bluuebunny/crossref_metadata_2025_split huggingface dataset:
A comparison of background correction methods for two-colour microarrays
Authors: Ritchie Matthew E. , Silver Jeremy , Oshlack Alicia , Holmes Melissa , Diyagama Dileepa , Holloway Andrew , Smyth Gordon K. 
Published: August 2007

AbstractMotivation: Microarray data must be background corrected to remove the effects of non-specific binding or spatial heterogeneity across the array, but this practice typically causes other problems such as negative corrected intensities and high variability of low intensity log-ratios. Different estimators of background, and various model-based processing methods, are compared in this study in search of the best option for differential expression analyses of small microarray experiments.Results: Using data where some independent truth in gene expression is known, eight different background correction alternatives are compared, in terms of precision and bias of the resulting gene expression measures, and in terms of their ability to detect differentially expressed genes as judged by two popular algorithms, SAM and limma eBayes. A new background processing method (normexp) is introduced which is based on a convolution model. The model-based correction methods are shown to be markedly superior to the usual practice of subtracting local background estimates. Methods which stabilize the variances of the log-ratios along the intensity range perform the best. The normexp+offset method is found to give the lowest false discovery rate overall, followed by morph and vsn. Like vsn, normexp is applicable to most types of two-colour microarray data.Availability: The background correction methods compared in this article are available in the R package limma (Smyth, 2005) from http://www.bioconductor.org.Contact: smyth@wehi.edu.auSupplementary information: Supplementary data are available from http://bioinf.wehi.edu.au/resources/webReferences.html.
An improved algorithm for clustering gene expression data
Authors: Bandyopadhyay Sanghamitra , Mukhopadhyay Anirban , Maulik Ujjwal 
Published: August 2007

AbstractMotivation: Recent advancements in microarray technology allows simultaneous monitoring of the expression levels of a large number of genes over different time points. Clustering is an important tool for analyzing such microarray data, typical properties of which are its inherent uncertainty, noise and imprecision. In this article, a two-stage clustering algorithm, which employs a recently proposed variable string length genetic scheme and a multiobjective genetic clustering algorithm, is proposed. It is based on the novel concept of points having significant membership to multiple classes. An iterated version of the well-known Fuzzy C-Means is also utilized for clustering.Results: The significant superiority of the proposed two-stage clustering algorithm as compared to the average linkage method, Self Organizing Map (SOM) and a recently developed weighted Chinese restaurant-based clustering method (CRC), widely used methods for clustering gene expression data, is established on a variety of artificial and publicly available real life data sets. The biological relevance of the clustering solutions are also analyzed.Contact: anirbanbuba@yahoo.comSupplementary information: The processed and normalized data sets, supplementary figures, tables and other related materials are available at http://d.1asphost.com/anirbanmukhopadhyay/simmts.html
Silver eel mortality during downstream migration in the River Meuse, from a population perspective
Authors: Winter Hendrik V. , Jansen Henrice M. , Breukelaar André W. 
Published: August 2007

Abstract
Winter, H. V., Jansen, H. M., and Breukelaar, A. W. 2007. Silver eel mortality during downstream migration in the River Meuse, from a population perspective. – ICES Journal of Marine Science, 64: 1444–1449. The European eel (Anguilla anguilla) population has decreased sharply over the past few decades owing to a combination of many factors. To determine the impact of hydropower and fisheries during the downstream migration of silver eel in the River Meuse, telemetry experiments were performed during the years 2002–2006, using 18 detection stations (NedapTrail-System®) in the river and two at the entrance to the hydropower turbines. Recaptures in fisheries were used to assess fisheries mortality. In all, 300 silver eels were surgically implanted with Nedap-transponders. For each stretch between subsequent stations, mortality rates were assessed and related to the different factors. However, to determine the overall effect on the escapement of silver eels from the River Meuse, insight into the distribution of silver eels in the entire catchment of the River Meuse is required. At two locations, mark-recapture experiments in 2002 revealed that the estimated number of migrating silver eels increased strongly in a downstream direction, suggesting that a large proportion of silver eels start their migration from the downstream stretches and tributaries of the River Meuse. Approaches and monitoring requirements that can be used to determine the impact on silver eel populations in a river basin are discussed.
INSULIN AS A VASCULAR HORMONE: IMPLICATIONS FOR THE PATHOPHYSIOLOGY OF CARDIOVASCULAR DISEASE
Authors: Cleland Stephen J , Petrie John R , Ueda Shinichiro , Elliott Henry L , Connell John MC 
Published: August 2007

1. Metabolic disorders, such as obesity and non‐insulin‐dependent diabetes mellitus, and cardiovascular disorders, such as essential hypertension, congestive cardiac failure and atherosclerosis, have two features in common, namely relative resistance to insulin‐mediated glucose uptake and vascular endothelial dysfunction.2. Significant increases in limb blood flow occur in response to systemic hyperinsulinaemia, although there is marked variation in the results due to a number of confounding factors, including activation of the sympathetic nervous system. Local hyperinsulinaemia has a less marked vasodilator action despite similar plasma concentrations, but this can be augmented by co‐infusing D‐glucose.3. Insulin may stimulate endothelial nitric oxide production or may act directly on vascular smooth muscle via stimulation of the Na+–H+ exchanger and Na+/K+‐ATPase, leading to hyperpolarization of the cell membrane and consequent closure of voltage‐gated Ca2+ channels.4. There is evidence both for and against the existence of a functional relationship between insulin‐mediated glucose uptake (insulin sensitivity) and insulin‐mediated vasodilation (which can be regarded as a surrogate measure for endothelial function).5. If substrate delivery is the rate‐limiting step for insulin‐mediated glucose uptake (in other words, if skeletal muscle blood flow is a determinant of glucose uptake), then endothelial dysfunction, resulting in a relative inability of mediators, including insulin, to stimulate muscle blood flow, may be the underlying mechanism accounting for the association of atherosclerosis and other cardiovascular disorders with insulin resistance.6. Glucose uptake may determine peripheral blood flow via stimulation of ATP‐dependent ion pumps with consequent vasorelaxation.7. A ‘third factor’ may cause both insulin resistance and endothelial dysfunction in cardiovascular disease. Candidates include skeletal muscle fibre type and capillary density, distribution of adiposity and endogenous corticosteroid production.8. A complex interaction between endothelial dysfunction, abnormal skeletal muscle blood flow and reduced insulin‐ mediated glucose uptake may be central to the link between insulin resistance, blood pressure, impaired glucose tolerance and the risk of cardiovascular disease. An understanding of the primary mechanisms resulting in these phenotypes may reveal new therapeutic targets in metabolic and cardiovascular disease.
ALLOSTERIC INTERACTIONS AT MUSCARINIC CHOLINOCEPTORS
Authors: Christopoulos Arthur , Lanzafame Alfred , Mitchelson Fred 
Published: August 2007

1. An allosteric interaction occurs when the binding of a ligand to its site on a receptor is able to modify the binding of another ligand to a topographically distinct site on the same receptor and vice versa. The muscarinic cholinoceptors represent the best‐studied examples of allosteric phenomena among the G‐protein‐coupled receptor superfamily.2. The simplest model describing allosteric interactions at muscarinic cholinoceptors is the ternary complex model, which allows for a three‐way interaction between the receptor, a classical (orthosteric) ligand and an allosteric modulator. The interaction may be quantified using the dissociation constant of each ligand for its respective binding site on the free receptor and the ‘co‐operativity factor’α. This latter term is the ratio of affinities of a ligand for the occupied versus the unoccupied receptor and is a measure of the magnitude of the co‐ operativity between two concomitantly bound ligands.3. Identification of allosteric phenomena requires the utilization of both radioligand binding and functional approaches. Manifestations of allosterism include: (i) a limited ability to influence radioligand binding as the concentration of the latter is increased; (ii) alterations in the dissociation rate of orthosteric ligands; (iii) curvilinear Schild regressions; and (iv) non‐ additivity of agonist/orthosteric antagonist/allosteric modulator combination concentration ratios.4. Allosteric modulators of muscarinic cholinoceptors represent a diverse range of compounds. Some of the most studied agents include gallamine, alcuronium and thebis‐ammonium compounds, C7/3′‐phth and W84. Alcuronium has proven a most useful pharmacological tool, as it has been shown to display both positive and negative co‐operativity, depending on the receptor subtype and orthosteric ligand involved in the interaction.5. Evidence has accumulated pointing to the existence of a common allosteric binding site on the muscarinic cholinoceptors, located close to the orthosteric site, but at a more extracellular level. However, the possibility of more than one accessory binding site on various receptor subtypes cannot be excluded.6. Allosteric modulators offer a number of potential therapeutic advantages, including a ceiling level to their effects and the possibility of ‘absolute selectivity’ of action, based on the degree of co‐operativity rather than the affinity of the modulator for any one receptor subtype.
SODIUM BALANCE AND JEJUNAL ION AND WATER ABSORPTION IN DAHL SALT‐SENSITIVE AND SALT‐RESISTANT RATS
Authors: Pácha Jirˇí 
Published: August 2007

1. Apparent Na+ absorption and jejunal water, Na+, Cl− and K+ absorption in vivo was evaluated in young (prepubertal) and adult Dahl salt‐sensitive (DS) and Dahl salt‐resistant (DR) rats kept on a low‐salt (low‐salt rat chow + distilled water) or a high‐salt diet (HS1 diet: NaCl‐enriched rat chow + distilled water; HS2 diet: standard rat chow + 1% saline as drinking fluid). These two high‐salt diets were chosen because the HS1 regimen has been shown to increase blood pressure (BP) in DS rats and the HS2 regimen decreases jejunal water and ion absorption in normotensive Wistar rats.2. The HS1 or HS2 diet increased BP in young and adult DS rats but had no effect on the BP of young and adult DR rats.3. Irrespective of dietary Na+ intake, no significant difference of apparent Na+ absorption (dietary Na+ intake minus faecal Na+ output) was observed between DS and DR rats both in prepuberty and in adulthood. Young DS rats kept on a low‐salt diet had increased faecal Na+ output in comparison with young DR rats. This difference disappeared with increasing dietary Na+ intake.4. There were no interstrain differences on the effect of a high‐salt diet on jejunal Na+ and K+ absorption in young and adult DS and DR rats. However, high‐salt diets stimulated jejunal water and Cl− absorption in young DS rats, but not in adult DS rats and young and adult DR rats. Interstrain differences of water and Cl− absorption were observed only in adulthood. Adult DR rats kept on an HS2 diet absorbed more water and Cl− than their DS counterparts.5. Our results do not indicate any abnormalities of apparent Na+ absorption and jejunal water and electrolyte transport in DS and DR rats. We conclude that there is no relationship between intestinal Na+ absorption and sensitivity or resistance to induction of experimental salt hypertension.
THE EFFECT OF DAYLENGTH AND LIGHT INTENSITY ON THE GROWTH RATE OF THE MARINE DIATOM DETONULA CONFERVACEA (CLEVE) GRAN1
Authors: Holt Marjorie G. , Smayda Theodore J. 
Published: August 2007

SUMMARYThe influence of 40 combinations of temperature (2, 7 C), light intensity (50, 200, 600, 1200, 1800 ft‐c), and photoperiod (24, 15:9, 12:12, and 8:16 LD) at 30% salinity on the rate of cell division of the Narragansett Bay clone of Detonula confervacea (Det‐1) was examined following appropriate preconditioning. At 2 C Detonula is a long day species (24 L) and prefers low light intensities (200–600 ft‐c); poorest growth occurred at 12:12 and 8:16 LD, and the compensation intensity was about 10 ft‐c. Increasing temperature to 7 C increased the mean growth rate, reduced the optimal daylength (15:9 LD), even though Detonula remained a long day species and increased the optimal light intensity (600–800 ft‐c). The compensation intensity varied with daylength and ranged from about 10–50 ft‐c. Photoperiods of 12:12 and 8:16 LD were least favorable for growth at both temperatures; light limitation and inhibition were observed at 50 and 1800 ft‐c. respectively; inhibition was less pronounced at 7 C. There is some indication that the conditions of growth that the stock cultures were exposed to prior to preconditioning for use in the experiments may have sometimes influenced response. Detonula produced resting spores without nutrient depletion at 2 and 7 C at all light intensities when the photoperiod was lengthened. Auxospore formation was also observed.Although short daylengths (9:15 LD) limit Detonula's growth during the early stages of the winter bloom, it competes successfully against Skeletonema costatum initially. This results from its higher rates of growth and of photosynthesis at the prevailing temperature and light conditions and a lower compensation intensity than reported for Skeletonema. The main causes of Detonula's growth inception and termination in Narragansett Bay differ.
ULTRASTRUCTURE OF THE FILAMENTOUS HABIT IN THE DIATOM NAVICULA CONFERVACEA (KÜTZ.) GRUN.1
Authors: Busch David E. 
Published: August 2007

SUMMARYFrustules of the filamentous diatom Navicula confervacea (Kütz.) Grun. are united by the overlapping of marginal teeth located alongside the junction of valve face and mantle. Scanning and transmission electron microscopy show this connecting mechanism to differ from the previously reported inter‐digitating spines or teeth in the genera Melosira, Stephanodisus, and Fragilaria.
MICROAUTORADIOGRAPHIC STUDIES OF THE MARINE PHYCOBIONTS RHIZOSOLENIA AND RICHELIA1
Authors: Weare N. M. , Azam F. , Mague T. H. , Holm‐Hansen O. 
Published: August 2007

SUMMARYMicroautoradiography was used to study photosynthetic and heterotrophic activities in cells of the diatom Rhizosolenia styliformis var. longispina containing the nitrogen‐fixing, endophytic, blue‐green alga Richelia intracellularis. In field studies with 14C‐labeled bicarbonate, the blue‐green alga appeared to be actively photosynthesizing but the diatom did not. Neither Richelia nor Rhizosolenia assimilated, 3H‐labeled acetate, glucose, or an amino acid mixture. The diatom lacked cytoplasmic streaming and appeared, to be in a senescent condition. Implications of these observations for the nature of this algal association are discussed.
CELL DIVISION INCHLAMYDOMONAS MOEWUSII1
Authors: Triemer Richard E. , Brown R. Malcolm 
Published: August 2007

SUMMARYCell division inChlamydomonas moewusiiis described. The cells become immobile with flagellar abscission prior to mitosis. The basal bodies migrate toward the nucleus and become intimately associated with the nuclear membrane which is devoid, of ribosomes where adjacent to the basal bodies. The basal bodies replicate at preprophase. The nucleolus fragments at this stage. By prophase the basal body pairs have migrated, to the nuclear poles. Spindle fibers become prominent in the nucleus. The nuclear membrane does not fragment. The nucleus assumes a crescent‐form by metaphase. Polar fenestrae are absent. Kinetochores appear at anaphase. An interzonal spindle elongates as the chromosomes move to the nuclear poles. Daughter nuclei become abscised by an ingrowth of nuclear membrane, leaving behind a separated, degenerating interzonal spindle. Ribosomes reappear on the outer nuclear membrane at late telophase. Nucleoli reform early in cytokinesis. The cleavage furrow, associated microtubules, and endoplasmic reticulum comprise the phycoplast. Cytokinesis proceeds rapidly after the completion of telophase. The basal body‐nucleus relationship becomes reorganized into the typical interphase condition late in cytokinesis. Specific and predictable organelle rearrangements during mitosis have been described. Cell division inC. moewusiiis compared with other algae, especiallyC. reinhardi.
A NUTRITIONAL ANALYSIS OF A SUBLITTORAL DIATOM ASSEMBLAGE EPIPHYTIC ONENTEROMORPHAFROM A LONG ISLAND SALT MARSH1,2
Authors: Lee John J. , McEnery Marie E. , Kennedy Eileen M. , Rubin Howard 
Published: August 2007

SUMMARYThe diatom population structure of a salt marsh epiphytic community growing onEnteromorpha intestinaliswas studied at one station throughout the summer. A total of 218 species or varieties were recognized. Six species— Fragilaria construens, Cocconeis scutellum, Cocconeis placentula, Achnanthes hauckianavarieties,Achnanthes pinnata, andAmphora coffeaeformis(var.acutiuscula)–dominated theEnteromorphaepiphytic community during the summer months and comprised ∼ 40% of the total populations.Melosira nummuloides, Opephora martyi, Synedra fasiculatavar.tabulata, S. affinis, Navicula platyventris, andN. pavillardiwere also very common species (13% of the total population). The distribution of many species in the community was seasonal. A series of differential media have been developed which are effective as tools for the isolation and nutritional characterization of the algae and bacteria from the community. Many diatom species can be recognized by their colony type or growth pattern on solidified media. A key and illustrated plates aid in identification. Changes in population structure of the community were reflected by changes in the nutritional patterns as judged by differences in the growth of diatoms and bacteria on the differential media tested. The nutritional requirements, selectivity, and rank order of media for individual species is given.Almost half of the colony types (32–33) grew on either unenriched seawater from the collection site or basal synthetic seawater. Erdschreiber was a poorer medium for the isolation of algae than seawater alone. Few algal colonies grew on either marine nutrient agar or trypticase soy agar. Nitrite inhibited algal growth. Media enriched with thiamine, biotin, or nitrate, phosphate, and B12were stimulatory. Soil extract or an acetone extract ofEnteromorphatripled growth; a complex vitamin mixture, or glycerol, or mannitol, or an autoclaved extract ofEnteromorphadoubled colony numbers. The greatest numbers of diatom types (43) and total colonies (655) were recovered on media enriched with acetone extract ofEnteromorpha, suggesting a possible nutritional relationship betweenEnteromorphaand its epiphytes.The representativeness of the isolations from the natural community as a function of time was also considered. Concentrations of selected dissolved potential growth‐stimulating nutrients were measured within and external toEnteromorphacommunities. We conclude that the algal assemblage growing epiphytically onEnteromorpha intestinalishas a diverse auxotrophic profile which contributes to the productivity and stability within this important component of the epiphytic community and that much of the organic substrates used by individual species originate within and are recycled among the community members.
ENHANCEMENT OF PHYTOPLANKTON GROWTH BY MARINE BACTERIA12
Authors: Ukeles Ravenna , Bishop Jean 
Published: August 2007

SUMMARYInvestigations were conducted into the effect of 3 marine bacteria,Vibrio anguillarum #19264,V. anguillarum #19109, andEscherichia coli, on the growth of 10 phytoplakters. A disc method on agar plates was used to evaluate growth responses. Growth enhancement of all algae in the presence ofV. anguillarum #19264 occurred on an enriched agar medium; the other bacteria yielded variable responses. Evidence available is consistent with the hypothesis that growth enhancement of algae is related to the release of stimulating substances through bacterial hydrolysis of the agar.
A MORPHOLOGICAL AND TAXONOMIC CONSIDERATION OF TABELLARIA (BACILLARIOPHYCEAE) FROM THE NORTHCENTRAL UNITED STATES1,2
Authors: Koppen John D. 
Published: August 2007

SUMMARYThe taxonomy, distribution, and ecology of the diatom genus Tabellaria Ehr. from a portion of the northcentral United States were studied from collections made from August 1968 to October 1971. Using the transmission electron microscope with carbon replicas of the frustule surfaces, taxonomically significant characters were identified and related to those visible with the light microscope, four morphologically distinguishable taxa were recognized. The frustular morphology of T. fenestrata (Lyngbye) kütz. em. Knudson var. fenestrata was confirmed by both light and electron microscopy. T. flocculosa (Roth) Kütz. var. flocculosa is composed of 3 morphologically distinguishable strains. One of which is sufficiently different from the nominate variety to be described as T. flocculosa var. linearis var. nov. Also, a planktonic ecotype of one of the strains was identified.
RELATIONSHIP BETWEEN PHOTOSYNTHESIS AND CELL SIZE OF MARINE DIATOMS12
Authors: Taguchi Satoru 
Published: August 2007

SUMMARYThree photosynthetic parameters of 7 species of marine diatoms were studied using Na214CO3 at 5–8 C using log phase axenic cultures. The cell volumes of the different species varied from 70 μm3 to 40 × 105μm3. The present experiment is consistent with the interpretation that the initial slope α (mg C · [mg chl a]−1· h−1· w−1· m2) of photosynthesis vs. light curves is controlled by self‐shading of chlorophyll a in the cell. Pm, the rate of photosynthesis at light saturation (mg C · [mg cell, C]−1· h−1) and R, the intercept at zero light intensity (mg C · [mg cell C]−1· H−1) are both dependent on the ratio of surface area to volume of cell.
BACTERIAL ENDOSYMBIONTS INVOLVOX CARTERI(CHLOROP HYCEAE)1
Authors: Lee Wen‐Shen Betty , Kochert Gary 
Published: August 2007

SUMMARYThe morphology of the bacterial endosymbiont ofVolvox carteriStein (Clone KA‐1) was studied with the electron microscope. Endosymbionts were found in the cytoplasm of somatic cells, gonidia and sperm, but never in nuclei, chloroplasts or mitochondria. DNA preparations contained, an extra DNA species assumed to be endosymbiont DNA. Attempts to isolate the endosymbionts or to “cure” the alga with antibiotics were unsuccessful. All progeny from crosses of infected and noninfected strains contained the endosymbiont.