bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stochastic approaches in systems biology
Authors: Ullah Mukhtar , Wolkenhauer Olaf 
Published: December 2009

AbstractThe discrete and random occurrence of chemical reactions far from thermodynamic equilibrium, and low copy numbers of chemical species, in systems biology necessitate stochastic approaches. This review is an effort to give the reader a flavor of the most important stochastic approaches relevant to systems biology. Notions of biochemical reaction systems and the relevant concepts of probability theory are introduced side by side. This leads to an intuitive and easy‐to‐follow presentation of a stochastic framework for modeling subcellular biochemical systems. In particular, we make an effort to show how the notion of propensity, the chemical master equation (CME), and the stochastic simulation algorithm arise as consequences of the Markov property. Most stochastic modeling reviews focus on stochastic simulation approaches—the exact stochastic simulation algorithm and its various improvements and approximations. We complement this with an outline of an analytical approximation. The most common formulation of stochastic models for biochemical networks is the CME. Although stochastic simulations are a practical way to realize the CME, analytical approximations offer more insight into the influence of randomness on system's behavior. Toward that end, we cover the chemical Langevin equation and the related Fokker–Planck equation and the two‐moment approximation (2MA). Throughout the text, two pedagogical examples are used to key illustrate ideas. With extensive references to the literature, our goal is to clarify key concepts and thereby prepare the reader for more advanced texts. Copyright © 2009 John Wiley & Sons, Inc.This article is categorized under:Analytical and Computational Methods > Computational Methods
Pancreatitis bundles
Authors: Mayumi Toshihiko , Takada Tadahiro , Hirata Koichi , Yoshida Masahiro , Sekimoto Miho , Hirota Masahiko , Kimura Yasutoshi , Takeda Kazunori , Amano Hodaka , Wada Keita , Gabata Toshifumi , Arata Shinjyu , Hirota Morihisa , Yokoe Masamichi , Kiriyama Seiki , Shikata Satoru , Shirai Kunihiro , Nakayama Takeo , Ohtomo Kuni , Tanaka Masao , Shimosegawa Tooru 
Published: December 2009

AbstractClinical indicators set forth in the guidelines have been found to contribute to the improvement in compliance with the guidelines. On the other hand, it has been shown that clinical indicators are more effective when individual indicators are presented in the form of a bundle than when they are given separately. Accordingly, in the JPN Guidelines 2010 for management of acute pancreatitis, those indicators that are judged to be important on the basis of a recommendation classification of “A or B” are presented as a pancreatitis bundle. Each item includes assessment of severity after a diagnosis of pancreatitis has been made, differentiation of pathogenesis, management of gallstone‐induced pancreatitis, a sufficient dose of fluid replacement and monitoring, pain control, prophylactic administration of wide‐spectrum antibiotics and cholecystectomy following resolution of pancreatic symptoms caused by cholecystolithiasis. Hereafter, the efficacy of these indicators and the significance of their achievement should be examined carefully. Then, the assessment of the compliance rate with the guidelines as well as the assessment of the guidelines and pancreatitis itself should become possible.
The Consumption of Food Products from Linseed‐Fed Animals Maintains Erythrocyte Omega‐3 Fatty Acids in Obese Humans
Authors: Legrand Philippe , Schmitt B. , Mourot J. , Catheline D. , Chesneau G. , Mireaux M. , Kerhoas N. , Weill P. 
Published: December 2009

AbstractBased on mechanistic and epidemiological data, we raise the question of the relationship between qualitative dietary polyunsaturated fatty acids (PUFA) changes and increase in obesity. In this double‐blind trial, we studied the effects on 160 overweight volunteers (body mass index, BMI >30) of a 90 days experimental diet rich principally in animal fat with a low PUFA/saturated fatty acid (SFA) ratio but a low n‐6/n‐3 ratio, using animal products obtained from linseed‐fed animals. The control diet provided less animal fat, a higher PUFA/SFA ratio and a higher n‐6/n‐3 ratio. Both diets excluded seafood. In the experimental group, we observed a significant increase in red blood cell (RBC) α‐linolenic acid content and a slight increase in EPA and DHA derivatives, while in the control group we observed a significant reduction in EPA and DHA content. Between groups now, the difference in the three n‐3 fatty acids changes in RBC was significant. This demonstrates that plasma EPA and DHA levels can be maintained without fish if products from linseed‐fed animals are used. During the diets, we noted a significant reduction in weight, BMI and hip circumference within both groups of volunteers. However, no significant difference was observed between the control group and the experimental group. Interestingly, 150 days after the end of the trial (i.e., day 240), we noted a significant weight gain in the control group, whereas no significant weight gain was observed in the experimental group. This was also observed for the BMI and hip circumference. Moreover, significant differences in BMI (P < 0.05) and weight (P = 0.05) appeared between the two groups, showing in both cases a smaller increase in the experimental group. During the 90 days trial, we did not observe any differences between groups in terms of total cholesterol, HDL cholesterol, LDL cholesterol or triglycerides, suggesting that the saturate content and the P/S ratio are not as important as the n‐6 and n‐3 fatty acid composition.
Tolerance of arabinoxylan-oligosaccharides and their prebiotic activity in healthy subjects: a randomised, placebo-controlled cross-over study
Authors: Cloetens Lieselotte , Broekaert Willem F. , Delaedt Yasmine , Ollevier Frans , Courtin Christophe M. , Delcour Jan A. , Rutgeerts Paul , Verbeke Kristin 
Published: December 2009

The tolerance and prebiotic effect following oral intake by healthy human subjects of arabinoxylan-oligosaccharides (AXOS), produced by partial enzymic hydrolysis of the wheat fibre arabinoxlyan, were studied. A total of twenty healthy subjects participated in the present randomised, placebo-controlled cross-over study. They consumed 10 g AXOS or placebo per d each for 3 weeks with a 4-week wash-out period in between. Before and immediately after each intake period, blood samples were taken to measure haematological and clinical chemistry parameters and the subjects completed a questionnaire about gastrointestinal symptoms. Additionally, urine was collected over 48 h for analysis ofp-cresol and phenol content by GC–MS, and faeces were collected over 72 h for analysis of microbiota using real-time PCR. Of the subjects, ten also performed a urine and faeces collection 2 weeks after the start of intake (during intervention). A limited number of tested blood parameters were influenced in a statistically significantly way by either AXOS or placebo intake, but these changes remained within the normal range. Blood lipids remained unchanged. AXOS had no statistically significant effect on the range of gastrointestinal symptoms, except for a mild increase in flatulence. Urinaryp-cresol excretion, an indicator of protein fermentation, was significantly decreased after 2 weeks of AXOS intake. The levels of bifidobacteria were significantly increased after 2 and 3 weeks of AXOS intake as well as after 3 weeks of placebo. However, the effect of AXOS on bifidobacteria was more pronounced than that of placebo. In conclusion, AXOS are a well-tolerated prebiotic at the dose of 10 g/d. AXOS intake increases faecal bifidobacteria and reduces urinaryp-cresol excretion.
Effect of dietary sodium phytate and microbial phytase on the lipase activity and lipid metabolism of broiler chickens
Authors: Liu Ning , Ru Yingjun , Wang Jianping , Xu Tingsheng 
Published: December 2009

The objective of the present study was to investigate the effect of dietary phytate and microbial phytase on the lipase activity, lipid metabolism and mRNA expressions of fatty acid synthase (FASN) and leptin in broiler chickens. The study was conducted as a 2 × 3 factorial arrangement of treatments with phytate phosphorus at 0·20 and 0·40 % (added as the sodium phytate) and supplemental microbial phytase at 0, 500, or 1000 phytase units/kg. The results showed that phytase improved (P < 0·05) the growth performance and ileal digestibility of nutrients of broilers, but phytate had no effect (P>0·05) on these parameters, except the decrease (P < 0·01) in the digestibility of Ca. Phytate decreased (P < 0·05) the lipase activity, serum total cholesterol (T-CHO) and hepatic TAG, and elevated (P < 0·01) serum NEFA and HDL cholesterol. Phytase decreased (P < 0·05) serum NEFA, but increased (P < 0·01) serum T-CHO and hepatic TAG. Phytate and phytase also influenced (P < 0·01) the mRNA expressions of leptin in the liver. There were significant (P < 0·05) interactions of phytate and phytase on the concentrations of serum TAG and LDL cholesterol, hepatic NEFA and T-CHO, and the mRNA expressions of FASN. The results suggest that phytate and phytase can affect lipase activity and lipid metabolism of broiler chickens.
Reflections of men and women in advanced old age on being born the other sex
Authors: ALÉX LENA , LUNDMAN BERIT , HAMMARSTRÖM ANNE 
Published: December 2009

ABSTRACTThe study reported in this paper is part of the Umeå 85+ project in Sweden. The aim was to investigate gender perspectives among ‘the oldest old’, by asking men and women in advanced old age living in a sparsely populated area of northern Sweden to reflect on how life might have been if they had been born the other sex. Thematic narratives from nine men and seven women were analysed using qualitative content analysis. The content of these narratives was resolved into eight categories in two domains, respectively men's and women's reflections about being born the opposite sex. The narratives of both the men and women indicated that they were satisfied with their actual birth sex. The men were aware that if they had been born female, they would probably have experienced more hard work and had a more restricted life, and they were conscious of both women's relative powerlessness and their greater ability to manage and organise work within the home. The women's narratives described a femininity characterised by longing for a state of being unconcerned when young, and their narratives also displayed awareness of women's physical strength and that men's lives had also been hard.
A reconfigurable modular robotic endoluminal surgical system: vision and preliminary results
Authors: Harada Kanako , Oetomo Denny , Susilo Ekawahyu , Menciassi Arianna , Daney David , Merlet Jean-Pierre , Dario Paolo 
Published: December 2009

SUMMARYMiniaturized surgical devices are promising for the future development of minimally invasive and endoluminal surgery. However, the dexterity and therapeutic functions of these devices are limited. In this paper, a reconfigurable modular robotic system is proposed to perform screening and interventions in the gastrointestinal tract. In the proposed system, millimeter-sized robotic modules are ingested and tasked to assemble into an articulated mechanism in the stomach cavity. The modules are assembled according to the target location to perform precise intervention. Based on this concept, a preliminary report is presented covering the robotic schemes for the endoluminal reconfigurable platform, the design with structural functions, the control strategy, and the interval-based constraint satisfaction algorithm to determine the suitable topologies of the reconfigurable robot for the given task.
Molecular detection of anammox bacteria in terrestrial ecosystems: distribution and diversity
Authors: Humbert Sylvia , Tarnawski Sonia , Fromin Nathalie , Mallet Marc-Philippe , Aragno Michel , Zopfi Jakob 
Published: December 2009

Abstract
Anaerobic oxidation of ammonium (anammox) is recognized as an important process in the marine nitrogen cycle yet nothing is known about the distribution, diversity and activity of anammox bacteria in the terrestrial realm. In this study, we report on the detection of anammox sequences of Candidatus ‘Brocadia’, ‘Kuenenia’, ‘Scalindua’ and ‘Jettenia’ in marshes, lakeshores, a contaminated porous aquifer, permafrost soil, agricultural soil and in samples associated with nitrophilic or nitrogen-fixing plants. This suggests a higher diversity of anammox bacteria in terrestrial than in marine ecosystems and could be a consequence of the larger variety of suitable niches in soils. Anammox bacteria were not ubiquitously present but were only detected in certain soil types and at particular depths, thus reflecting specific ecological requirements. As opposed to marine water column habitats where Candidatus ‘Scalindua’ dominates anammox guilds, ‘Kuenenia’ and ‘Brocadia’ appear to be the most common representatives in terrestrial environments.
Binary and ternary crystal structure analyses of a novel inhibitor with 17β-HSD type 1: a lead compound for breast cancer therapy
Authors: Mazumdar Mausumi , Fournier Diane , Zhu Dao-Wei , Cadot Christine , Poirier Donald , Lin Sheng-Xiang 
Published: December 2009

Oestradiol is a well-characterized sex hormone that stimulates breast cancer and other oestrogen-related diseases. 17β-hydroxysteroid dehydrogenase type 1 (17β-HSD1) catalyses the last step in the synthesis of oestradiol and androstenediol in breast tumour tissue. The enzyme's high expression and activity after simultaneous blockade of oestrogen receptors and inhibition of aromatase in the tumour shows the necessity for its inhibition as a requirement for breast cancer therapy. In the present paper, we report structures of the binary and ternary complexes of 17β-HSD1 with a new inhibitor E2B {3-[3′,17′β-dihydroxyestra-1′,3′,5′(10′)-trien-16′β-methyl]benzamide}, and the enzyme inhibition by the later. The IC50 value for E2B was determined to be 42 nM in T47D cells. Multiple interactions between E2B and the enzyme include hydrogen bonds and hydrophobic interactions, as well as π–π interactions. A kinetic study demonstrated that E2B inhibits the enzyme's reduction forming oestradiol from oestrone, with a Ki of 0.9±0.15 nM. Such strong inhibition is in agreement with its extensive interaction with the enzyme, suggesting its potential as a lead compound for breast cancer therapy. In fact, this possibility is enhanced by its capacity for cell penetration similar to natural steroids. Such inhibitors that block oestrogen synthesis to suppress the sulfatase pathway producing oestradiol can be used in adjuvant therapies with oestrogen receptor blockade, opening a new orientation of breast cancer treatment.
Countervailing vascular effects of rosiglitazone in high cardiovascular risk mice: role of oxidative stress and PRMT-1
Authors: Savoia Carmine , Ebrahimian Talin , Lemarié Catherine A. , Paradis Pierre , Iglarz Marc , Amiri Farhad , Javeshgani Danesh , Schiffrin Ernesto L. 
Published: December 2009

In the present study, we tested the hypothesis that the PPARγ (peroxisome-proliferator-activated receptor γ) activator rosiglitazone improves vascular structure and function in aged hyperhomocysteinaemic MTHFR (methylene tetrahydrofolate reductase) gene heterozygous knockout (mthfr+/−) mice fed a HCD (high-cholesterol diet), a model of high cardiovascular risk. One-year-old mthfr+/− mice were fed or not HCD (6 mg·kg−1 of body weight·day−1) and treated or not with rosiglitazone (20 mg·kg−1 of body weight·day−1) for 90 days and compared with wild-type mice. Endothelium-dependent relaxation of carotid arteries was significantly impaired (−40%) only in rosiglitazone-treated HCD-fed mthfr+/− mice. Carotid M/L (media-to-lumen ratio) and CSA (cross-sectional area) were increased (2-fold) in mthfr+/− mice fed or not HCD compared with wild-type mice (P&lt;0.05). Rosiglitazone reduced M/L and CSA only in mthfr+/− mice fed a normal diet. Superoxide production was increased in mthfr+/− mice fed HCD treated or not with rosiglitazone, whereas plasma nitrite was decreased by rosiglitazone in mice fed or not HCD. PRMT-1 (protein arginine methyltransferase-1), involved in synthesis of the NO (nitric oxide) synthase inhibitor ADMA (asymmetric ω-NG,NG-dimethylarginine), and ADMA were increased only in rosiglitazone-treated HCD-fed mthfr+/− mice. Rosiglitazone had both beneficial and deleterious vascular effects in this animal model of high cardiovascular risk: it prevented carotid remodelling, but impaired endothelial function in part through enhanced oxidative stress and increased ADMA production in mice at high cardiovascular risk.
David Zeisberger’s Description of Delaware Morphology (1827)
Authors: Swiggers Pierre 
Published: December 2009

Summary
This article proposes an analysis of the linguistic work of the Moravian missionary David Zeisberger (1721–1808), and more particularly of his grammar of the Delaware language (= [Lenni-]Lenape), which was published in 1827 in an English translation by Peter S. Du Ponceau (1760–1844), on the basis of the author’s German manuscript. A life-sketch and a short presentation of Zeisberger’s missionary work are intended to place the Delaware grammar in the context of his scholarly output, thus allowing the reader to adequately appreciate the practical orientation of the work. The analysis of the grammar, which is essentially a description of Delaware verb morphology, focuses on the parts-of-speech model, and on the treatment of the various word classes, with special attention being paid to the verb. The article offers a detailed study of the organization of the verb paradigms, of the division into conjugations and into ‘forms’ (positive, negative, etc.), and of the description of verbal ‘transitions’. The practical and analytical outlook of Zeisberger is confirmed by the lexicographically oriented treatment of the undeclinable parts of speech: the adverb, the preposition, the conjunction and the interjection. The conclusion insists on the fact that Zeisberger’s grammar was an important source for 19th-century linguists interested in language typology and more particularly in the structure of polysynthetic languages.
Translating Non-Denominational Concepts in Describing a Religious System
Authors: Pharo Lars Kirkhusmo 
Published: December 2009

SummaryIn an earlier article (Pharo 2007), the author investigated how Spanish ethnographer-missionaries and missionary-linguists of the Colonial period translated the concept of ‘religion’ into various indigenous Mesoamerican languages. In the present article, he concedes that “assorted Mesoamerican notions may well together, as a family of concepts, be subordinated to the abstract superior concept of ‘religion’. Other relevant modern Spanish concepts like ‘sagrado’, ‘creencia’, ‘ritual’ and ‘costumbre’ etc. can thus be studied in the dictionaries.” In particular ‘costumbre’ (“custom”, “habit”) proves to be a central word among present-day Mesoamericans, not only to circumscribe their own religious practice, but also to designate ‘religion’ as well. As a result, the author, this time, analyses Spanish concepts associated with religion – but not exclusively with Christianity, i.e., neutral religious notions are the object of the analysis – translated into Nahuatl and Yucatec as recorded in colonial period dictionaries. The general hypothesis is that the dictionaries, in particular theVocabulario(1555 and 1571) by the Franciscan Alonso de Molina (1514–1585), constituted a pedagogical strategy of transculturation at this early stage of the mission, not a radical linguistic attempt at acculturation, in order to transmit the unfamiliar Christian notions (such as conversion) to the natives of Mesoamerica.
Portuguese and Other European Missionaries in Africa
Authors: Levi Joseph Abraham 
Published: December 2009

Summary
This study looks at some of the works produced by Catholic missionaries in Africa from the pre-dawn of the Modern Era (Fall of Constantinople, 1453), in particular the Fall of Ceuta (1415), to the Berlin Conference (1884–1885). Particular emphasis will be placed on the linguistic production of a few Franciscan, Augustinian, Capuchin, Dominican, and/or Jesuit clerics, working under the aegis of the Portuguese Crown, who – with the invaluable help of native assistants, usually members of the clergy or closely affiliated with the Church – compiled the first grammars, word lists, glossaries, and dictionaries of the indigenous languages with which they worked and interacted on a daily basis. Their endeavour, though meritorious and not always free from preconceived ideas of the ‘other’, paved the way for future studies in the field.
Emotion Modelling Towards Affective Pathogenesis
Authors: Bas James Le 
Published: December 2009

Objective: There is a need in psychiatry for models that integrate pathological states with normal systems. The interaction of arousal and emotion is the focus of an exploration of affective pathogenesis. Method: Given that the explicit causes of affective disorder remain nascent, methods of linking emotion and disorder are evaluated. Results: A network model of emotional families is presented, in which emotions exist as quantal gradients. Morbid emotional states are seen as the activation of distal emotion sites. The phenomenology of affective disorders is described with reference to this model. Recourse is made to non-linear dynamic theory. Conclusions: Metaphoric emotion models have face validity and may prove a useful heuristic.
Academics of the Future? A Survey of Final Year Medical Students
Authors: Galletly Cherrie , Chur-Hansen Anna , Air Tracy , Chapman Ian 
Published: December 2009

Objective: The aim of this study was to survey final year medical students at an Australian medical school about their views and experiences regarding academic medicine Methods: A four page questionnaire was developed and administered to each group of final (6th) year medical students upon completion of their psychiatry rotation Results: For 82% clinical teaching would probably or definitely be part of their future careers, while 63% expected that they would undertake formal teaching. Thirty-three percent of students anticipated limited or no involvement in research. While 26% of students expected that they would undertake a higher degree, only 13% were interested in pursuing an academic career Conclusions: The dearth of academics in medicine and in psychiatry in particular is of considerable concern. This study provides some possible avenues for further exploration to address this professional challenge
PCIT: an R package for weighted gene co-expression networks based on partial correlation and information theory approaches
Authors: Watson-Haigh Nathan S. , Kadarmideen Haja N. , Reverter Antonio 
Published: December 2009

Abstract
Summary: We make the PCIT algorithm, used for detecting meaningful gene–gene associations in co-expression networks, available as an R package. Automatic detection of a suitable parallel environment is used such that scripts are portable between parallel and non-parallel environments with no modification of the script.
Availability and implementation: Source code and binaries freely available (under GPL-3) for download via CRAN at http://cran.r-project.org/package=PCIT, implemented in R and supported on Linux and MS Windows.
Contact: nathan.watson-haigh@csiro.au