bluuebunny/crossref_metadata_2025 huggingface dataset:
Role and Functions of Local Communities in Earthquake Rescue, Shelter Administration and Reconstruction
Authors: Iwasaki Nobuhiko
Published: January 2009

Abstract  Major conditions of mitigation during earthquake disasters are quake‐proof built‐environment, administrative ability for crisis management and mutual aid functions of local communities. In this monograph focus is on local communities that played a role in helping victim residents in the Great Hanshin Earthquake. In Japan chonai‐kais are organized in almost all areas as basic associations of local communities. We explored the functions of three levels of community: neighborhoods, chonai‐kais and precincts. During the earthquake neighborhoods were active while precincts were recognized as contributing significantly to the process of rescue. In shelter administration teachers and resident volunteers played leading roles in many cases but some chonai‐kais and precincts showed remarkable activities. Various conflicts occurred in the process of community reconstruction but many chonai‐kais played an important role in coordinating opinions and interests of residents. We could confirm that the active role of each community during disaster period were based on their activities related to neighborhood welfare and community improvement.
Fathers Who Kill Their Children: An Analysis of the Literature
Authors: West Sara G. , Friedman Susan Hatters , Resnick Phillip J.
Published: January 2009

Abstract:  Roughly half of filicidal acts are committed by fathers, though the majority of the literature focuses on maternal filicide. This paper reviews the existing literature on paternal filicide with the goal of identifying characteristics common among these fathers. Fathers who killed their children were, on average, in their mid thirties. The mean age of their victims was five. They may have multiple victims. Sons and daughters were killed in equal numbers. Reasons included death related to abuse, mental illness (including psychosis and depression), and revenge against a spouse. The method often involved wounding violence. Suicide following the act occurred frequently. After being tried for their crimes, filicidal fathers were more frequently incarcerated than hospitalized. Given the range of those capable of this act, mental health professionals must be alert to the possibility of filicide in a variety of fathers. Considering this risk, clinicians should inquire about thoughts of harming children, partners, and themselves.
“Theory of Mind” and Executive Functioning in Forensic Patients with Schizophrenia
Authors: Majorek Karina , Wolfkühler Wiebke , Küper Christian , Saimeh Nahlah , Juckel Georg , Brüne Martin
Published: January 2009

Abstract:  Previous studies in forensic patients with schizophrenia have shown that delinquent patients may outperform nondelinquent patients with regards to “theory of mind” (ToM). Findings were, however, confounded by a lack of control for executive functioning. We examined 33 forensic patients with schizophrenia regarding ToM, intelligence, executive functioning, and psychopathology. Results were compared with a nonforensic schizophrenia sample and a group of healthy controls. Both patient groups performed more poorly on most measures compared with controls. Forensic and nonforensic patients did not differ in task performance. In the forensic group ToM correlated inversely with “excitement” and cognitive symptoms. When “excitement” was covaried out, forensic patients outperformed nonforensic patients with regards to ToM. This study supports the hypothesis that schizophrenic patients with a criminal record are equally impaired in their ability to infer mental states compared with nonforensic patients, but for different reasons associated with a divergent psychopathological profile.
Inducible nitric oxide synthase in pityriasis lichenoides lesions
Authors: Di Giunta Gabriella , Gonçalves da Silva Ana M. , Sotto Mirian N.
Published: January 2009

Background:  Pityriasis lichenoides (PL) is an inflammatory skin disease of unknown etiology. Nitric oxide (NO) has emerged as an important mediator of many physiological functions. The importance of NO‐mediated signaling in skin diseases has been reported by several studies.

Methods:  A review of clinical records and histopathological slides of 34 patients diagnosed with PL was performed. Three different groups of skin biopsies including PL chronica (24 patients), PL et varioliformis acuta (10 patients) and 15 normal skin samples were subjected to the immunohistochemistry technique for inducible nitric oxide synthase (iNOS) detection.

Results:  Normal skin group exhibited a few number of iNOS‐positive cells in the dermis and rare positive cells in the upper epidermis, unlike abundant epidermal and dermal iNOS expression observed in both PL groups.

Conclusion:  According to our results, we hypothesize that NO produced by iNOS could participate in PL pathogenesis. Abnormal and persistent responses to unknown antigens, probably a pathogen, associated with NO immunoregulatory functions could contribute to the relapsing course observed in PL. NO anti‐apoptotic effect on T‐cell lymphocytes could play a role on maintenance of reactive T cells, leading to a T‐cell lymphoid dyscrasia.
Life history tradeoffs influence mortality associated with the amphibian pathogen Batrachochytrium dendrobatidis
Authors: Garner Trenton W. J. , Walker Susan , Bosch Jaime , Leech Stacey , Marcus Rowcliffe J. , Cunningham Andrew A. , Fisher Matthew C.
Published: January 2009

Fatal amphibian chytridiomycosis has typically been associated with the direct costs of infection. However the relationship between exposure to the pathogen, infection and mortality may not be so straightforward. Using results from both field work and experiments we report how exposure of common toads to Batrachochytrium dendrobatidis influences development and survival and how developmental stage influences host responses. Our results show that costs are accrued in a dose dependent manner during the larval stage and are expressed at or soon after metamorphosis. Exposure to B. dendrobatidis always incurs a growth cost for tadpoles and can lead to larval mortality before or soon after metamorphosis even when individuals do not exhibit infection at time of death. In contrast, exposure after metamorphosis almost always results in infection, but body size dictates survival to a greater extent than does dose. These data show that amphibian survival in the face of challenge by an infectious agent is dependent on host condition as well as life history stage. Under current models of climate change, many species of amphibia are predicted to increasingly occur outside their environmental optima. In this case, condition‐dependent traits such as we have demonstrated may weigh heavily on species survival.
The Feminist Periodical Press: Women, Periodical Studies, and Modernity
Authors: Green Barbara
Published: January 2009

The study of feminist periodical culture is playing an increasingly important role in the larger fields of modernist periodical studies and of feminist or women's print culture. Treated as important objects of study in their own right and for their own sake, the feminist periodicals of the early twentieth century – suffrage papers, avant‐garde feminist journals, feminist literary reviews and more – give researchers a glimpse into the intersection of gender and discourses of modernity. Feminist periodicals embed literary texts – plays, short stories, poems as well as book and theater reviews – in the context of economic and political discussions, personal journalism, investigative journalism and advertisements to highlight connections between Edwardian feminist literature and the central issues for feminism – the vote, imperialism, socialism, women's professional labor, and women's engagement with commodity culture.
Risk management dilemmas in dementia care: an organizational survey in three UK countries
Authors: Clarke Charlotte L. , Gibb Catherine E. , Keady John , Luce Anna , Wilkinson Heather , Williams Linda , Cook Ailsa
Published: January 2009

Aims and objectives.  The overall project aimed to understand the variability of the construction of risk in dementia care from the perspective of the person with dementia, family carers and practitioners with the intention of developing negotiated partnerships in risk management. This paper focuses on the objective of identifying the understandings of risk by practitioners.

Background.  Risk management can result in a ‘safety first’ approach to care practices, but this may be disempowering for people with dementia.

Design.  This paper describes the results of the first stage of the study: a survey to service managers or equivalent in health, social and voluntary sector care organizations in three countries of the UK.

Methods.  Data from this stage was collection by postal questionnaire (n = 46).

Results.  Risk was portrayed as a multidimensional concept and clustered around three themes: (1) Risk and Independence, (2) Risk and Resource, and (3) Organizational Risk Management.

Conclusions.  Very wide understandings of risk are identifiable, ranging from avoidance of physical harm through to managed risk taking to improve quality of life, and to an appreciation of the impact of organizational and professional patterns of behaviour resulting in harm to the person with dementia.

Relevance to clinical practice.  Obtaining information about the perspectives of others may help to illuminate some of the dilemmas experienced by staff in this study, and the development of risk assessment frameworks may assist staff to resolve some of these.
Autosomal and sex‐linked microsatellite loci in the green oak leaf roller Tortrix viridana L. (Lepidoptera, Tortricidae)
Authors: SCHROEDER H. , ARENS P. , SMULDERS M. J. M.
Published: January 2009

Eight microsatellite markers were developed for the lepidopteran species Tortrix viridana using an enrichment protocol. The loci were highly variable with number of alleles ranging from four to 38. Six of the eight loci were in Hardy–Weinberg equilibrium. The other two were linked to the Z‐chromosome. Values of observed heterozygosity ranged for the autosomal loci from 0.510 to 0.957. All loci will be useful to study dispersal and the autosomal loci, as well for phylogeographical studies.
Chloroplast simple sequence repeat markers for evolutionary studies in the sexually deceptive orchid genus Chiloglottis
Authors: EBERT DANIEL , HAYES CHRISTINE , PEAKALL ROD
Published: January 2009

The orchids in the genus Chiloglottis are pollinated exclusively by sexual deception. Extensive sequencing (> 19.5 kb) of noncoding chloroplast DNA revealed that simple sequence repeats (cpSSRs) were abundant, enabling a set of 41 cpSSR markers to be developed. All markers were polymorphic across the genus. Polymorphism reflected variation at both mononucleotide repeats and indels. For a subset of four taxa with 40 samples each, locus polymorphism varied from 46 to 81%, while the number of haplotypes ranged from seven to 21 per taxon. Extensive differentiation among the taxa was detected. These cpSSRs markers will enable novel insights into the evolution of this unique genus.
Effects of storage type and time on DNA amplification success in tropical ungulate faeces
Authors: SOTO‐CALDERÓN IVÁN D. , NTIE STEPHAN , MICKALA PATRICK , MAISELS FIONA , WICKINGS ELIZABETH J. , ANTHONY NICOLA M.
Published: January 2009

The present study compares the effect of three storage media (silica, RNAlater®, ethanol) and time to extraction (1 week, 1 month and 3 months) on mitochondrial and nuclear marker amplification success in faecal DNA extracts from a sympatric community of small to medium‐sized Central African forest ungulates (genera Cephalophus, Tragelaphus, Hyemoschus). The effect of storage type and time on nuclear DNA concentrations, genotyping errors and percentage recovery of consensus genotypes was also examined. Regardless of storage method, mitochondrial and nuclear amplification success was high in DNA extracted within the first week after collection. Over longer storage periods, RNAlater yielded better amplification success rates in the mitochondrial assay. However, samples stored on silica showed (i) highest nuclear DNA concentrations, (ii) best microsatellite genotyping success, (iii) lowest genotyping errors, and (iv) greatest percentage recovery of the consensus genotype. The quantity of nuclear DNA was generally a good predictor of microsatellite performance with 83% amplification success or greater achieved with sample DNA concentrations of ≥ 50 pg/µL. If faecal DNA samples are to be used for nuclear microsatellite analyses, we recommend silica as the best storage method. However, for maximum mitochondrial amplification success, RNAlater appears to be the best storage medium. In contrast, ethanol appeared inferior to the other two methods examined here and should not be used to store tropical ungulate faeces. Regardless of storage method, samples should be extracted as soon as possible after collection to ensure optimal recovery of DNA.
The Reserve Capacity Model as a Framework for Understanding Psychosocial Factors in Health Disparities
Authors: Gallo Linda C.
Published: January 2009

Substantial research has identified a robust, linear association between socioeconomic status (SES) and health, across many different populations and outcomes. Among myriad influences, psychosocial factors may contribute to SES‐related gradients in health. In the current manuscript, we describe the Reserve Capacity Model (Gallo & Matthews, 2003) as a potential framework through which to examine psychosocial pathways in health disparities. The model posits that SES is connected to health, in part through associations with stress and concomitant negative emotions, and their subsequent links with bio‐behavioral functioning. In addition, low SES may predict enhanced emotional and physiological reactivity to stress due to a deficiency in resilient psychosocial resources (i.e. “reserve capacity”) and limited opportunities to replenish resource reserves. In addition, resources might represent a direct mediational pathway from SES to health. We describe several studies in which we have examined various tenets of the Reserve Capacity Model, and comment on future research directions to better understand the roles of psychosocial variables in health disparities.
Passion Does Make a Difference in People's Lives: A Look at Well‐Being in Passionate and Non‐Passionate Individuals
Authors: Philippe Frederick L. , Vallerand Robert J. , Lavigne Geneviève L.
Published: January 2009

The purpose of the present research was to examine the differences in well‐being between passionate and non‐passionate individuals of various age groups. The results of two studies (total n = 885) provided support for the hypothesis that being harmoniously passionate for an activity contributes significantly to both hedonic and eudaimonic well‐being, while being obsessively passionate for an activity or having no passion at all does not contribute to well‐being. Furthermore, results from Study 2 showed that only harmoniously passionate people experienced an increase in subjective vitality over a 1‐year period compared to obsessively passionate and non‐passionate people who did not differ from each other. These results also held true after controlling for the effect of age and gender. It would thus appear that passion does make a difference in people's lives, as long as such passion is harmonious in nature.
Personality Assessment with the MMPI‐2: Historical Roots, International Adaptations, and Current Challenges
Authors: Butcher James N. , Williams Carolyn L.
Published: January 2009

The Minnesota Multiphasic Personality Inventory‐2 (MMPI‐2) is the most widely used personality test in psychological practice. Although originally developed during the middle of the last century in the United States, its use today extends around the world. The MMPI‐2 is a robust measure given its strong empirical tradition and many innovations. Recent years have seen controversial changes to this standard of psychological assessment. New scales were added in 2003 (i.e. the Restructured Clinical or RC Scales) and the Fake Bad Scale (FBS) was included in the MMPI‐2 in 2007. A new instrument called the MMPI‐2 Restructured Form (MMPI‐2‐RF) was released in 2008 with the RC Scales replacing the well‐validated MMPI‐2 Clinical Scales; 40 per cent of its items eliminated; a shortened FBS included; and most of its 50 scales introduced for the first time. This article traces the history of the evolving MMPI‐2 with special attention to its international applications, and offers a perspective on the radical departure from past MMPI‐2 research represented by the RC Scales, FBS, the MMPI‐2‐RF, and other recent changes to this standard in the field.
Revealing the Maximum Strength in Nanotwinned Copper
Authors: Lu L. , Chen X. , Huang X. , Lu K.
Published: January 2009

The strength of polycrystalline materials increases with decreasing grain size. Below a critical size, smaller grains might lead to softening, as suggested by atomistic simulations. The strongest size should arise at a transition in deformation mechanism from lattice dislocation activities to grain boundary–related processes. We investigated the maximum strength of nanotwinned copper samples with different twin thicknesses. We found that the strength increases with decreasing twin thickness, reaching a maximum at 15 nanometers, followed by a softening at smaller values that is accompanied by enhanced strain hardening and tensile ductility. The strongest twin thickness originates from a transition in the yielding mechanism from the slip transfer across twin boundaries to the activity of preexisting easy dislocation sources.
Faulty Transmission
Authors: Wolfe Audra J.
Published: January 2009

Science on the Air
. Popularizers and Personalities on Radio and Early Television.
By Marcel Chotkowski LaFollette
. University of Chicago Press, Chicago, 2008. 324 pp. $$27.50, £14.50. ISBN 9780226467597.

LaFollette explores how scientists, journalists, and the conflicting goals of education and entertainment interacted to shape the content and format of science broadcasts from the rise of radio to the early days of television.
Prevalence of Anti-Varicella-Zoster Virus Antibodies in French Infants under 15 Months of Age
Authors: Pinquier Didier , Gagneur Arnaud , Balu Laurent , Brissaud Olivier , Gras Le Guen Christèle , Hau-Rainsard Isabelle , Mory Olivier , Picherot Georges , De Pontual Loïc , Stephan Jean-Louis , Maple Peter , Breuer Judith , Aubert Marie , Caulin Evelyne , Sana Claudine , Pradat Pierre , Soubeyrand Benoît , Reinert Philippe
Published: January 2009

Varicella is a widespread disease of childhood resulting from primary infection with varicella-zoster virus (VZV). The objective of this study was to determine the kinetics of the decline of maternal anti-VZV antibodies in French infants between birth and the age of 15 months in order to estimate the duration of passively acquired maternal anti-VZV immunoglobulin G (IgG). This prospective multicenter study was conducted between October 2005 and January 2007 in the pediatric wards and/or pediatric emergency units of seven French hospitals scattered throughout the country. The level of anti-VZV IgG antibodies in serum was measured by a time-resolved fluorescence immunoassay (TRFIA) (the threshold considered positive is 150 mIU/ml). A total of 345 infants were included. Seventy-seven percent of mothers reported a history of varicella. A rapid decline in the prevalence of anti-VZV antibodies was observed during the first few months of life, with the mean antibody titer decreasing from 536 mIU/ml at birth and through 1 month to below the 150-mIU/ml threshold at 3 to 4 months. The half-life of passively acquired maternal immunoglobulins was around 6 weeks. Based on a large number of subjects, this study clearly demonstrated, for the first time in France, high levels of passively acquired maternal antibodies during the neonatal period, and it allowed us to estimate the duration of passively acquired maternal anti-VZV IgG in French infants. After 4 to 5 months, infants had very low levels of maternal anti-VZV IgG, below the 150-mIU/ml cutoff of the VZV IgG TRFIA.
From Genome-Based In Silico Predictions to Ex Vivo Verification of Leprosy Diagnosis
Authors: Geluk Annemieke , Spencer John S. , Bobosha Kidist , Pessolani Maria C. V. , Pereira Geraldo M. B. , Banu Sayera , Honoré Nadine , Reece Stephen T. , MacDonald Murdo , Sapkota Bishwa Raj , Ranjit Chaman , Franken Kees L. M. C. , Zewdie Martha , Aseffa Abraham , Hussain Rabia , Stefani Mariane M. , Cho Sang-Nae , Oskam Linda , Brennan Patrick J. , Dockrell Hazel M.
Published: January 2009

The detection of hundreds of thousands of new cases of leprosy every year suggests that transmission of
Mycobacterium leprae
infection still continues. Unfortunately, tools for identification of asymptomatic disease and/or early-stage
M. leprae
infection (likely sources of transmission) are lacking. The recent identification of
M. leprae
-unique genes has allowed the analysis of human T-cell responses to novel
M. leprae
antigens. Antigens with the most-promising diagnostic potential were tested for their ability to induce cytokine secretion by using peripheral blood mononuclear cells from leprosy patients and controls in five different areas where leprosy is endemic; 246 individuals from Brazil, Nepal, Bangladesh, Pakistan, and Ethiopia were analyzed for gamma interferon responses to five recombinant proteins (ML1989, ML1990, ML2283, ML2346, and ML2567) and 22 synthetic peptides. Of these, the
M. leprae
-unique protein ML1989 was the most frequently recognized and ML2283 the most specific for
M. leprae
infection/exposure, as only a limited number of tuberculosis patients responded to this antigen. However, all proteins were recognized by a significant number of controls in areas of endemicity. T-cell responses correlated with in vitro response to
M. leprae
, suggesting that healthy controls in areas where leprosy is endemic are exposed to
M. leprae
. Importantly, 50% of the healthy household contacts and 59% of the controls in areas of endemicity had no detectable immunoglobulin M antibodies to
M. leprae
-specific PGL-I but responded in T-cell assays to ≥1
M. leprae
protein. T-cell responses specific for leprosy patients and healthy household contacts were observed for ML2283- and ML0126-derived peptides, indicating that
M. leprae
peptides hold potential as diagnostic tools. Future work should concentrate on the development of a sensitive and field-friendly assay and identification of additional peptides and proteins that can induce
M. leprae
-specific T-cell responses.
Immune Responses and Protection against Experimental Challenge after Vaccination of Bison withBrucella abortusStrain RB51 or RB51 Overexpressing Superoxide Dismutase and Glycosyltransferase Genes
Authors: Olsen S. C. , Boyle S. M. , Schurig G. G. , Sriranganathan N. N.
Published: January 2009

Vaccination is a tool that could be beneficial in managing the high prevalence of brucellosis in free-ranging bison in Yellowstone National Park. In this study, we characterized immunologic responses and protection against experimental challenge after vaccination of bison withBrucella abortusstrain RB51 (RB51) or a recombinant RB51 strain overexpressing superoxide dismutase (sodC) and glycosyltransferase (wboA) genes (RB51+sodC,wboA). Bison were vaccinated with saline only or with 4.6 × 1010CFU of RB51 or 7.4 × 1010CFU of RB51+sodC,wboA(n= eight animals/treatment). Bison vaccinated with RB51 or RB51+sodC,wboAhad greater (P< 0.05) antibody responses, proliferative responses, and production of gamma interferon to RB51 after vaccination than did nonvaccinates. However, bison vaccinated with RB51+sodC,wboAcleared the vaccine strain from draining lymph nodes faster than bison vaccinated with the parental RB51 strain. Immunologic responses of bison vaccinated with RB51+sodC,wboAwere similar to responses of bison vaccinated with RB51. Pregnant bison were intraconjunctivally challenged in midgestation with 107CFU ofB. abortusstrain 2308. Bison vaccinated with RB51, but not RB51+sodC,wboAvaccinates, had greater protection from abortion, fetal/uterine, mammary, or maternal infection than nonvaccinates. Our data suggest that the RB51+sodC,wboAstrain is less efficacious as a calfhood vaccine for bison than the parental RB51 strain. Our data also suggest that the RB51 vaccine is a currently available management tool that could be utilized to help reduce brucellosis in free-ranging bison.
Identification of Functional Domains in Reovirus Replication Proteins μNS and μ2
Authors: Kobayashi Takeshi , Ooms Laura S. , Chappell James D. , Dermody Terence S.
Published: January 2009

Mammalian reoviruses are nonenveloped particles containing a genome of 10 double-stranded RNA (dsRNA) gene segments. Reovirus replication occurs within viral inclusions, which are specialized nonmembranous cytoplasmic organelles formed by viral nonstructural and structural proteins. Although these structures serve as sites for several major events in the reovirus life cycle, including dsRNA synthesis, gene segment assortment, and genome encapsidation, biochemical mechanisms of virion morphogenesis within inclusions have not been elucidated because much remains unknown about inclusion anatomy and functional organization. To better understand how inclusions support viral replication, we have used RNA interference (RNAi) and reverse genetics to define functional domains in two inclusion-associated proteins, μNS and μ2, which are interacting partners essential for inclusion development and viral replication. Removal of μNS N-terminal sequences required for association with μ2 or another μNS-binding protein, σNS, prevented the capacity of μNS to support viral replication without affecting inclusion formation, indicating that μNS-μ2 and μNS-σNS interactions are necessary for inclusion function but not establishment. In contrast, introduction of changes into the μNS C-terminal region, including sequences that form a putative oligomerization domain, precluded inclusion formation as well as viral replication. Mutational analysis of μ2 revealed a critical dependence of viral replication on an intact nucleotide/RNA triphosphatase domain and an N-terminal cluster of basic amino acid residues conforming to a nuclear localization motif. Another domain in μ2 governs the capacity of viral inclusions to affiliate with microtubules and thereby modulates inclusion morphology, either globular or filamentous. However, viral variants altered in inclusion morphology displayed equivalent replication efficiency. These studies reveal a modular functional organization of inclusion proteins μNS and μ2, define the importance of specific amino acid sequences and motifs in these proteins for viral replication, and demonstrate the utility of complementary RNAi-based and reverse genetic approaches for studies of reovirus replication proteins.
Noncytolytic Clearance of Sindbis Virus Infection from Neurons by Gamma Interferon Is Dependent on Jak/Stat Signaling
Authors: Burdeinick-Kerr Rebeca , Govindarajan Dhanasekaran , Griffin Diane E.
Published: January 2009

The alphavirus Sindbis virus (SINV) causes encephalomyelitis in mice by infecting neurons of the brain and spinal cord. The outcome is age dependent. Young animals develop fatal disease, while older animals recover from infection. Recovery requires noncytolytic clearance of SINV from neurons, and gamma interferon (IFN-γ) is an important contributor to clearance in vivo. IFN-γ-dependent clearance has been studied using immortalized CSM14.1 rat neuronal cells that can be differentiated in vitro. Previous studies have shown that differentiated, but not undifferentiated, cells develop prolonged SINV replication and respond to IFN-γ treatment with noncytolytic clearance of virus preceded by suppression of genomic viral RNA synthesis and reactivation of cellular protein synthesis. To determine the signaling mechanisms responsible for clearance, the responses of SINV-infected differentiated neurons to IFN-γ were examined. IFN-γ treatment of SINV-infected differentiated CSM14.1 cells, AP-7 olfactory neuronal cells, and primary dorsal root ganglia neurons triggered prolonged Stat-1 Tyr701phosphorylation, Stat-1 Ser727phosphorylation, and transient Stat-5 phosphorylation. Inhibition of Jak kinase activity with Jak inhibitor I completely reversed the neuroprotective and antiviral activities of IFN-γ in differentiated cells. We conclude that activation of the Jak/Stat pathway is the primary mechanism for IFN-γ-mediated clearance of SINV infection from mature neurons.
Non-Cleavage Site Gag Mutations in Amprenavir-Resistant Human Immunodeficiency Virus Type 1 (HIV-1) Predispose HIV-1 to Rapid Acquisition of Amprenavir Resistance but Delay Development of Resistance to Other Protease Inhibitors
Authors: Aoki Manabu , Venzon David J. , Koh Yasuhiro , Aoki-Ogata Hiromi , Miyakawa Toshikazu , Yoshimura Kazuhisa , Maeda Kenji , Mitsuya Hiroaki
Published: January 2009

In an attempt to determine whether mutations in Gag in human immunodeficiency virus type 1 (HIV-1) variants selected with a protease inhibitor (PI) affect the development of resistance to the same or a different PI(s), we generated multiple infectious HIV-1 clones carrying mutated Gag and/or mutated protease proteins that were identified in amprenavir (APV)-selected HIV-1 variants and examined their virological characteristics. In an HIV-1 preparation selected with APV (33 passages, yielding HIVAPVp33), we identified six mutations in protease and six apparently critical mutations at cleavage and non-cleavage sites in Gag. An infectious recombinant clone carrying the six protease mutations but no Gag mutations failed to replicate, indicating that the Gag mutations were required for the replication of HIVAPVp33. An infectious recombinant clone that carried wild-type protease and a set of five Gag mutations (rHIVWTpro12/75/219/390/409gag) replicated comparably to wild-type HIV-1; however, when exposed to APV, rHIVWTpro12/75/219/390/409gagrapidly acquired APV resistance. In contrast, the five Gag mutations significantly delayed the acquisition of HIV-1 resistance to ritonavir and nelfinavir (NFV). Recombinant HIV-1 clones containing NFV resistance-associated mutations, such as D30N and N88S, had increased susceptibilities to APV, suggesting that antiretroviral regimens including both APV and NFV may bring about favorable antiviral efficacy. The present data suggest that the preexistence of certain Gag mutations related to PI resistance can accelerate the emergence of resistance to the PI and delay the acquisition of HIV resistance to other PIs, and these findings should have clinical relevance in the therapy of HIV-1 infection with PI-including regimens.
Foot-and-Mouth Disease Virus Can Induce a Specific and Rapid CD4+T-Cell-Independent Neutralizing and Isotype Class-Switched Antibody Response in Naïve Cattle
Authors: Juleff Nicholas , Windsor Miriam , Lefevre Eric A. , Gubbins Simon , Hamblin Pip , Reid Elizabeth , McLaughlin Kerry , Beverley Peter C. L. , Morrison Ivan W. , Charleston Bryan
Published: January 2009

The role of T-lymphocyte subsets in recovery from foot-and-mouth disease virus (FMDV) infection in calves was investigated by administering subset-specific monoclonal antibodies. The depletion of circulating CD4+or WC1+γδ T cells was achieved for a period extending from before challenge to after resolution of viremia and peak clinical signs, whereas CD8+cell depletion was only partial. The depletion of CD4+cells was also confirmed by analysis of lymph node biopsy specimens 5 days postchallenge. Depletion with anti-WC1 and anti-CD8 antibodies had no effect on the kinetics of infection, clinical signs, and immune responses following FMDV infection. Three of the four CD4+T-cell-depleted calves failed to generate an antibody response to the nonstructural polyprotein 3ABC but generated a neutralizing antibody response similar to that in the controls, including rapid isotype switching to immunoglobulin G antibody. We conclude that antibody responses to sites on the surface of the virus capsid are T cell independent, whereas those directed against the nonstructural proteins are T cell dependent. CD4 depletion was found to substantially inhibit antibody responses to the G-H peptide loop VP1135-156on the viral capsid, indicating that responses to this particular site, which has a more mobile structure than other neutralizing sites on the virus capsid, are T cell dependent. The depletion of CD4+T cells had no adverse effect on the magnitude or duration of clinical signs or clearance of virus from the circulation. Overall, we conclude that CD4+T-cell-independent antibody responses play a major role in the resolution of foot-and-mouth disease in cattle.
System-scenario-based design of dynamic embedded systems
Authors: Gheorghita Stefan Valentin , Palkovic Martin , Hamers Juan , Vandecappelle Arnout , Mamagkakis Stelios , Basten Twan , Eeckhout Lieven , Corporaal Henk , Catthoor Francky , Vandeputte Frederik , Bosschere Koen De
Published: January 2009

In the past decade, real-time embedded systems have become much more complex due to the introduction of a lot of new functionality in one application, and due to running multiple applications concurrently. This increases the dynamic nature of today's applications and systems, and tightens the requirements for their constraints in terms of deadlines and energy consumption. State-of-the-art design methodologies try to cope with these novel issues by identifying several most used cases and dealing with them separately, reducing the newly introduced complexity. This article presents a generic and systematic design-time/run-time methodology for handling the dynamic nature of modern embedded systems, which can be utilized by existing design methodologies to increase their efficiency. It is based on the concept of
system scenarios
, which group system behaviors that are similar from a multidimensional cost perspective—such as resource requirements, delay, and energy consumption—in such a way that the system can be configured to exploit this cost similarity. At design-time, these scenarios are individually optimized. Mechanisms for predicting the current scenario at run-time, and for switching between scenarios, are also derived. This design trajectory is augmented with a run-time calibration mechanism, which allows the system to learn on-the-fly during its execution, and to adapt itself to the current input stimuli, by extending the scenario set, changing the scenario definitions, and both the prediction and switching mechanisms. To show the generality of our methodology, we show how it has been applied on four very different real-life design problems. In all presented case studies, substantial energy reductions were obtained by exploiting scenarios.
Model checking sequential software programs via mixed symbolic analysis
Authors: Yang Zijiang , Wang Chao , Gupta Aarti , Ivančić Franjo
Published: January 2009

We present an efficient symbolic search algorithm for software model checking. Our algorithms perform word-level reasoning by using a combination of decision procedures in Boolean and integer and real domains, and use novel symbolic search strategies optimized specifically for sequential programs to improve scalability. Experiments on real-world C programs show that the new symbolic search algorithms can achieve several orders-of-magnitude improvements over existing methods based on bit-level (Boolean) reasoning.
Interconnect customization for a hardware fabric
Authors: Mehta Gayatri , Stander Justin , Baz Mustafa , Hunsaker Brady , Jones Alex K.
Published: January 2009

This article describes several multiplexer-based interconnection strategies designed to improve energy consumption of stripe-based coarse-grain reconfigurable fabrics. Application requirements for the architecture as well as two dense subgraphs are extracted from a suite of signal and image processing benchmarks. These statistics are used to drive the strategy of the composition of multiplexer-based interconnect. The article compares interconnects that are fully connected between stripes, those with a cardinality of 8:1 to 4:1, and extensions that provide a 5:1 cardinality, limited 6:1 cardinality, and hybrids between 5:1 and 3:1 cardinalities. Additionally, dedicated vertical routes are considered replacing some computational units with dedicated pass-gates. Using a fabric interconnect model (FIM) written in XML, we demonstrate that fabric instances and mappers can be automatically generated using a Web-based design flow. Upon testing these instances, we found that using an 8:1 cardinality interconnect with 33% of the computational units replaced with dedicated pass-gates provided the best energy versus mappability tradeoff, resulting in a 50% energy improvement over fully connected rows and 20% energy improvement over an 8:1 cardinality interconnect without dedicated vertical routes.
Straightforward construction of depth-size optimal, parallel prefix circuits with fan-out 2
Authors: Lin Yen-Chun , Hung Li-Ling
Published: January 2009

Prefix computation is used in various areas and is considered as a primitive operation. Parallel prefix circuits are parallel prefix algorithms on the combinational circuit model. The depth of a prefix circuit is a measure of its processing time; smaller depth implies faster computation. The size of a prefix circuit is the number of operation nodes in it. Smaller size implies less power consumption, less VLSI area, and less cost. A prefix circuit with
n
inputs is depth-size optimal if its depth plus size equals 2
n
− 2. A circuit with a smaller fan-out is in general faster and occupies less VLSI area. To be of practical use, the depth and fan-out of a prefix circuit should be small. In this paper, a family of depth-size optimal, parallel prefix circuits with fan-out 2 is presented. This family of prefix circuits is easier to construct and more amenable to automatic synthesis than two other families of the same type, although the three families have the same minimum depth among all depth-size optimal prefix circuits with fan-out 2. The balanced structure of the new family is also a merit.
Specifying norm-governed computational societies
Authors: Artikis Alexander , Sergot Marek , Pitt Jeremy
Published: January 2009

Electronic markets, dispute resolution and negotiation protocols are three types of application domains that can be viewed as open agent societies. Key characteristics of such societies are agent heterogeneity, conflicting individual goals and unpredictable behavior. Members of such societies may fail to, or even choose not to, conform to the norms governing their interactions. It has been argued that systems of this type should have a formal, declarative, verifiable, and meaningful semantics. We present a theoretical and computational framework being developed for the executable specification of open agent societies. We adopt an external perspective and view societies as instances of normative systems. In this article, we demonstrate how the framework can be applied to specifying and executing a contract-net protocol. The specification is formalized in two action languages, the
C
+ language and the Event Calculus, and executed using respective software implementations, the Causal Calculator and the Society Visualizer. We evaluate our executable specification in the light of the presented case study, discussing the strengths and weaknesses of the employed action languages for the specification of open agent societies.
Arithmetic complexity
Authors: Dries Lou Van Den , Moschovakis Yiannis N.
Published: January 2009

We obtain
lower bounds
on the cost of computing various arithmetic functions and deciding various arithmetic relations from specified primitives. This includes lower bounds for computing the greatest common divisor and deciding coprimeness of two integers, from primitives like addition, subtraction, division with remainder and multiplication. Some of our results are in terms of recursive programs, but they generalize directly to most (plausibly all) algorithms from the specified primitives. Our methods involve some elementary number theory as well as the development of some basic notions and facts about recursive algorithms.
Certainty closure
Authors: Yorke-Smith Neil , Gervet Carmen
Published: January 2009

Constraint Programming (CP) has proved an effective paradigm to model and solve difficult combinatorial satisfaction and optimization problems from disparate domains. Many such problems arising from the commercial world are permeated by data uncertainty. Existing CP approaches that accommodate uncertainty are less suited to uncertainty arising due to incomplete and erroneous data, because they do not build reliable models and solutions guaranteed to address the user's genuine problem as she perceives it. Other fields such as reliable computation offer combinations of models and associated methods to handle these types of uncertain data, but lack an expressive framework characterizing the resolution methodology independently of the model.

We present a unifying framework that extends the CP formalism in both model and solutions, to tackle ill-defined combinatorial problems with incomplete or erroneous data. Thecertainty closure frameworkbrings together modeling and solving methodologies from different fields into the CP paradigm to provide reliable and efficient approches for uncertain constraint problems. We demonstrate the applicability of the framework on a case study in network diagnosis. We define resolution forms that give generic templates, and their associated operational semantics, to derive practical solution methods for reliable solutions.
A finite equational base for CCS with left merge and communication merge
Authors: Aceto Luca , Fokkink Wan , Ingolfsdottir Anna , Luttik Bas
Published: January 2009

Using the left merge and the communication merge from ACP, we present an equational base (i.e., a ground-complete and ω-complete set of valid equations) for the fragment of CCS without recursion, restriction and relabeling modulo (strong) bisimilarity. Our equational base is finite if the set of actions is finite.
Static and Dynamic Memory Footprint Reduction for FPGA Routing Algorithms
Authors: Chin Scott Y. L. , Wilton Steven J. E.
Published: January 2009

This article presents techniques to reduce the static and dynamic memory requirements of routing algorithms that target field-programmable gate arrays. During routing, memory is required to store both architectural data and temporary routing data. The architectural data is static, and provides a representation of the physical routing resources and programmable connections on the device. We show that by taking advantage of the regularity in FPGAs, we can reduce the amount of information that must be explicitly represented, leading to significant memory savings. The temporary routing data is dynamic, and contains scoring parameters and traceback information for each routing resource in the FPGA. By studying the lifespan of the temporary routing data objects, we develop several memory management schemes to reduce this component. To make our proposals concrete, we applied them to the routing algorithm in VPR and empirically quantified the impact on runtime memory footprint, and place and route time.
Searching for Transient Pulses with the ETA Radio Telescope
Authors: Patterson C. D. , Ellingson S. W. , Martin B. S. , Deshpande K. , Simonetti J. H. , Kavic M. , Cutchin S. E.
Published: January 2009

Array-based, direct-sampling radio telescopes have computational and communication requirements unsuited to conventional computer and cluster architectures. Synchronization must be strictly maintained across a large number of parallel data streams, from A/D conversion, through operations such as beamforming, to dataset recording. FPGAs supporting multigigabit serial I/O are ideally suited to this application. We describe a recently-constructed radio telescope called ETA having all-sky observing capability for detecting low frequency pulses from transient events such as gamma ray bursts and primordial black hole explosions. Signals from 24 dipole antennas are processed by a tiered arrangement of 28 commercial FPGA boards and 4 PCs with FPGA-based data acquisition cards, connected with custom I/O adapter boards supporting InfiniBand and LVDS physical links. ETA is designed for unattended operation, allowing configuration and recording to be controlled remotely.
RAT
Authors: Holland Brian , Nagarajan Karthik , George Alan D.
Published: January 2009

While the promise of achieving speedup and additional benefits such as high performance per watt with FPGAs continues to expand, chief among the challenges with the emerging paradigm of reconfigurable computing is the complexity in application design and implementation. Before a lengthy development effort is undertaken to map a given application to hardware, it is important that a high-level parallel algorithm crafted for that application first be analyzed relative to the target platform, so as to ascertain the likelihood of success in terms of potential speedup. This article presents the RC Amenability Test, or RAT, a methodology and model developed for this purpose, supporting rapid exploration and prediction of strategic design tradeoffs during the formulation stage of application development.
Traveling to Rome
Authors: Wilkes John
Published: January 2009

Starting in 1994/5, the Storage Systems Program at HP Labs embarked on a decade-long journey to automate the management of enterprise storage systems by means of a technique we initially called attribute-managed storage. The key idea was to provide declarative specifications of workloads and their needs, and of storage devices and their capabilities, and to automate the mapping of one to the other. One of many outcomes of the project was a specification language we called Rome 1 -- hence the title of this paper, which offers a short retrospective on the approach and some of the lessons we learned along the way.
The CHART system
Authors: Brassil Jack , McGeer Rick , Rajagopalan Raj , Sharma Puneet , Yalagandula Praveen , Banerjee Sujata , Reed David P. , Lee Sung-Ju
Published: January 2009

TCP/IP is known to have poor performance under conditions of moderate to high packet loss (5%-20%) and end-to-end latency (20-200 ms). The CHART system, under development by HP and its partners under contract to the US Defense Advanced Research Projects Agency, is a careful re-engineering of Internet Layer 3 and Layer 4 protocols to improve TCP/IP performance in these cases. The CHART system has just completed the second phase of a three-phase, 42-month development cycle. The goal for the 42-month program was a 10x improvement in the performance of TCP/IP under conditions of loss and delay. In independent tests for DARPA at Science Applications In-ternational Corporation, the CHART System demonstrated a 20x performance improvement over TCP/IP, exceeding the goals for the program by a factor of two. Fairness to legacy TCP and UDP ows was further demonstrated in DARPA testing. We describe the CHART System as a set of five interacting services and protocol improvements which act together to make TCP/IP robust under conditions of loss and latency, and we describe and detail the test regime and performance results.