGINS C.R. , PWAKEEL R.A. , CERIO R.
Published: July 2006

We report a case of Jessner's lymphocytic infiltrate of the skin in an 11-year-old boy. This benign lymphocytic infiltrate was originally described in 1953, and classically occurs in middle-aged men. Its occurrence in children appears to be very rare, and there are only two other case reports in the literature.
Mucosal lichen sclerosus/lichen planus overlap syndromes
Authors: MARREN P. , MILLARD P. , CHIA Y. , WOJNAROWSKA F.
Published: July 2006

Lichen sclerosus and lichen planus affecting cutaneous sites are easily distinguishable clinically. Clinical signs on mucosal sites, however, may not allow differentiation between these diseases, and reliance is frequently placed on histopathological findings.

We report a series of seven patients with clinical evidence of coexisting vulval lichen sclerosus and lichenoid oral lesions. All patients had vulval biopsies, and four had oral biopsies. Histology of all the vulval biopsy specimens showed features consistent with lichen sclerosus. Two of these patients developed vulval intraepithelial neoplasia during the course of their disease, and one progressed to a well-differentiated squamous carcinoma. Histology of the oral lesions showed features that were predominantly those of lichen planus. There are, however, few reports of histologically proven oral lichen sclerosus. Variations in histopathological descriptions of lichen sclerosus, depending on duration of disease, have been reported, particularly with regard to the position of the inflammatory infiltrate in relation to the dermo-epidermal junction. We believe that these patients may have oral lichen sclerosus, or at the very least make up a distinctive group who need to be identified and followed up, as their risk of oral dysplasia is unknown.
The Hoard of Cyzicenes and Shrine of Demeter at Myrmekion
Authors: Chistov Dmitrii , Butyagin Alexander
Published: July 2006

On August 20, 2003, in the course of excavations of the ancient settlement of Myrmekion (Ukraine, town of Kerch) the State Hermitage expedition discovered a hoard of electrum staters from the town of Cyzicus. The hoard had been kept in a bronze jug hidden under masonry. It contained 99 well-preserved coins that belong to 53 types, mostly dating from the 5th century BC (2nd and 3rd groups according to H. Fritze). One of the types (a sitting warrior wearing a helmet with a bow placed to the right of him) is unique. The building under which the hoard was found had been a sanctuary constructed in the 4th century BC. However the wall where the hoard comes from was constructed not before the 370s BC, so coins from Cyzicus cannot be dated to an earlier period. Most probably the hoard was not a private property but part of the temple's treasures concealed in some unclear circumstances. The hoard, by its size, is comparable to similar finds from Prinkipo, Clazomenae, Piraeus and Orlovka. The hoard from Myrmekion is the only one obtained by a museum in its integrity and whose archaeological origin is clear. The sanctuary, in which the hoard was found, is known as the "Demeter sanctuary". It occupied an area of more than 500 m2, in the center of which there was a premise with a stone altar. The archaeological context proves that the hoard could have been hidden not earlier than 375-350 BC.
The Bosporus and Sindike in the Era of Leukon I. New Epigraphic Publications
Authors: Tokhtas'ev Sergei
Published: July 2006

I. The author returns to the analysis (see Hyperboreus. 1998, 4/2, 286-301; cf. SEG, XLVIII, 1027) of an epigram of the Bosporan tyrant Leukon I from the Semibratnee site (Labrys) on the occasion of Yu. G. Vinogradov's posthumous publication (VDI, 2002, No 3). Although Vinogradov accepted the most important of the author's readings, some of the interpretations suggested by him were erroneous, as the author strives to prove (see also A. J. Graham's observations). The inscription is analyzed from the point of view of its language and style. As a historical source, the epigram is discussed in the second part of the article together with a new inscription from Nymphaion.II. As early as the end of the 5th c. BC (or even earlier) Bosporan tyrant Satyros I made Sindike Bosporus' vassal (Polyaen. VIII. 55). The Labrys epigram tells us about Leukon I, «archon of the Bosporus and Theodosia» helping Hekataios, king of the Sindoi, dethroned by his own son, obviously in order to take possession of Sindike de jure. A new votive inscription from Nymphaion published by O. Yu. Sokolova and N. A. Pavlichenko (Hyperboreus, 2002, 8/1, 99-121) sheds new light on the further history of the forming of the Bosporan state in the 1st half of the 4th century BC. Leukon is called here «archon of the Bosporus, Theodosia, all Sindike, Toretai, Dandarioi, Psessoi». The author believes that the epithet «all» is applied to Sindike for expressiveness and implies in fact the land which belonged to Hekataios. The author supposes that the neighboring barbarians were annexed by a treaty, and the power of their own kings was abolished, this fact explaining why Greek poleis and the barbarians were politically equal. No doubt, Leukon soon had to be disappointed in the possibility of governing barbarians in the same way as Greeks. According to the inscription CIRB 6a Sindoi were still under Leukon's rule as archon, but for the rest of the barbarians he was a king. However, in the later inscriptions CIRB 6, 8, 1037, 1038 the standard formula appears: «Leukon, archon of the Bosporus and Theodosia, king of Sindoi, Toretai, etc.» The change in the political status of the barbarians was probably connected with their efforts to get free from the power of the Bosporus. The Greek cities of the Bosporus and Theodosia preserved their formal autonomy and citizenship, but the barbarians were turned into dependent population.
Marine Boundaries: States and the United States
Authors: Mangone Gerard
Published: July 2006

Marine boundaries between states of the United States and between the states and the United States have a long and contentious history. Disputes have arisen between states separated by a river and between states in extending their land boundaries seaward. Especially since the Submerged Lands Act of 1953, disputes between states and the federal United States over title to valuable resources in the three-mile coastal area measured from the shoreline have been sharp and continuous. The legal basis for the delimitation of marine zones, including common law, statutes and international law, has been explored, indicating the reliance of courts on all three sources plus equitable principles.
A review of the biology and genetics of sea lice
Authors: Boxaspen Karin
Published: July 2006

Studies of the biology of sea lice have been conducted from various perspectives for two decades. For Lepeophtheirus spp., most of the published literature has centred on the economically important Lepeophtheirus salmonis, while for Caligus spp., research has focused on a wider range of species. The most numerous species of Caligus in North Atlantic waters, however, is Caligus elongatus, which is also economically important to salmon farming. Since the last review by Pike, A. W., and Wadsworth, S. L. (1999. Sea lice on salmonids: their biology and control. Advances in Parasitology, 44: 234–337.), research on sea lice has developed considerably, including the application of genetic methods. This new research has focused on life history biology, studying developmental stages under different environmental conditions (e.g. temperature and salinity), behaviour, distribution and the dispersal of free-living stages, monitoring practices, population structure, and modelling. The results of this research have informed risk analyses and allowed the refinement of management strategies to reduce sea lice infestations in wild and farmed populations of anadromous salmonids. Molecular techniques have been used to describe population structure and identify differences in genetic characterization of geographically separate populations and population markers. Research has been initiated to understand the parasite–host relationship at a molecular level and to develop a vaccine against sea lice.
The feeding behaviour of cultured and wild Atlantic salmon, Salmo salar L., in the Louvenga River, Kola Peninsula, Russia
Authors: Orlov Alexander V. , Gerasimov Yuri V. , Lapshin Oleg M.
Published: July 2006

An underwater survey was conducted in the Louvenga River to investigate the behaviour and distribution of juvenile Atlantic salmon, Salmo salar L., and the adaptation of cultured fish to the natural environment. The food and feeding habits of 34 wild and 44 cultured parr released from the Kandalaksha hatchery were also studied. The cultured salmon fed mostly in the bottom 15 cm of the water column in current velocities of 0.2–0.35 m s−1. In contrast to wild fish, when cultured fish moved away from these areas and into areas with higher current velocities (average speeds of 0.52 m s−1) and lower drift density (2.66 particles m−3), they did not show a tendency to return to slower moving water. The diet of cultured parr was made up of benthic invertebrates (20%), terrestrial insects (32%), and drift items (33%), but these proportions were different in the diet of wild parr (2%, 24%, and 67%, respectively), with drift items predominating. The mean quantity of food per stomach indicated that the wild parr were feeding more actively than cultured parr. Invertebrates made up 3% of items in the drift, with the remaining 97% being exuvia of aquatic and terrestrial insects, algae, and various plant remains. Poor quality food items were found in 13% and 25% of the stomachs of wild and cultured parr, respectively, demonstrating that the cultured parr were less able to differentiate food items in the water column and made 20–30% more false feeding attempts than wild fish. The cultured parr were also more aggressive in terms of the frequency of aggressive interactions and reacted to each other at greater distances than wild fish. Thus, wild parr were able to optimize their feeding conditions by choosing habitats with preferred sizes of food items, higher densities of drift items, and current velocities that allowed them to maintain station and to feed more effectively. Conversely, cultured parr usually occupied suboptimal areas.
Joint estimation of calibration and expression for high-density oligonucleotide arrays
Authors: Oberg Ann L. , Mahoney Douglas W. , Ballman Karla V. , Therneau Terry M.
Published: July 2006

Motivation: The need for normalization in microarray experiments has been well documented in the literature. Currently, many analysis methods treat normalization and analysis as a series of steps, with summarized data carried forward to the next step.

Results: We present a unified algorithm which incorporates normalization and class comparison in one analysis using probe level perfect match and mismatch data. The algorithm is based on calibration models common to most biological assays, and the resulting chip-specific parameters have a natural interpretation. We show that the algorithm fits into the statistical generalized linear models framework, describe a practical fitting strategy and present results of the algorithm applied to an example dataset as well as based on metrics used in affycomp. The algorithm ranks amongst the top third of the affycomp competitors, performing best in measures of bias.

Availability: R functions are available on request from the authors.

Contact:  oberg.ann@mayo.edu
The deoxyribonucleic acid (DNA) skin test in systemic lupus erythematosus.
Authors: JOHANSSON E.A , NIEMI K-M. , LASSUS A.
Published: July 2006

A total of fifty-five biopsies from fifty-two intradermal DNA skin tests were studied. The biopsies were taken 6, 8–10,24 or 48 h after the injection of the DNA material. Necrosis of the vessel wall was taken to be the main characteristic of a specific reaction. In forty of the fifty-two tests the results of the histological evaluation closely matched the clinical results. In five of the fifteen cases with discrepancies, the histological evaluation ruled out clinically false positive test results.

In three cases of SLE on corticosteroid treatment, the histological examination gave a positive result despite a clinically negative result.

In seven of the fifteen cases the discrepancies occurred in borderline cases with reactions of 5 to 6 mm diameter.

The amount of inflammatory cells in positive as well as in negative reactions was also recorded. The number of polymorphonuclear cells in positive reactions increased with the age of the reaction. The number of lymphocytes was not found to increase in the positive reactions, thus differing from the delayed hypersensitivity type of reactions. Rather, the reaction was characterized by an Arthus type of hypersensitivity.

On the basis of the present study it may be concluded that clinically positive tests at 6 or 8 h may merely be expressions of nonspecific vascular alterations. On the other hand, in late reactions, even in patients on systemic treatment, histological examination revealed clinically negative results to be positive. By using the histological picture of hypersensitivity angiitis as the main diagnostic criterion the specificity of the clinical reactions may be established.
An improved method of assessing topical corticosteroid activity
Authors: BARNES H. , GAYLARDE P.M , BROCK A.P , SARKANY I.
Published: July 2006

Topical application of ointment bases causes varying degrees of epidermal thickening in guinea-pigs This is reproducible and can be accurately measured. Suppression of these changes was produced by addition of beta-methasone 17-valerate, fluocinolone acetonide, fluocinonide and hydrocortisone acetate. The inhibitory effect of these steroids was related to the type of corticosteroid, its concentration and the ointment base. The effect was still evident at extremely high dilutions of the steroids and could be measured at concentrations as low as 5 × 10-5% of fluocinonide in FAPG.

This technique has the merits of being reproducible, sensitive and accurate. It should find a place among existing methods in assaying the efficacy of topical corticosteroids and in aiding the selection of bases most suitable for formulation of these preparations.
The mitotic index in psoriatic plaques and their response to PUVA therapy
Authors: GOLDBERG L. H. , COX A. J. , ABEL E. A.
Published: July 2006

The mitotic index of pretreatment plaques of chronic psoriasis was determined before treatment with PUVA. There was a wide variation in mitotic indices in different patients.

Treatment was given with UV-A 2 h after oral ingestion of 8-methoxypsoralen (8-MOP) two or three times per week, with increasing doses of UV-A. Patients were considered cleared if there was 95% clearing of all psoriatic plaques.

There was no correlation between the mitotic index and the response to treatment, as measured by either the number of joules administered or the number of treatments until the lesions cleared. This suggests that the action of PUVA in psoriasis is not dependent on the amount of increase in epidermal proliferation.
Methotrexate induced liver cirrhosis
Authors: ZACHARIAE H. , KRAGBALLE K. , SøGAARD H.
Published: July 2006

Seven hundred and sixty-four liver biopsies were performed in 328 psoriatics on treatment with methotrexate or being considered for systemic treatment either with methotrexate or with psoralens and long-wave ultraviolet light. The diagnosis of cirrhosis was established histologically in twenty-one patients. Two patients had cirrhosis in their premethotrexate biopsy and were not given methotrexate. The remainder all showed no signs of cirrhosis or fibrosis in their premethotrexate biopsy. The difference between the methotrexate treated psoriatics and the premethotrexate group was highly significant. Among thirty-nine patients treated for more than 5 years, ten developed cirrhosis (25.6%). Almost all patients were on a divided dose intermittent oral dosage schedule. The cumulative dose of methotrexate, when cirrhosis was first found, ranged from 590 to 8105 mg, with an average dosage of 2200 mg. Other factors contributing to cirrhosis in this study seem to be previous treatment with arsenic, a previous intake of alcohol, and lowered renal function.

Data on later serial biopsies from fourteen patients, of which eleven continued to receive methotrexate due to very severe psoriasis, seem to indicate that methotrexate induced liver cirrhosis is not of a very aggressive nature. When evaluated blind no progression was found in most of the later biopsies, and a ‘cumulative cirrhosis index’ composed of the combined gradings for fibrosis, assessment of membrana limitans, fibrous destruction and regeneration showed a tendency to decrease. In three patients the latest of the serial biopsies showed no cirrhosis. The observation period on continued methotrexate therapy ranged from 1 to 7 years. None of the patients with cirrhosis differed from the remaining patients on methotrexate in their laboratory results for evaluating liver damage, and apart from transient increases in serum glutamic pyruvic transaminases no abnormalities were found.

The data support the necessity of liver biopsies in the control of psoriatics treated with methotrexate. Liver biopsies should be performed at least in all psoriatics in whom a cumulative dosage of methotrexate exceeds 1.5g. The data also indicate that methotrexate can be continued at least for a while in patients where the indication is strong enough, if the dosage is maintained as low as possible and alcohol consumption avoided.
Transient acantholytic dermatosis
Authors: HEENAN P. J. , QUIRK C. J.
Published: July 2006

A series of twenty-four cases of transient acantholytic dermatosis (TAD) is presented. All patients were male and their eruptions tended to be more persistent than those of previously reported cases. The epidermal changes included four patterns of acantholysis, of which the pemphigus-like pattern was associated with the more persistent eruptions. Although twenty-three of the twenty-four patients had other actinic-associated skin lesions, no direct relationship between the onset of TAD and episodes of excessive sun exposure was found. Oral vitamin A treatment has been effective in some cases.
Histochemical staining of sunburn cells for sulphhydryl and disulphide groups: a time course study
Authors: DANNO KIICHIRO , HORIO TAKESHI
Published: July 2006

Ultraviolet light (UV)-exposed rabbit skin was stained with a fluorescent thiol reagent or haematoxylin and eosin to investigate a time relationship between histochemical stainings for sulphhydryl (-SH) and disulphide (S-S) groups and sunburn cell (SBC) production. SBCs appeared by 8 h after irradiation, increased and showed a peak at 48 h, then declined to zero by 96 h. SBCs showing -SH staining increased to a maximum of 41–59% at 24–48 h and declined to 26–45% by 72 h, whereas S-S-stained SBCs were only a few at 8–24 h and then increased up to 65–85% by 72 h. The results seem to indicate that S-S linkage may occur in the process of SBC production.
Clinical value of serum γ-glutamyl transferase estimation in porphyria cutanea tarda
Authors: ADJAROV D. , IVANOV E.
Published: July 2006

Serum γ-glutamyl transferase was elevated fourfold in all thirty-four new cases of porphyria cutanea tarda. Phlebotomy treatment decreased it. The twelve patients in relapse showed a considerable increase, while those in remission tended to a gradual elevation in the enzyme over the course of years. γ-Glutamyl transferase is a useful auxiliary parameter in porphyria cutanea tarda particularly in untreated cases.
A histometric and autoradiographic study of hydrocortisone action in cultured human epidermis
Authors: TAMMI RAIJA
Published: July 2006

Pieces of human skin maintained their viability, grew and differentiated for at least 10 days in chemically defined (serum-free) culture conditions. Physiological concentrations of hydrocorti sone, added to the cultures, were shown to cause thinning of epidermis, which was due to decreased rate of epidermal proliferation. The relative volume of normal, orthokeratotic stratum corneum with underlying granular cells was increased concomitantly with epidermal thinning. The present findings show that even small concentrations of the hormone influence epidermal cell proliferation and suggest that hydrocortisone has a physiological role in keratinization. The possibility of using human skin culture in the assessment of the antiproliferative and atrophogenic action of synthetic glucocorticoids is discussed.
Sclerosing lipogranuloma of the male genitalia: ultrastructural study
Authors: CLAUDY A. , GARCIER F. , SCHMITT D.
Published: July 2006

Ultrastructural study of a case of sclerosing lipogranuloma showed a predominantly histiocytic-like cell infiltrate with numerous intracytoplasmic vacuoles of varied sizes without any limiting membrane and located in the deep dermis and subcutaneous fat. Fibroblasts appeared normal. Polymorphonuclear cells and macrophages were absent. This appearance was different from that described in ‘classical’ phagocytosis, mucopolysaccharidoses or polyvinylpyrrolidone storage syndrome.
Circulating testosterone, sex hormone binding globulin and prolactin in women with late onset or persistent acne vulgaris
Authors: DARLEY C.R. , KIRBY J.D. , BESSER G.M. , MUNRO D.D. , EDWARDS C.R.W. , REES L.H.
Published: July 2006

Serum testosterone, sex hormone binding globulin (SHBG) and prolactin were measured in thirty-eight women with acne which persisted or started after the age of 18 years. One or more of these levels were abnormal in 76% of patients. Increased testosterone or low SHBG were present alone or in combination in 60% of patients. This group was presumed to have a raised level of non-protein bound, metabolically-available testosterone. Hyperprolactinaemia, which was present in 45% of patients, may be important in view of the reported association with increased adrenal androgens. The hormonal abnormalities may be causally related to the acne and a greater understanding of them may lead to better treatment.
Primary onycholysis of the big toenails: a review of 113 cases
Authors: BARAN R. , BADILLET G.
Published: July 2006

We have reviewed the clinical and microbiological features of 113 cases of idiopathic onycholysis primarily affecting the great toenails. It is suggested that the majority of these cases were traumatic in origin. Although dermatophytes and potentially pathogenic bacteria were frequently found in the lesions, they were thought to be commensal in most cases. This is of considerable significance with regard to the selection of appropriate therapy.
Monetary Circulation and the Political History of Archaic Borysthenes
Authors: Solovyov Sergei
Published: July 2006

The paper is devoted to the monetary circulation of Borysthenes, which was founded in the lower reaches of the rivers Hypanis and Borysthenes, and was one of the earliest Milesian colonies in the northern Black Sea area. In the second half of the 6th century BC, its monetary production consisted of cast bronze coins in the shape of small 'arrowheads' and large trapezoid segments with relief images of an arrowhead and a head of tuna fish on the both sides. If 'arrowhead' money was widespread in the region previously, the segments were found on Berezan and in its vicinity only. The issue of such money, especially those of large face-values, was the purposeful demarche of Borysthenes in the development of its own coin denomination based both on 'arrowheads' and on the weight standard of Cyzicus' coinage. Authorities of the polis appeared to attempt to underline the connection of the new money with the Phocaean weight standard or Cyzicus' coins, taking into account the major orientation of Borysthenes' economy, which was mainly based on trading and handicraft. However, both 'arrowheads' and segments were only the mark of value exchange at a conditional rate. Other cast money of the region in the Late Archaic period was 'dolphins'. They appeared to be the first Olbia polis coins. The foundation of Olbia followed Borysthenes, when, in the last quarter of the 6th century BC, a significant group of new colonists arrived to the region. The social conflict between the first settlers and the newcomers expressed in the form of a dispute between worshippers of Apollo the Healer and Apollo Delphinios. The recovery of social peace in the region was owed to an oracle of Apollo of Didyma; its text was found on Berezan. The expression of the peaceful coexistence of two forms of the cult and two groups of the settlers was obviously permitting the equivalent circulation of different polis coin forms, which were those of 'arrowheads' and 'dolphins' probably authorized by the temples of the two deities. Their symbolism was directly connected to the cults of Apollo the Healer and Apollo Delphinios, who was the patron of the Milesian colonies. Due to military and political instability in the steppe zone of the northern Black Sea area in the second and third quarters of the 5th century BC, Borysthenes lost its political independence, and was transformed into an emporion dependant on the Olbia polis, forfeiting its right to issue its own money. Some part of Borysthenes' population appeared to resettle to Kerkinitis in the northwestern Crimea, which started to issue cast cooper 'arrowhead-fish' and 'arrowhead' money in the 5th century BC.
The Caspian Conundrum: Reflections on the Interplay Between Law, the Environment and Geopolitics
Authors: Joyner Christopher , Walters Kelly Zack
Published: July 2006

Rising world demand for petroleum and natural gas makes the Caspian Sea and its resources the focus of increased international attention. This article examines the controversy over the legal condition of the Caspian Sea, both in terms of delimination questions and its status as a lake or a semi-enclosed sea. The natural resource potential of the Caspian is assessed, with a view to highlighting its hydrocarbon and fishery resources, as well as the environmental implications posed by development of industry and pipelines throughout the region. Also examined are the geopolitical priorities of the five Caspian littoral states, as well as the need to maintain the region as a zone for peaceful commercial enterprise and economic development. Toward these ends, the study concludes with an evaluation of the realistic prospects for collaboration among the Caspian states to protect the environment as evidenced by the recent negotiation of a special convention dedicated to that purpose.
Synthesis and properties of organic‐silica nanocomposites with perhydropolysilazane
Authors: Saito Reiko
Published: July 2006

The synthesis and properties of the organic polymer‐silica nanocomposites by blending perhydropolysilazane with organic polymer having hydroxyl groups have been described. Poly(methyl methacrylate) (PMMA)‐silica nanocomposites with a PMMA/silica lamellar structure and spherical silica domains in a PMMA matrix were obtained with random copolymers and block copolymers. The effect of the architecture of the random and block copolymers on the morphology of composites has been summarized. The thermal stability, electrical properties, such as field break down, leakage current, etc., and surface hardness of the composites have been discussed. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 5174–5181, 2006
Polyploidization increases the sensitivity to DNA‐damaging agents in mammalian cells
Authors: Hau Pok Man , Siu Wai Yi , Wong Nathalie , Lai Paul B.S. , Poon Randy Y.C.
Published: July 2006

Polyploidization occurs during normal development as well as during tumorigenesis. In this study, we investigated if the responses to genotoxic stress in cancer cells are influenced by the ploidy. Prolonged treatment of Hep3B cells with the spindle inhibitor nocodazole resulted in mitotic slippage, followed by re‐replication of the DNA to produce polyploids. Reintroduction of p53 restored the checkpoints and suppressed polyploidization. Remarkably, a stable tetraploidy cell line could be generated from Hep3B by a transient nocodazole treatment followed by a period of recovery. Using this novel tetraploid system, we found that tetraploidization increased the cell volume without significantly affecting the cell cycle. Although tetraploidization was accompanied by an increase in centrosome number, the majority of mitoses in the tetraploid cells remained bipolar. Polyploidization sensitized cells to genotoxic stress inflicted by ionizing radiation and topoisomerase inhibitors without affecting the sensitivity to spindle inhibitors. Accordingly, more gamma‐H2AX foci were induced by radiation in tetraploids than in normal Hep3B cells. Likewise, primary tetraploid human fibroblasts displayed higher gamma‐H2AX foci formation than diploid human fibroblasts. An implication for chemotherapy is that some cancer cells can be sensitized to genotoxic agents by a preceding step that induces polyploidization.
Sonic tracking of wild cod, Gadus morhua, in an inshore region of the Bay of Fundy: a contribution to understanding the impact of cod farming for wild cod and endangered salmon populations
Authors: Brooking Paul , Doucette Gino , Tinker Steve , Whoriskey Frederick G.
Published: July 2006

Sea cage trials of Atlantic cod farming have begun in the Bay of Fundy region. We fitted inshore wild cod (n = 10) captured in the Quoddy region with sonic tags during the late summer of 2004 to provide data on their temporal and spatial residency and habitat usage, with a view to understanding the potential for impact between escaped farmed cod and wild cod and other fish species, particularly Atlantic salmon. Most of the tagged cod remained within a restricted corridor in the inshore zone, occupied deep water (75–130 m) within several kilometres of the release point, and undertook local movements. Three cod undertook more extensive movements; one fish emigrated offshore immediately, and two fish moved as far as 14 km from the release point before returning, 52–54 h later, to the area in which the other cod were located. The mean residence time in the inshore zone was 55 days. In the late autumn, there was a staggered pattern of departure from the coastal zone, although one fish over-wintered in Passamaquoddy Bay. Three of the nine cod that migrated offshore in autumn 2004 returned within a three-week period in May 2005, after a mean absence of 172 days, and reoccupied the inshore region inhabited the previous year. These cod left the region again after a mean residence of 120 days during the spring and summer. The presence of some of the tagged cod in the principal migration corridor for wild salmon smolts during the period of their migration suggests that escapes from cod farms could result in increased predation on salmon smolts from endangered populations.
Construction and Characterization of ack Deleted Mutant of Clostridium tyrobutyricum for Enhanced Butyric Acid and Hydrogen Production
Authors: Liu Xiaoguang , Zhu Ying , Yang Shang‐Tian
Published: July 2006

Clostridium tyrobutyricum produces butyrate, acetate, H2, and CO2 as its main fermentation products from glucose and xylose. To improve butyric acid and hydrogen production, integrational mutagenesis was used to create a metabolically engineered mutant with inactivated ack gene, encoding acetate kinase (AK) associated with the acetate formation pathway. A non‐replicative plasmid containing the acetate kinase gene (ack) fragment was constructed and introduced into C. tyrobutyricum by electroporation. Integration of the plasmid into the homologous region on the chromosome should inactivate the target ack gene and produce ack‐deleted mutant, PAK‐Em. Enzyme activity assays showed that the AK activity in PAK‐Em decreased by ∼50%; meanwhile, phosphotransacetylase (PTA) and hydrogenase activities each increased by ∼40%. The sodium dodecyl sulfate‐polyacrylamide gel electrophoresis (SDS‐PAGE) results showed that the expression of protein with ∼32 kDa molecular mass was reduced significantly in the mutant. Compared to the wild type, the mutant grew more slowly at pH 6.0 and 37 °C, with a lower specific growth rate of 0.14 h−1 (vs 0.21 h−1 for the wild type), likely due to the partially impaired PTA‐AK pathway. However, the mutant produced 23.5% more butyrate (0.42 vs 0.34 g/g glucose) at a higher final concentration of 41.7 g/L (vs 19.98 g/L) as a result of its higher butyrate tolerance as indicated in the growth kinetics study using various intial concentrations of butyrate in the media. The mutant also produced 50% more hydrogen (0.024 g/g) from glucose than the wild type. Immobilized‐cell fermentation of PAK‐Em in a fibrous‐bed bioreactor (FBB) further increased the final butyric acid concentration (50.1 g/L) and the butyrate yield (0.45 g/g glucose). Furthermore, in the FBB fermentation at pH 5.0 with xylose as the substrate, only butyric acid was produced by the mutant, whereas the wild type produced large amounts of acetate (0.43 g/g xylose) and lactate (0.61 g/g xylose) and little butyrate (0.05 g/g xylose), indicating a dramatic metabolic pathway shift caused by the ack deletion in the mutant.
Genetic diversity ofSinapis albagermplasm as revealed by AFLP markers
Authors: Fu Yong-Bi , Gugel Richard K. , Katepa-Mupondwa Felicitas
Published: July 2006

Sinapis albaL. is a major specialty crop grown as a condiment in western Canada, but little is known about its genetic diversity. The objective of this study was to assess the level and pattern of genetic diversity in a collection of 127S. albaaccessions held at Plant Gene Resources of Canada using amplified fragment length polymorphism (AFLP) markers. Five AFLP primer pairs were applied, and 134 polymorphic bands were scored for each accession. These scored bands had frequencies of occurrence ranging from 0.02 to 0.99 with an average of 0.69. More AFLP variation was found within single (79.1%) than between (20.9%)S. albaaccessions. A small degree of AFLP difference (1.7%) was observed among the accessions of various regions, while relatively large variation (9.2%) existed among the accessions of various countries. A large AFLP difference (15.6%) also existed between the yellow- and brown-seeded accessions, but only 6.2% difference was observed between the cultivar and landrace accessions. Two distinct groups ofS. albagermplasm were identified on the basis of the seed colour (yellow or brown), although a few mixtures also existed. No apparent ‘duplicated’ accessions were observed. The most diverse accessions were from Italy, Spain, France and Greece. Among the most genetically distinct accessions were SA97 from Portugal, SA89 and SA88 from France, SA83 from Russia and SA57 from Italy. These findings are significant not only for managingS. albagermplasm, but also for identifying diverse germplasm that can be used by plant breeders to improveS. albaseed yield and quality parameters.
Out-crossing between genetically modified herbicide-tolerant and other winter oilseed rape cultivars
Authors: Simpson Euan , McRoberts Neil , Sweet Jeremy
Published: July 2006

Out-crossing between genetically modified herbicide-tolerant (GMHT) and non-GM rape cultivars was studied using GMHT source field plots of approximately 0.8 ha. Levels of cross-pollination between adjacent fully fertile rape varieties declined rapidly with increasing distance from the interface between plots. A varietal association with low levels of male sterility showed higher levels of out-crossing than other varieties. Out-crossing data were used to compare negative exponential and inverse power-law models for their fit to describe the observed relationship between cross-pollination and distance from source. Results showed that the inverse power-law model provided a better fit of the data.
Partition resampling and extrapolation averaging: approximation methods for quantifying gene expression in large numbers of short oligonucleotide arrays
Authors: Goldstein Darlene R.
Published: July 2006

Motivation: Studies of gene expression using high-density short oligonucleotide arrays have become a standard in a variety of biological contexts. Of the expression measures that have been proposed to quantify expression in these arrays, multi-chip-based measures have been shown to perform well. As gene expression studies increase in size, however, utilizing multi-chip expression measures is more challenging in terms of computing memory requirements and time.

Results: A strategic alternative to exact multi-chip quantification on a full large chip set is to approximate expression values based on subsets of chips. This paper introduces an extrapolation method, Extrapolation Averaging (EA), and a resampling method, Partition Resampling (PR), to approximate expression in large studies.

An examination of properties indicates that subset-based methods can perform well compared with exact expression quantification. The focus is on short oligonucleotide chips, but the same ideas apply equally well to any array type for which expression is quantified using an entire set of arrays, rather than for only a single array at a time.

Availability: Software implementing Partition Resampling and Extrapolation Averaging is under development as an R package for the BioConductor project.

Contact:  Darlene.Goldstein@epfl.ch
Variance stabilization and normalization for one-color microarray data using a data-driven multiscale approach
Authors: Motakis E. S. , Nason G. P. , Fryzlewicz P. , Rutter G. A.
Published: July 2006

Motivation: Many standard statistical techniques are effective on data that are normally distributed with constant variance. Microarray data typically violate these assumptions since they come from non-Gaussian distributions with a non-trivial mean–variance relationship. Several methods have been proposed that transform microarray data to stabilize variance and draw its distribution towards the Gaussian. Some methods, such as log or generalized log, rely on an underlying model for the data. Others, such as the spread-versus-level plot, do not. We propose an alternative data-driven multiscale approach, called the Data-Driven Haar–Fisz for microarrays (DDHFm) with replicates. DDHFm has the advantage of being ‘distribution-free’ in the sense that no parametric model for the underlying microarray data is required to be specified or estimated; hence, DDHFm can be applied very generally, not just to microarray data.

Results: DDHFm achieves very good variance stabilization of microarray data with replicates and produces transformed intensities that are approximately normally distributed. Simulation studies show that it performs better than other existing methods. Application of DDHFm to real one-color cDNA data validates these results.

Availability: The R package of the Data-Driven Haar–Fisz transform (DDHFm) for microarrays is available in Bioconductor and CRAN.

Contact:  g.p.nason@bristol.ac.uk
Hierarchical classification of hydrolases catalytic sites
Authors: Gariev Igor A. , Varfolomeev Sergey D.
Published: July 2006

Summary: Universal ontology of catalytic sites is required to systematize enzyme catalytic sites, their evolution as well as relations between catalytic sites and protein families, organisms and chemical reactions. Here we present a classification of hydrolases catalytic sites based on hierarchical organization. The web-accessible database provides information on the catalytic sites, protein folds, EC numbers and source organisms of the enzymes and includes software allowing for analysis and visualization of the relations between them.

Availability:  

Contact:  gariev@hotmail.com
SANTA domain: a novel conserved protein module in Eukaryota with potential involvement in chromatin regulation
Authors: Zhang Dapeng , Martyniuk Christopher J. , Trudeau Vance L.
Published: July 2006

Since packaging of DNA in the chromatin structure restricts the accessibility for regulatory factors, chromatin remodeling is required to facilitate nuclear processes such as gene transcription, replication, and genome recombination. Many conserved non-enzymatic protein domains have been identified that contribute to the activities of multiprotein remodeling complexes. Here we identified a novel conserved protein domain in Eukaryota whose putative function may be in regulating chromatin remodeling. Since this domain is associated with a known SANT domain in several vertebrate proteins, we named it the SANTA (SANT Associated) domain. Sequence analysis showed that the SANTA domain is approximately a 90 amino acid module and likely composed of four central β-sheets and three flanking α-helices. Many hydrophobic residues exhibited high conservation along the domain, implying a possible function in protein–protein interactions. The SANTA domain was identified in mammals, chicken, frog, fish, sea squirt, sea urchin, worms and plants. Furthermore, a phylogenetic tree of SANTA domains showed that one plant-specific duplication event happened in the Viridiplantae lineage.

Contact:  trudeauv@uottawa.ca

Supplementary Information:  Supplementary Figure S1 for this paper is available at Bioinformatics online.
Absorption and biotransformation of topically applied 8-(methylthio)cyclic AMP
Authors: DREYFUSS JACQUES , MISCHLER TERRENCE W. , NEISS EDWARD S. , SHAW JAMES M. , SCHREIBER ERIC C.
Published: July 2006

8-(Methylthio)cyclic AMP-35S was applied topically to the intact or abraded skin of dogs at a dose of about 2.5 mg/kg. In this species, an average of 7% of the dose was absorbed through the intact and 62% through abraded skin. Half-lives for radioactivity in plasma averaged 3.6 h. After the topical application of the drug to the intact skin of dogs, the average concentration in plasma of glucose, but not of insulin, was increased by as much as 21% after application to abraded skin, glucose and insulin were increased, on average, by as much as 84 and 221%, respectively. 8-(methylthio)adenosine and two unidentified compounds were present as metabolites in the urine of dogs; some unchanged 8-(methylthio)cyclic AMP-35S was also excreted. 8-(methylthio)cyclic AMP-35S was also applied topically (25 mg; 0.32 mg/kg) to the intact and stripped skin of normal human subjects under conditions similar to those used for dogs. Three subjects with intact skin did not absorb any of the drug, whereas three subjects with stripped skin absorbed 0.5, 8.3, and 23.3% of the dose. The half-life of radioactivity in the plasma of the subject with the greatest absorption was 0.5 h during the first 2 h, and 11 h for the next 10 h. During the first 2 h, this same subject excreted unchanged drug and 8-(methylthio)adenosine in his urine. No changes in glucose or insulin concentrations in plasma were observed in any of the subjects nor was there any apparent irritation of the skin.
Lysosomal hydrolases of the epidermis
Authors: MIER P.D , VAN DEN HURK JOSÉ J.M.A.
Published: July 2006

Five distinct ester hydrolases (EC 3.1) have been characterized in guinea-pig epidermis. These are carboxylic esterase, acid phosphatase, pyrophosphatase, and arylsulphatases A and B. Their properties are consistent with those of lysosomal enzymes.
The deoxyribonucleic acid (DNA) skin test in systemic lupus erythematosus.
Authors: JOHANSSON E.A , KIISTALA U. , NIEMI K-M. , HALME H. , LASSUS A.
Published: July 2006

A clinical evaluation of the intradermal DNA-test was carried out on a series of patients with untreated or with treated definite systemic lupus erythematosus (SLE), or with suspected SLE with or without circulating antinuclear factors. A saline solution of a commercially available DNA-preparation was used. The course of the DNA reaction was followed for 24–48 h after the injection.

All nine cases of untreated definite SLE had a positive DNA test 6 h after the injection, and eight cases a positive result at 24 h. All seven patients with definite SLE who were on low-dosage systemic steroid treatment had a clinically positive DNA test at 6 h. In all except one of these cases the test was still positive at 24 h. All five patients with definite SLE on antimalarial treatment had a positive test at 6 h which had become negative at 24 h after the injection. Eleven of the twelve patients with suspected SLE and circulating antinuclear factors had a positive DNA test at 6 h, which in nine cases persisted for 24 h. On the other hand, of the eleven ANF negative patients with various connective tissue diseases five had a positive test at 6 h. In only one of these cases it persisted for 24 h. Two of the eighteen control patients with various dermatoses exhibited a positive test at 6 h, and in one of these the positive reaction persisted for 24 h.

It is concluded that the intradermal skin test using native DNA is a useful diagnostic tool for the detection of SLE when the reaction is followed up for 24 h. Antimalarial treatment seems to decrease skin reactivity to native DNA.
Lichen planus and ulcerative colitis
Authors: WYATT EDWARD H.
Published: July 2006

Three patients with ulcerative colitis and lichen planus are reported and similar cases in the literature discussed. Similarities in the pathology of the two conditions are outlined.