bluuebunny/crossref_metadata_2025_split huggingface dataset:
Perfect simulation with exponential tails on the running time
Authors: Huber Mark 
Published: April 2008

AbstractMonte Carlo algorithms typically need to generate random variates from a probability distribution described by an unnormalized density or probability mass function. Perfect simulation algorithms generate random variates exactly from these distributions, but have a running timeTthat is itself an unbounded random variable. This article shows that commonly used protocols for creating perfect simulation algorithms, such as Coupling From the Past can be used in such a fashion that the running time is unlikely to be very much larger than the expected running time. © 2008 Wiley Periodicals, Inc. Random Struct. Alg., 2008
Enquiring into skills development with SSM: a South African experience
Authors: Córdoba José‐Rodrigo , Farquharson Fiona 
Published: April 2008

AbstractSince the first democratic elections in 1994, vocational education and training (VET) in South Africa has undergone major changes in order to equip the country to enhance its skills base, and to face post apartheid and globalization challenges. Part of the change has involved the adoption (by some players) of ‘Mode 2’ ideas of knowledge production as suggested by Gibbons and those studying the sociology of knowledge in modern societies. Mode 2 production is trans‐disciplinary and uses socially accountable forms to generate scientific knowledge in contrast to ‘Mode 1’ which is mainly based on single scientific disciplines and knowledge generation by the scholarly community. The objective of this adoption in the South African context is to enable a variety of stakeholders to be involved both in enhancing research in South Africa and responding to the needs of different economic sectors. However, the dynamics of stakeholder interaction can be complex. In this paper, we report on a skills capacity building intervention involving the application of Systems Thinking approaches and methodologies in a South African setting. Our intervention was informed by the use of soft systems methodology (SSM) as a means of assisting different groups of researchers firstly to share their perceptions about research in the skills development context, and secondly to collaborate together in generating suggestions for improvements. A key objective was to improve the interactions between researchers and other stakeholders in the organization of skills development research projects. The use of SSM methodology enabled us to ‘qualify’ the nature of these interactions. It also gave us clues about particular issues (e.g. power) that need to be tackled to improve capacity building in this area. Copyright © 2008 John Wiley & Sons, Ltd.
Adapting organizations: the instance of business process re‐engineering
Authors: Dekkers Rob 
Published: April 2008

AbstractThe question whether the often‐radical approach of Business Process Re‐engineering constitutes a viable option for restructuring is at the heart of this study. It appraises the case of Business Process Re‐engineering and its kin—process innovation and the Delft School Approach—from an evolutionary perspective based on an analogy between organisms and organizations. The research introduces a reference model that originates in evolutionary biological theories and models. The study undertaken—archival research for Business Process Re‐engineering and process innovation, and six case studies for the Delft School Approach—confirms that organizations evolve slower than expected, that Business Process Re‐engineering as a radical approach is hardly viable, that it and its kin seem to be directed at optimization and that the initiatives hardly connect to external opportunities. The primary yield of this research is the reference model that makes it possible to describe these (often slower) evolutionary processes. Copyright © 2008 John Wiley & Sons, Ltd.
Toward a property based requirements theory: System requirements structured as a semilattice
Authors: Micouin Patrice 
Published: April 2008

AbstractIn this paper, we outline a property‐based requirement (PBR) theory. After introducing the mathematical notion of semilattice, we express the ontological and epistemological assumptions on which our theory is built. We provide a definition of a “well formed (wf‐)requirement,” based on the property concept, distinguished from that of an “expectation.” Then, we introduce two relationships between wf‐requirements called respectively “conjunction” operation and “stringency” relationship. So, we state that a set of wf‐requirements, assigned to a system, is structured as a semilattice and that the maximum element of this semilattice matches the system specification. The network including all the expectations and wf‐requirements related to a system are linked together through two very unlike categories of relationships. “De dicto” relationships are linguistic dependencies while “de re” relationships among requirements are extralinguistic dependencies among material properties refereed by wf‐requirements. We highlight two types of “de re” relationship among wf‐requirements. The first one is the well known “derivation” relationship that links together a “parent” requirement with its “child” requirements during the system design process. We introduce a second one, called “coupling” relationship. Wf‐requirements are coupled when the change of one of them collides with others. We claim that our PBR theory belongs to the same paradigm as the model‐based systems engineering (MBSE) approaches whereas TBR belongs to the same field as empirical design approaches. Then, we relate our requirements formulation to features of the OMG SysMLTM language. We conclude on our prospects for research, which connect our requirement theory with reflections carried out on the bodies of knowledge and their specification, i.e. ontologies. © 2008 Wiley Periodicals, Inc. Syst Eng
Thirty years of advocacy in San Francisco: Lessons learned and the next generation of leadership
Authors: Lee NTanya 
Published: April 2008

AbstractProfessional advocacy organizations are often challenged by the question of their authentic community representation and their ability to balance short‐term pragmatism with strategic plans for long‐term, systemic change. Coleman Advocates, one of the nation's most effective child advocacy organizations, has taken up this challenge under the leadership of a next‐generation leader of color who followed a dynamic director of the baby boom generation. In this piece, Coleman's thirty years of social change strategies are analyzed from the perspective of this new executive director, who has facilitated the latest organizational shift that deepens its commitment to building bottom‐up grassroots leadership and community power while keeping the best of the professional, staff‐led advocacy model. Issues of race, accountability, power, and movement building are addressed through the lens of one organization's evolution, with the goal of building a long‐term movement that will achieve racial and economic equity for all children and families.
The development of collective moral leadership among parents through education organizing
Authors: Evans Michael P. , Shirley Dennis 
Published: April 2008

AbstractIt is often assumed that parent participation in schools is primarily based on self‐interest and that this is a frequent source of contention between parents and teachers. This article examines the experiences of members of the Jamaica Plain Parent Organizing Project (JP‐POP), a community‐based organization in Boston, and reveals that some parents have learned to act beyond their individual self‐interest and to organize on behalf of the entire community as a result of their participation. The authors present qualitative data from interviews with JP‐POP members to ascertain the motivations behind their initial decisions to become involved in education, the benefits they derive from their participation, and the gradual evolution of narrow definitions of self‐interest to more communal understandings. Finally, they draw out implications for the potential capacity enhancement of community‐based organizations in education at both the institutional and district levels.
Parkin‐co‐regulated gene (PACRG) product interacts with tubulin and microtubules
Authors: Ikeda Takashi 
Published: April 2008

MINT‐6439731, MINT‐6439753, MINT‐6439768:

PACRG (genbank_protein_gi:169219363), tubulin alpha (uniprotkb:P02550), tubulin beta (uniprotkb:Q2XVP4) bind (MI:0407) by cosedimentation (MI:0027)
MINT‐6439796:

PACRG (genbank_protein_gi:169219363), tubulin alpha (uniprotkb:P02550), tubulin beta (uniprotkb:Q2XVP4) bind (MI:0407) by pull-down (MI:0096)
Mapping of interaction domains of putative telomere‐binding proteins AtTRB1 and AtPOT1b from Arabidopsis thaliana
Authors: Schrumpfová Petra Procházková , Kuchař Milan , Paleček Jan , Fajkus Jiří 
Published: April 2008

MINT‐6440051:

AtTRB1 (uniprotkb:Q8VWK4) physically interacts (MI:0218) with AtTRB1 (uniprotkb:Q8VWK4) by two‐hybrid (MI:0018)
MINT‐6440068:

AtTRB2 (uniprotkb:Q8VX38) physically interacts (MI:0218) with AtTRB1 (uniprotkb:Q8VWK4) by two‐hybrid (MI:0018)
MINT‐6440083:

AtTRB3 (uniprotkb:Q9M2X3) physically interacts (MI:0218) with AtTRB1 (uniprotkb:Q8VWK4) by two‐hybrid (MI:0018)
MINT‐6440099:

AtPOT1b (uniprotkb:Q6Q835) physically interacts (MI:0218) with AtTRB1 (uniprotkb:Q8VWK4) by two‐hybrid (MI:0018)
MINT‐6440119:

AtPOT1b (uniprotkb:Q6Q835) physically interacts (MI:0218) with AtTRB2 (uniprotkb:Q8VX38) by two‐hybrid (MI:0018)
MINT‐6440138:

AtPOT1b (uniprotkb:Q6Q835) physically interacts (MI:0218) with AtTRB3 (uniprotkb:Q9M2X3) by two‐hybrid (MI:0018)
MINT‐6440216:

AtPOT1b (uniprotkb:Q6Q835) physically interacts (MI:0218) with AtTRB1 (uniprotkb:Q8VWK4) by coimmunoprecipitation (MI:0019)
MINT‐6440157:

AtTRB2 (uniprotkb:Q8VX38) physically interacts (MI:0218) with AtTRB1 (uniprotkb:Q8VWK4) by coimmunoprecipitation (MI:0019)
MINT‐6440177:

AtTRB3 (uniprotkb:Q9M2X3) physically interacts (MI:0218) with AtTRB1 (uniprotkb:Q8VWK4) by coimmunoprecipitation (MI:0019)
Epigenetics and cancer, 2nd IARC meeting, Lyon, France, 6 and 7 December 2007
Authors: Lambert Marie-Pierre , Herceg Zdenko 
Published: April 2008

It is becoming widely accepted that epigenetic alterations are universally present in human malignancies and that cancer is as much a disease of abnormal epigenetics as it is a genetic disease. The potential utility of epigenetics and epigenomics in cancer research and cancer control is highlighted by the fact that many funding agencies put cancer epigenetics on the priority list. The goal of this meeting, held at the offices of the International Agency for Research on Cancer in Lyon, France, 6 and 7 December 2007, was to discuss recent conceptual and technological advances in cancer epigenetics and epigenomics, the future research needs in the field, and their implications for early detection, risk assessment and prevention of cancer.While epigenetics has been historically linked to phenomena that do not follow normal genetic principles of heritability, recent mechanistic advances have begun to change our understanding of complex diseases including cancer, traditionally viewed as genetic in origin. It is now known that epigenetic mechanisms play critical roles in regulation of many cellular functions and their deregulation may disrupt the control of fundamental processes leading to tumour formation. A flurry of screening and functional studies revealed that most key processes found in cancer cells, such as silencing of tumour suppressor genes, activation of oncogenes, aberrant cell cycle processes, defects in DNA repair, and deregulation of cell death, can be triggered by epigenetic deregulation. Two important features that distinguish epigenetic changes from genetic alterations are the gradual appearance and reversibility of epigenetic events. These features make epigenetic alterations an attractive target for therapeutic intervention and the development of preventive strategies. For example, aberrant patterns of DNA methylation and histone acetylation and methylation can be targeted by drugs aiming to re‐activate epigenetically silenced genes. Until now, most studies on epigenetic changes in cancer were generally focused on specific genes. However, this meeting also stressed the need to take advantage of recent progress in epigenomics and emergence of powerful technologies for detection of epigenetic changes in high throughput and genome‐wide settings. This may further advance our capacity to evaluate the contribution of epigenetic changes induced by environmental epimutagens to human cancer. This information may prove critical for the design of efficient strategies for early diagnosis, therapy, and prevention of cancer.
Generalized Euler constants
Authors: DIAMOND HAROLD G. , FORD KEVIN 
Published: April 2008

AbstractWe study the distribution of a family $\{\g(\P)\}$ of generalized Euler constants arising from integers sieved by finite sets of primes $\P$. For $\P=\P_r$, the set of the first r primes, $\g(\P_r) \to \exp(-\g)$ as r → ∞. Calculations suggest that $\g(\P_r)$ is monotonic in r, but we prove it is not. Also, we show a connection between the distribution of $\g(\P_r) - \exp(-\g)$ and the Riemann hypothesis.
Idiosyncratic evolution of conserved eukaryote proteins that are similar in sequence to archaeal or bacterial proteins
Authors: Britten Roy 
Published: April 2008

Abstract	Sequence comparisons have been made between the proteins of 571 prokaryote species including 46 archaea and 525 bacteria and the set of human proteins. Highly conserved eukaryotic proteins are often strikingly similar in sequence to archaeal and bacterial proteins. Yet in many cases similarity to archaeal proteins is not correlated to the similarity to bacterial proteins. In these comparisons there are hundreds of eukaryote proteins that match well archeal proteins, but do not match recognizably to bacterial proteins, while thousands of proteins match well to bacterial proteins but not recognizably to archeal proteins. Forty percent of the 21,440 human proteins that significantly match prokaryote proteins are in this extreme idiosyncratic category. These relationships have been preserved over billions of years since the last common ancestor or sharing of protein genes between prokaryotes and eukaryotes. For each of the 21,440 members of this set of human proteins (that make significant matches to any of the 1.8 million proteins in this set of prokaryote species protein libraries) it is certain that each protein has important functions both in prokaryotes and eukaryotes and the precursor proteins have been important in the precursor species of both. That is the only explanation for the preservation of amino acid sequence similarity for the billions of years since the last common ancestor or period of sharing of proteins. Comparisons were made between the proteins of Arabidopsis thaliana and Saccharomyces cerevisiae to the proteins of the 571 prokaryote species. The results agreed with the human comparisons indicating that the conclusions apply to eukaryotes generally.
Long-term hyperglucagonaemia induces early metabolic and renal phenotypes of Type 2 diabetes in mice
Authors: Li Xiao C. , Liao Tang-dong , Zhuo Jia L. 
Published: April 2008

Clinical studies have shown that patients with early Type 2 diabetes often have elevated serum glucagon rather than insulin deficiency. Imbalance of insulin and glucagon in favouring the latter may contribute to impaired glucose tolerance, persistent hyperglycaemia, microalbuminuria and glomerular injury. In the present study, we tested the hypothesis that long-term glucagon infusion induces early metabolic and renal phenotypes of Type 2 diabetes in mice by activating glucagon receptors. Five groups of adult male C57BL/6J mice were treated with vehicle, glucagon alone (1 μg/h via an osmotic minipump, intraperitoneally), glucagon plus the glucagon receptor antagonist [Des-His1-Glu9]glucagon (5 μg/h via an osmotic minipump), [Des-His1-Glu9]glucagon alone or a high glucose load alone (2% glucose in the drinking water) for 4 weeks. Glucagon infusion increased serum glucagon by 129% (P&lt;0.05), raised systolic BP (blood pressure) by 21 mmHg (P&lt;0.01), elevated fasting blood glucose by 42% (P&lt;0.01), impaired glucose tolerance (P&lt;0.01), increased the kidney weight/body weight ratio (P&lt;0.05) and 24 h urinary albumin excretion by 108% (P&lt;0.01) and induced glomerular mesangial expansion and extracellular matrix deposition. These responses were associated with marked increases in phosphorylated ERK1/2 (extracellular-signal-regulated kinase 1/2) and Akt signalling proteins in the liver and kidney (P&lt;0.01). Serum insulin did not increase proportionally. Concurrent administration of [Des-His1-Glu9]glucagon with glucagon significantly attenuated glucagon-increased BP, fasting blood glucose, kidney weight/body weight ratio and 24 h urinary albumin excretion. [Des-His1-Glu9]glucagon also improved glucagon-inpaired glucose tolerance, increased serum insulin by 56% (P&lt;0.05) and attenuated glomerular injury. However, [Des-His1-Glu9]glucagon or high glucose administration alone did not elevate fasting blood glucose levels, impair glucose tolerance or induce renal injury. These results demonstrate for the first time that long-term hyperglucagonaemia in mice induces early metabolic and renal phenotypes of Type 2 diabetes by activating glucagon receptors. This supports the idea that glucagon receptor blockade may be beneficial in treating insulin resistance and Type 2 diabetic renal complications.
Initiation factors for translation of proteins in the rectus abdominis muscle from patients on overnight standard parenteral nutrition before surgery
Authors: Iresjö Britt-Marie , Körner Ulla , Hyltander Anders , Ljungman David , Lundholm Kent 
Published: April 2008

Previous studies have provided conflicting conclusions concerning the efficacy of improving protein balance in patients by standard intravenous nutrition [TPN (total parenteral nutrition)], which is either explained by suboptimal nutritional regimens or insensitive clinical methods. The aim of the present study was therefore to evaluate the effects on the initiation of translation of skeletal muscle proteins by standard overnight TPN. A total of 12 patients who underwent standard surgery were included. TPN was provided as an all-in-one treatment by constant infusion [0.16 gN·kg−1 of body weight·day−1 (30 kcal·kg−1 of body weight·day−1)]. Saline-infused patients served as controls. Rectus abdominis muscle biopsies were taken at the time of the operation. The phosphorylation state of the proteins for initiation of translation was quantified. Plasma glucose, and serum insulin, glycerol, triacylglycerols (triglycerides) and NEFAs (non-esterified fatty acids; ‘free fatty acids’) were not significantly altered during TPN infusion, whereas total plasma amino acids increased, as shown by increases in methionine, phenylalanine, threonine, alanine, arginine, aspartic acid, glycine and histidine (P&lt;0.05). Overnight TPN increased the formation of active eIF4G–eIF4E (where eIF is eukaryotic-initiation factor) complexes (P&lt;0.05), whereas the inhibitory complex 4E-BP1 (eIF4E-binding protein)–eIF4E was moderately decreased (P&lt;0.06). TPN increased the amount of the most phosphorylated form of 4E-BP1 (P&lt;0.05), and increased the amount (P&lt;0.04) and phosphorylation (P&lt;0.01) of p70S6K (70 kDa ribosomal protein S6 kinase). In conclusion, an overnight pre-operative constant infusion of standard TPN altered initiation factor complexes, indicating activation of the initiation of protein translation in rectus abdominis muscle in the presence of increased plasma amino acid levels, but without a concomitant increase in energy substrates and insulin. In contrast with our results from previous studies, the methodology used in the present study appears to be more sensitive in reflecting directional changes in human muscle protein synthesis compared with traditional methods, particularly based on measurements of amino acid flux.
Expected gene-order distances and model selection in bacteria
Authors: Dalevi Daniel , Eriksen Niklas 
Published: April 2008

AbstractMotivation: The evolutionary distance inferred from gene-order comparisons of related bacteria is dependent on the model. Therefore, it is highly important to establish reliable assumptions before inferring its magnitude.Results: We investigate the patterns of dotplots between species of bacteria with the purpose of model selection in gene-order problems. We find several categories of data which can be explained by carefully weighing the contributions of reversals, transpositions, symmetrical reversals, single gene transpositions and single gene reversals. We also derive method of moments distance estimates for some previously uncomputed cases, such as symmetrical reversals, single gene reversals and their combinations, as well as the single gene transpositions edit distance.Contact: ner@math.chalmers.seSupplementary information: Supplementary data are available at Bioinformatics online.
FT-COMAR: fault tolerant three-dimensional structure reconstruction from protein contact maps
Authors: Vassura Marco , Margara Luciano , Di Lena Pietro , Medri Filippo , Fariselli Piero , Casadio Rita 
Published: April 2008

Abstract
Summary: Fault Tolerant Contact Map Reconstruction (FT-COMAR) is a heuristic algorithm for the reconstruction of the protein three-dimensional structure from (possibly) incomplete (i.e. containing unknown entries) and noisy contact maps. FT-COMAR runs within minutes, allowing its application to a large-scale number of predictions.
Availability: http://bioinformatics.cs.unibo.it/FT-COMAR
Contact: vassura@cs.unibo.it
Supplementary information: Supplementary data are available on Bioinformatics online.
New serotype of mutans streptococci isolated from pig oral cavity
Authors: Takada Kazuko , Igarashi Mitsuhiko , Yamaguchi Yasutaka , Hirasawa Masatomo 
Published: April 2008

ABSTRACTGram‐positive streptococcal mutans‐like strains, but with clearly different colony formation than S. orisuis on Mitis Salivarius agar, were isolated from the pig oral cavity and identified by 16S rRNA sequencing, G+C content, DNA‐DNA homology and extensive biochemical and serological testing. The phenotypic data showed that the strains were similar to S. orisuis except for susceptibility to bacitracin. DNA‐DNA homology between the isolates and S. orisuis was 72∼81%. However, serological data showed that they have a different sero‐specific antigen from S. orisuis and other mutans streptococci. A new serotype, designated p, strains are classified in a serovar of S. orisuis, one of mutans streptococci.