bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of inulin on the human gut microbiota: stimulation ofBifidobacterium adolescentisandFaecalibacterium prausnitzii
Authors: Ramirez-Farias Carlett , Slezak Kathleen , Fuller Zoë , Duncan Alan , Holtrop Grietje , Louis Petra 
Published: July 2008

Prebiotics are food ingredients that improve health by modulating the colonic microbiota. The bifidogenic effect of the prebiotic inulin is well established; however, it remains unclear which species ofBifidobacteriumare stimulatedin vivoand whether bacterial groups other than lactic acid bacteria are affected by inulin consumption. Changes in the faecal microbiota composition were examined by real-time PCR in twelve human volunteers after ingestion of inulin (10 g/d) for a 16-d period in comparison with a control period without any supplement intake. The prevalence of most bacterial groups examined did not change after inulin intake, although the low G+C % Gram-positive speciesFaecalibacterium prausnitziiexhibited a significant increase (10·3 % for control periodv.14·5 % during inulin intake,P = 0·019). The composition of the genusBifidobacteriumwas studied in four of the volunteers by clone library analysis. Between three and fiveBifidobacteriumspp. were found in each volunteer.Bifidobacterium adolescentisandBifidobacterium longumwere present in all volunteers, andBifidobacterium pseudocatenulatum,Bifidobacterium animalis,Bifidobacterium bifidumandBifidobacterium dentiumwere also detected. Real-time PCR was employed to quantify the four most prevalentBifidobacteriumspp.,B. adolescentis,B. longum,B. pseudocatenulatumandB. bifidum, in ten volunteers carrying detectable levels of bifidobacteria.B. adolescentisshowed the strongest response to inulin consumption, increasing from 0·89 to 3·9 % of the total microbiota (P = 0·001).B. bifidumwas increased from 0·22 to 0·63 % (P < 0·001) for the five volunteers for whom this species was present.
Administration of a dietary supplement (N-oleyl-phosphatidylethanolamine and epigallocatechin-3-gallate formula) enhances compliance with diet in healthy overweight subjects: a randomized controlled trial
Authors: Rondanelli Mariangela , Opizzi Annalisa , Solerte Sebastiano Bruno , Trotti Rosita , Klersy Catherine , Cazzola Roberta 
Published: July 2008

Many studies have found thatN-oleyl-ethanolamine (NOE), a metabolite ofN-oleyl-phosphatidylethanolamine (NOPE), and epigallocatechin-3-gallate (EGCG) inhibit food intake. The main aim of this study was to evaluate the efficacy of 2 months of administration of an oily NOPE–EGCG complex (85 mg NOPE and 50 mg EGCG per capsule) and its effect on compliance with diet in healthy, overweight people. Secondary end-points of the study were to compare body composition, metabolic parameters, sensation of appetite, depressive symptoms and severity of binge eating. Using a parallel-arm, double-blind, placebo-controlled design, 138 healthy, overweight women (106) and men (thirty-two) were randomly assigned to one of two groups: (1) the treatment group (seventy-one patients: fifty-three females, eighteen males) taking two capsules per day of an oral supplement or (2) the placebo group (sixty-seven patients: fifty-three females, fourteen males). Both groups observed a 3344 kJ/d energy restriction. All parameters were assessed both before onset and after 2 months on the supplement. Dropout was 6 % in the NOPE–EGCG group and 27 % in the placebo group (P < 0·001). The treatment induced a significant weight reduction in both groups ( − 3·28 kg and − 2·67 kg in NOPE–EGCG and placebo, respectively); the weight changes were not significantly different between the groups. NOPE–EGCG treatment improved insulin resistance (P < 0·001), the sensation feelings of fullness (P < 0·05), depressive symptoms (P < 0·004) and severity of binge eating (P < 0·0001).
Growth hormone improves lipoprotein concentration and arylesterase activity in mice with an atherogenic lipid profile induced by lactalbumin
Authors: López-Oliva Elvira , Nus Meritxell , Agis-Torres Angel , Villaro Wilma , Sánchez-Montero José M. , Muñoz-Martínez Emilia , Sánchez-Muniz Francisco J. 
Published: July 2008

The effect of growth hormone (GH) on arylesterase (AE), one of the activities of paraoxonase, has never been studied. The aims of the present study in mice were: (a) to compare the effect of age and sex on serum lipid and lipoprotein levels after consumption of lactalbumin-v.chow-based diets and (b) to study the effect of GH administration, age and sex on serum AE activity, lipid and lipoprotein and body fat levels in mice fed a lactalbumin diet. Seventy-two mice were divided into three age- and sex-matched experimental groups: (1) control chow (CC), (2) non-GH lactalbumin (NGL) and (3) GH-treated lactalbumin (GL) mice. Lactalbumin increased total cholesterol, (LDL+VLDL)-cholesterol and TAG and diminished HDL-cholesterol in all animals (P < 0·05). In comparison with their NGL counterparts, old GL males presented lower total cholesterol (15 %) and (LDL+VLDL)-cholesterol (17 %) levels (P < 0·05), whereas values of the same parameters were higher in adult GL males (P < 0·05) (22 and 23 %, respectively). Adult GL females displayed higher serum HDL-cholesterol concentrations (26 %) (P < 0·05) than adult NGL females. AE activity was lower in old GL females (78 %) and old GL males (20 %) (P < 0·05), but higher in adult GL males (100 %) (P < 0·01). GH, that was inversely related to food intake, decreased abdominal and gonadal fat in all mice (P < 0·05). To conclude, lactalbumin induced an atherogenic lipoprotein profile in NGL mice that was reverted by GH, preferentially in old males, suggesting that GH therapy will be more effective in aged men. The present results suggest that AE activity was age-, sex- and body fat level-dependent and that it diminished as a consequence of improved antioxidant status.
Discrimination of Cricotopus species (Diptera: Chironomidae) by DNA barcoding
Authors: Sinclair C.S. , Gresens S.E. 
Published: July 2008

AbstractChironomids (Diptera) typically comprise the most abundant group of macroinvertebrates collected in water quality surveys. Species in the genus Cricotopus display a wide range of tolerance for manmade pollutants, making them excellent bioindicators. Unfortunately, the usefulness of Cricotopus is overshadowed by the difficulty of accurately identifying larvae using current morphological keys. Molecular approaches are now being used for identification and taxonomic resolution in many animal taxa. In this study, a sequence-based approach for the mitochondrial gene, cytochrome oxidase I (COI), was developed to facilitate identification of Cricotopus species collected from Baltimore area streams. Using unique COI sequence variations, we developed profiles for seven described Cricotopus sp., four described Orthocladius sp., one described Paratrichocladius sp. and one putative species of Cricotopus. In addition to providing an accurate method for identification of Cricotopus, this method will make a useful contribution to the development of keys for Nearctic Cricotopus.
Tracking pyrethroid resistance in the polyphagous bollworm, Helicoverpa armigera (Lepidoptera: Noctuidae), in the shifting landscape of a cotton-growing area
Authors: Brévault T. , Achaleke J. , Sougnabé S.P. , Vaissayre M. 
Published: July 2008

AbstractIn cotton-growing areas of Central Africa, timing of host crops and pest management practices in annual rainfed cropping systems result in a shifting mosaic of habitats that influence the dynamics and resistance of Helicoverpa armigera (Hübner) populations on spatial scales, both within and across seasons. From 2002 to 2006, regional and local resistance was monitored among cotton fields and among the major host plants of the bollworm. From 2002, pyrethroid resistance increased within and across cotton-growing seasons to reach a worrying situation at the end of the 2005 growing season. Cotton crops played a fundamental role in the increase in seasonal resistance, even if the intensive use of insecticides on local tomato crops strongly concentrated resistance alleles in residual populations throughout the off-season. Due to the relative stability of resistance in H. armigera populations despite a long off-season, we believe that after the dispersal of the moths southwards at the end of the growing season, reverse migration mainly accounts for the reconstitution of populations at the onset of the following growing season. In addition, local resistance monitoring in 2005 and 2006 showed that it was possible to control the increase in resistance by temporarily stopping the use of pyrethroids during the period of peak infestation of cotton by H. armigera. On the other hand, the similar resistance frequency of populations sampled from sprayed and unsprayed synchronous hosts confirmed the absence of reproductive isolation between adults. As a result, diversity in cropping systems should be encouraged by planting alternative host plants to provide a mosaic of habitats, which in return would provide insecticide-free refuges. The implications for insecticide resistance management in annual cropping systems are discussed.
Quackgrass- and ryegrass-adapted populations of the cereal rust mite, Abacarus hystrix (Acari: Eriophyidae), differ in their potential for wheat, Triticum aestivum, colonization
Authors: Skoracka A. 
Published: July 2008

AbstractThe cereal rust mite, Abacarus hystrix, is one of the most notable among mites causing losses in cultivated grasslands. It is one of a few eriophyoid species for which a broad host range has been reported. Recent studies, however, have shown that host specialization is very likely in this species. For two populations of A. hystrix (one inhabiting perennial ryegrass, the second inhabiting quackgrass), host-associated differences correlated with strong host fidelity, distinct phenotypes and reproductive barriers have been found. In the present study, the ability of wheat colonization by quackgrass- and ryegrass-adapted cereal rust mite was studied. The hypothesis that the potential for wheat colonization by the quackgrass strain is more likely was tested by comparing the colonization performance (assessed by female survival and fecundity) of quackgrass- and ryegrass-associated A. hystrix on their familiar hosts and on wheat. The ryegrass population had no success in wheat colonization (expressed by extremely low fecundity and female survival). Fecundity and survival of quackgrass strain were similar on wheat and the familiar host, or even higher on wheat. Phylogenetic similarity of quackgrass and wheat is discussed as a possible factor that might influence such patterns of host colonization. Since A. hystrix is the only vector of the ryegrass mosaic virus (RgMV), the presented results may be helpful in explaining the inability of RgMV to successfully infest wheat. The conclusions are that (i) quackgrass- and ryegrass-adapted strains of the cereal rust mite have different physiological host ranges and (ii) phylogenetic relationships between host plant species appear to be drivers for host specialization in this mite species.
The Voluntariness of Virtue – and Belief
Authors: Montmarquet James A. 
Published: July 2008

AbstractThis paper examines the relative voluntariness of three types of virtue: ‘epistemic’ virtues like open-mindedness; ‘motivational’ virtues like courage, and more robustly ‘moral’ virtues like justice. A somewhat novel conception of the voluntariness of belief is offered in terms of the limited, but quite real, voluntariness of certain epistemic virtues.
Religious Dialogue in the Nicaraguan Revolution
Authors: Reed Jean-Pierre 
Published: July 2008

AbstractThis article is an historical study of the Nicaraguan revolution that makes a case in favor of interpreting revolutionary stances/action as driven by religious dialogue. To this end, seminary dialogues that assumed revolutionary significance during the 1970s in Solentiname, Nicaragua, are studied. Institutional shifts in religious meaning, both in the region and Nicaragua, are historically detailed. Three dialogues fromThe Gospel in Solentiname, a four-volume collection of Bible-centered dialogues, are analyzed. These are evaluated in terms of their role for revolutionary outlooks. Innovative and developmental features of dialogue are identified in order to underscore the revolutionary potential of dialogue.
Dissecting the Biological Motherboard (Systems Biology and Beyond)
Authors: Krishna Abhay , Narayanan Ajit 
Published: July 2008

AbstractGenome-scale molecular networks, including gene pathways, gene regulatory networks and protein interactions, are central to the investigation of the nascent disciplines of systems biology and bio-complexity. Dissecting these genome-scale molecular networks in its all-possible manifestations is paramount in our quest for a genotype-input phenotype-output application which will also take environment-genome interactions into account.Machine learning approaches are now increasingly being used for reverse engineering such networks. Our work stresses the importance of a system approach in biological research and how artificial neural networks are at the forefront of Artificial Intelligence techniques that are increasingly being used to construct as well as dissect molecular networks, the building blocks of the living system.Our paper will show the application of artificial neural networks to reverse engineer a temporal gene pathway In this paper we will also explore the pruning of nodes of these artificial neural networks to simulate gene silencing and thus generate novel biological insight into these molecular networks (The Biological Motherboard).The research described is novel, in that this may be the first time that the application of neural networks to temporal gene expression data is described. It will be shown that a trained artificial neural network, with pruning, can also be described as a gene network with minimal re-interpretation, where the weights on links between nodes reflect the probability of one gene affecting another gene in time.
Inferior Colliculus
Authors:   Allen Institute for Brain Science, Solan Beth , Ng Lydia , Morris John 
Published: July 2008

AbstractThis report contains a gene expression summary of the inferior colliculus (IC), derived from the Allen Brain Atlas (ABA) in-situ hybridization (ISH) mouse data set. The structure’s location and morphological characteristics in the mouse brain are described using the Nissl data found in the Allen Reference Atlas. Using an established algorithm, the expression values of the IC were compared to the values of the macro/parent-structure, in this case the midbrain, for the purpose of extracting regionally specific gene expression data. The highest ranking ratios were then manually curated and verified. The 50 Select Genes were compiled for expression characterization. The experimental data for each gene may be accessed via the links provided; complementary sagittal data may also be accessed using the ABA. Correlation between gene expression in the IC and the rest of the brain, across all genes in the coronal dataset (~4300 genes), were derived computationally and are presented below. A gene ontology table (derived from DAVID Bioinformatics Resources 2007) is also included, highlighting possible functions of these 50 Select Genes.
Does quality of sleep mediate the effect of depression on hopelessness?
Authors: Mystakidou Kyriaki , Parpa Efi , Tsilika Eleni , Galanos Antonis , Vlahos Lambros 
Published: July 2008

The objectives of the study were to evaluate the relationship between sleep quality, depression, and hopelessness in advanced cancer patients and whether sleep quality mediated the effect of depression on hopelessness. The final sample consisted of 102 advanced cancer patients under palliative treatment. Patients completed the Greek Pittsburgh Sleep Quality Index, a sleep quality instrument, the Greek Beck Depression Inventory for measuring depression, and finally the Beck Hopelessness Scale. Patients' performance status was assessed by their overall physical functioning, as defined by the Eastern Cooperative Oncology Group. Depression was highly associated with hopelessness (r = .52, p<.001). Statistically significant associations were found between sleep quality with hopelessness (r = .37, p<.001), as well as with depression (r = .36, p<.001). Mediation analyses indicated that depression influenced hopelessness directly as well as indirectly by its effect on sleep quality. About 14.58% of the variation in hopelessness was explained by depression; 4% of the variance in hopelessness explained by depression was accounted for by the mediation pathway indicating that sleep quality mediated the relationship between depression and hopelessness. Similarly, in the reverse mediation analysis, depression mediated the relationship between sleep quality and hopelessness; 43% of the variation in hopelessness was explained by sleep quality. In conclusion, some of the effect of depression on hopelessness was mediated by sleep quality, but depression had a direct effect on hopelessness as well. Additionally, some of the effect of sleep quality on hopelessness was mediated by depression. The current findings are important because improving sleep quality by treating depression may contribute to decreased hopelessness scores and vice versa: Treating depression by improving sleep quality may also contribute to lower hopelessness scores.
Accelerating and focusing protein–protein docking correlations using multi-dimensional rotational FFT generating functions
Authors: Ritchie David W. , Kozakov Dima , Vajda Sandor 
Published: July 2008

Abstract
Motivation: Predicting how proteins interact at the molecular level is a computationally intensive task. Many protein docking algorithms begin by using fast Fourier transform (FFT) correlation techniques to find putative rigid body docking orientations. Most such approaches use 3D Cartesian grids and are therefore limited to computing three dimensional (3D) translational correlations. However, translational FFTs can speed up the calculation in only three of the six rigid body degrees of freedom, and they cannot easily incorporate prior knowledge about a complex to focus and hence further accelerate the calculation. Furthemore, several groups have developed multi-term interaction potentials and others use multi-copy approaches to simulate protein flexibility, which both add to the computational cost of FFT-based docking algorithms. Hence there is a need to develop more powerful and more versatile FFT docking techniques.
Results: This article presents a closed-form 6D spherical polar Fourier correlation expression from which arbitrary multi-dimensional multi-property multi-resolution FFT correlations may be generated. The approach is demonstrated by calculating 1D, 3D and 5D rotational correlations of 3D shape and electrostatic expansions up to polynomial order L=30 on a 2 GB personal computer. As expected, 3D correlations are found to be considerably faster than 1D correlations but, surprisingly, 5D correlations are often slower than 3D correlations. Nonetheless, we show that 5D correlations will be advantageous when calculating multi-term knowledge-based interaction potentials. When docking the 84 complexes of the Protein Docking Benchmark, blind 3D shape plus electrostatic correlations take around 30 minutes on a contemporary personal computer and find acceptable solutions within the top 20 in 16 cases. Applying a simple angular constraint to focus the calculation around the receptor binding site produces acceptable solutions within the top 20 in 28 cases. Further constraining the search to the ligand binding site gives up to 48 solutions within the top 20, with calculation times of just a few minutes per complex. Hence the approach described provides a practical and fast tool for rigid body protein-protein docking, especially when prior knowledge about one or both binding sites is available.
Availability: http://www.csd.abdn.ac.uk/hex/
Contact: d.w.ritchie@abdn.ac.uk
Automated mapping of large-scale chromatin structure in ENCODE
Authors: Lian Heng , Thompson William A. , Thurman Robert , Stamatoyannopoulos John A. , Noble William Stafford , Lawrence Charles E. 
Published: July 2008

Abstract
Motivation: A recently developed DNaseI assay has given us our first genome-wide view of chromatin structure. In addition to cataloging DNaseI hypersensitive sites, these data allows us to more completely characterize overall features of chromatin accessibility. We employed a Bayesian hierarchical change-point model (CPM), a generalization of a hidden Markov Model (HMM), to characterize tiled microarray DNaseI sensitivity data available from the ENCODE project.
Results: Our analysis shows that the accessibility of chromatin to cleavage by DNaseI is well described by a four state model of local segments with each state described by a continuous mixture of Gaussian variables. The CPM produces a better fit to the observed data than the HMM. The large posterior probability for the four-state CPM suggests that the data falls naturally into four classes of regions, which we call major and minor DNaseI hypersensitive sites (DHSs), regions of intermediate sensitivity, and insensitive regions. These classes agree well with a model of chromatin in which local disruptions (DHSs) are concentrated within larger domains of intermediate sensitivity, the accessibility islands. The CPM assigns 92% of the bases within the ENCODE regions to the insensitive regions. The 5.8% of the bases that are in regions of intermediate sensitivity are clearly enriched in functional elements, including genes and activating histone modifications, while the remaining 2.2% of the bases in hypersensitive regions are very strongly enriched in these elements.
Availability: The CPM software is available upon request from the authors.
Contact: jstam@stamlab.org; noble@gs.washington.edu; Charles_Lawrence@brown.edu
Supplementary information: Supplementary data are available at Bioinformatics online. Source code is available at http://noble.gs.washington.edu/proj/segment.
Identification of Differential Genes by Suppression Subtractive Hybridization: I. Preparation of Subtracted cDNA or Genomic DNA Library
Authors: Rebrikov Denis V. 
Published: July 2008

INTRODUCTIONSuppression subtractive hybridization (SSH) is one of the most powerful and popular methods for generating subtracted cDNA or genomic DNA libraries. This technique can be used to compare two mRNA populations and obtain cDNAs representing genes that are either overexpressed or exclusively expressed in one population as compared to another. It can also be used for comparison of genomic DNA populations. This protocol describes the preparation of a subtracted cDNA or genomic DNA library, and includes methods for cDNA synthesis, tester and driver DNA digestion, and adapter ligation.
Identification of Differential Genes by Suppression Subtractive Hybridization: III. PCR Amplification of Differentially Presented DNAs
Authors: Rebrikov Denis V. 
Published: July 2008

INTRODUCTIONSuppression subtractive hybridization (SSH) is one of the most powerful and popular methods for generating subtracted cDNA or genomic DNA libraries. This technique can be used to compare two mRNA populations and obtain cDNAs representing genes that are either overexpressed or exclusively expressed in one population as compared to another. It can also be used for comparison of genomic DNA populations. In this protocol, differentially presented DNAs are selectively amplified using PCR. It is strongly recommended that subtractions be performed in both directions for each tester/driver DNA pair. Forward subtraction is designed to enrich for differentially presented molecules present in the tester but not in the driver; reverse subtraction is designed to enrich for differentially presented sequences present in the driver but not in the tester. Therefore, each experiment should have at least four reactions: (1) subtracted tester DNAs, (2) unsubtracted tester control, (3) reverse-subtracted tester DNAs, and (4) unsubtracted control for the reverse subtraction.