bluuebunny/crossref_metadata_2025 huggingface dataset:
Cyclic Loading of 3 Achilles Tendon Repairs Simulating Early Postoperative Forces
Authors: Lee Steven J. , Sileo Michael J. , Kremenic Ian J. , Orishimo Karl , Ben-Avi Simon , Nicholas Stephen J. , McHugh Malachy
Published: February 2009

Background

Accelerated rehabilitation has been advocated after Achilles tendon repair, but it produces significant forces at the repair site.

Hypothesis

Stresses applied to the repaired Achilles tendon simulating postoperative forces may exceed the strength of some repairs.

Study Design

Controlled laboratory study.

Methods

Fifteen Achilles tendons were incised 4 cm proximal to the calcaneal insertion, then were repaired using either a percutaneous, 4-strand Krackow, or an epitendinous augmented 4-strand Krackow technique. Tendons were cyclically loaded to 1000 cycles each at 100, 190, and 369 N. The number of cycles to initial gapping, 5-mm gapping, and total failure were compared using Mann-Whitney U tests with adjustments for multiple comparisons.

Results

Gap resistance was significantly greater for augmented Krackow repairs (2208 cycles to initial gapping) versus nonaugmented repairs (502 cycles, P = .024) and for nonaugmented Krackow repairs versus percutaneous repairs (5 cycles, P = .024). All percutaneous repairs failed during the 100-N cycling (102 ± 135 cycles). All nonaugmented Krackow repairs failed during the 190-N cycles (total cycles to failure: 1268 ± 345). All augmented Krackow repairs were intact (no gapping) after the 190-N cycles. Four failed during 369-N cycling (total cycles to failure, 2017 ± 11), and 1 remained intact for 3000 cycles.

Conclusion

Epitendinous cross-stitch weave augmentation of Achilles tendon repairs significantly increased repair strength and gap resistance.

Clinical Relevance

Epitendinous cross-stitch weave augmentation of Achilles tendon repairs may better allow for early stretching and ambulation after Achilles tendon repair.
An Insight Into the Delivery of a Palliative Approach in Residential Aged Care
Authors: Phillips Jane , Davidson Patricia M. , Willcock Simon
Published: February 2009

Managing the complex care needs of older people is a global concern. General practitioners (GPs) play a pivotal role in aged care, yet little is known about their capacity to provide palliative care in nursing homes. This study aimed to investigate GPs' perceptions and understanding of a palliative approach. A convenience sample of rural GPs ( n = 13) participated in a series of three focus groups undertaken in August, 2005. These focus groups were all audio-taped, transcribed, and analyzed using thematic content analysis. Four key themes emerged: uncertainty about a palliative approach, a need to reorientate providers, the challenges of managing third parties, and making it work and moving forward. These preliminary findings suggest that integrating a palliative approach in aged care requires GPs to have a greater awareness of this paradigm and to be more effectively engaged in multidisciplinary care planning.
Subacute Sclerosing Panencephalitis (SSPE) Presenting as Acute Disseminated Encephalomyelitis in a Child
Authors: Goraya Jatinder , Marks Harold , Khurana Divya , Legido Agustin , Melvin Joseph
Published: February 2009

Subacute sclerosing panencephalitis (SSPE) typically presents with progressive mental deterioration, behavioral changes, and myoclonic jerks. Atypical presentations are not unknown and may result in diagnostic delays. A 9-year-old girl presented with poor balance and ataxia following an episode of upper respiratory tract infection. Neurological examination revealed mild hemiparesis and ataxia. Brain magnetic resonance imaging revealed scattered areas of T2 and fluid-attenuated inversion recovery hyperintensities in the white matter consistent with acute disseminated encephalomyelitis. Despite treatment with intravenous methylprednisolone, intravenous immunoglobulins, and plasmapheresis, progressive neurological worsening occurred. Later during the course of her illness, subacute sclerosing panencephalitis was suspected from the appearance of burst-suppression pattern on electroencephalogram, and the diagnosis confirmed by elevated titers of measles antibodies in cerebrospinal fluid. Physicians taking care of children need to be aware of atypical presentations of subacute sclerosing panencephalitis and must have a high index of suspicion to prevent diagnostic delays and avoid unnecessary diagnostic and therapeutic interventions.
Blood Compatibility of Surface Modified Poly(ethylene terephthalate) (PET) by Plasma Polymerized Acetobromo-α-D-glucose
Authors: Kumar D. Sakthi , Nair Baiju G. , Varghese Saino H. , Nair Remya , Hanajiri T. , Maekawa T. , Yoshida Yasuhiko , John Rajan K. , Jayakrishnan A.
Published: February 2009

Poly (ethylene terephthalate) (PET) was surface modified by plasma polymerization of acetobromo-α-D-glucose (ABG) at different radio frequency (RF) powers. Plasma polymerization was carried out by vaporizing ABG in the powder form by heating at 135°C. Surface modification resulted in improved hydrophilicity and smoothness of the surface especially at low RF powers (30—50 W), but at high RF powers, the surface was found to be etched and the hydrophilicity decreased as evidenced by atomic force microscopy (AFM) and contact angle measurements. The plasma polymerized ABG film was found to be extensively cross-linked as evidenced by its insolubility in water. Infra red (IR) and X-ray photoelectron spectroscopy (XPS) were employed to characterize the plasma polymerized ABG films. IR studies revealed that at lower RF powers, polymerization was taking place mainly by breaking up of acetoxy group while retaining the ring structures to a major extent during the polymerization process whereas at high RF powers, the rupture of ring structures was indicated. XPS indicated a reduction in the percentage of oxygen in the polymers going from low to high RF powers suggestive of complete destruction of the acetoxy group at high RF powers. Cross-cut tests showed excellent adhesive properties of the plasma polymerized ABG films onto PET. Static platelet adhesion tests using platelet rich human plasma showed significantly reduced adhesion of platelets onto modified PET surface as evidenced by scanning electron microscopy. Polymerization of glucose and its derivatives using RF plasma has not been reported so far and the preliminary results reported in this study shows that this could be an interesting approach in the surface modification of biomaterials.
Three-Year Measured Weight Change in the African American Health Study
Authors: Wolinsky Fredric D. , Andresen Elena M. , Malmstrom Theodore K. , Schootman Mario , Miller J. Philip , Miller Douglas K.
Published: February 2009

Objective: This study examines 3-year weight change in African Americans. Method: Nine hundred and ninety-eight participants 49 to 65 years old were assessed at baseline and 3 years later. Weight was measured, and weight change was defined as clinically meaningful increases or decreases (± 5 kg). Potential risk factors were investigated using multinomial logistic regression. Results: In-home measured weights were available for 752 participants (75%): 504 (67%) had stable weights, 131 (17%) gained more than 5 kg, and 117 (16%) lost more than 5 kg. Among all participants, the risks for weight gains were cancer, chronic obstructive pulmonary disease, lower income, and Medicaid status; the risks for weight losses were angina, cancer, high measured systolic blood pressure, asthma, and physical inactivity. Sex-stratified analyses reveal differences involving age, socioeconomic status, cancer, blood pressure, and lower body function. Discussion: Three-year weight changes in middle-aged African Americans were frequent and significantly associated with several risk factors.
Damage Identification Using Piezoelectric Impedance Approach and Spectral Element Method
Authors: Wang X. , Tang J.
Published: February 2009

The basic idea of the impedance-based damage detection is that the electrical impedance of the piezoelectric transducer attached to a structure is directly related to the mechanical impedance of the host structure. Therefore, damage effect can be reflected in the change of the piezoelectric impedance curves before and after damage occurrence. As the piezoelectric impedance information can be extracted at relatively high-frequency range, such a method is considered to be sensitive to small-sized damage. Previous studies on this approach mainly focus on declaring damage occurrence. In this research, we develop a model-based method that can identify both the location and the severity of the damage. The model is built upon the spectral element method, which has high computational accuracy and numerical efficiency in the high-frequency range. Using the difference between the impedance curves of the system monitored and the system at its healthy baseline state as input, an inverse identification procedure is formulated to extract directly the property change of the structural elements. Extensive numerical and experimental studies are carried out to demonstrate the effectiveness of the proposed method.
Into the Abyss of Someone Else's Dying
Authors: Phillips Linda R. , Reed Pamela G.
Published: February 2009

This study was undertaken to better understand family caregivers' perspectives of providing end-of-life (EOL) care to elders facing expected deaths from life-limiting, chronic illnesses, and the study involved understanding the nature of EOL caregiving using caregivers' own words. The study employed a cross-sectional, exploratory descriptive design. The data source was intensive interviews with 27 EOL caregivers. Eight themes were extracted from data that exemplify the core characteristics of EOL caregiving. The themes intersected at a central idea expressed in the voice of one caregiver as “jumping . . . into the abyss of someone else's dying.” Data suggested that caregivers of elders with life-limiting illnesses needed nursing guidance about EOL care earlier than it is usually provided and that all nurses providing care to elders in any setting should be ready to offer early education in the practical, technical, and emotional dimensions of end-of-life caregiving.
Scheduling Accommodations Among Students Who Persist in High School Music Ensembles
Authors: Baker Vicki D.
Published: February 2009

The purpose of this study was to investigate scheduling patterns of high school students who earn multiple credits in music ensembles and to investigate why high school students elect to enroll in ensembles. Participants ( N = 443) were freshman music majors enrolled in 10 Texas universities. They completed questionnaires about enrollment in ensembles, classes taken outside of the traditional school day, and types of high school schedules. In a free-response format, participants listed any scheduling obstacles and reasons for taking ensemble classes in high school. Results indicated that the primary obstacles involved schedule conflicts. Respondents ( n = 55) who took summer school and correspondence courses had the highest average number of music ensemble classes (7.9) for Grades 9 through 12. The primary motivating factors for ensemble membership were the pleasures associated with performing music and social networking. Implications of research include the potential improvement of retention rates.
Inside and Outside the Undergraduate Music Education Curriculum
Authors: Hourigan Ryan M. , Scheib John W.
Published: February 2009

This study examined the perceived requisite skills and understandings needed for a successful student teaching experience. Six instrumental music student teachers served as participants. Findings included that students perceived curricular, co-curricular, and extra-curricular music teaching and non- music teaching experiences to be valuable prior to student teaching. Valuable curricular and co-curricular (e.g. fieldwork) skills included: (a) administrative skills; (b) classroom management skills; (c) musicianship skills; and (d) content and pedagogical knowledge. The participants reported that not only did they acquire these skills from coursework, applied lessons, and ensemble participation, but also experiences outside of their curricular requirements (e.g., skills relating to work ethic, interpersonal and intrapersonal skills). The researchers compared these results to the forms of Ethical and Intellectual Development (Perry, 1968/1999) and determined that preservice music teachers' perceptions of the importance of acquired skills prior to student teaching may depend on their intellectual development.
African American Women's Satisfaction with the Design and Marketing of Ready‐to‐Wear Clothing
Authors: MacDonald Nora M. , Lazorchak Shirley A. , Currie Kristi M.
Published: February 2009

The African American market has increased in terms of percentage of the United States population and income, with purchasing power estimated at more than $800 billion. This pilot study assessed older African American women's perception of how well their clothing needs were being met using focus group discussion methodology. The primary objective was to determine African American women's satisfaction with marketing clothing, clothing fit, cultural dress, and accessories. The dress‐body clothing purchase decision‐making factors model was used as the theoretical framework. Thirty‐two African American women from the Charleston, West Virginia, area participated in the study. Results indicated dissatisfaction with the portrayal of African American females in targeted advertisements and the fit of clothing. Suggestions are provided to overcome these reservations.
Needs and Issues of Latino and Native American Nonparental Relative Caregivers: Strengths and Challenges Within a Cultural Context
Authors: Kopera‐Frye Karen
Published: February 2009

While custodial grandparenting historically has been more prevalent among African Americans, kinship care is increasing nationally among all culturally diverse groups. Custodial grandparenting and kinship care are becoming more common among Latino and Native American cultures. However, there are few studies examining needs and issues faced by these relative caregivers, particularly grandparents. In‐depth interviews were conducted with Latino and Native American caregivers of one or more children. Interviews focused on the child's needs, caregiving issues, and the caregiver's impact on the children. Results indicate that both groups reported concerns involving finances and health of child; Native Americans noted legal custodial issues as critical. Latino caregivers reported having inadequate resources for the child's medical care; Native Americans reported legal aid as a significant need. Differential impact on children was reported: with Latinos, family and education, with Native Americans, cultural identity. The findings suggested differential needs, concerns, and impact among these diverse caregivers.
Engaging Latinos in Culturally Specific Educational Programming: A Multidisciplinary Approach
Authors: Springer Paul , Hollist Cody , Buchfink Karen
Published: February 2009

Results from the 2000 United States census highlighted that the Latino population had exceeded the African American population as the largest U.S. minority group. Furthermore, during the past 20 years, migration patterns for Latino families have spread throughout the West, Midwest, and South and not merely in the border states. To meet the rising educational and human service needs, professionals have sought to develop programs that are effective at helping the Latino populations. This article presents a theoretical model for engaging Latinos in family and consumer science education and outreach programs. The model was designed for family and consumer science educators and draws from both the education and human service literature. A case study is used to outline the application of the model and suggestions for implementation are described.
Ecocultural Adaptive Research: A Synthesis of Ecocultural Theory, Participatory Research, and Adaptive Designs
Authors: Phenice Lillian A. , Griffore Robert J. , Hakoyama Mikiyasu , Silvey Le Anne
Published: February 2009

Recently ethical codes of conduct for research with ethnic families, communities, and groups have emerged. Therefore, a model that includes ethical codes of conduct for researchers and ethnic participants is needed to advocate for change. By integrating aspects of ecocultural theory with the strengths of various research designs and approaches, revisions and strategic changes during the course of planning, proposing, and conducting research can result in specific applications congruent with a unique ethnic population as well as optimized outcomes. The proposed research model is a synthesis of ecocultural theory, participatory research, and adaptive designs. This research model is built on the uniqueness of the ethnic community, issues of participatory social justice and the need for sense making, and valuing the balance of power between the professional researcher and the participants of communities and groups.
Aging Out of Place: Cambodian Refugee Elders in the United States
Authors: Lewis Denise C.
Published: February 2009

Experiences of aging refugees or immigrants are significantly different from elders who have not experienced international migration. Eighty‐nine interviews with 38 elderly Cambodian refugees were conducted to understand their aging experiences in the United States. This paper explores multiple meanings of aging in place that go beyond the ability to remain in one's preferred geographic location, maintenance of independence and autonomy, and attachment and meanings assigned to place. Of the components normally used in defining aging in place, meaning making had the most salience for this group of elders. One's sense of place, whether such “place” is defined geographically, socially, or culturally, often created challenges for these elders. This group exhibits different forms of coping and require different services than non‐refugee elders. An infrastructure that supports aging refugees or immigrants must include a remarkably different set of parameters than one designed to support native‐born elders.
The Role of Discipline in Hutterite Child Rearing
Authors: Smith Suzanne R. , Ingoldsby Bron
Published: February 2009

The Hutterian Brethren are an Anabaptist religious group who live communally and have flourished since coming to North America in the 1870s. Colony life is structured so as to resist the modernizing influences of the greater society and to instill conformity to traditional values and behaviors in their children. The authors examine the role of discipline in the child‐rearing behaviors of the Hutterites over time in the context of overall family change in recent years via qualitative ethnography. The Hutterites have only been able to slow the rate of change but not to completely avoid the values and practices of the outside culture. Generational changes in parental discipline, and what that means for the Hutterites, is discussed.
The Limits of Regional Data Sharing and Regional Problem Solving
Authors: Boba Rachel , Weisburd David , Meeker James W.
Published: February 2009

This article examines regional data sharing for regional problem solving, drawing on the process evaluation findings of the East Valley, California COMPASS. The findings confirm prior research of regional data-sharing difficulties, such as technological and database expertise and participation. Our study points to more fundamental limitations of regional data-sharing development for regional problem solving. Problems in many communities are simply local phenomena that may not be aided by a regional approach. Consequently, the development of a data system for regional problem solving ignores the specific nature of problems and the practical barriers inherent to accessing diverse databases. We agree that regional data sharing is important, but may be better tailored toward sharing data for short-term tactical purposes (e.g., pattern analysis) or for simply identifying problems, the first step in the problem-solving process, regionally.
In situ scanning electron microscopy observation of fracture crack propagation in the welding interface between aluminium alloy and steel
Authors: Qiu R. , Iwamoto C. , Satonaka S.
Published: February 2009

Reaction products formed at the welding interface of aluminium/steel can deteriorate mechanical properties. It would therefore be quite beneficial to analyse the mechanism of crack propagation to obtain strong joints. In this study, we directly observed the fracture process of the aluminium/steel sample by in situ scanning electron microscopy. In situ observation revealed that the crack propagated in the reaction layer and aluminium, and that crack propagation was arrested by the interface between the reaction layer and steel.
Inconsistent wear behaviour of cryotreated tool steels: Role of mode and mechanism
Authors: Das D. , Dutta A. K. , Ray K. K.
Published: February 2009

This report aims to reveal the cause of wide variation in the reported degree of improvement in wear resistance of cryotreated tool steels. Sliding wear tests at different normal loads have been carried out on conventional and cryotreated AISI D2 steel specimens together with SEM examinations and EDX microanalyses of the surfaces and subsurfaces of the worn specimens and that of the generated debris. The obtained results reveal that when the modes and mechanisms of wear are similar for both types of specimens, mild oxidative at lower load or severe delaminative at higher load, the improvement in wear resistance is 1·6–2·2 times. At the intermediate load, the modes and mechanisms are dissimilar, and the observed improvement is as high as 53·2 times. The reported varied degree of improvement in wear resistance by cryotreatment has been attributed to the operating test conditions that govern the modes and mechanisms of wear.
Microstructure and mechanical properties of ZM6 magnesium alloy produced by extrusion of machined chips
Authors: Wen L. H. , Ji Z. S. , Xin M. D.
Published: February 2009

The microstructure and room temperature mechanical properties of a ZM6 magnesium alloy produced by extrusion of machined chips were investigated. The tensile properties of the material were evaluated for the magnesium alloy in a series of tempers, including as cast, cast-T6, as extruded, extruded-T4, extruded-T5 and extruded-T6 conditions. Refined grains and broken particles during hot extrusion were attained. All the extruded alloy tempers showed better tensile properties than the cast alloy. The extruded-T4 alloy exhibited the best elongation to failure. The aging treatment resulted in an increase in tensile yield strength and ultimate tensile strength because of the dispersive particles or the fine precipitates. The morphology of the fracture surfaces was examined using scanning electron microscope.
Distinctive localization and opposed roles of vasohibin-1 and vasohibin-2 in the regulation of angiogenesis
Authors: Kimura Hiroshi , Miyashita Hiroki , Suzuki Yasuhiro , Kobayashi Miho , Watanabe Kazuhide , Sonoda Hikaru , Ohta Hideki , Fujiwara Takashi , Shimosegawa Tooru , Sato Yasufumi
Published: February 2009

We recently isolated a novel angiogenesis inhibitor, vasohibin-1, and its homologue, vasohibin-2. In this study we characterize the role of these 2 molecules in the regulation of angiogenesis. In a mouse model of subcutaneous angiogenesis, the expression of endogenous vasohibin-1 was low in proliferating ECs at the sprouting front but high in nonproliferating endothelial cells (ECs) in the termination zone. In contrast, endogenous vasohibin-2 was preferentially expressed in mononuclear cells mobilized from bone marrow that infiltrated the sprouting front. When applied exogenously, vasohibin-1 inhibited angiogenesis at the sprouting front where endogenous vasohibin-1 was scarce but did not influence vascularity in the termination zone where endogenous vasohibin-1 was enriched. Exogenous vasohibin-2 prevented the termination of angiogenesis in the termination zone and increased vascularity in this region. Angiogenesis was persistent in the termination zone in the vasohibin-1 knockout mice, whereas angiogenesis was deficient at the sprouting front in the vasohibin-2 knockout mice. Supplementation of deficient proteins normalized the abnormal patterns of angiogenesis in the vasohibin knockout mice. These results indicate that vasohibin-1 is expressed in ECs in the termination zone to halt angiogenesis, whereas vasohibin-2 is expressed in infiltrating mononuclear cells in the sprouting front to promote angiogenesis.
Contribution of STAT3 and SMAD4 pathways to the regulation of hepcidin by opposing stimuli
Authors: Huang Hua , Constante Marco , Layoun Antonio , Santos Manuela M.
Published: February 2009

Hepcidin, a key regulator of iron metabolism, is a small antimicrobial peptide produced by the liver that regulates intestinal iron absorption and iron recycling by macrophages. Hepcidin is stimulated when iron stores increase and during inflammation and, conversely, is inhibited by hypoxia and augmented erythropoiesis. In many pathologic situations, such as in the anemia of chronic disease (ACD) and iron-loading anemias, several of these factors may be present concomitantly and may generate opposing signaling to regulate hepcidin expression. Here, we address the question of dominance among the regulators of hepcidin expression. We show that erythropoiesis drive, stimulated by erythropoietin but not hypoxia, down-regulates hepcidin in a dose-dependent manner, even in the presence of lipopolysaccharide (LPS) or dietary iron-loading, which may act additively. These effects are mediated through down-regulation of phosporylation of Stat3 triggered by LPS and of Smad1/5/8 induced by iron. In conclusion, hepcidin expression levels in the presence of opposing signaling are determined by the strength of the individual stimuli rather than by an absolute hierarchy among signaling pathways. Our findings also suggest that erythropoietic drive can inhibit both inflammatory and iron-sensing pathways, at least in part, via the suppression of STAT3 and SMAD4 signaling in vivo.
MytiBase: a knowledgebase of mussel (M. galloprovincialis) transcribed sequences
Authors: Venier Paola , De Pittà Cristiano , Bernante Filippo , Varotto Laura , De Nardi Barbara , Bovo Giuseppe , Roch Philippe , Novoa Beatriz , Figueras Antonio , Pallavicini Alberto , Lanfranchi Gerolamo
Published: February 2009

Background

Although Bivalves are among the most studied marine organisms due to their ecological role, economic importance and use in pollution biomonitoring, very little information is available on the genome sequences of mussels. This study reports the functional analysis of a large-scale Expressed Sequence Tag (EST) sequencing from different tissues ofMytilus galloprovincialis(the Mediterranean mussel) challenged with toxic pollutants, temperature and potentially pathogenic bacteria.

Results

We have constructed and sequenced seventeen cDNA libraries from different Mediterranean mussel tissues: gills, digestive gland, foot, anterior and posterior adductor muscle, mantle and haemocytes. A total of 24,939 clones were sequenced from these libraries generating 18,788 high-quality ESTs which were assembled into 2,446 overlapping clusters and 4,666 singletons resulting in a total of 7,112 non-redundant sequences. In particular, a high-quality normalized cDNA library (Nor01) was constructed as determined by the high rate of gene discovery (65.6%). Bioinformatic screening of the non-redundantM. galloprovincialissequences identified 159 microsatellite-containing ESTs. Clusters, consensuses, related similarities and gene ontology searches have been organized in a dedicated, searchable databasehttp://mussel.cribi.unipd.it.

Conclusion

We defined the first species-specific catalogue ofM. galloprovincialisESTs including 7,112 unique transcribed sequences. Putative microsatellite markers were identified. This annotated catalogue represents a valuable platform for expression studies, marker validation and genetic linkage analysis for investigations in the biology of Mediterranean mussels.
Three LIF-dependent signatures and gene clusters with atypical expression profiles, identified by transcriptome studies in mouse ES cells and early derivatives
Authors: Trouillas Marina , Saucourt Claire , Guillotin Bertrand , Gauthereau Xavier , Ding Li , Buchholz Frank , Doss Michael Xavier , Sachinidis Agapios , Hescheler Jurgen , Hummel Oliver , Huebner Norbert , Kolde Raivo , Vilo Jaak , Schulz Herbert , Bœuf Hélène
Published: February 2009

Background

Mouse embryonic stem (ES) cells remain pluripotentin vitrowhen grown in the presence of the cytokine Leukaemia Inhibitory Factor (LIF). Identification of LIF targets and of genes regulating the transition between pluripotent and early differentiated cells is a critical step for understanding the control of ES cell pluripotency.

Results

By gene profiling studies carried out with mRNAs from ES cells and their early derivatives treated or not with LIF, we have identified i) LIF-dependent genes, highly expressed in pluripotent cells, whose expression level decreases sharply upon LIF withdrawal [Plurigenes], ii) LIF induced genes [Lifindgenes] whose expression is differentially regulated depending upon cell context and iii) genes specific to the reversible or irreversible committed states. In addition, by hierarchical gene clustering, we have identified, among eight independent gene clusters, two atypical groups of genes, whose expression level was highly modulated in committed cells only. Computer based analyses led to the characterization of different sub-types ofPluriandLifindgenes, and revealed their differential modulation byOct4orNanogmaster genes. Individual knock down of a selection ofPluriandLifindgenes leads to weak changes in the expression of early differentiation markers, in cell growth conditions in which these master genes are still expressed.

Conclusion

We have identified different sets of LIF-regulated genes depending upon the cell state (reversible or irreversible commitment), which allowed us to present a novel global view of LIF responses. We are also reporting on the identification of genes whose expression is strictly regulated during the commitment step. Furthermore, our studies identify sub-networks of genes with a restricted expression in pluripotent ES cells, whose down regulation occurs while the master knot (composed of OCT4, SOX2 and NANOG) is still expressed and which might be down-regulated together for driving cells towards differentiation.
Dynamic evolution of V1R putative pheromone receptors between Mus musculus and Mus spretus
Authors: Kurzweil Vanessa C , Getman Mike ,   NISC Comparative Sequencing Program, Green Eric D , Lane Robert P
Published: February 2009

Background

The mammalian vomeronasal organ (VNO) expresses two G-protein coupled receptor gene families that mediate pheromone responses, the V1R and V2R receptor genes. In rodents, there are ~150 V1R genes comprising 12 subfamilies organized in gene clusters at multiple chromosomal locations. Previously, we showed that several of these subfamilies had been extensively modulated by gene duplications, deletions, and gene conversions around the time of the evolutionary split of the mouse and rat lineages, consistent with the hypothesis that V1R repertoires might be involved in reinforcing speciation events. Here, we generated genome sequence for one large cluster containing two V1R subfamilies in Mus spretus, a closely related and sympatric species to Mus musculus, and investigated evolutionary change in these repertoires along the two mouse lineages.

Results

We describe a comparison of spretus and musculus with respect to genome organization and synteny, as well as V1R gene content and phylogeny, with reference to previous observations made between mouse and rat. Unlike the mouse-rat comparisons, synteny seems to be largely conserved between the two mouse species. Disruption of local synteny is generally associated with differences in repeat content, although these differences appear to arise more from deletion than new integrations. Even though unambiguous V1R orthology is evident, we observe dynamic modulation of the functional repertoires, with two of seven V1Rb and one of eleven V1Ra genes lost in spretus, two V1Ra genes becoming pseudogenes in musculus, two additional orthologous pairs apparently subject to strong adaptive selection, and another divergent orthologous pair that apparently was subjected to gene conversion.

Conclusion

Therefore, eight of the 18 (~44%) presumptive V1Ra/V1Rb genes in the musculus-spretus ancestor appear to have undergone functional modulation since these two species diverged. As compared to the rat-mouse split, where modulation is evident by independent expansions of these two V1R subfamilies, divergence between musculus and spretus has arisen more by mutations within coding sequences. These results support the hypothesis that adaptive changes in functional V1R repertoires contribute to the delineation of very closely related species.
Exploring and dissecting genome-wide gene expression responses of Penicillium chrysogenum to phenylacetic acid consumption and penicillinG production
Authors: Harris Diana M , van der Krogt Zita A , Klaassen Paul , Raamsdonk Leonie M , Hage Susanne , van den Berg Marco A , Bovenberg Roel AL , Pronk Jack T , Daran Jean-Marc
Published: February 2009

Background

Since the discovery of the antibacterial activity of penicillin by Fleming 80 years ago, improvements of penicillin titer were essentially achieved by classical strain improvement through mutagenesis and screening. The recent sequencing of Penicillium chrysogenum strain Wisconsin1255-54 and the availability of genomics tools such as DNA-microarray offer new perspective.

Results

In studies on β-lactam production by P. chrysogenum, addition and omission of a side-chain precursor is commonly used to generate producing and non-producing scenarios. To dissect effects of penicillinG production and of its side-chain precursor phenylacetic acid (PAA), a derivative of a penicillinG high-producing strain without a functional penicillin-biosynthesis gene cluster was constructed. In glucose-limited chemostat cultures of the high-producing and cluster-free strains, PAA addition caused a small reduction of the biomass yield, consistent with PAA acting as a weak-organic-acid uncoupler. Microarray-based analysis on chemostat cultures of the high-producing and cluster-free strains, grown in the presence and absence of PAA, showed that: (i) Absence of a penicillin gene cluster resulted in transcriptional upregulation of a gene cluster putatively involved in production of the secondary metabolite aristolochene and its derivatives, (ii) The homogentisate pathway for PAA catabolism is strongly transcriptionally upregulated in PAA-supplemented cultures (iii) Several genes involved in nitrogen and sulfur metabolism were transcriptionally upregulated under penicillinG producing conditions only, suggesting a drain of amino-acid precursor pools. Furthermore, the number of candidate genes for penicillin transporters was strongly reduced, thus enabling a focusing of functional analysis studies.

Conclusion

This study demonstrates the usefulness of combinatorial transcriptome analysis in chemostat cultures to dissect effects of biological and process parameters on gene expression regulation. This study provides for the first time clear-cut target genes for metabolic engineering, beyond the three genes of the β-lactam pathway.
Characterisation of porin genes from Mycobacterium fortuitumand their impact on growth
Authors: Sharbati Soroush , Schramm Kira , Rempel Sonja , Wang Hwa , Andrich Ronny , Tykiel Verena , Kunisch Ralph , Lewin Astrid
Published: February 2009

Background

Highly pathogenic mycobacteria like Mycobacterium tuberculosis are characterised by their slow growth and their ability to reside and multiply in the very hostile phagosomal environment and a correlation between the growth rate of mycobacteria and their pathogenicity has been hypothesised. Here, porin genes from M. fortuitum were cloned and characterised to address their impact on the growth rate of fast-growing and pathogenic mycobacteria.

Results

Two genes encoding porins orthologous to MspA from M. smegmatis, porM1 and porM2, were cloned from M. fortuitum strains, which were originally isolated from human patients. Both porin genes were at least partially able to complement the mutations of a M. smegmatis mutant strain lacking the genes mspA and mspC with respect to the growth rate. PorM1 and porM2 were present in different strains of M. fortuitum including the type strain. Comparative expression analysis of porM genes revealed divergent porin expression among analysed M. fortuitum strains. Repression of the expression of porins by antisense technique decreased the growth rates of different M. fortuitum. The effects of over-expression of porM1 as well as porM2 varied depending on the strain and the concentration of antibiotic added to the medium and indicated that PorM1 and PorM2 enhance the growth of M. fortuitum strains, but also the diffusion of the antibiotic kanamycin into the cells.

Conclusion

This study demonstrates the important role of porin expression in growth as well as antibiotic susceptibility of the opportunistic bacterium M. fortuitum.
Influence of vector design and host cell on the mechanism of recombination and emergence of mutant subpopulations of replicating retroviral vectors
Authors: Paar Matthias , Klein Dieter , Salmons Brian , Günzburg Walter H , Renner Matthias , Portsmouth Daniel
Published: February 2009

Background

The recent advent of murine leukaemia virus (MLV)-based replication-competent retroviral (RCR) vector technology has provided exciting new tools for gene delivery, albeit the advances in vector efficiency which have been realized are also accompanied by a set of fresh challenges. The expression of additional transgene sequences, for example, increases the length of the viral genome, which can lead to reductions in replication efficiency and in turn to vector genome instability. This necessitates efforts to analyse the rate and mechanism of recombinant emergence during the replication of such vectors to provide data which should contribute to improvements in RCR vector design.

Results

In this study, we have performed detailed molecular analyses on packaged vector genomes and proviral DNA following propagation of MLV-based RCR vectors both in cell culture and in pre-formed subcutaneous tumours in vivo. The effects of strain of MLV, transgene position and host cell type on the rate of emergence of vector recombinants were quantitatively analysed by applying real-time PCR and real-time RT-PCR assays. Individual mutants were further characterized by PCR, and nucleotide sequence and structural motifs associated with these mutants were determined by sequencing. Our data indicate that virus strain, vector design and host cell influence the rate of emergence of predominating vector mutants, but not the underlying recombination mechanisms in vitro. In contrast, however, differences in the RNA secondary structural motifs associated with sequenced mutants emerging in cell culture and in solid tumours in vivo were observed.

Conclusion

Our data provide further evidence that MLV-based RCR vectors based on the Moloney strain of MLV and containing the transgene cassette in the 3' UTR region are superior to those based on Akv-MLV and/or containing the transgene cassette in the U3 region of the LTR. The observed discrepancies between the data obtained in solid tumours in vivo and our own and previously published data from infected cells in vitro demonstrates the importance of evaluating vectors designed for use in cancer gene therapy in vivo as well as in vitro.
A semiparametric Bayesian proportional hazards model for interval censored data with frailty effects
Authors: Henschel Volkmar , Engel Jutta , Hölzel Dieter , Mansmann Ulrich
Published: February 2009

Background

Multivariate analysis of interval censored event data based on classical likelihood methods is notoriously cumbersome. Likelihood inference for models which additionally include random effects are not available at all. Developed algorithms bear problems for practical users like: matrix inversion, slow convergence, no assessment of statistical uncertainty.

Methods

MCMC procedures combined with imputation are used to implement hierarchical models for interval censored data within a Bayesian framework.

Results

Two examples from clinical practice demonstrate the handling of clustered interval censored event times as well as multilayer random effects for inter-institutional quality assessment. The software developed is called survBayes and is freely available at CRAN.

Conclusion

The proposed software supports the solution of complex analyses in many fields of clinical epidemiology as well as health services research.
Genetic analysis of the vitamin D receptor gene in two epithelial cancers: melanoma and breast cancer case-control studies
Authors: Barroso Eva , Fernandez Lara P , Milne Roger L , Pita Guillermo , Sendagorta Elena , Floristan Uxua , Feito Marta , Aviles Jose A , Martin-Gonzalez Manuel , Arias Jose I , Zamora Pilar , Blanco Monserrat , Lazaro Pablo , Benitez Javier , Ribas Gloria
Published: February 2009

Background

Vitamin D serum levels have been found to be related to sun exposure and diet, together with cell differentiation, growth control and consequently, cancer risk. Vitamin D receptor (VDR) genotypes may influence cancer risk; however, no epidemiological studies in sporadic breast cancer (BC) or malignant melanoma (MM) have been performed in a southern European population. In this study, the VDR gene has been evaluated in two epithelial cancers BC and MM.

Methods

We have conducted an analysis in 549 consecutive and non-related sporadic BC cases and 556 controls, all from the Spanish population, and 283 MM cases and 245 controls. Genotyping analyses were carried out on four putatively functional SNPs within the VDR gene.

Results

An association with the minor allele A of the non-synonymous SNP rs2228570 (rs10735810, FokI, Met1Thr) was observed for BC, with an estimated odds ratio (OR) of 1.26 (95% CI = 1.02–1.57; p = 0.036). The synonymous variant rs731236 (TaqI) appeared to be associated with protection from BC (OR = 0.80, 95%CI = 0.64–0.99; p = 0.047). No statistically significant associations with MM were observed for any SNP. Nevertheless, sub-group analyses revealed an association between rs2228570 (FokI) and absence of childhood sunburns (OR = 0.65, p = 0.003), between the 3'utr SNP rs739837 (BglI) and fair skin (OR = 1.31, p = 0.048), and between the promoter SNP rs4516035 and the more aggressive tumour location in head-neck and trunk (OR = 1.54, p = 0.020).

Conclusion

In summary, we observed associations between SNPs in the VDR gene and BC risk, and a comprehensive analysis using clinical and tumour characteristics as outcome variables has revealed potential associations with MM. These associations required confirmation in independent studies.
The impact of demographic and risk factor changes on coronary heart disease deaths in Beijing, 1999–2010
Authors: Cheng Jun , Zhao Dong , Zeng Zhechun , Critchley Julia Alison , Liu Jing , Wang Wei , Sun Jiayi , Capewell Simon
Published: February 2009

Background

Recent, dramatic increases in coronary heart disease (CHD) mortality in China can be mostly explained by adverse changes in major cardiovascular risk factors. Our study aimed to assess the potential impact of subsequent changes in risk factors and population ageing on CHD deaths in Beijing between 1999 and 2010.

Methods

The previously validated IMPACT model was used to estimate the CHD deaths expected in 2010, with treatment uptakes being held constant at levels measured in 1999, comparing three scenarios: a) taking into account the ageing of the population but assuming no further changes in major risk factor levels from 1999 or, b) if recent risk factor trends continued until 2010 or, c) if there was a 0.5% annual reduction in each risk factor.

Results

Population ageing alone would result in approximately 1990 additional deaths in 2010 compared with 1999, representing an increase of 27%. Continuation of current risk factor trends would result in approximately 3,015 extra deaths in 2010, [a 40% increase]; three quarters of this increase would be attributable to rises in total cholesterol levels. Thus, demographic changes and worsening risk factors would together result in a 67% increase in CHD deaths. Conversely, assumed 0.5% annual reductions in risk factors (a mean population level decline of 0.3 mmol/L for total cholesterol in both genders, and smoking prevalence declining by 3.0% for men and 4.1% for women, body mass index by 1.3 kg/m2 for men and 1.4 kg/m2 for women, diabetes prevalence by 0.4% in both genders, and diastolic blood pressure by 4.7 mmHg for men and 4.4 mmHg for women) would result in some 3,730 fewer deaths, representing a 23% decrease overall. These findings remained consistent in sensitivity analyses.

Conclusion

CHD death rates are continuing to rise in Beijing. This reflects worsening risk factor levels, compounded by demographic trends. However, the adverse impact of population ageing on CHD burden could be completely offset by eminently feasible improvements in diet and smoking.
Simple high-cell density fed-batch technique for high-level recombinant protein production with Pichia pastoris: Application to intracellular production of Hepatitis B surface antigen
Authors: Gurramkonda Chandrasekhar , Adnan Ahmad , Gäbel Thomas , Lünsdorf Heinrich , Ross Anton , Nemani Satish Kumar , Swaminathan Sathyamangalam , Khanna Navin , Rinas Ursula
Published: February 2009

Background

Hepatitis B is a serious global public health concern. Though a safe and efficacious recombinant vaccine is available, its use in several resource-poor countries is limited by cost. We have investigated the production of Hepatitis B virus surface antigen (HBsAg) using the yeast Pichia pastoris GS115 by inserting the HBsAg gene into the alcohol oxidase 1 locus.

Results

Large-scale production was optimized by developing a simple fed-batch process leading to enhanced product titers. Cells were first grown rapidly to high-cell density in a batch process using a simple defined medium with low salt and high glycerol concentrations. Induction of recombinant product synthesis was carried out using rather drastic conditions, namely through the addition of methanol to a final concentration of 6 g L-1. This methanol concentration was kept constant for the remainder of the cultivation through continuous methanol feeding based on the on-line signal of a flame ionization detector employed as methanol analyzer in the off-gas stream. Using this robust feeding protocol, maximum concentrations of ~7 grams HBsAg per liter culture broth were obtained. The amount of soluble HBsAg, competent for assembly into characteristic virus-like particles (VLPs), an attribute critical to its immunogenicity and efficacy as a hepatitis B vaccine, reached 2.3 grams per liter of culture broth.

Conclusion

In comparison to the highest yields reported so far, our simple cultivation process resulted in an ~7 fold enhancement in total HBsAg production with more than 30% of soluble protein competent for assembly into VLPs. This work opens up the possibility of significantly reducing the cost of vaccine production with implications for expanding hepatitis B vaccination in resource-poor countries.