bluuebunny/crossref_metadata_2025 huggingface dataset:
"Teachers Know You Can Do More"
Authors: Rodríguez Louie F.
Published: October 2007

Urban high school reform is one of the most significant challenges facing education today. In response to this challenge, reformers have put significant energy toward restructuring the large high school primarily through creating smaller school settings. Although the research literature often draws connections between school size and student outcomes, an examination of life within these settings remains a large void. From the voices and experiences of students, this article examines how relationships are connected to school culture. The nature of student-adult relationships is disentangled by exploring how students experience personalized, respectful, and encouraging interactions with school adults. Then relationships are connected to student dispositions in schools by examining the question, relationships for the purpose of what? The author concludes that the silver bullet for high school reform is a commitment to forging deliberate "cultures of success" for low-income Black and Latina or Latino students in U.S. high schools. Implications for research, policy, and practice are explored.
Poor politics — poor housing. Policy under the Collor government in Brazil (1990—92)
Authors: Valença Márcio Moraes
Published: October 2007

This paper(1) describes the ways in which clientelism was a factor in the formal structures promoting housing during the Collor government in Brazil, a country where frequent institutional changes have provided the opportunity for new client—patron chains to penetrate the government apparatus. While the institutional and organizational aspects of housing provision are of paramount interest to social scientists and practitioners, it is necessary to go beyond the surface of these formal structures to find out how the system works in practice. This paper analyzes the institutional arrangements that supported housing promotion under the Ministry of Social Action in Brazil during the Collor government and examines their private nature as well as the often loose ways in which the housing authorities actually operated the system.
Securing inclusion: strategies for community empowerment and state redistribution
Authors: Muller Anna , Mitlin Diana
Published: October 2007

This study draws together the experiences of the Shack Dwellers Federation of Namibia (SDFN) in using finance to secure access to land and infrastructure. Thefederation uses strategies of collective solidarity, political presence and financial capacity to encourage local authorities to reconsider traditional approaches to urban development, and to date they have assisted about 5 per cent of urban dwellers in need in Namibia with housing improvements. The federation believes that local groups must define solutions that work for them, seeking to draw on the resources of the local authority to ensure affordability for all. These solutions need to build the power of the collective, enabling successive community actions to achieve additional development aspirations for the community. The community-driven process incorporates self-help as one of a number of strategies to achieve affordability but, more importantly, also to embed a social process across the community. Social movements strongly rooted in local neighbourhoods can secure the political advancement of the poor through effective political pressure on political decision makers. The grassroots location of the movement allows the shelter process to develop relevant tools and methods, which in turn are embedded within the negotiation processes towards the more egalitarian redistribution of state resources.(1)
Reconceptualizing housing finance in informal settlements: the case of Dar es Salaam, Tanzania
Authors: Sheuya Shaaban A.
Published: October 2007

Most urban dwellers in developing countries live in informal settlements in housing that is built incrementally. Low-income households most often have no access to formal housing finance institutions and largely depend on informal housing finance mechanisms in addition to the recently established shelter microfinance institutions. However, both formal and informal shelter-financing institutions have a requirement for savings. Based on empirical investigations in two informal settlements in Dar es Salaam, Tanzania, this paper explores the nature of savings in incremental housing development. The findings show that unpacking the concept of savings has the potential to uncover new opportunities for promoting housing finance in informal settlements, other than shelter microfinance.
Strategies for grassroots control of international aid
Authors: Mitlin Diana , Satterthwaite David
Published: October 2007

Official aid agencies and development banks are not set up to work with poor groups or to be directly accountable to them, even if their work is legitimized on the basis of these groups' needs. The bureaucracy of such agencies works primarily with and through national governments and is generally unable to catalyze or support the local social processes needed to make external finance effective in addressing many aspects of poverty. This paper describes an initiative to overcome these constraints — an international fund to support grassroots initiatives, managed by a transnational network of slum/shack/homeless people's federations and their support NGOs. This fund makes small grants available to savings groups that are members of these federations, to support them in securing land for housing and getting basic services. Over the last five years, more than 40 initiatives in 17 nations have received support. The fund demonstrates to international agencies what their monies could do if they were willing to relinquish more decision-making powers and more financial control to local organizations formed by and accountable to the urban poor.
From Computer to Compost
Authors: Randall William L.
Published: October 2007

This paper introduces the compost heap as a metaphor for autobiographical memory. As an alternative to the computer, such a metaphor, it is argued, comes closer to capturing the dynamics of memory across the lifespan and how it feels to us as we age, particularly memory's narrative dimensions. After citing concerns expressed by psychologists and others regarding computationalism, the paper considers four entailments of the compost heap analogy that may serve, very roughly, as counterparts to such concepts as encoding, storage, and retrieval. They are: laying it on, breaking it down, stirring it up, and mixing it in. The paper concludes with reflections on the advantages of a more organic model of memory and some suggestions for further inquiry concerning issues of interest to the psychology of aging.
On Mediation
Authors: Roth Wolff-Michael
Published: October 2007

Mediation is a key notion in dialectical approaches to understanding consciousness, thinking, and thought. However, the scholarly literature is replete with uses of the notion that are inconsistent with the dialectical framework within it, which has the specific function to articulate and explain the unit of a phenomenon and the corresponding unit of scientific analysis. The purpose of this paper is to clarify the term and its possible uses in the theoretical and methodological approaches of present-day cultural-historical activity theory.
Paranormal Belief and the Avowal of Prior Scepticism
Authors: Lamont Peter
Published: October 2007

A common way in which people warrant their belief in the paranormal is by employing an avowal of prior scepticism. That such avowals are used so often, and cited by others as relevant, suggest they are an effective means of warranting not only the facticity of ostensibly paranormal events but also a belief about the paranormal nature of the event. Their function, it is argued, is to head off potential accusations of gullibility or wishful thinking, and they are analogous to avowals of prior belief by `sceptics', which head off potential accusations of narrow-mindedness. However, such avowals also point up key theoretical and methodological problems in current paranormal belief research. Problems of representation and constitution are discussed, and greater stress upon functional aspects of expressions of paranormal belief is suggested.
Essay Review: Taking a Good Look at Why Scientific Images Don't Speak for Themselves
Authors: de Rijcke Sarah , Beaulieu Anne
Published: October 2007

This review focuses on what scientific images can do, by considering three books in which they are central. We problematize the assumption that images can simply show and that the viewer can simply see what is at hand. Images are neither self-explanatory nor transparent, but rather partake in a specific visual culture. If they are to serve as bridges (e.g. to popularize scientific results), then they are only effective insofar as cultural conventions are shared. Felice Frankel's how-to book demonstrates the complexity of making photographs transparent, while keeping these processes backstage. Joseph Dumit's anthropological analysis of brain scans focuses on tensions between uses of scans inside and outside the lab. In Matthews and McQuain's book, pairings of scans with Shakespearean theatre stand in for neuroscientific and artistic approaches to human nature. The attempt to join these very different spheres shows the dangers of going beyond shared understandings of visual material.
On improving research methodology in clinical trials
Authors: Berger Vance W , Matthews J Rosser , Grosch Eric N
Published: October 2007

Research plays a vital role within biomedicine. Scientifically appropriate research provides a basis for appropriate medical decisions; conversely, inappropriate research may lead to flawed `best medical practices' which, when followed, contribute to avoidable morbidity and mortality. Although an all-encompassing definition of `appropriate medical research' is beyond the scope of this article, the concept clearly entails (among other things) that research methods be continually revised and updated as better methods become available. Despite the advent of evidence-based medicine, many research methods have become `standard' even though there are legitimate scientific reasons to question the conclusions reached by such methods. We first illustrate prominent examples of inappropriate (yet regimented) research methods that are in widespread use. Second, as a way to improve the situation, we suggest a model of research that relies on standardized statistical analyses that individual researchers must consider as a default, but are free to challenge when they can marshal sufficient scientific evidence to demonstrate that the challenge is warranted. Third, we characterize the current system as analogous to `unnatural selection' in the biological world and argue that our proposed model of research will enable `natural' to replace `unnatural' selection in the choice of research methodologies. Given the pervasiveness of inappropriate research methods, we believe that there are strong scientific and ethical reasons to create such a system, that, if properly designed, will both facilitate creativity and ensure methodological rigor while protecting the public at large from the threats posed by poor medical treatment decisions resulting from flawed research methodology.
The Biomarker-Surrogacy Evaluation Schema: a review of the biomarker-surrogate literature and a proposal for a criterion-based, quantitative, multidimensional hierarchical levels of evidence schema for evaluating the status of biomarkers as surrogate endpoints
Authors: Lassere Marissa N
Published: October 2007

There are clear advantages to using biomarkers and surrogate endpoints, but concerns about clinical and statistical validity and systematic methods to evaluate these aspects hinder their efficient application. Section 2 is a systematic, historical review of the biomarker-surrogate endpoint literature with special reference to the nomenclature, the systems of classification and statistical methods developed for their evaluation. In Section 3 an explicit, criterion-based, quantitative, multidimensional hierarchical levels of evidence schema — Biomarker-Surrogacy Evaluation Schema — is proposed to evaluate and co-ordinate the multiple dimensions (biological, epidemiological, statistical, clinical trial and risk-benefit evidence) of the biomarker clinical endpoint relationships. The schema systematically evaluates and ranks the surrogacy status of biomarkers and surrogate endpoints using defined levels of evidence. The schema incorporates the three independent domains: Study Design, Target Outcome and Statistical Evaluation. Each domain has items ranked from zero to five. An additional category called Penalties incorporates additional considerations of biological plausibility, risk-benefit and generalizability. The total score (0—15) determines the level of evidence, with Level 1 the strongest and Level 5 the weakest. The term `surrogate' is restricted to markers attaining Levels 1 or 2 only. Surrogacy status of markers can then be directly compared within and across different areas of medicine to guide individual, trial-based or drug-development decisions. This schema would facilitate communication between clinical, researcher, regulatory, industry and consumer participants necessary for evaluation of the biomarker-surrogate-clinical endpoint relationship in their different settings.
Commitments, Transnational Interests, and Congress
Authors: McCormick James M. , Mitchell Neil J.
Published: October 2007

The authors seek to explain the membership of the Congressional Human Rights Caucus (CHRC). Focusing on human rights violations abroad, the Caucus offers few incentives for representatives to join this organization, yet it consistently has a large membership. Drawing on theoretical literature on Congress and interest groups, the authors argue that members' policy motivation and the subsidizing role of national and transnational human rights interest groups account for the decision to join. Documentary and interview evidence for House members in the 107th and 108th Congresses support these arguments. The results have substantive and theoretical implications for the study of the CHRC, the interactions between members of Congress and interest groups, and the study of congressional caucuses generally.
Goal Salience and the 2006 Race for House Majority Leader
Authors: Green Matthew N. , Harris Douglas B.
Published: October 2007

In intraparty congressional leadership races, the characteristics of candidates and the nature of their campaigns increase the salience of particular legislator goals and, in doing so, influence legislators' support of particular leadership candidates. Using multinomial logit regression analysis, the authors test this “goal salience” theory to determine what factors predict individual legislators' commitments to candidates in the 2006 House Republican majority leader's race. Notably, among other factors, the level of campaign donations made to Republican House members had a positive and statistically significant relationship with the choice of specific candidates.
Two-dimensional Legendre Wavelets Method for the Mixed Volterra-Fredholm Integral Equations
Authors: Banifatemi E. , Razzaghi M. , Yousefi S.
Published: October 2007

This article presents a numerical method for solving nonlinear mixed Volterra-Fredholm integral equations. The method is based on two-dimensional Legendre wavelet approximations. The properties of Legendre wavelets are utilized together with the Gaussian integration method to reduce the mixed integral equations to the solution of algebraic equations. Illustrative examples are included to demonstrate the validity and applicability of the technique.
LPV Model Based Gain-scheduling Controller for a Full Vehicle Active Suspension System
Authors: Onat Cem , Kucukdemiral Ibrahim B. , Sivrioglu Selim , Yuksek Ismail
Published: October 2007

This article addresses the design of a gain-scheduling type nonlinear controller for a full-vehicle active suspension system. The proposed method is based on a Linear Parameter Varying (LPV) model of the system. In this model, the variations in suspension deflection and mass are chosen as the scheduling parameters. During the simulations, the full-vehicle system that is controlled by the proposed method is tested with different road profiles, having high and low bumps, hollows and combinations of the two. The simulation results demonstrate that the proposed method successfully maximizes the ride comfort when suspension deflection is far away from the structural limits and minimizes the suspension deflection by changing its behavior when the suspension limits are reached.
Compliance with Home Telehealth Clinical Guidelines
Authors: Gingerich Barbara Stover
Published: October 2007

In this world of high tech and telehealth, many programs and services are expanding into the home care setting. As these new services and programs are established and grow, the importance of maintaining consistency and meeting established guidelines also increases. This “Compliance Corner” focuses on the telemedicine and telehealth guidelines and specialty services provided within the home care setting.
Delineation of Risk Through the Exploration of a Culture of Safety in Community Home Health
Authors: Stevenson Lynn , McRae Cora , Mughal Waqar Ali
Published: October 2007

In one large Canadian healthcare region, there was no consistent way of identifying factors impacting safety and risk in community home healthcare. A participatory action research approach was employed to explore client safety risks in this environment. Staff identified a lack of adequate information as their primary safety concern. A novel chart review tool was developed to capture baseline information regarding client risks, including frequency, context and severity. Very little documentation regarding safety was identified in the reviewed charts. The most frequent risks identified were mobility, falls prevention and medication concerns, which is consistent with the literature.
Improving Quality of Life at Home for Pediatric Patients and Families With Primary Immune Deficiencies Using Subcutaneous Immune Globulin Infusions
Authors: Zampelli Annette R.
Published: October 2007

Pediatric patients diagnosed with primary antibody deficiencies often require lifelong immune globulin replacement to help protect them from life-threatening infections. Although this is not a cure or a treatment for the disorder, replacement therapy is necessary to maintain health. The two current viable routes for immune globulin replacement are intravenous or subcutaneous. For many patients, subcutaneous infusions improve quality of life by offering greater independence and better control of the therapy situation and daily life. Subcutaneous infusions have been shown to be easy for both adult patients and children and their parents and to be safe, with minimal or no systemic reactions and no transmission of the hepatitis C virus. All of these factors are very important when considering replacement therapy. Home nursing care and support can also help provide additional support to improve treatment outcomes to enhance quality of life.
Non-Invasive Ventilation: The Impact of a Home Health Support
Authors: Stabinski Jodie W.
Published: October 2007

Non-invasive ventilation seems to have gained in popularity in the past few years for pediatric patients with a variety of disease processes. Although it is infrequently used for acute respiratory failure, it is becoming a popular choice for ventilation assistance in a variety of chronic disease processes and not just limited to asthma, cystic fibrosis and other neurological disorders that impair breathing. As the medical team acquires more experience in non-invasive ventilation, a new frontier in the home setting is now being explored.
Overt reference to speaker and recipient in Korean
Authors: Oh Sun-Young
Published: October 2007

In Korean, reference forms can be omitted so long as the referent can be understood by the interlocutor(s); speaker/recipient reference terms are most readily omitted because they are easily retrievable from the physical interactional context. The current study represents the first attempt to examine specifically when and why Korean speakers do use an overt reference form in referring to themselves or their recipients even when reference can be understood without such overt forms. It demonstrates that Korean speakers build their talk to incorporate an overt form of speaker/ recipient reference in order to accomplish various interactional projects (e.g. (self-)praising/blaming, responsibility-attribution, disagreement, projecting further talk by the current speaker, or selecting next speaker), often marking that reference form with a particle relevant to the specific action being implemented. Doing overt reference to speaker or recipient is thus a means by which speakers can accomplish other than simple reference that is done with zero anaphora.
Self-referential gestures in conversation
Authors: Turk Monica J.
Published: October 2007

One way speakers can refer to themselves in conversation is with a stressed first-person pronoun accompanied by a movement of the hand to or toward the chest. This can be produced alone or in tandem with a reference and gesture to another person. Close analysis of several instances of self-referential gesture demonstrates that this form of self-reference is designed to achieve interactional work beyond simple reference, specifically relational disaggregation and self-referential extraction.
Structuring Gender's Impact
Authors: McCall Madhavi
Published: October 2007

The importance of judge gender as a factor in judicial votes continues to attract much scholarly attention. I contribute to the debate on the influence of judge gender by examining the voting behavior of male and female state supreme court justices in three areas of criminal justice. I find that female justices, controlling for institutional, political, and legal constraints, are more likely than are their male counterparts to rule for the criminal defendant and in a broader array of cases than commonly thought. I conclude that judge gender is a significant factor in the outcome of judicial decisions and that the number of women on the courts is a factor in judicial decision making.
Parastomal Hernia: Short-Term Outcome After Laparoscopic and Conventional Repairs
Authors: McLemore Elisabeth C. , Harold Kristi L. , Efron Jonathan E. , Laxa Bernadette U. , Young-Fadok Tonia M. , Heppell Jacques P.
Published: October 2007

The purpose of this study was to evaluate the short-term outcomes after laparoscopic and conventional parastomal hernia repairs. A retrospective review of parastomal hernia repairs was performed. Conventional repairs included primary suture repair, stoma relocation, and mesh repair. Laparoscopic repairs included the Sugarbaker and keyhole techniques. Forty-nine patients underwent repair of symptomatic parastomal hernias: 19 ileostomies, 13 colostomies, and 17 urostomies. Thirty patients underwent 39 conventional repairs. Nineteen patients underwent laparoscopic surgical repairs. Operative times were longer for laparoscopic repair (208 ± 58 vs 162 ± 114 minutes, P = .06). The mean length of stay was 6 days for both groups ( P = .74). The mean follow-up was shorter in the laparoscopic group (20 vs 65 months, P ≤ .001). There were no significant differences in the incidence of surgical site infections (11% laparoscopic vs 5% conventional, P = .60) or complication rates (63% laparoscopic vs 36% conventional, P = .67). Laparoscopic parastomal hernia repair is a feasible operation with similar short-term outcomes to conventional repairs.
Laparoscopic Heller Myotomy for Achalasia in 101 Patients: Can Successful Symptomatic Outcomes Be Predicted?
Authors: Rosen Michael J. , Novitsky Yuri W. , Cobb William S. , Kercher Kent W. , Todd Heniford B.
Published: October 2007

We aimed to evaluate the clinical outcomes of patients undergoing laparoscopic esophageal myotomy for achalasia and identify the factors that might predict postoperative dysphagia or symptomatic reflux. A retrospective analysis of all patients undergoing laparoscopic Heller myotomy from January 1997 to June 2004 was performed. Postoperative frequency and severity of reflux, dysphagia, chest pain, and regurgitation were evaluated using a standardized telephone interview. Forty-eight males and 53 females, with an average age of 45 years, underwent laparoscopic Heller myotomy during the study period. Prior to presentation, 65% of patients had undergone pneumatic dilatation (52%) and/or Botox injection (28%). The mean lower esophageal sphincter pressure was 44 mmHg. A Toupet fundoplication was performed in 89 patients, and 12 patients had no fundoplication. There were no intraoperative complications and 10 minor postoperative complications. During an average follow-up of 34 months (range 2-90), 15% of patients had a weekly dysphagia, and 16% had subjective reflux. Only an older age predicted higher incidence of postoperative dysphagia. No factors were identified to predict postoperative symptomatic reflux. Eighty-one percent of patients rated their outcome as excellent, 14% good, 4% fair, and 1% poor. Ninety-nine percent of patients would choose surgery over other treatment options again. Laparoscopic anterior esophageal myotomy is a safe and effective treatment for achalasia. Improvement in dysphagia can be expected in more than 95% of patients. Younger patients tended to have better improvement of dysphagia. Predicting the patients at higher risk for postoperative reflux remains elusive at this time.
Laparoscopic Revision of Gastrogastric Stricture With a Transoral Circular Stapler
Authors: Parikh Manish , Gagner Michel
Published: October 2007

Most anastomotic strictures can be effectively managed by endoscopic dilations. Patients with severe strictures refractory to balloon dilations may require surgical revision. Revision of a strictured anastomosis (open or laparoscopic) is often technically demanding because of the severity of adhesion formation and difficulty in correctly identifying the anatomy. We discuss a laparoscopic method of safely revising an anastomotic stricture with a circular stapler.
Targeting Notch signaling in autoimmune and lymphoproliferative disease
Authors: Teachey David T. , Seif Alix E. , Brown Valerie I. , Bruno Marlo , Bunte Ralph M. , Chang Yueh J. , Choi John K. , Fish Jonathan D. , Hall Junior , Reid Gregor S. , Ryan Theresa , Sheen Cecilia , Zweidler-McKay Patrick , Grupp Stephan A.
Published: October 2007

Patients with autoimmune lymphoproliferative syndrome (ALPS) and systemic lupus erythematosis (SLE) have T-cell dysregulation and produce abnormal, activated T lymphocytes and an atypical peripheral T-cell population, termed double negative T cells (DNTs). T-cell functions, including DNT transition in T-cell development and T-cell activation, are critically dependent on Notch signaling. We hypothesized that inhibiting Notch signaling would be effective in ALPS and SLE by reducing the production of abnormal DNTs and by blocking aberrant T-cell activation. We tested this hypothesis using murine models of ALPS and SLE. Mice were randomized to treatment with the notch pathway inhibitor (gamma-secretase inhibitor), N-S-phenyl-glycine-t-butyl ester (DAPT), or vehicle control. Response to treatment was assessed by measurement of DNTs in blood and lymphoid tissue, by monitoring lymph node and spleen size with ultrasound, by quantifying cytokines by bead-array, by ELISA for total IgG and anti–double-stranded DNA (dsDNA) specific antibodies, and by histopathologic assessment for nephritis. We found a profound and statistically significant decrease in all disease parameters, comparing DAPT-treated mice to controls. Using a novel dosing schema, we avoided the reported toxicities of gamma-secretase inhibitors. Inhibiting the Notch signaling pathway may thus present an effective, novel, and well-tolerated treatment for autoimmune and lymphoproliferative diseases.
Common variation in the C-terminal region of the fibrinogen β-chain: effects on fibrin structure, fibrinolysis and clot rigidity
Authors: Ajjan Ramzi , Lim Bernard C. B. , Standeven Kristina F. , Harrand Robert , Dolling Sarah , Phoenix Fladia , Greaves Richard , Abou-Saleh Radwa H. , Connell Simon , Smith D. Alastair M. , Weisel John W. , Grant Peter J. , Ariëns Robert A. S.
Published: October 2007

Fibrinogen BβArg448Lys is a common polymorphism, positioned within the carboxyl terminus of the Bβ-chain of the molecule. Studies suggest that it is associated with severity of coronary artery disease and development of stroke. The effects of the amino acid substitution on clot structure remains controversial, and the aim of this study was to investigate the effect(s) of this polymorphism on fibrin clot structure using recombinant techniques. Permeation, turbidity, and scanning electron microscopy showed that recombinant Lys448 fibrin had a significantly more compact structure, with thin fibers and small pores, compared with Arg448. Clot stiffness, measured by means of a novel method using magnetic tweezers, was significantly higher for the Lys448 compared with the Arg448 variant. Clots made from recombinant protein variants had similar lysis rates outside the plasma environment, but when added to fibrinogen-depleted plasma, the fibrinolysis rates for Lys448 were significantly slower compared with Arg448.

This study demonstrates for the first time that clots made from recombinant BβLys448 fibrinogen are characterized by thin fibers and small pores, show increased stiffness, and appear more resistant to fibrinolysis. Fibrinogen BβArg448Lys is a primary example of common genetic variation with a significant phenotypic effect at the molecular level.
Increased survival is a selective feature of human circulating antigen-induced plasma cells synthesizing high-affinity antibodies
Authors: González-García Inés , Rodríguez-Bayona Beatriz , Mora-López Francisco , Campos-Caro Antonio , Brieva José A.
Published: October 2007

The present study shows that tetanus toxoid (tet) booster releases to the human circulation 2 subsets of specific plasma cells (PCs), as defined by phenotype and morphology, which clearly differed in the staining capacity of their cytoplasmic antibodies (Abs) with fluorescein isothiocyanate (FITC)–labeled tet–fragment C (tetC). These cells, called tetCHIGH and tetCINT PCs according to their either high or intermediate FITC-tetC staining capacity, exhibit similar rapid temporary kinetics in the blood (5-8 days after boost), contain many cycling cells, express equivalent amounts of BLIMP-1 mRNA, and produce similar quantities of IgG. However, Abs synthesized by tetCHIGH PCs show a tetC affinity more than 10 times higher than that exhibited by tetCINT PC Abs, and indicated by IGVH sequence analysis. Chemotaxis to CXCL12, a requisite for bone marrow (BM) PC homing, is similar for both cell types. Circulating nonspecific and tetCINT PCs, but not tetCHIGH PCs, tend to undergo spontaneous apoptosis, as demonstrated by APO2.7 and activated caspase-3 expression, and cell recovery. These results indicate that tet booster generates 2 discrete subsets of specific PCs exhibiting different ranges of Ab affinity for the immunogen, and that only those synthesizing high-affinity Abs show enhanced survival. This inherent property may be essential for determining the BM fate of PCs secreting high-affinity Ab.
RECOVIR: An application package to automatically identify some single stranded RNA viruses using capsid protein residues that uniquely distinguish among these viruses
Authors: Zhu Dianhui , Fox George E , Chakravarty Sugoto
Published: October 2007

Background

Most single stranded RNA (ssRNA) viruses mutate rapidly to generate large number of strains having highly divergent capsid sequences. Accurate strain recognition in uncharacterized target capsid sequences is essential for epidemiology, diagnostics, and vaccine development. Strain recognition based on similarity scores between target sequences and sequences of homology matched reference strains is often time consuming and ambiguous. This is especially true if only partial target sequences are available or if different ssRNA virus families are jointly analyzed. In such cases, knowledge of residues that uniquely distinguish among known reference strains is critical for rapid and unambiguous strain identification. Conventional sequence comparisons are unable to identify such capsid residues due to high sequence divergence among the ssRNA virus reference strains. Consequently, automated general methods to reliably identify strains using strain distinguishing residues are not currently available.

Results

We present here RECOVIR ("recognize viruses"), a software tool to automatically detect strains of caliciviruses and picornaviruses by comparing their capsid residues with built-in databases of residues that uniquely distinguish among known reference strains of these viruses. The databases were created by constructing partitioned phylogenetic trees of complete capsid sequences of these viruses. Strains were correctly identified for more than 300 complete and partial target sequences by comparing the database residues with the aligned residues of these sequences. It required about 5 seconds of real time to process each sequence. A Java-based user interface coupled with Perl-coded computational modules ensures high portability of the software. RECOVIR currently runs on Windows XP and Linux platforms. The software generalizes a manual method briefly outlined earlier for human caliciviruses.

Conclusion

This study shows implementation of an automated method to identify virus strains using databases of capsid residues. The method is implemented to detect strains of caliciviruses and picornaviruses, two of the most highly divergent ssRNA virus families, and therefore, especially difficult to identify using a uniform method. It is feasible to incorporate the approach into classification schemes of caliciviruses and picornaviruses and to extend the approach to recognize and classify other ssRNA virus families.
Dynamic transcription programs during ES cell differentiation towards mesoderm in serum versus serum-freeBMP4 culture
Authors: Bruce Stephen J , Gardiner Brooke B , Burke Les J , Gongora M Milena , Grimmond Sean M , Perkins Andrew C
Published: October 2007

Background

Expression profiling of embryonic stem (ES) cell differentiation in the presence of serum has been performed previously. It remains unclear if transcriptional activation is dependent on complex growth factor mixtures in serum or whether this process is intrinsic to ES cells once the stem cell program has been inactivated. The aims of this study were to determine the transcriptional programs associated with the stem cell state and to characterize mesoderm differentiation between serum and serum-free culture.

Results

ES cells were differentiated as embryoid bodies in 10% FBS or serum-free media containing BMP4 (2 ng/ml), and expression profiled using 47 K Illumina(R) Sentrix arrays. Statistical methods were employed to define gene sets characteristic of stem cell, epiblast and primitive streak programs. Although the initial differentiation profile was similar between the two culture conditions, cardiac gene expression was inhibited in serum whereas blood gene expression was enhanced. Also, expression of many members of the Kruppel-like factor (KLF) family of transcription factors changed dramatically during the first few days of differentiation. KLF2 and KLF4 co-localized with OCT4 in a sub-nuclear compartment of ES cells, dynamic changes in KLF-DNA binding activities occurred upon differentiation, and strong bio-informatic evidence for direct regulation of many stem cell genes by KLFs was found.

Conclusion

Down regulation of stem cell genes and activation of epiblast/primitive streak genes is similar in serum and defined media, but subsequent mesoderm differentiation is strongly influenced by the composition of the media. In addition, KLF family members are likely to be important regulators of many stem cell genes.
Saccharomyces cerevisiae: a versatile eukaryotic system in virology
Authors: Galao Rui P , Scheller Nicoletta , Alves-Rodrigues Isabel , Breinig Tanja , Meyerhans Andreas , Díez Juana
Published: October 2007

The yeastSaccharomyces cerevisiaeis a well-established model system for understanding fundamental cellular processes relevant to higher eukaryotic organisms. Less known is its value for virus research, an area in whichSaccharomyces cerevisiaehas proven to be very fruitful as well. The present review will discuss the main achievements of yeast-based studies in basic and applied virus research. These include the analysis of the function of individual proteins from important pathogenic viruses, the elucidation of key processes in viral replication through the development of systems that allow the replication of higher eukayotic viruses in yeast, and the use of yeast in antiviral drug development and vaccine production.
Gene expression profiling of cuticular proteins across the moult cycle of the crab Portunus pelagicus
Authors: Kuballa Anna V , Merritt David J , Elizur Abigail
Published: October 2007

Background

Crustaceans represent an attractive model to study biomineralization and cuticle matrix formation, as these events are precisely timed to occur at certain stages of the moult cycle. Moulting, the process by which crustaceans shed their exoskeleton, involves the partial breakdown of the old exoskeleton and the synthesis of a new cuticle. This cuticle is subdivided into layers, some of which become calcified while others remain uncalcified. The cuticle matrix consists of many different proteins that confer the physical properties, such as pliability, of the exoskeleton.

Results

We have used a custom cDNA microarray chip, developed for the blue swimmer crabPortunus pelagicus, to generate expression profiles of genes involved in exoskeletal formation across the moult cycle. A total of 21 distinct moult-cycle related differentially expressed transcripts representing crustacean cuticular proteins were isolated. Of these, 13 contained copies of the cuticle_1 domain previously isolated from calcified regions of the crustacean exoskeleton, four transcripts contained a chitin_bind_4 domain (RR consensus sequence) associated with both the calcified and un-calcified cuticle of crustaceans, and four transcripts contained an unannotated domain (PfamB_109992) previously isolated fromC. pagurus. Additionally, cryptocyanin, a hemolymph protein involved in cuticle synthesis and structural integrity, also displays differential expression related to the moult cycle. Moult stage-specific expression analysis of these transcripts revealed that differential gene expression occurs both among transcripts containing the same domain and among transcripts containing different domains.

Conclusion

The large variety of genes associated with cuticle formation, and their differential expression across the crustacean moult cycle, point to the complexity of the processes associated with cuticle formation and hardening. This study provides a molecular entry path into the investigation of the gene networks associated with cuticle formation.
Defending legitimate epidemiologic research: combating Lysenko pseudoscience
Authors: Enstrom James E
Published: October 2007

This analysis presents a detailed defense of my epidemiologic research in the May 17, 2003British Medical Journalthat found no significant relationship between environmental tobacco smoke (ETS) and tobacco-related mortality. In order to defend the honesty and scientific integrity of my research, I have identified and addressed in a detailed manner several unethical and erroneous attacks on this research. Specifically, I have demonstrated that this research is not "fatally flawed," that I have not made "inappropriate use" of the underlying database, and that my findings agree with other United States results on this relationship. My research suggests, contrary to popular claims, that there is not a causal relationship between ETS and mortality in the U.S. responsible for 50,000 excess annual deaths, but rather there is a weak and inconsistent relationship. The popular claims tend to damage the credibility of epidemiology.

In addition, I address the omission of my research from the 2006 Surgeon General's Report on Involuntary Smoking and the inclusion of it in a massive U.S. Department of Justice racketeering lawsuit. I refute erroneous statements made by powerful U.S. epidemiologists and activists about me and my research and I defend the funding used to conduct this research. Finally, I compare many aspect of ETS epidemiology in the U.S. with pseudoscience in the Soviet Union during the period of Trofim Denisovich Lysenko. Overall, this paper is intended to defend legitimate research against illegitimate criticism by those who have attempted to suppress and discredit it because it does not support their ideological and political agendas. Hopefully, this defense will help other scientists defend their legitimate research and combat "Lysenko pseudoscience."
Role of reaction kinetics and mass transport in glucose sensing with nanopillar array electrodes
Authors: Anandan Venkataramani , Yang Xiaoling , Kim Euihyeon , Rao Yeswanth L , Zhang Guigen
Published: October 2007

The use of nanopillar array electrodes (NAEs) for biosensor applications was explored using a combined experimental and simulation approach to characterize the role of reaction kinetics and mass transport in glucose detection with NAEs. Thin gold electrodes with arrays of vertically standing gold nanopillars were fabricated and their amperometric current responses were measured under bare and functionalized conditions. Results show that the sensing performances of both the bare and functionalized NAEs were affected not only by the presence and variation of the nanoscale structures on the electrodes but also by the reaction kinetics and mass transport of the analyte species involved. These results will shed new light for enhancing the performance of nanostructure based biosensors.
Comparative and functional genomics reveals genetic diversity and determinants of host specificity among reference strains and a large collection of Chinese isolates of the phytopathogen Xanthomonas campestris pv. campestris
Authors: He Yong-Qiang , Zhang Liang , Jiang Bo-Le , Zhang Zheng-Chun , Xu Rong-Qi , Tang Dong-Jie , Qin Jing , Jiang Wei , Zhang Xia , Liao Jie , Cao Jin-Ru , Zhang Sui-Sheng , Wei Mei-Liang , Liang Xiao-Xia , Lu Guang-Tao , Feng Jia-Xun , Chen Baoshan , Cheng Jing , Tang Ji-Liang
Published: October 2007

Background

Xanthomonas campestris pathovar campestris (Xcc) is the causal agent of black rot disease of crucifers worldwide. The molecular genetic diversity and host specificity of Xcc are poorly understood.

Results

We constructed a microarray based on the complete genome sequence of Xcc strain 8004 and investigated the genetic diversity and host specificity of Xcc by array-based comparative genome hybridization analyses of 18 virulent strains. The results demonstrate that a genetic core comprising 3,405 of the 4,186 coding sequences (CDSs) spotted on the array are conserved and a flexible gene pool with 730 CDSs is absent/highly divergent (AHD). The results also revealed that 258 of the 304 proved/presumed pathogenicity genes are conserved and 46 are AHD. The conserved pathogenicity genes include mainly the genes involved in type I, II and III secretion systems, the quorum sensing system, extracellular enzymes and polysaccharide production, as well as many other proved pathogenicity genes, while the AHD CDSs contain the genes encoding type IV secretion system (T4SS) and type III-effectors. A Xcc T4SS-deletion mutant displayed the same virulence as wild type. Furthermore, three avirulence genes (avrXccC, avrXccE1 and avrBs1) were identified. avrXccC and avrXccE1 conferred avirulence on the hosts mustard cultivar Guangtou and Chinese cabbage cultivar Zhongbai-83, respectively, and avrBs1 conferred hypersensitive response on the nonhost pepper ECW10R.

Conclusion

About 80% of the Xcc CDSs, including 258 proved/presumed pathogenicity genes, is conserved in different strains. Xcc T4SS is not involved in pathogenicity. An efficient strategy to identify avr genes determining host specificity from the AHD genes was developed.
Systemic inflammation and end organ damage following trauma involves functional TLR4 signaling in both bone marrow-derived cells and parenchymal cells
Authors: Mollen Kevin P , Levy Ryan M , Prince Jose M , Hoffman Rosemary A , Scott Melanie J , Kaczorowski David J , Vallabhaneni Raghuveer , Vodovotz Yoram , Billiar Timothy R
Published: October 2007

Endogenous damage-associated molecular pattern (DAMP) molecules are released from cells during traumatic injury, allowing them to interact with pattern recognition receptors such as the toll-like receptors (TLRs) on other cells and subsequently, to stimulate inflammatory signaling. TLR4, in particular, plays a key role in systemic and remote organ responses to hemorrhagic shock (HS) and peripheral tissue injury in the form of bilateral femur fracture. TLR4 chimeric mice were generated to investigate the cell lineage in which functional TLR4 is needed to initiate the injury response to trauma. Chimeric mice were generated by adoptive bone marrow (BM) transfer, whereby donor marrow was given to an irradiated host using reciprocal combinations of TLR4 wild-type (WT; C3H/HeOuJ) and TLR4 mutant (Mu; C3H/HeJ) mice. After a period of engraftment, chimeric mice were then subjected to HS or bilateral femur fracture. Control groups, including TLR4-WT mice receiving WT BM and TLR4-Mu mice receiving Mu BM, responded to injury in a similar pattern to unaltered HeOuJ and HeJ mice, and protection was afforded to those mice lacking functional TLR4. In contrast, TLR4-WT mice receiving Mu BM and TLR4-Mu mice receiving WT BM demonstrated intermediate inflammatory and cellular damage profiles. These data demonstrate that functional TLR4 is required in BM-derived cells and parenchymal cells for an optimal inflammatory response to trauma.
A Quantitative Trait Locus on Chromosome 13q Affects Fasting Glucose Levels in Hispanic Children
Authors: Cai Guowen , Cole Shelley A. , Butte Nancy F. , Voruganti V. Saroja , Comuzzie Anthony G.
Published: October 2007

Objective: The prevalence of childhood obesity has increased dramatically in the United States. Early presentation of type 2 diabetes has been observed in children and adolescents, especially in the Hispanic population. The genetic contribution of glucose homeostasis related to childhood obesity is poorly understood. The objective of this study was to localize quantitative trait loci influencing fasting serum glucose levels in Hispanic children participating in the Viva La Familia Study.

Design: Subjects were 1030 children ascertained through an overweight child from 319 Hispanic families. Fasting serum glucose levels were measured enzymatically, and genetic linkage analyses were conducted using SOLAR software.

Results: Fasting glucose was heritable, with a heritability of 0.62 ± 0.08 (P < 0.01). Genome-wide scan mapped fasting serum glucose to markers D13S158–D13S173 on chromosome 13q (LOD score of 4.6). A strong positional candidate gene is insulin receptor substrate 2, regulator of glucose homeostasis and a candidate gene for obesity. This region was reported previously to be linked to obesity- and diabetes-related phenotypes.

Conclusions: A quantitative trait locus on chromosome 13q contributes to the variation in fasting serum glucose levels in Hispanic children at high risk for obesity.