bluuebunny/crossref_metadata_2025_split huggingface dataset:
Normal levels of Rac1 are important for dendritic but not axonal development in hippocampal neurons
Authors: Gualdoni Sara , Albertinazzi Chiara , Corbetta Sara , Valtorta Flavia , de Curtis Ivan 
Published: July 2007

Background information. Rho family GTPases are required for cytoskeletal reorganization and are considered important for the maturation of neurons. Among these proteins, Rac1 is known to play a crucial role in the regulation of actin dynamics, and a number of studies indicate the involvement of this protein in different steps of vertebrate neuronal maturation. There are two distinct Rac proteins expressed in neurons, namely the ubiquitous Rac1 and the neuron‐specific Rac3. The specific functions of each of these GTPases during early neuronal development are largely unknown.Results. The combination of the knockout of Rac3 with Rac1 down‐regulation by siRNA (small interfering RNA) has been used to show that down‐regulation of Rac1 affects dendritic development in mouse hippocampal neurons, without affecting axons. F‐actin levels are strongly decreased in neuronal growth cones following down‐regulation of Rac1, and time‐lapse analysis indicated that the reduction of Rac1 levels decreases growth‐cone dynamics.Conclusions. These results show that normal levels of endogenous Rac1 activity are critical for early dendritic development, whereas dendritic outgrowth is not affected in hippocampal neurons from Rac3‐null mice. On the other hand, early axonal development appears normal after Rac1 down‐regulation. Our findings also suggest that the initial establishment of neuronal polarity is not affected by Rac1 down‐regulation.
A2breceptor mediates adenosine inhibition of taurine efflux from pituicytes
Authors: Pierson Patricia M. , Peteri‐Brunbäck Brigitta , Pisani Didier F. , Abbracchio Maria Pia , Mienville Jean‐Marc , Rosso Lia 
Published: July 2007

Background information. Recent work suggests that part of the control of vasopressin output is mediated by taurine released from pituicytes, the astroglial cells of the neurohypophysis. Taurine release, in turn, is stimulated by hypotonic conditions and by vasopressin itself. As adenosine is generated from ATP co‐released with vasopressin, it appeared important to study its effects on taurine efflux from pituicytes.Results. We measured radioactive efflux from cultured pituicytes and whole neurohypophyses pre‐loaded with [3H]taurine. Cultured pituicytes were also used to study adenosine‐receptor mRNA expression. Taurine efflux elicited by hypotonic shocks is ∼30–50% smaller in the presence of 10 μM adenosine or 1 μM NECA (5′‐N‐ethylcarboxamidoadenosine). Both compounds also inhibited basal efflux in a manner that was not immediately reversible. Agonists of the adenosine A1‐, A2a‐ or A3‐receptor subtypes have no relevant effect on basal taurine release, and the A1‐receptor antagonist DPCPX (8‐cyclopentyl‐1,3‐dipropylxanthine) has no effect on the inhibition of release by NECA. In turn, the A2b‐receptor antagonists MRS 1706 {N‐(4‐acetylphenyl)‐2‐[4‐(2,3,6,7‐tetrahydro‐2,6‐dioxo‐1,3‐dipropyl‐1H‐purin‐8‐yl)phenoxy]acetamide} or alloxazine partially reverse the inhibition of basal or hypotonicity‐evoked efflux by NECA. Both A1‐ and A2b‐receptor mRNAs are expressed in pituicytes, which is consistent with an A1‐receptor‐mediated effect on cell morphology and an A2b‐receptor‐mediated effect on taurine release. Forskolin and dibutyryl cAMP mimic the inhibitory effects of purinergics on basal taurine efflux, and the adenylate cyclase inhibitor DDA (2′,5′‐dideoxyadenosine) partially reverses the inhibition of the hypotonic response by NECA.Conclusions. Our results suggest that purinergic inhibition of taurine efflux from pituicytes operates through A2breceptors coupled to intracellular cAMP increase. They point to a possible modulation of neurohypophysial hormone output by endogenous adenosine released in either physiological or pathological situations.
Mechanisms underlying agonist efficacy
Authors: Strange P.G. 
Published: July 2007

Agonist efficacy is a measure of how well an agonist can stimulate a response system linked to a receptor. Efficacy can be assessed in functional assays and various parameters (Emax, KA/EC50, Emax·KA/EC50) determined. The Emax·KA/EC50 parameter provides a good estimate of efficacy across the full range of efficacy. A convenient assay for the efficacy of agonists for some receptors is provided by the [35S]GTP[S] (guanosine 5′-[γ-[35S]thio]triphosphate)-binding assay. In this assay, the normal GTP-binding event in GPCR (G-protein-coupled receptor) activation is replaced by the binding of the non-hydrolysable analogue [35S]GTP[S]. This assay may be used to profile ligands for their efficacy, and an example here is the D2 dopamine receptor where an efficacy scale has been set up using this assay. The mechanisms underlying the assay have been probed. The time course of [35S]GTP[S] binding follows a pseudo-first-order reaction with [35S]GTP[S] binding reaching equilibrium after approx. 3 h. The [35S]GTP[S]-binding event is the rate-determining step in the assay. Agonists regulate the maximal level of [35S]GTP[S] bound, rather than the rate constant for binding. The [35S]GTP[S]-binding assay therefore determines agonist efficacy on the basis of the amount of [35S]GTP[S] bound rather than the rate of binding.
Selection and validation of normalization methods for c-DNA microarrays using within-array replications
Authors: Fan Jianqing , Niu Yue 
Published: July 2007

AbstractMotivation: Normalization of microarray data is essential for multiple-array analyses. Several normalization protocols have been proposed based on different biological or statistical assumptions. A fundamental problem arises whether they have effectively normalized arrays. In addition, for a given array, the question arises how to choose a method to most effectively normalize the microarray data.Results: We propose several techniques to compare the effectiveness of different normalization methods. We approach the problem by constructing statistics to test whether there are any systematic biases in the expression profiles among duplicated spots within an array. The test statistics involve estimating the genewise variances. This is accomplished by using several novel methods, including empirical Bayes methods for moderating the genewise variances and the smoothing methods for aggregating variance information. P-values are estimated based on a normal or χ approximation. With estimated P-values, we can choose a most appropriate method to normalize a specific array and assess the extent to which the systematic biases due to the variations of experimental conditions have been removed. The effectiveness and validity of the proposed methods are convincingly illustrated by a carefully designed simulation study. The method is further illustrated by an application to human placenta cDNAs comprising a large number of clones with replications, a customized microarray experiment carrying just a few hundred genes on the study of the molecular roles of Interferons on tumor, and the Agilent microarrays carrying tens of thousands of total RNA samples in the MAQC project on the study of reproducibility, sensitivity and specificity of the data.Availability: Code to implement the method in the statistical package R is available from the authors.Contact: jqfan@princeton.edu
Robustness analysis and tuning of synthetic gene networks
Authors: Batt Grégory , Yordanov Boyan , Weiss Ron , Belta Calin 
Published: July 2007

AbstractMotivation: The goal of synthetic biology is to design and construct biological systems that present a desired behavior. The construction of synthetic gene networks implementing simple functions has demonstrated the feasibility of this approach. However, the design of these networks is difficult, notably because existing techniques and tools are not adapted to deal with uncertainties on molecular concentrations and parameter values.Results: We propose an approach for the analysis of a class of uncertain piecewise-multiaffine differential equation models. This modeling framework is well adapted to the experimental data currently available. Moreover, these models present interesting mathematical properties that allow the development of efficient algorithms for solving robustness analyses and tuning problems. These algorithms are implemented in the tool RoVerGeNe, and their practical applicability and biological relevance are demonstrated on the analysis of the tuning of a synthetic transcriptional cascade built in Escherichia coli.Availability: RoVerGeNe and the transcriptional cascade model are available at http://iasi.bu.edu/%7Ebatt/rovergene/rovergene.htmContact: gregory.batt@imag.fr
Quality estimation of multiple sequence alignments by Bayesian hypothesis testing
Authors: Tomovic Andrija , Oakeley Edward J. 
Published: July 2007

AbstractSummary: In this work we present a web-based tool for estimating multiple alignment quality using Bayesian hypothesis testing. The proposed method is very simple, easily implemented and not time consuming with a linear complexity. We evaluated method against a series of different alignments (a set of random and biologically derived alignments) and compared the results with tools based on classical statistical methods (such as sFFT and csFFT). Taking correlation coefficient as an objective criterion of the true quality, we found that Bayesian hypothesis testing performed better on average than the classical methods we tested. This approach may be used independently or as a component of any tool in computational biology which is based on the statistical estimation of alignment quality.Availability: http://www.fmi.ch/groups/functional.genomics/tool.htmContact: edward.oakeley@fmi.chSupplementary information: Supplementary data are available from http://www.fmi.ch/groups/functional.genomics/tool-Supp.htm
Comparative modeling without implicit sequence alignments
Authors: Kolinski Andrzej , Gront Dominik 
Published: July 2007

AbstractMotivation: The number of known protein sequences is about thousand times larger than the number of experimentally solved 3D structures. For more than half of the protein sequences a close or distant structural analog could be identified. The key starting point in a classical comparative modeling is to generate the best possible sequence alignment with a template or templates. With decreasing sequence similarity, the number of errors in the alignments increases and these errors are the main causes of the decreasing accuracy of the molecular models generated. Here we propose a new approach to comparative modeling, which does not require the implicit alignment — the model building phase explores geometric, evolutionary and physical properties of a template (or templates).Results: The proposed method requires prior identification of a template, although the initial sequence alignment is ignored. The model is built using a very efficient reduced representation search engine CABS to find the best possible superposition of the query protein onto the template represented as a 3D multi-featured scaffold. The criteria used include: sequence similarity, predicted secondary structure consistency, local geometric features and hydrophobicity profile. For more difficult cases, the new method qualitatively outperforms existing schemes of comparative modeling. The algorithm unifies de novo modeling, 3D threading and sequence-based methods. The main idea is general and could be easily combined with other efficient modeling tools as Rosetta, UNRES and others.Contact: dgront@chem.uw.edu.pl
Polyketide synthase genes and the natural products potential ofDictyostelium discoideum
Authors: Zucko J. , Skunca N. , Curk T. , Zupan B. , Long P.F. , Cullum J. , Kessin R.H. , Hranueli D. 
Published: July 2007

AbstractMotivation: The genome of the social amoeba Dictyostelium discoideum contains an unusually large number of polyketide synthase (PKS) genes. An analysis of the genes is a first step towards understanding the biological roles of their products and exploiting novel products.Results: A total of 45 Type I iterative PKS genes were found, 5 of which are probably pseudogenes. Catalytic domains that are homologous with known PKS sequences as well as possible novel domains were identified. The genes often occurred in clusters of 2–5 genes, where members of the cluster had very similar sequences. The D.discoideum PKS genes formed a clade distinct from fungal and bacterial genes. All nine genes examined by RT–PCR were expressed, although at different developmental stages. The promoters of PKS genes were much more divergent than the structural genes, although we have identified motifs that are unique to some PKS gene promoters.Contact: dhranueli@pbf.hrSupplementary information: Supplementary data are available at Bioinformatics online.
PRESEMO—a predictive model of codend selectivity—a tool for fishery managers
Authors: O'Neill F. G. , Herrmann B. 
Published: July 2007

Abstract
O'Neill, F. G., and Herrmann, B. 2007. PRESEMO—a predictive model of codend selectivity—a tool for fishery managers. – ICES Journal of Marine Science, 64: 1558–1568. The codend selectivity simulation model PRESEMO is a predictive model based on an understanding of the physical, biological, and behavioural mechanisms that underpin codend selection. In this paper, PRESEMO is used to predict the selectivity of a large range of codends of varying design. In particular, the selectivity of codends with mesh sizes in the range 80–160 mm, number of meshes around in the range 60–140, and netting twine thickness in the range 3–6 mm are predicted and, where possible, the predictions are validated with experimental data. Using the simulated data, the codend selectivity parameters are expressed in terms of the gear design parameters and in terms of both catch size and gear design parameters. The potential use of these results in a management context and for the development of more selective gears is highlighted by plotting iso-l50 and iso-sr curves used to identify gear design parameters that give equal estimates of the 50% retention length and the selection range, respectively. It is emphasized that this approach can be extended to consider the influence of other design parameters and, if sufficient relevant quantitative information exists, biological and behavioural parameters. As such, the model presented here will provide a better understanding of the selection process, permit a more targeted approach to codend selectivity experiments, and assist fishery managers to assess the impact of proposed technical measures that are introduced to reduce the catch of undersized fish and unwanted bycatch.
Seasonal variation in the trawl codend selectivity of picarel (Spicare smaris)
Authors: Özbilgin Hüseyin , Tosunoğlu Zafer , Tokaç Adnan , Metin Gülnur 
Published: July 2007

AbstractÖzbilgin, H., Tosunoğlu, Z., Tokaç, A., and Metin, G. 2007. Seasonal variation in the trawl codend selectivity of picarel (Spicare smaris). – ICES Journal of Marine Science, 64: 1569–1572. Seasonal selectivity of commercial 40 mm polyethylene codend was tested for picarel (Spicara smaris) in spring (4–18 April 2002), summer (10–25 July 2002), autumn (26 September–2 October 2002), and winter (22–23 January 2003) in the Aegean Sea. Data were collected using the covered codend technique and analysed using the logistic equation with the maximum likelihood method. Four sets of selection curves were analysed and compared using the model developed by Fryer (1991). Highest L50 is in autumn (13.82 cm; s.e. 0.62), when water temperature is highest and the fish are expected to be in their best condition after summer feeding. Lowest L50 is in spring (11.09 cm; s.e. 0.51), when water temperature is lowest and the fish are at their spawning stage. However, there is not sufficient evidence to say that the seasonal variation in the selectivity of 40 mm polyethylene codend for picarel is statistically significant (p > 0.05).
Pediatric Short Bowel Syndrome: Adaptation After Massive Small Bowel Resection
Authors: Rossi Ljubomir , Kadamba Padmalatha , Hugosson Claes , De Vol Edward B , Habib Zakaria , Al‐Nassar Saleh 
Published: July 2007

ABSTRACTBackground:Short bowel syndrome (SBS) develops after massive small bowel resections. Patients with less than 12 cm of jejunoileum have a slim possibility of being weaned from parenteral nutrition (PN).Patients and Methods:In a retrospective review of records of consecutive patients with SBS, 8 patients were evaluated for treatment by adaptation and weaning from PN. These included 4 patients with class I SBS (0–10 cm of small bowel), one with class II SBS (>10–25 cm), one with class III SBS (>25–50 cm), and 2 with class IV SBS (>50–75 cm). Adaptation was assessed by measuring growth in the small bowel and the ability to be weaned from PN.Results:Adaptation was achieved primarily by extending the length of jejunoileum by approximately 450% over the first 2.5 years after resection and by increasing the degree of colonic fermentation and absorption of nutrients. As of July 1, 2005, all of the patients were off PN, with the exception of 2 patients with class I‐A SBS: patient 3 had a remaining jejunoileum of only 2.5 cm and patient 4 had a remaining jejunoileum of 9 cm but developed eosinophilic enterocolitis. These 2 patients continued with PN on alternate months.Conclusions:Bowel growth after massive small bowel resection provides an objective parameter of adaptation and a means of predicting ability to be weaned from PN. Aggressive nutritional support makes even patients with class I SBS, whose disease was previously considered hopeless, likely candidates to achieve freedom from PN.
Infant Feeding Patterns in the First 6 Months: An Assessment in Full‐term Infants
Authors: Nevo Neta , Rubin Lisa , Tamir Ada , Levine Arie , Shaoul Ron 
Published: July 2007

ABSTRACTBackground:The infant formula market has grown significantly and offers a wide range of products for the different stages of healthy infant growth. Healthy infants often go through a series of unnecessary changes of formulas. The present study aimed to identify the factors leading to switches to alternative formulas. We studied the feeding patterns in the first 6 months of babies born at term, particularly changes in infant formulas. We also investigated the reasons for choosing the first formula, infant formula changes, the addition of formulas to supplement breast‐feeding, and various aspects related to formula thickening.Patients and Methods:Two hundred parents of babies ages 6 to 18 months were interviewed. The interviews included a detailed questionnaire and were conducted in child and maternal health care centers.Results:Forty‐seven percent of these infants underwent changes in their formula in the first 6 months of life, most of which (67%) were to another cow's milk–based formula. The main reasons for switching a formula were regurgitation or vomiting (24%) followed by restlessness (18%). Lower z scores at birth and a higher Δz2 (z score at the time of the questionnaire minus z score at birth) were associated with significantly more formula changes. The impact of pediatricians and other health care professionals on the choice of infant nutrition was surprisingly negligible.Conclusions:The most common reason for switching a formula was concern regarding common infantile symptoms or behavior patterns perceived by parents to be related to formula intolerance. The decision to switch formula was usually made by the parents without consulting a health professional.
Lack of Effect of Lactobacillus GG in Breast‐fed Infants With Rectal Bleeding: A Pilot Double‐blind Randomized Controlled Trial
Authors: Szajewska H , Gawrońska A , Woś H , Banaszkiewicz A , Grzybowska‐Chlebowczyk U 
Published: July 2007

ABSTRACTObjectives:For breast‐fed infants with rectal bleeding, maternal restriction of dietary protein such as cow's milk proteins is often recommended; however, poor response to dietary protein restriction is of concern. This pilot study was designed to assess the effectiveness of Lactobacillus GG (LGG) in breast‐fed infants with rectal bleeding.Patients and Methods:Breast‐fed infants <6 months of age with rectal bleeding (defined as the presence of visible specks or streaks of blood mixed with mucus in the stool in otherwise healthy infants) were enrolled in a double‐blind randomized controlled trial in which they received LGG 3 × 109 colony‐forming units (n = 14) or placebo (n = 15) twice daily for 4 weeks as an adjunct to cow's milk restriction in the mother's diet. Analyses were based on allocated treatment and included data from 26 infants.Results:Mean duration of rectal bleeding was similar in the LGG and control groups (17.3 ± 10.6 vs 15.4 ± 11 days; mean difference −1.9 (95% confidence interval [CI] −4 to 7). No difference was found in the number of infants with clinical resolution of rectal bleeding within 72 hours and no relapse afterward (2/11 vs 3/15, relative risk [RR] 0.9, 95% CI 0.2–3.9) and the number of infants with clinical resolution of rectal bleeding within 72 hours followed by relapse of symptoms (5/11 vs 5/15, RR 1.4, 95% CI 0.5–3.5). Breast‐feeding cessation was not needed in any infant.Conclusions:These results do not support the use of LGG as an adjunct to maternal cow's milk restriction in breast‐fed infants with rectal bleeding.
Disaccharidase Activity in Infants and Comparison Based on Symptoms and Histological Changes
Authors: Tori Alvaro J , Carroll Aaron E , Gupta Sandeep K 
Published: July 2007

ABSTRACTObjectives:There is uncertainty regarding disaccharidase activity (DA) in infants. In this study, values for DA in infants were established and compared with symptoms and intestinal mucosal histological appearance.Patients and Methods:Disaccharidase activity and histological appearance of endoscopically obtained intestinal mucosal biopsy specimens from 131 infants (75 males; mean age 180 days; range 20–364 days) obtained during an 8‐year period were reviewed. Patients were divided into 2 groups on the basis of absence (group 1; n = 56) or presence (group 2; n = 75) of failure to thrive (FTT) and/or diarrhea. These groups were subdivided into 3 subgroups on the basis of histological findings: normal histological appearance (A), mild histological abnormalities (B), and moderate to severe histological abnormalities (C).Results:The DA from patients in group 1A represent values in infants who were free of diarrhea/FTT and who had normal intestinal mucosal histological appearance. The geometric means (95% CI) in units of DA were as follows: lactase 33.7 (normal range 29.0–39.1), sucrase 48.9 (normal range 44.2–54.1), maltase 160.5 (normal range 144.4–178.3), and palatinase 11.2 (normal range 9.7–12.9). Differences in DA were not related to symptoms, in the absence of histological abnormalities (1A vs 2A), but rather on the presence of histological abnormalities even in the absence of symptoms (1A vs 1B). Differences were also found when patients with FTT and/or diarrhea with abnormal histological appearance (2B and 2C) were compared with patients with no FTT and/or diarrhea with a normal brush border (1A).Conclusions:We outline DA values in a large cohort of infants. DA in infants, as in children, relates to intestinal mucosal histological appearance rather than to symptoms.