bluuebunny/crossref_metadata_2025 huggingface dataset:
Dis-embedding Health Care
Authors: Wilson Caroline
Published: April 2009

From the early 1990s, so-called ‘five-star’ hospitals have sprouted up in small towns and cities across the state of Kerala, South India. Equipped with expensive diagnostic technologies and super-specialist consultants, these institutions are now leading players in the vibrant local health care economy. Markets in health are often understood to increase inequalities by creating a two-tier system of provision for the rich and the poor (for example, Johnson 1995). This paper examines how the processes of marketisation have significantly increased the cost of treatment across the public and private health care systems. It contrasts earlier approaches to corruption in medicine that emphasised the over-use or misuse of technologies (Yesudian 1994) to contemporary Kerala, in which technology has become an important value in everyday medical practice. As a result of growing competition and income aspirations, the health care system is gradually being decoupled from local cost considerations, while doctors and private hospitals are increasingly viewed as exploitative and lacking in moral legitimacy.
‘There is Peace Here’
Authors: Heitmeyer Carolyn
Published: April 2009

This article describes the relations between Hindus and Muslims in a small town in central Gujarat following the massive violence against the Muslim minority community throughout many parts of the state between February and May 2002. While the ‘communal divide’ has become more pronounced following the 2002 attacks in many parts of the state as well as in the town in which the research was conducted, concerted efforts are made by members of both communities as a means of re-imposing a sense of ‘everyday peace’. As such, normative discourses presenting the 2002 violence as an aberration with respect to the state of local communal relations in the town represent a collective strategy of containing the tension and mutual suspicion which remain constant undercurrents in daily life. This article, moreover, explores the ongoing caste– and class-based social networks and interactions underlying public declarations of ‘everyday peace’ which have played a central role in, if not averting violence altogether, discouraging the development of further communal segregation and division in the aftermath of the 2002 attacks in the town.
A Pyramidal Modeling Scheme for Laminates - Identification of Transverse Cracking
Authors: Lubineau G.
Published: April 2009

Modern approaches to the modeling of composites are no longer limited to the use of a single approach for the whole structure or for all the degradation mechanisms. On the contrary, modern advances enable the definition of truly multiscale models in order to describe the degradation. Thus, homogenized models can be rigorously deduced from the underlying micromechanics. In the past few years, LMT-Cachan has made a number of contributions to the three key points of these multiscale approaches: (1) the improvement of the reference model on the fine scale, (2) the definition of a controlled correspondence between the scales, and (3) the definition of the associated homogenized model. Here, the complete approach is formalized as a modeling pyramid. Each mechanism of degradation is described on the more relevant scale within an ‘hybrid micromechanical model’. Based on the reference modeling, constitutive laws can be transfered within the unique framework of damage mechanics for being applied within commercial softwares. As an illustration, we focus more specifically on the homogenized law obtained for transverse cracking. The constitutive law and the material parameters issued from the homogenization, which define the model on the higher scale, are reviewed. Their identification is studied in detail. An important key point of the pyramidal approach appears here. Since it allows the interpretation of every quantity on different scales (both at the micromechanical and at the mesomechanical scales), the most relevant scale can be used for the identification of a chosen property. We limit ourselves to a ‘classical’ identification. We mean by classical identification a procedure based on straight specimens. This process, to a certain extent, uses a parametric simulation of the nonlinear model based on a finite element representation of the test samples. The complete model is then used for the simulation of an industrial sample with hole. That example emphasizes the interest of underlying micromechanial variables for experimental validation.
Continuum Models of Ductile Fracture: A Review
Authors: Besson J.
Published: April 2009

The past 20 years have seen substantial work on the modeling of ductile damage and fracture. Several factors explain this interest. (i) There is a growing demand to provide tools which allow to increase the efficiency of structures (reduce weight, increase service temperature or load, etc.) while keeping or increasing safety. This goal is indeed first achieved by using better materials but also by improving design tools. Better tools have been provided which consist (ii) of material constitutive equations integrating a physically-based description of damage processes and (iii) of better numerical tools which allow to use the improved constitutive equations in structural computations which become more and more realistic. This article reviews the material constitutive equations and computational tools, which have been recently developed to simulate ductile rupture.
Electric Delayed Fracture and Localized Polarization Switching of Cracked Piezoelectric Ceramics in Three-point Bending
Authors: Narita Fumio , Shindo Yasuhide , Hirama Mitsuru
Published: April 2009

This article discusses the delayed fracture and localized polarization switching near a crack tip in three-point bending piezoceramics under electromechanical loading. We have used finite element analysis to study delayed fracture experiments with single-edge precracked-beam method. A nonlinear finite element analysis was employed to calculate the fracture mechanics parameters such as energy release rate for the permeable, impermeable, and open crack face boundary conditions. Recent proposed energetically consistent boundary conditions were also considered. The effects of applied electric field and localized polarization switching on the fracture mechanics parameters were then examined.
Computational Evaluation of Elasto-Viscoplastic Deformation and Strength of Rubber Blended Semi-crystalline Polymer
Authors: Uchida Makoto , Tada Naoya , Tomita Yoshihiro
Published: April 2009

In order to clarify the elasto-viscoplastic deformation behavior and strength of rubber blended semi-crystalline polymer, micro- to mesoscopic mechanical behavior was modeled by using large deformation finite element homogenization method. In this model, dimension of mesostructure is identified by the volume fraction of interface region around the rubber particles. The effects of strain rate and the size of rubber particles on the mesoscopic true stress—strain relation, strain rate distribution in mesoscopic area, and change in mesoscopic morphology with deformation are investigated by numerical simulation of uniaxial tensile deformation of semi-crystalline polymer with nonuniformly distributed rubber particles. A series of computational simulations clarified that mechanical behavior of blend polymer is strongly affected by the size of rubber particles. Mesoscopic true stress—strain relationship shows softening for blend polymer with large rubber particles, which is closely related to the distribution of strain rate on mesoscopic scale. When the rubber particles are large, local strain rate is highly concentrated in the ligament area between adjacent rubber particles, while it distributes in larger area of semi-crystalline polymer matrix in case of small rubber particles. The difference in these localized deformation leads to characteristic change in the size and shape of rubber particles with straining. Nonuniform deformation in mesoscopic area caused by heterogeneous rubber particle distribution is emphasized by high strain rate and large rubber particles. Furthermore, maximum mean stress generated in semi-crystalline polymer matrix is very high when the size of rubber particles is smaller than or ligament thickness is larger than a specific value. The specific thickness corresponds to the critical value for brittle-ductile transition of rubber blended semi-crystalline polymer obtained by impact test.
Elastic-plastic Behavior of WC-Co Cemented Carbide Used for Forging Tool Considering Anisotropic Damage and Stress Unilaterality
Authors: Hayakawa Kunio , Nakamura Tamotsu , Tanaka Shigekazu
Published: April 2009

Elastic—plastic constitutive equation of hard metal for cold forging tools such as WC-Co cemented carbide with anisotropic damage is proposed to predict a precise service life of cold forging tools. A second rank symmetric damage tensor is introduced in order to express the anisotropic material damage and damage-induced stress unilaterality, namely a salient difference in uniaxial behavior between tension and compression. The conventional framework of irreversible thermodynamics is used to derive the constitutive equation. The Gibbs potential is formulated as a function of stress tensor, damage tensor, isotropic hardening variable, and kinematic hardening variable tensor. The elastic-damage constitutive equation, conjugate forces of damage, isotropic hardening, and kinematic hardening variable is derived from the potential. For the kinematic hardening variable, the superposition of three kinematic hardening laws is employed in order to improve the cyclic behavior of the material. For the evolution equation of the damage tensor, the damage is assumed to progress by fracture of the Co matrix—WC particle interface and by the mechanism of fatigue, i.e., the accumulation of microscopic plastic strain in matrix and particles. By using the constitutive equations, calculation of uniaxial tensile, and compressive test is performed and the results are compared with the experimental ones in the literature. Furthermore, finite element analysis on the behavior of cemented carbide as a die-insert of cold forward extrusion die set was carried out. The proposed constitutive equation was implemented to commercial FE software MSC.Marc2005 using User Subroutines. It is found that the anisotropic damage component can describe the different failure modes of the die-insert, namely fatigue crack and forced rupture.
Development and Criterion Validity of Differentiated and Elevated Vocational Interests in Adolescence
Authors: Hirschi Andreas
Published: April 2009

Interest differentiation and elevation are supposed to provide important information about a person’s state of interest development, yet little is known about their development and criterion validity. The present study explored these constructs among a group of Swiss adolescents. Study 1 applied a cross-sectional design with 210 students in 11th grade. Study 2 applied a 1-year longitudinal design with 289 students in 7th to 8th grade. Gender, personality traits, and career exploration were significant predictors of state and development of differentiation and elevation. Increase in differentiation predicted increase in career decidedness above traits. Elevation could not predict increase in exploration behavior over traits. The results provide support for differentiation and elevation as important aspects of adolescents’ vocational interests.
Medical and Dental Care Utilization and Expenditures Under Medicaid and Private Health Insurance
Authors: Ku Leighton
Published: April 2009

Data from the 2005 Medical Expenditure Panel Survey were used to conduct a disaggregated comparison of utilization and expenditures under Medicaid and private health insurance for low-income adults and children. After adjustment for health status and other factors, Medicaid adults and children had greater use of prescription drugs than the privately insured, but there were no significant differences in prescription expenditures. Adults on Medicaid had lower utilization of office-based medical and dental care and much lower expenditures than the privately insured. Contrary to stereotypes, there were no significant differences between Medicaid adults and children and the privately insured in emergency, outpatient, or inpatient hospital use, and the former had significantly lower expenditures.
Awareness and Knowledge of Andropause Among Chinese Males in Hong Kong
Authors: Yuk Yee Yan
Published: April 2009

This is a pilot study that explored the awareness and knowledge of andropause among Chinese males in Hong Kong. The study employed a structured questionnaire and a convenience sample of 500 individuals at the age ≥40 years participated in the survey. A total of 397 (79.4%) of the respondents were identified as andropause-enlightened, 88.2% of whom believed that andropause was a natural aging process. Mass media was the main source of andropausal information. The andropause-enlightened respondents had poor knowledge with the mean knowledge score of 5.94. The majority identified irritability (72.5%), loss of energy (66.5%), and loss of libido (60.7%) as symptoms. Less than half of the andropause-enlightened respondents expressed that andropause could be treated and only 34 knew testosterone replacement therapy as a treatment. The present findings underscore the need for provision of health education to increase the knowledge of andropause among adult males.
Sedaghatian Type of Spondylometaphyseal Dysplasia and Concurrent Anomalies
Authors: Witters Ingrid , Moerman Philippe , Catte Luc De , Jean-Pierre Fryns
Published: April 2009

To date 16 cases of Sedaghatian type of spondylometaphyseal dysplasia have been reported mainly in the neonatal period. We report on a female fetus with increased nuchal thickness at 12 weeks and Sedaghatian type of spondylometaphyseal dysplasia with absence of the corpus callosum and pachygyria at 18 weeks of gestation. A follow-up ultrasound at 18 weeks was performed due to the increased nuchal thickness with normal karyotype; rhizomelic shortening of the long bones, a small fetal thorax and cerebral ventriculomegaly were present. Pathological examination revealed Sedaghatian type of spondylometaphyseal dysplasia with pachygyria and absence of the corpus callosum. To our knowledge, this is the earliest diagnosis of Sedaghatian type of spondylometaphyseal dysplasia with absence of the corpus callosum and the first reported case with increased nuchal thickness.
The Characteristics and Applications of Metamaterials
Authors: Wright Derek W , Cobbold Richard S C
Published: April 2009

The past 10 years have seen remarkable developments in microwave, optical and acoustic methods that make use of the unique wave transmission properties of a class of ordered composites known as metamaterials. These materials differ from regular materials in that wave propagation is dramatically affected by the size and arrangement of their small-scale structure, and not just by the choice of constituent materials. Their characteristic feature sizes can be much less than, or on the same order as a wavelength. They have a variety of potential applications ranging from super-lenses, to enabling subwavelength imaging resolution, to the creation of a Harry Potter-like ‘invisibility cloak’. In this review we provide an overview of some of these achievements, much of which has been proposed and demonstrated with optical and electromagnetic waves. However, more recently these ideas have been extended to acoustic waves, offering the opportunity of controlling ultrasound wave propagation in a unique manner.
Sub-involution of Placental Site After First Trimester Miscarriage: Sonographic Appearances and A New Approach to Management
Authors: Arora Suruchi , Williams Roger M , Torrie Peter , Gibson M , Musa Fawaz
Published: April 2009

Delayed postpartum bleeding can be caused by retained products of conception (RPOC), secondary infection, or more unusually, by sub-involution of placental site. Sub-involution of placental site is suspected when there is delayed onset, abrupt and heavy uterine bleeding in the absence of RPOC following a delivery or miscarriage. It is a histologic diagnosis and imaging and other investigations have not been reported to help in diagnosing this condition. We report the sonographic findings in a patient who was later diagnosed, histologically, to have placental site sub-involution. Also, we report a new approach to managing the condition by embolising the uterine arteries before undertaking evacuation of uterus.
Umbilical Cord Anomalies
Authors: Ashington Gail
Published: April 2009

Cord cysts are a rare occurrence and are usually insignificant to the pregnancy if an isolated finding. True cysts have an epithelial lining and may represent a remnant of the allantois during cord formation1 Cysts can reach several centimeters in diameter and maybe detected in the first trimester.2 Pseuodocysts represent embryological remnant or cystic degeneration of Wharton's jelly that surrounds the cord and have no epithelial lining.1 They can be seen as multiple masses and are associated with aneuploidy. Other more rare cord anomalies are tumours, such as teratomas originating from germ cells. Angiomyxoma is a tumour deriving from abnormal vascularisation of the cord, emanating from the umbilical arteries. Cord compression from these masses means that there can be serious complications in pregnancy.3 Haematomas are rare in pregnancies that have not had intervention such as amniocentesis or fetal cord sampling. A mass can be demonstrated with internal echoes. Even more rare is the ompahlomesenteric cyst, an enteric lined cyst that connects with the Meckel's diverticulum. Allantoic cysts are where remnants of the communication between the bladder and cord still exist. Extravasation of the bladder into the cord creates a cyst. These cysts are often seen in connection with urinary tract anomalies and can sometimes be identified if the connection between the cord and bladder is present.4
Diagnosis of An Interstitial Ectopic Pregnancy with Two-Dimensional Transvaginal Sonography
Authors: Peel Alison
Published: April 2009

Interstitial ectopic pregnancy is a medical emergency affecting women of reproductive age. Its presentation is late and is often misinterpreted as early miscarriage. If undiagnosed and allowed to progress to a significant gestation, rupture will occur with devastating maternal consequences. There are several treatment options available depending on a number of clinical factors; surgical, medical and expectant management. The most significant outcome is from early treatment, resulting in reduced maternal morbidity and preservation of fertility. The key to successful treatment is early detection. Ultrasound plays a major role in detection of this life threatening condition.
Assessment and Localisation of Response to Primary Systemic Therapy in Breast Cancer
Authors: Noble Frith
Published: April 2009

Primary systemic therapy (PST) is used in non-metastatic breast cancer to decrease tumour size and reduce the extent of surgery. This article reviews imaging and surgical issues associated with the increasing use of PST in the management of breast cancer. The role of imaging, with a special focus on ultrasound, is evaluated.
Incidental Splenic Cyst Simulating A Supernumerary Kidney
Authors: Christie Andrew
Published: April 2009

This case represents an incidental splenic cyst misinterpreted as a supernumerary kidney, resulting in a computed tomography scan to confirm the ultrasound (US) findings. A 55-year-old man presenting with renal failure had an US examination which showed a mass adjacent to the left kidney. It resembled a kidney with a dilated collecting system rather than a spleen. Supernumerary kidneys are extremely rare in the published literature. Splenic cysts are more common, but are still relatively unusual. The possible diagnoses and US findings in splenic cysts are discussed.
Ultrasound Evaluation of Stem Cell Treated Tendon Injuries in the Horse: Repair or Regeneration?
Authors: Avella Charlotte S , Smith Roger K
Published: April 2009

Ultrasonography is widely used in the diagnosis and monitoring of equine tendon injuries. More recently it has been used to perform ultrasound guided intra-lesional administration of growth factor and cell based therapies including autologus bone marrow derived mesenchymal stem cells (BM-MSCs). Re-injury rates in horses following tendon injury are high with conventional treatment, however the use of BM-MSCs has resulted in a significant reduction in tendon re-injury in National Hunt racehorses. This article reviews the methods of tendon ultrasound used in the horse and the techniques used for BM-MSC therapy to treat tendon injury.
Deformation twinning in zircaloy 2
Authors: Sahoo S. K. , Hiwarkar V. D. , Samajdar I. , Pant P. , Dey G. K. , Srivastav D. , Tewari R. , Banerjee S.
Published: April 2009

Fully recrystallised zircaloy 2 samples were subjected to different degrees of uniaxial compression. Grains of high Taylor factors showed {1012}〈1011〉 deformation twins, noticeable up to 13–16% compression. Twinning strongly affected the crystallographic texture and also brought in clear differences in stored energy and residual stress between the suspected parent and product grains/orientations of twinning. At later stages of deformation, where presence of twinning was insignificant, aforementioned heterogeneity was further supplemented by heterogeneity in microstructure – clear presence of fragmenting and non-fragmenting grains. Direct observations on twin fraction, twin deviation and twin continuity had shown an apparent peak in twinning by ∼7·5% compression, an observation explainable through a simple model of twin decay by in grain misorientation development.
Endobrevin/VAMP-8–dependent dense granule release mediates thrombus formation in vivo
Authors: Graham Gwenda J. , Ren Qiansheng , Dilks James R. , Blair Price , Whiteheart Sidney W. , Flaumenhaft Robert
Published: April 2009

Individuals whose platelets lack dense or α-granules suffer various degrees of abnormal bleeding, implying that granule cargo contributes to hemostasis. Despite these clinical observations, little is known regarding the effects of impaired platelet granule secretion on thrombus formation in vivo. In platelets, SNARE proteins mediate the membrane fusion events required for granule cargo release. Endobrevin/VAMP-8 is the primary vesicle-SNARE (v-SNARE) responsible for efficient release of dense and α-granule contents; thus, VAMP-8−/− mice are a useful model to evaluate the importance of platelet granule secretion in thrombus formation. Thrombus formation, after laser-induced vascular injury, in these mice is delayed and decreased, but not absent. In contrast, thrombus formation is almost completely abolished in the mouse model of Hermansky-Pudlak syndrome, ruby-eye, which lacks dense granules. Evaluation of aggregation of VAMP-8−/− and ruby-eye platelets indicates that defective ADP release is the primary abnormality leading to impaired aggregation. These results demonstrate the importance of dense granule release even in the earliest phases of thrombus formation and validate the distal platelet secretory machinery as a potential target for antiplatelet therapies.
Gene synteny comparisons between different vertebrates provide new insights into breakage and fusion events during mammalian karyotype evolution
Authors: Kemkemer Claus , Kohn Matthias , Cooper David N , Froenicke Lutz , Högel Josef , Hameister Horst , Kehrer-Sawatzki Hildegard
Published: April 2009

Background

Genome comparisons have made possible the reconstruction of the eutherian ancestral karyotype but also have the potential to provide new insights into the evolutionary inter-relationship of the different eutherian orders within the mammalian phylogenetic tree. Such comparisons can additionally reveal (i) the nature of the DNA sequences present within the evolutionary breakpoint regions and (ii) whether or not the evolutionary breakpoints occur randomly across the genome. Gene synteny analysis (E-painting) not only greatly reduces the complexity of comparative genome sequence analysis but also extends its evolutionary reach.

Results

E-painting was used to compare the genome sequences of six different mammalian species and chicken. A total of 526 evolutionary breakpoint intervals were identified and these were mapped to a median resolution of 120 kb, the highest level of resolution so far obtained. A marked correlation was noted between evolutionary breakpoint frequency and gene density. This correlation was significant not only at the chromosomal level but also sub-chromosomally when comparing genome intervals of lengths as short as 40 kb. Contrary to previous findings, a comparison of evolutionary breakpoint locations with the chromosomal positions of well mapped common fragile sites and cancer-associated breakpoints failed to reveal any evidence for significant co-location. Primate-specific chromosomal rearrangements were however found to occur preferentially in regions containing segmental duplications and copy number variants.

Conclusion

Specific chromosomal regions appear to be prone to recurring rearrangement in different mammalian lineages ('breakpoint reuse') even if the breakpoints themselves are likely to be non-identical. The putative ancestral eutherian genome, reconstructed on the basis of the synteny analysis of 7 vertebrate genome sequences, not only confirmed the results of previous molecular cytogenetic studies but also increased the definition of the inferred structure of ancestral eutherian chromosomes. For the first time in such an analysis, the opossum was included as an outgroup species. This served to confirm our previous model of the ancestral eutherian genome since all ancestral syntenic segment associations were also noted in this marsupial.
Two-stage genome-wide association study identifies integrin beta 5 as having potential role in bull fertility
Authors: Feugang Jean M , Kaya Abdullah , Page Grier P , Chen Lang , Mehta Tapan , Hirani Kashif , Nazareth Lynne , Topper Einko , Gibbs Richard , Memili Erdogan
Published: April 2009

Background

Fertility is one of the most critical factors controlling biological and financial performance of animal production systems and genetic improvement of lines. The objective of this study was to identify molecular defects in the sperm that are responsible for uncompensable fertility in Holstein bulls. We performed a comprehensive genome wide analysis of single nucleotide polymorphisms (SNP) for bull fertility followed by a second-stage replication in additional bulls for a restricted set of markers.

Results

In the Phase I association study, we genotyped the genomic sperm DNA of 10 low-fertility and 10 high-fertility bulls using Bovine SNP Gene Chips containing approximately 10,000 random SNP markers. In these animals, 8,207 markers were found to be polymorphic, 97 of which were significantly associated with fertility (p < 0.01). In the Phase II study, we tested the four most significant SNP from the Phase I study in 101 low-fertility and 100 high-fertility bulls, with two SNPs (rs29024867 and rs41257187) significantly replicated. Rs29024867 corresponds to a nucleotide change of C → G 2,190 bp 3' of the collagen type I alpha 2 gene on chromosome 4, while the rs41257187 (C → T) is in the coding region of integrin beta 5 gene on chromosome 1. The SNP rs41257187 induces a synonymous (Proline → Proline), suggesting disequilibrium with the true causative locus (i), but we found that the incubation of bull spermatozoa with integrin beta 5 antibodies significantly decreased the ability to fertilize oocytes. Our findings suggest that the bovine sperm integrin beta 5 protein plays a role during fertilization and could serve as a positional or functional marker of bull fertility.

Conclusion

We have identified molecular markers associated with bull fertility and established that at least one of the genes harboring such variation has a role in fertility. The findings are important in understanding mechanisms of uncompensatory infertility in bulls, and in other male mammals. The findings set the stage for more hypothesis-driven research aimed at discovering the role of variation in the genome that affect fertility and that can be used to identify molecular mechanisms of development.
A high resolution RH map of the bovine major histocompatibility complex
Authors: Brinkmeyer-Langford Candice L , Childers Christopher P , Fritz Krista L , Gustafson-Seabury Ashley L , Cothran Marian , Raudsepp Terje , Womack James E , Skow Loren C
Published: April 2009

Background

The cattle MHC is termed the bovine leukocyte antigen (BoLA) and, along with the MHCs of other ruminants, is unique in its genomic organization. Consequently, correct and reliable gene maps and sequence information are critical to the study of the BoLA region. The bovine genome sequencing project has produced two assemblies (Btau_3.1 and 4.0) that differ substantially from each other and from conventional gene maps in the BoLA region. To independently compare the accuracies of the different sequence assemblies, we have generated a high resolution map of BoLA using a 12,000rad radiation hybrid panel. Seventy-seven unique sequence tagged site (STS) markers chosen at approximately 50 kb intervals from the Btau 2.0 assembly and spanning the IIa-III-I and IIb regions of the bovine MHC were mapped on a 12,000rad bovine radiation hybrid (RH) panel to evaluate the different assemblies of the bovine genome sequence.

Results

Analysis of the data generated a high resolution RH map of BoLA that was significantly different from the Btau_3.1 assembly of the bovine genome but in good agreement with the Btau_4.0 assembly. Of the few discordancies between the RH map and Btau_4.0, most could be attributed to closely spaced markers that could not be precisely ordered in the RH panel. One probable incorrectly-assembled sequence and three missing sequences were noted in the Btau_4.0 assembly. The RH map of BoLA is also highly concordant with the sequence-based map of HLA (NCBI build 36) when reordered to account for the ancestral inversion in the ruminant MHC.

Conclusion

These results strongly suggest that studies using Btau_3.1 for analyses of the BoLA region should be reevaluated in light of the Btau_4.0 assembly and indicate that additional research is needed to produce a complete assembly of the BoLA genomic sequences.
Characterization of the bovine pregnancy-associated glycoprotein gene family – analysis of gene sequences, regulatory regions within the promoter and expression of selected genes
Authors: Telugu Bhanu Prakash VL , Walker Angela M , Green Jonathan A
Published: April 2009

Background

The Pregnancy-associated glycoproteins (PAGs) belong to a large family of aspartic peptidases expressed exclusively in the placenta of species in the Artiodactyla order. In cattle, the PAG gene family is comprised of at least 22 transcribed genes, as well as some variants. Phylogenetic analyses have shown that the PAG family segregates into 'ancient' and 'modern' groupings. Along with sequence differences between family members, there are clear distinctions in their spatio-temporal distribution and in their relative level of expression. In this report, 1) we performed an in silico analysis of the bovine genome to further characterize the PAG gene family, 2) we scrutinized proximal promoter sequences of the PAG genes to evaluate the evolution pressures operating on them and to identify putative regulatory regions, 3) we determined relative transcript abundance of selected PAGs during pregnancy and, 4) we performed preliminary characterization of the putative regulatory elements for one of the candidate PAGs, bovine (bo) PAG-2.

Results

From our analysis of the bovine genome, we identified 18 distinct PAG genes and 14 pseudogenes. We observed that the first 500 base pairs upstream of the translational start site contained multiple regions that are conserved among all boPAGs. However, a preponderance of conserved regions, that harbor recognition sites for putative transcriptional factors (TFs), were found to be unique to the modern boPAG grouping, but not the ancient boPAGs. We gathered evidence by means of Q-PCR and screening of EST databases to show that boPAG-2 is the most abundant of all boPAG transcripts. Finally, we provided preliminary evidence for the role of ETS- and DDVL-related TFs in the regulation of the boPAG-2 gene.

Conclusion

PAGs represent a relatively large gene family in the bovine genome. The proximal promoter regions of these genes display differences in putative TF binding sites, likely contributing to observed differences in spatial and temporal expression. We also discovered that boPAG-2 is the most abundant of all boPAG transcripts and provided evidence for the role of ETS and DDVL TFs in its regulation. These experiments mark the crucial first step in discerning the complex transcriptional regulation operating within the boPAG gene family.
Cross-species mapping of bidirectional promoters enables prediction of unannotated 5' UTRs and identification of species-specific transcripts
Authors: Piontkivska Helen , Yang Mary Q , Larkin Denis M , Lewin Harris A , Reecy James , Elnitski Laura
Published: April 2009

Background

Bidirectional promoters are shared regulatory regions that influence the expression of two oppositely oriented genes. This type of regulatory architecture is found more frequently than expected by chance in the human genome, yet many specifics underlying the regulatory design are unknown. Given that the function of most orthologous genes is similar across species, we hypothesized that the architecture and regulation of bidirectional promoters might also be similar across species, representing a core regulatory structure and enabling annotation of these regions in additional mammalian genomes.

Results

By mapping the intergenic distances of genes in human, chimpanzee, bovine, murine, and rat, we show an enrichment for pairs of genes equal to or less than 1,000 bp between their adjacent 5' ends ("head-to-head") compared to pairs of genes that fall in the same orientation ("head-to-tail") or whose 3' ends are side-by-side ("tail-to-tail"). A representative set of 1,369 human bidirectional promoters was mapped to orthologous sequences in other mammals. We confirmed predictions for 5' UTRs in nine of ten manual picks in bovine based on comparison to the orthologous human promoter set and in six of seven predictions in human based on comparison to the bovine dataset. The two predictions that did not have orthology as bidirectional promoters in the other species resulted from unique events that initiated transcription in the opposite direction in only those species. We found evidence supporting the independent emergence of bidirectional promoters from the family of five RecQ helicase genes, which gained their bidirectional promoters and partner genes independently rather than through a duplication process. Furthermore, by expanding our comparisons from pairwise to multispecies analyses we developed a map representing a core set of bidirectional promoters in mammals.

Conclusion

We show that the orthologous positions of bidirectional promoters provide a reliable guide to directly annotate over one thousand regulatory regions in sequences of mammalian genomes, while also serving as a useful tool to predict 5' UTR positions and identify genes that are novel to a single species.
Quantitation of DNA methylation by melt curve analysis
Authors: Smith Eric , Jones Michael E , Drew Paul A
Published: April 2009

Background

Methylation of DNA is a common mechanism for silencing genes, and aberrant methylation is increasingly being implicated in many diseases such as cancer. There is a need for robust, inexpensive methods to quantitate methylation across a region containing a number of CpGs. We describe and validate a rapid, in-tube method to quantitate DNA methylation using the melt data obtained following amplification of bisulfite modified DNA in a real-time thermocycler.

Methods

We first describe a mathematical method to normalise the raw fluorescence data generated by heating the amplified bisulfite modified DNA. From this normalised data the temperatures at which melting begins and finishes can be calculated, which reflect the less and more methylated template molecules present respectively. Also the T50, the temperature at which half the amplicons are melted, which represents the summative methylation of all the CpGs in the template mixture, can be calculated. These parameters describe the methylation characteristics of the region amplified in the original sample.

Results

For validation we used synthesized oligonucleotides and DNA from fresh cells and formalin fixed paraffin embedded tissue, each with known methylation. Using our quantitation we could distinguish between unmethylated, partially methylated and fully methylated oligonucleotides mixed in varying ratios. There was a linear relationship between T50 and the dilution of methylated into unmethylated DNA. We could quantitate the change in methylation over time in cell lines treated with the demethylating drug 5-aza-2'-deoxycytidine, and the differences in methylation associated with complete, clonal or no loss of MGMT expression in formalin fixed paraffin embedded tissues.

Conclusion

We have validated a rapid, simple in-tube method to quantify methylation which is robust and reproducible, utilizes easily designed primers and does not need proprietary algorithms or software. The technique does not depend on any operator manipulation or interpretation of the melt curves, and is suitable for use in any laboratory with a real-time thermocycler. The parameters derived provide an objective description and quantitation of the methylation in a specimen, and can be used to for statistical comparisons of methylation between specimens.
Single-embryo transfer reduces clinical pregnancy rates and live births in fresh IVF and Intracytoplasmic Sperm Injection (ICSI) cycles: a meta-analysis
Authors: Baruffi Ricardo LR , Mauri Ana L , Petersen Claudia G , Nicoletti Andréia , Pontes Anagloria , Oliveira João Batista A , Franco José G
Published: April 2009

Background

It has become an accepted procedure to transfer more than one embryo to the patient to achieve acceptable ongoing pregnancy rates. However, transfers of more than a single embryo increase the probability of establishing a multiple gestation. Single-embryo transfer can minimize twin pregnancies but may also lower live birth rates. This meta-analysis aimed to compare current data on single-embryo versus double-embryo transfer in fresh IVF/ICSI cycles with respect to implantation, ongoing pregnancy and live birth rates.

Methods

Search strategies included on-line surveys of databases from 1995 to 2008. Data management and analysis were conducted using the Stats Direct statistical software. The fixed-effect model was used for odds ratio (OR). Fixed-effect effectiveness was evaluated by the Mantel Haenszel method. Seven trials fulfilled the inclusion criteria.

Results

When pooling results under the fixed-effect model, the implantation rate was not significantly different between double-embryo transfer (34.5%) and single-embryo transfer group (34.7%) (P = 0.96; OR = 0.99, 95% CI 0.78, 1.25). On the other hand, double-embryo transfer produced a statistically significantly higher ongoing clinical pregnancy rate (44.5%) than single-embryo transfer (28.3%) (P < 0.0001; OR:2.06, 95% CI = 1.64,2.60). At the same time, pooling results presented a significantly higher live birth rate when double-embryo transfer (42.5%) (P < 0.001; OR: 1.87, 95% CI = 1.44,2.42) was compared with single-embryo transfer (28.4%).

Conclusion

Meta-analysis with 95% confidence showed that, despite similar implantation rates, fresh double-embryo transfer had a 1.64 to 2.60 times greater ongoing pregnancy rate and 1.44 to 2.42 times greater live birth rate than single-embryo transfer in a population suitable for ART treatment.
A novel promoter controls Cyp19a1 gene expression in mouse adipose tissue
Authors: Zhao Hong , Innes Joy , Brooks David C , Reierstad Scott , Yilmaz Mehmet B , Lin Zhihong , Bulun Serdar E
Published: April 2009

Background

Aromatase, the key enzyme in estrogen biosynthesis, is encoded by the Cyp19a1 gene. Thus far, 3 unique untranslated first exons associated with distinct promoters in the mouse Cyp19a1 gene have been described (brain, ovary, and testis-specific). It remains unknown whether aromatase is expressed in other mouse tissues via novel and tissue-specific promoters.

Methods

Real-time PCR was used to examine the aromatase expression levels in various C57BL/6 mouse tissues. 5'-rapid amplification of cDNA ends (5'-RACE) was used to determine the transcriptional start sites of Cyp19a1 transcripts. Promoter activity was measured using serial deletion mutants of DNA fused to the luciferase reporter gene. Primary mouse adipose fibroblasts were isolated and cultured from 16-week-old mouse gonadal fat pads.

Results

We systematically analyzed Cyp19a1 expression in a large number of mouse tissues, and demonstrated for the first time that aromatase was expressed in the male but not female gonadal fat pad. Subcutaneous and brown adipose tissue did not contain detectable Cyp19a1 mRNA. We used 5'-RACE to clone a novel gonadal fat-specific untranslated first exon, which is spliced onto a common junction 15 bp upstream of the translation start site. This adipose-specific first exon was mapped to approximately 75 kb upstream of the translation start site. Transfection of luciferase reporter gene plasmids containing the promoter region upstream of the adipose-specific first exon into murine 3T3-L1 adipose fibroblasts demonstrated significant basal promoter activity conferred primarily by the sequence located at -343/-1 bp. Dexamethasone significantly induced activity of this adipose-specific promoter region. Adipose-specific Cyp19a1 mRNA was expressed in primary mouse adipose fibroblasts and significantly induced by dexamethasone alone or serum plus dexamethasone.

Conclusion

Taken together, this research identified a novel, adipose-specific first exon of Cyp19a1 and its hormonally regulated promoter region in male murine gonadal fat. These results expand the known 5'-regulatory region of the murine Cyp19a1 gene to 75 kb upstream of the translation start site. Cyp19a1 expression in mouse adipose tissue may play an important role in reproductive biology and lipid metabolism.
Incorporation of membrane-bound, mammalian-derived immunomodulatory proteins into influenza whole virus vaccines boosts immunogenicity and protection against lethal challenge
Authors: Herbert Andrew S , Heffron Lynn , Sundick Roy , Roberts Paul C
Published: April 2009

Background

Influenza epidemics continue to cause morbidity and mortality within the human population despite widespread vaccination efforts. This, along with the ominous threat of an avian influenza pandemic (H5N1), demonstrates the need for a much improved, more sophisticated influenza vaccine. We have developed an in vitro model system for producing a membrane-bound Cytokine-bearing Influenza Vaccine (CYT-IVAC). Numerous cytokines are involved in directing both innate and adaptive immunity and it is our goal to utilize the properties of individual cytokines and other immunomodulatory proteins to create a more immunogenic vaccine.

Results

We have evaluated the immunogenicity of inactivated cytokine-bearing influenza vaccines using a mouse model of lethal influenza virus challenge. CYT-IVACs were produced by stably transfecting MDCK cell lines with mouse-derived cytokines (GM-CSF, IL-2 and IL-4) fused to the membrane-anchoring domain of the viral hemagglutinin. Influenza virus replication in these cell lines resulted in the uptake of the bioactive membrane-bound cytokines during virus budding and release.In vivoefficacy studies revealed that a single low dose of IL-2 or IL-4-bearing CYT-IVAC is superior at providing protection against lethal influenza challenge in a mouse model and provides a more balanced Th1/Th2humoral immune response, similar to live virus infections.

Conclusion

We have validated the protective efficacy of CYT-IVACs in a mammalian model of influenza virus infection. This technology has broad applications in current influenza virus vaccine development and may prove particularly useful in boosting immune responses in the elderly, where current vaccines are minimally effective.
Quality of life and the impact of drug toxicities in a South African community‐based antiretroviral programme
Authors: Pitt Jennifer , Myer Landon , Wood Robin
Published: April 2009

Background

The impact of highly active antiretroviral therapy (HAART) on health‐related quality of life has been widely researched in the developed world, but there are few data from sub‐Saharan Africa, where the vast majority of HIV‐infected individuals live. This study examined health‐related quality of life among HIV‐positive individuals initiating HAART in Cape Town, South Africa, and explored the impact of HAART‐related drug toxicities on quality of life.

Methods

Health‐related quality of life was assessed using a standardised questionnaire, the Medical Outcomes Survey Short Form 36. Physical health summary scores and mental health summary scores were compared pre‐HAART and at regular intervals during the first 48 weeks of HAART. The relationships between socio‐demographic, baseline and on‐treatment variables and decline in health‐related quality of life, as well as the impact of drug toxicities on quality of life, were assessed in unadjusted bivariate and adjusted multivariate analyses.

Results

Two hundred and ninety‐five patients were enrolled into the study. There was a significant increase in health‐related quality of life during the first 48 weeks on HAART. The median physical health summary score increased from 45 to 53 units (p < 0.001) and median mental health summary score increased from 45 to 50 units (p < 0.001).

The bulk of this increase occurred during the first 16 weeks. Overall, 23% of participants experienced a decline in their physical health summary score, while 34% showed a decline in the mental health summary score. Average drops in median physical and mental health summary scores were 8.4 units (SD 9.31) and 9.9 (SD 11.4) units respectively. Participants with drug toxicity had lower physical health summary scores than participants without drug toxicity at all time points. However, only three participants with toxicity (27%) reported an actual decline in health‐related quality of life by week 48. Drug toxicities had little impact on mental health summary scores.

Conclusion

These results confirm the health‐related quality of life benefits of HAART. While the majority of patients experienced a significant improvement in health‐related quality of life on HAART, up to a third of patients reported declines in this quality of life. This was largely related to better baseline clinical state. HAART‐related drug toxicities did not have a significant impact on health‐related quality of life during the first year of HAART, which supports the ongoing use of the current national first‐line regimen.