bluuebunny/crossref_metadata_2025_split huggingface dataset:
Major lipids and fatty acids in the liver and rumen fluid of the goat (Capra hircus) infected with the trematodeParamphistomum cervi
Authors: Ghosh D. , Misra K.K. 
Published: September 2010

AbstractThe present study records the occurrence of major lipid fractions and their fatty acids in a digenetic trematode parasiteParamphistomum cervi, and the rumen fluid and liver of the goat (Capra hircus). The amount of neutral lipids (NL), glycolipids (GL) and phospholipids (PL) of goat liver, rumen fluid and of the parasite shows that the rumen fluid is rich in NL, which is also in maximum quantity in the parasite, while the liver is rich in PL followed by NL. The number of fatty acids of total lipids (TL), NL and PL is greater in the parasite than those of the liver and rumen fluid. The number of fatty acids of GL is higher in the liver than in the parasite and the rumen fluid. Comparison of unsaturated fatty acid (UFA), C18total and C18UFA of TL, NL, GL and PL of the liver, rumen fluid and the parasite shows that the amount of C18UFA is higher inP. cerviin all the lipid fractions, except for GL, than in the rumen fluid and the liver. The results reveal thatP. cerviabsorbs a greater number of fatty acids than its host.
Sepúlveda, Las Casas, and the Other: Exploring the Tension between Moral Universalism and Alterity
Authors: Brunstetter Daniel R. 
Published: September 2010

AbstractModern politics is at times a balancing act between universal claims about the human (equal rights, dignity, and respect) and political actions which may seem to violate these claims (torture, just wars, repudiation of certain cultural practices, tacit discrimination). An exploration of some of the philosophical roots of the modern understanding of the person, when it was the subject of debate, provides a perspective at the origin of Modernity from which to evaluate the tenuous relationship between moral universalism and alterity at the heart of this tension. The debates at Valladolid in 1550–51 between Las Casas and Sepúlveda, arguing their conceptions of the human, can shed light on how and why arguments for inequality creep back into the modern discourse on alterity. The lessons from Valladolid, therefore, might help to limit or clarify recourse to such arguments.
The Beginning that Never Was: Mediation and Freedom in Rousseau's Political Thought
Authors: Einspahr Jennifer 
Published: September 2010

AbstractUpon close examination of Rousseau's accounts of human development, we find that Rousseau presents us with paradoxical chronologies in which the experience of supposed immediacy from which humans are said to originate always seems to be informed by, and even require, previous mediation. More specifically, reflection, comparison, and imagination are thought to exist only after the onset of perfectibility, but these mediating capacities are always already present in pity and self-love, as well as for the “independent” savage, calling into question the possibility that any human sentiment or condition could be immediately accessible and fundamentally imbuing human life with ambiguity, fluidity, and disorder. Consequently, morality and freedom for Rousseau require the negotiation, stabilization, or management of the unstable “things between” human beings and their experiences, the object world, and others, even as such management is best hidden from view and experienced as given and true.
Rousseau's Use of the Jewish Example
Authors: Marks Jonathan D. 
Published: September 2010

AbstractRousseau refers to the Jews in major and minor works, setting them alongside the Greeks and Romans as models for republican politics. Yet Rousseau's use of the Jewish example has been almost entirely neglected. I argue that this example, which for Rousseau stands between paganism and Christianity, plays a unique role in Rousseau's political thought. In particular, Judaism, as Rousseau presents it, surpasses Christianity in its this-worldly emphasis on compassion and justice, an emphasis that even the classical republics that are Rousseau's usual models for social and political well-being cannot match. It does so, moreover, without fostering the dogmatism that, along with Christian otherworldiness, has, in Rousseau's estimation, helped to spoil European politics.
Particle‐resolved simulation of aerosol size, composition, mixing state, and the associated optical and cloud condensation nuclei activation properties in an evolving urban plume
Authors: Zaveri Rahul A. , Barnard James C. , Easter Richard C. , Riemer Nicole , West Matthew 
Published: September 2010

The recently developed particle‐resolved aerosol box model PartMC‐MOSAIC (Particle Monte Carlo model–Model for Simulating Aerosol Interactions and Chemistry) was used to rigorously simulate the evolution of aerosol mixing state and the associated optical and cloud condensation nuclei (CCN) activation properties in an idealized urban plume. The model explicitly resolved the size and composition of individual particles from a number of sources and tracked their evolution due to condensation, evaporation, coagulation, emission, and dilution. The ensemble black carbon (BC)–specific absorption cross section increased by 40% over the course of 2 days due to BC aging by condensation and coagulation. Threefold and fourfold enhancements in CCN/CN ratios were predicted to occur within 6 h for 0.2% and 0.5% supersaturations (S), respectively. The particle‐resolved results were used to evaluate the errors in the optical and CCN activation properties that would be predicted by a conventional sectional framework that assumes monodisperse, internally mixed particles within each bin. This assumption artificially increased the ensemble BC‐specific absorption by 14–30% and decreased the single scattering albedo (SSA) by 0.03–0.07, while the bin resolution had a negligible effect. In contrast, the errors in CCN/CN ratios were sensitive to the bin resolution for a chosen supersaturation. For S = 0.2%, the CCN/CN ratio predicted using 100 internally mixed bins was up to 25% higher than the particle‐resolved results, while it was up to 125% higher using 10 internally mixed bins. Neglecting coagulation overpredicted aerosol water content and number concentrations (<0.2 μm), causing errors in SSA from −0.02 to 0.035 and overprediction of CCN concentrations by 25–80% at S = 0.5%.
Baroreflex sensitivity is higher during acute psychological stress in healthy subjects under β-adrenergic blockade
Authors: Truijen Jasper , Davis Shyrin C.A.T. , Stok Wim J. , Kim Yu-Sok , van Westerloo David J. , Levi Marcel , van der Poll Tom , Westerhof Berend E. , Karemaker John M. , van Lieshout Johannes J. 
Published: September 2010

Acute psychological stress challenges the cardiovascular system with an increase in BP (blood pressure), HR (heart rate) and reduced BRS (baroreflex sensitivity). β-adrenergic blockade enhances BRS during rest, but its effect on BRS during acute psychological stress is unknown. This study tested the hypothesis that BRS is higher during acute psychological stress in healthy subjects under β-adrenergic blockade. Twenty healthy novice male bungee jumpers were randomized and studied with (PROP, n=10) or without (CTRL, n=10) propranolol. BP and HR responses and BRS [cross-correlation time-domain (BRSTD) and cross-spectral frequency-domain (BRSFD) analysis] were evaluated from 30 min prior up to 2 h after the jump. HR, cardiac output and pulse pressure were lower in the PROP group throughout the study. Prior to the bungee jump, BRS was higher in the PROP group compared with the CTRL group [BRSTD: 28 (24–42) compared with 17 (16–28) ms·mmHg−1, P&lt;0.05; BRSFD: 27 (20–34) compared with 14 (9–19) ms·mmHg−1, P&lt;0.05; values are medians (interquartile range)]. BP declined after the jump in both groups, and post-jump BRS did not differ between the groups. In conclusion, during acute psychological stress, BRS is higher in healthy subjects treated with non-selective β-adrenergic blockade with significantly lower HR but comparable BP.
The Chemical Translation Service—a web-based tool to improve standardization of metabolomic reports
Authors: Wohlgemuth Gert , Haldiya Pradeep Kumar , Willighagen Egon , Kind Tobias , Fiehn Oliver 
Published: September 2010

Abstract
Summary: Metabolomic publications and databases use different database identifiers or even trivial names which disable queries across databases or between studies. The best way to annotate metabolites is by chemical structures, encoded by the International Chemical Identifier code (InChI) or InChIKey. We have implemented a web-based Chemical Translation Service that performs batch conversions of the most common compound identifiers, including CAS, CHEBI, compound formulas, Human Metabolome Database HMDB, InChI, InChIKey, IUPAC name, KEGG, LipidMaps, PubChem CID+SID, SMILES and chemical synonym names. Batch conversion downloads of 1410 CIDs are performed in 2.5 min. Structures are automatically displayed.
Implementation: The software was implemented in Groovy and JAVA, the web frontend was implemented in GRAILS and the database used was PostgreSQL.
Availability: The source code and an online web interface are freely available. Chemical Translation Service (CTS): http://cts.fiehnlab.ucdavis.edu
Contact: ofiehn@ucdavis.edu
Robust and accurate data enrichment statistics via distribution function of sum of weights
Authors: Stojmirović Aleksandar , Yu Yi-Kuo 
Published: September 2010

AbstractMotivation: Term-enrichment analysis facilitates biological interpretation by assigning to experimentally/computationally obtained data annotation associated with terms from controlled vocabularies. This process usually involves obtaining statistical significance for each vocabulary term and using the most significant terms to describe a given set of biological entities, often associated with weights. Many existing enrichment methods require selections of (arbitrary number of) the most significant entities and/or do not account for weights of entities. Others either mandate extensive simulations to obtain statistics or assume normal weight distribution. In addition, most methods have difficulty assigning correct statistical significance to terms with few entities.Results: Implementing the well-known Lugananni–Rice formula, we have developed a novel approach, called SaddleSum, that is free from all the aforementioned constraints and evaluated it against several existing methods. With entity weights properly taken into account, SaddleSum is internally consistent and stable with respect to the choice of number of most significant entities selected. Making few assumptions on the input data, the proposed method is universal and can thus be applied to areas beyond analysis of microarrays. Employing asymptotic approximation, SaddleSum provides a term-size-dependent score distribution function that gives rise to accurate statistical significance even for terms with few entities. As a consequence, SaddleSum enables researchers to place confidence in its significance assignments to small terms that are often biologically most specific.Availability: Our implementation, which uses Bonferroni correction to account for multiple hypotheses testing, is available at http://www.ncbi.nlm.nih.gov/CBBresearch/qmbp/mn/enrich/. Source code for the standalone version can be downloaded from ftp://ftp.ncbi.nlm.nih.gov/pub/qmbpmn/SaddleSum/.Contact: yyu@ncbi.nlm.nih.govSupplementary information: Supplementary materials are available at Bioinformatics online.
SBML2TikZ: supporting the SBML render extension in LaTeX
Authors: Shen Si Yuan , Bergmann Frank , Sauro Herbert M. 
Published: September 2010

Abstract
Motivation: The SBML Render Extension enables coloring and shape information of biochemical models to be stored in the Systems Biology Markup Language (SBML). Rendering of this stored graphical information in a portable and well supported system such as TeX would be useful for researchers preparing documentation and presentations. In addition, since the Render Extension is not yet supported by many applications, it is helpful for such rendering functionality be extended to the more popular CellDesigner annotation as well.
Results: SBML2TikZ supports automatic generation of graphics for biochemical models in the popular TeX typesetting system. The library generates a script of TeX macro commands for the vector graphics languages PGF/TikZ that can be compiled into scalable vector graphics described in a model.
Availability: Source code, documentation and compiled binaries for the SBML2TikZ library can be found at http://www.sbml2tikz.org. In addition, a web application is available at http://www.sys-bio.org/layout
Contact: hsauro@u.washington.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
ODES: an overlapping dense sub-graph algorithm
Authors: Long James , Hartman Chris 
Published: September 2010

Abstract
Summary: Enumeration of the dense sub-graphs of a graph is of interest in community discovery and membership problems, including dense sub-graphs that overlap each other. Described herein is ODES (Overlapping DEnse Sub-graphs), pthreads parallelized software to extract all overlapping maximal sub-graphs whose densities are greater than or equal to a specified cutoff density of at least 1/2.
Availability and Implementation: http://dense.sf.net
Contact: jlong@alaska.edu
Fixed point characterization of biological networks with complex graph topology
Authors: Radde N. 
Published: September 2010

Abstract
Motivation: Feedback circuits are important motifs in biological networks and part of virtually all regulation processes that are needed for a reliable functioning of the cell. Mathematically, feedback is connected to complex behavior of the systems, which is often related to bifurcations of fixed points. Therefore, several approaches for the investigation of fixed points in biological networks have been developed in recent years. Many of them assume the fixed point coordinates to be known, and an efficient way to calculate the entire set of fixed points for interrelated feedback structures is highly desirable.
Results: In this article, we consider regulatory network models, which are differential equations with an underlying directed graph that illustrates independencies among variables. We introduce the circuit-breaking algorithm (CBA), a method that constructs one-dimensional characteristics for these network models, which inherit important information about the system. In particular, fixed points are related to the zeros of these characteristics. The CBA operates on the graph topology, and results from graph theory are used in order to make calculations efficient. Our framework provides a general scheme for analyzing network models in terms of interrelated feedback circuits. The efficiency of the approach is demonstrated on a model for calcium oscillations based on experiments in hepatocytes, which consists of several interrelated feedback circuits.
Contact: radde@ist.uni-stuttgart.de
Supplementary information: Supplementary data are available at Bioinformatics online.
A Novel method for similarity analysis and protein sub-cellular localization prediction
Authors: Liao Bo , Liao Benyou , Sun Xingming , Zeng Qingguang 
Published: September 2010

Abstract
Motivation: Biological sequence was regarded as an important study by many biologists, because the sequence contains a large number of biological information, what is helpful for scientists' studies on biological cells, DNA and proteins. Currently, many researchers used the method based on protein sequences in function classification, sub-cellular location, structure and functional site prediction, including some machine-learning methods. The purpose of this article, is to find a new way of sequence analysis, but more simple and effective.
Results: According to the nature of 64 genetic codes, we propose a simple and intuitive 2D graphical expression of protein sequences. And based on this expression we give a new Euclidean-distance method to compute the distance of different sequences for the analysis of sequence similarity. This approach contains more sequence information. A typical phylogenetic tree constructed based on this method proved the effectiveness of our approach. Finally, we use this sequence-similarity-analysis method to predict protein sub-cellular localization, in the two datasets commonly used. The results show that the method is reasonable.
Contact: dragonbw@163.com
Will depleted populations of Pacific salmon recover under persistent reductions in survival and catastrophic mortality events?
Authors: Holt Carrie A. 
Published: September 2010

Abstract
Holt, C. A. 2010. Will depleted populations of Pacific salmon recover under persistent reductions in survival and catastrophic mortality events? – ICES Journal of Marine Science, 67: 2018–2026. Under Canada's Wild Salmon Policy, benchmarks between zones of biological status are required to distinguish populations requiring conservation attention (Red and Amber zones) from those that can be managed for production (Green zone). The recovery of depleted populations (i.e. from Red to Green) will depend in part on the choice of the lower benchmark. At a minimum, that benchmark should be set high enough to allow recovery within an acceptable time-frame in the absence of targeted fishing. Currently, benchmarks are evaluated and selected using simulation models that assess the probability of recovery to spawner abundance associated with the maximum sustainable yield within a specified time-frame. Guided by case examples, the evaluation is extended to include two scenarios of future conditions: persistent reductions in survival rates below the replacement level; and increased frequency of catastrophic mortality (die-off) events. Probabilities of recovery appear to be more sensitive to persistent reductions in survival than to increased probability of die-off events. The current lower benchmarks on spawner abundance and fishing mortality might not be sufficiently precautionary to allow recovery under those conditions.
Hake catchability by the French trawler fleet in the Bay of Biscay: estimating technical and biological components
Authors: Mahévas Stéphanie , Trenkel Verena M. , Doray Mathieu , Peyronnet Arnaud 
Published: September 2010

AbstractMahévas, S., Trenkel, V. M., Doray, M., and Peyronnet, A. 2011. Hake catchability by the French trawler fleet in the Bay of Biscay: estimating technical and biological components. – ICES Journal of Marine Science, 68: 107–118. Several factors affect trawl catchability: (i) gear and vessel technical characteristics, (ii) anthropogenic factors, and (iii) biological factors. The objectives of this study were to assess the relative contribution of each factor to variations in hake (Merluccius merluccius) landings by the French trawler fleet operating on the shelf of the northern Bay of Biscay (ICES Subdivision VIIIa). Using generalized linear models, the impact of technical and anthropogenic factors was evaluated using landings per unit effort (lpue) obtained from logbooks. Variations in hake lpue were explained primarily by anthropogenic factors. For studying the biological components of catchability, the results of a scientific trawl survey in July 2006 involving three similar trawlers of the French trawler fleet were used. Daytime accessibility to large hake was lower than at night, and about zero for small hake (<19 cm). Estimates of spatial variation made using generalized linear mixed models showed a patchy fine-scale spatial distribution, but a random larger-scale distribution of hake over the area surveyed.
Calorie restriction‐induced maternal longevity is transmitted to their daughters in a rotifer
Authors: Kaneko Gen , Yoshinaga Tatsuki , Yanagawa Yoshiko , Ozaki Yori , Tsukamoto Katsumi , Watabe Shugo 
Published: September 2010

Summary1 Extension of life span by food shortage, often mimicked by calorie restriction (CR) in the laboratory, is one of the most common life‐history alterations in eukaryotes. Although the life‐history of offspring often changes in response to the parental environment, it has remained ambiguous whether or not CR‐induced longevity is transmitted to the next generation.2 Here, we investigated the effects of CR on life span, oxidative stress resistance and the expression levels of two antioxidant enzymes, catalase and manganese superoxide dismutase (Mn SOD), in the parthenogenetic rotiferBrachionus plicatilisduring two consecutive generations.3 Rotifers under CR lived 50% longer than those fedad libitum(AL) in association with enhancement of oxidative stress resistance and increased mRNA levels of catalase and Mn SOD.4 The daughters from the CR‐treated mothers lived 20% longer than those from the mothers fed AL regardless of food‐rich and CR conditions for the daughter. Furthermore, the daughters from the CR‐treated mothers were endowed at birth with a higher ability to resist oxidative stress and the increased mRNA levels for catalase, but not for Mn SOD. In agreement with the mRNA expression patterns, CR increased the protein levels of catalase and Mn SOD in eggs and the whole body of mothers, respectively.5 Our results for these asexually reproducing rotifers provide the first evidence that the longevity and oxidative stress resistance resulting from CR can be passed on to subsequent generations.
Development and psychometric testing of the Health Beliefs Related to Cardiovascular Disease Scale: preliminary findings
Authors: Tovar Elizabeth Gressle , Rayens Mary Kay , Clark Michele , Nguyen Hoang 
Published: September 2010

tovar e.g., rayens m.k., clark m. & nguyen h. (2010) Development and psychometric testing of the Health Beliefs Related to Cardiovascular Disease Scale: preliminary findings. Journal of Advanced Nursing 66(12), 2772–2784.AbstractAim.  This paper is a report of an evaluation of the psychometric properties of the Health Beliefs Related to Cardiovascular Disease Scale designed to measure beliefs related to cardiovascular disease risk and diet and exercise in adults with diabetes.Background.  Heart attack and stroke are 2–4 times more common among adults with diabetes than those without diabetes. To reduce this risk for patients with diabetes, understanding beliefs about cardiovascular disease risk and risk‐reduction strategies is important.Methods.  Item development for the 25‐item self‐report Likert scale was guided by literature review, expert panel review and focus‐group feedback. It consists of four subscales, measuring four constructs of the Health Belief Model: perceived susceptibility and severity of cardiovascular disease and benefits and barriers to diet and exercise. A convenience sample of 178 adults with self‐reported type 2 diabetes completed the survey between August 2006 and March 2007; 42 participants completed it again 2–3 weeks later to evaluate test–retest reliability.Results.  The instrument has more than one dimension, with the best fit identified using a two‐factor model specifying the Benefits and Susceptibility subscale items, rather than the four‐factor solution as predicted. The Susceptibility and Benefits subscales demonstrated stable factor structure and acceptable reliability (α = 0·93 and α = 0·82 respectively). The Barriers and Severity items demonstrated unstable factor structure and poor internal consistency (α = 0·70 and α = 0·61 respectively).Conclusion.  Only the Susceptibility and Benefits subscale items can be used in their current form. The Barriers and Severity items need further refinement including revised wording with clearer focus and evaluation with a larger, more diverse sample.