bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic variation in eight Chinese cattle breeds based on the analysis of microsatellite markers
Authors: Sun Weibin , chen Hong , Lei Chuzhao , Lei Xueqin , Zhang Yinghan 
Published: June 2009

Abstract
Genetic variability and genetic relationships were investigated among eight Chinese cattle breeds using 12 microsatellite markers. Three hundred and fifty-two alleles were detected and the average number of alleles per locus ranged from 8.33 ± 1.67 in the Jiaxian breed to 21.33 ± 5.60 in the Qinchuan breed with a mean value of 13.91. The total number of alleles per microsatellite ranged from 21 (INRA005, HEL1) to 40 (HEL13), with a mean of 29.33 per locus. The fixation indices at the 12 loci in the eight breeds were very low with a mean of 0.006. A principal components analysis and the construction of a neighborjoining tree showed that these eight Chinese cattle breeds cluster into three groups i.e. the Yanbian andChineseHolstein, theNanyang and Jiaxian, and the four remaining breeds.This clustering agrees with the origin and geographical distributions of these Chinese breeds.
Genomic selection of purebreds for crossbred performance
Authors: Ibánẽz-Escriche Noelia , Fernando Rohan L , Toosi Ali , Dekkers Jack CM 
Published: June 2009

Abstract

Background
One of the main limitations of many livestock breeding programs is that selection is in pure breeds housed in high-health environments but the aim is to improve crossbred performance under field conditions. Genomic selection (GS) using high-density genotyping could be used to address this. However in crossbred populations, 1) effects of SNPs may be breed specific, and 2) linkage disequilibrium may not be restricted to markers that are tightly linked to the QTL. In this study we apply GS to select for commercial crossbred performance and compare a model with breed-specific effects of SNP alleles (BSAM) to a model where SNP effects are assumed the same across breeds (ASGM). The impact of breed relatedness (generations since separation), size of the population used for training, and marker density were evaluated. Trait phenotype was controlled by 30 QTL and had a heritability of 0.30 for crossbred individuals. A Bayesian method (Bayes-B) was used to estimate the SNP effects in the crossbred training population and the accuracy of resulting GS breeding values for commercial crossbred performance was validated in the purebred population.

Results
Results demonstrate that crossbred data can be used to evaluate purebreds for commercial crossbred performance. Accuracies based on crossbred data were generally not much lower than accuracies based on pure breed data and almost identical when the breeds crossed were closely related breeds. The accuracy of both models (ASGM and BSAM) increased with marker density and size of the training data. Accuracies of both models also tended to decrease with increasing distance between breeds. However the effect of marker density, training data size and distance between breeds differed between the two models. BSAM only performed better than AGSM when the number of markers was small (500), the number of records used for training was large (4000), and when breeds were distantly related or unrelated.

Conclusion
In conclusion, GS can be conducted in crossbred population and models that fit breed-specific effects of SNP alleles may not be necessary, especially with high marker density. This opens great opportunities for genetic improvement of purebreds for performance of their crossbred descendents in the field, without the need to track pedigrees through the system.
Large-scale association study for structural soundness and leg locomotion traits in the pig
Authors: Fan Bin , Onteru Suneel K , Mote Benny E , Serenius Timo , Stalder Kenneth J , Rothschild Max F 
Published: June 2009

Abstract

Background
Identification and culling of replacement gilts with poor skeletal conformation and feet and leg (FL) unsoundness is an approach used to reduce sow culling and mortality rates in breeding stock. Few candidate genes related to soundness traits have been identified in the pig.

Methods
In this study, 2066 commercial females were scored for 17 traits describing body conformation and FL structure, and were used for association analyses. Genotyping of 121 SNPs derived from 95 genes was implemented using Sequenom's MassARRAY system.

Results
Based on the association results from single trait and principal components using mixed linear model analyses and false discovery rate testing, it was observed that APOE, BMP8, CALCR, COL1A2, COL9A1, DKFZ, FBN1 and VDBP were very highly significantly (P < 0.001) associated with body conformation traits. The genes ALOX5, BMP8, CALCR, OPG, OXTR and WNT16 were very highly significantly (P < 0.001) associated with FL structures, and APOE, CALCR, COL1A2, GNRHR, IHH, MTHFR and WNT16 were highly significantly (P < 0.01) associated with overall leg action. Strong linkage disequilibrium between CALCR and COL1A2 on SSC9 was detected, and haplotype -ACGACC- was highly significantly (P < 0.01) associated with overall leg action and several important FL soundness traits.

Conclusion
The present findings provide a comprehensive list of candidate genes for further use in fine mapping and biological functional analyses.
Changes in muscle cell cation regulation and meat quality traits are associated with genetic selection for high body weight and meat yield in broiler chickens
Authors: Sandercock Dale A , Barker Zoe E , Mitchell Malcolm A , Hocking Paul M 
Published: June 2009

AbstractBetween-breed genetic variation for muscle and meat quality traits was determined at eight weeks of age in 34 lines of purebred commercial broiler and layer lines and traditional breeds (categories) of chickens. Between-breed genetic variation for plasma ion concentrations and element concentration in muscle dry matter and ash were determined. Plasma from broilers had higher concentrations of Na+, K+, Mg++, total and free Ca++and lower free:total Ca++than plasma from layer and traditional lines. Muscle from broilers contained more Na and higher concentrations of K, Mg and Ca per mg of ash but not of dry matter compared with layer and traditional lines. In comparison with layer and traditional lines, broiler genotypes were over three times heavier, their plasma creatine kinase activity (CK), a marker of muscle tissue damage, was higher, their breast muscle colour was lighter (L*) and less red (a*) and yellow (b*) in appearance, the initial and final pH of their muscles were lower, the pH change was higher and their breast muscle was more tender. Thus, genetic selection for broiler traits has markedly altered cation regulation in muscle cells and may be associated with changes in muscle cell function and the development of pathology and meat quality problems.
Evaluating regional blood spinal cord barrier dysfunction following spinal cord injury using longitudinal dynamic contrast-enhanced MRI
Authors: Tatar Ilkan , Chou Peter Cheng-te , Desouki Mohamed Mokhtar , El Sayed Hanaa , Bilgen Mehmet 
Published: June 2009

Abstract

Background
In vivo preclinical imaging of spinal cord injury (SCI) in rodent models provides clinically relevant information in translational research. This paper uses multimodal magnetic resonance imaging (MRI) to investigate neurovascular pathology and changes in blood spinal cord barrier (BSCB) permeability following SCI in a mouse model of SCI.

Methods
C57BL/6 female mice (n = 5) were subjected to contusive injury at the thoracic T11 level and scanned on post injury days 1 and 3 using anatomical, dynamic contrast-enhanced (DCE-MRI) and diffusion tensor imaging (DTI). The injured cords were evaluated postmortem with histopathological stains specific to neurovascular changes. A computational model was implemented to map local changes in barrier function from the contrast enhancement. The area and volume of spinal cord tissue with dysfunctional barrier were determined using semi-automatic segmentation.

Results
Quantitative maps derived from the acquired DCE-MRI data depicted the degree of BSCB permeability variations in injured spinal cords. At the injury sites, the damaged barriers occupied about 70% of the total cross section and 48% of the total volume on day 1, but the corresponding measurements were reduced to 55% and 25%, respectively on day 3. These changes implied spatio-temporal remodeling of microvasculature and its architecture in injured SC. Diffusion computations included longitudinal and transverse diffusivities and fractional anisotropy index. Comparison of permeability and diffusion measurements indicated regions of injured cords with dysfunctional barriers had structural changes in the form of greater axonal loss and demyelination, as supported by histopathologic assessments.

Conclusion
The results from this study collectively demonstrated the feasibility of quantitatively mapping regional BSCB dysfunction in injured cord in mouse and obtaining complementary information about its structural integrity using in vivo DCE-MRI and DTI protocols. This capability is expected to play an important role in characterizing the neurovascular changes and reorganization following SCI in longitudinal preclinical experiments, but with potential clinical implications.
Beyond the EPR: Complementary roles of the hospital-wide electronic health record and clinical departmental systems
Authors: Vedvik Eivind , Tjora Aksel H , Faxvaag Arild 
Published: June 2009

Abstract

Background
Many hospital departments have implemented small clinical departmental systems (CDSs) to collect and use patient data for documentation as well as for other department-specific purposes. As hospitals are implementing institution-wide electronic patient records (EPRs), the EPR is thought to be integrated with, and gradually substitute the smaller systems. Many EPR systems however fail to support important clinical workflows. Also, successful integration of systems has proven hard to achieve. As a result, CDSs are still in widespread use. This study was conducted to see which tasks are supported by CDSs and to compare this to the support offered by the EPR.

Methods
Semi-structured interviews with users of 16 clinicians using 15 different clinical departmental systems (CDS) at a Medium-sized University hospital in Norway. Inductive analysis of transcriptions from the audio taped interviews.

Results
The roles of CDSs were complementary to those of the hospital-wide EPR system. The use of structured patient data was a characteristic feature. This facilitated quality development and supervision, tasks that were poorly supported by the EPR system. The structuring of the data also improved filtering of information to better support clinical decision-making. Because of the high value of the structured patient data, the users put much effort in maintaining their integrity and representativeness. Employees from the departments were also engaged in the funding, development, implementation and maintenance of the systems.

Conclusion
Clinical departmental systems are vital to the activities of a clinical hospital department. The development, implementation and clinical use of such systems can be seen as bottom-up, user-driven innovations.
Fatty acid desaturation index correlates with body mass and adiposity indices of obesity in Wistar NIN obese mutant rat strains WNIN/Ob and WNIN/GR-Ob
Authors: Jeyakumar Shanmugam M , Lopamudra Pratti , Padmini Suryaprakash , Balakrishna Nagalla , Giridharan Nappan V , Vajreswari Ayyalasomayajula 
Published: June 2009

Abstract

Background
Microsomal stearoyl-CoA desaturase1 (SCD1) is the rate limiting enzyme involved in the biosynthesis of monounsaturated fatty acids (MUFAs); palmitoleic (16:1) and oleic (18:1) acid from their respective substrates palmitic (16:0) and stearic (18:0) acids. The ratio of 18:1 to 18:0 has been implicated in the regulation membrane fluidity and function. SCD1 is abundantly expressed in obese humans as well as rodent models. However, no studies have correlated the fatty acid desaturation index (16:1/16:0 and 18:1/18:0), an indicator of SCD1 activity with the markers of obesity in terms of body mass index (BMI) and adiposity index (AI). Therefore, here, we attempted to relate the fatty acid desaturation index with BMI and AI in Wistar NIN-obese mutant rat strains namely, WNIN/Ob and WNIN/GR-Ob (with impaired glucose tolerance).

Methods
For this purpose, 200 days old male 6 lean and 6 obese rats of both strains were taken. Fatty acid composition was analyzed in plasma, various tissues such as liver, white adipose tissues (retroperitoneal, epididymal, omental, and subcutaneous) and brown adipose tissue.

Results
Fatty acid composition data showed significant increase in palmitoleic (16:1) and oleic (18:1) acid levels, which were reflected in increased desaturation index (16:1/16:0 and 18:1/18:0) in plasma and all the tissues of obese rats of both strains, when compared with their respective age and sex-matched lean rats. Further, we found a strong positive correlation between desaturation index, BMI and AI in plasma and most of the tissues analyzed.

Conclusion
So far, plasma Δ9 desaturation index has been well correlated with hypertriglyceridemia and we, by employing two models of obesity namely, WNIN/Ob and WNIN/GR-Ob, have shown Δ9 desaturation index of plasma correlated with physical markers of obesity such as BMI and AI. In conclusion, Δ9 desaturation index may serve as a potential sensitive biochemical marker to assess the degree of obesity and impact of therapeutic/nutritional interventions to combat obesity, along with other indicators.
The relationship between lower extremity alignment and Medial Tibial Stress Syndrome among non-professional athletes
Authors: Raissi Golam Reza D , Cherati Afsaneh D Safar , Mansoori Kourosh D , Razi Mohammad D 
Published: June 2009

Abstract

Objective
To determine the relationship between lower extremity alignment and MTSS amongst non-professional athletes

Design
In a prospective Study, sixty six subjects were evaluated. Bilateral navicular drop test, Q angle, Achilles angle, tibial angle, intermalleolar and intercondylar distance were measured. In addition, runner's height, body mass, history of previous running injury, running experience was recorded. Runners were followed for 17 weeks to determine occurrence of MTSS.

Results
The overall injury rate for MTSS was 19.7%. The MTSS injury rate in girls (22%) was not significantly different from the rate in boys (14.3%). Most MTSS injuries were induced after 60 hours of exercise, which did not differ between boys and girls. There was a significant difference in right and left navicular drop (ND) in athletes with MTSS. MTSS had no significant correlation with other variables including Quadriceps, Tibia and Achilles angles, intercondylar and intermaleolar lengths and lower extremity lengths.

Limitation
All measurements performed in this study were uniplanar and static. The small sample size deemed our main limitation. The accurate assessment of participants with previous history of anterior leg pain for MTSS was another limitation.

Conclusion
Although a significant relationship between navicular drop and MTSS was found in this study; there was not any significant relationship between lower extremity alignment and MTSS in our sample study.
The conservation and evolutionary modularity of metabolism
Authors: Peregrín-Alvarez José M , Sanford Chris , Parkinson John 
Published: June 2009

Abstract
Background
Cellular metabolism is a fundamental biological system consisting of myriads of enzymatic reactions that together fulfill the basic requirements of life. The recent availability of vast amounts of sequence data from diverse sets of organisms provides an opportunity to systematically examine metabolism from a comparative perspective. Here we supplement existing genome and protein resources with partial genome datasets derived from 193 eukaryotes to present a comprehensive survey of the conservation of metabolism across 26 taxa representing the three domains of life.

Results
In general, metabolic enzymes are highly conserved. However, organizing these enzymes within the context of functional pathways revealed a spectrum of conservation from those that are highly conserved (for example, carbohydrate, energy, amino acid and nucleotide metabolism enzymes) to those specific to individual taxa (for example, those involved in glycan metabolism and secondary metabolite pathways). Applying a novel co-conservation analysis, KEGG defined pathways did not generally display evolutionary coherence. Instead, such modularity appears restricted to smaller subsets of enzymes. Expanding analyses to a global metabolic network revealed a highly conserved, but nonetheless flexible, 'core' of enzymes largely involved in multiple reactions across different pathways. Enzymes and pathways associated with the periphery of this network were less well conserved and associated with taxon-specific innovations.

Conclusions
These findings point to an emerging picture in which a core of enzyme activities involving amino acid, energy, carbohydrate and lipid metabolism have evolved to provide the basic functions required for life. However, the precise complement of enzymes associated within this core for each species is flexible.
Paracrine Signals from the Mouse Conceptus Are Not Required for the Normal Progression of Decidualization
Authors: Herington Jennifer L. , Underwood Tawny , McConaha Melinda , Bany Brent M. 
Published: June 2009

Abstract
The purpose of this study was to determine whether the conceptus directs the formation of a tight- and adherens-dependent permeability barrier formed by the primary decidual zone and normal progression of decidual cell differentiation during embryo implantation. Four artificial models of decidualization were used, some apparently more physiological than others. The results show that both the formation of the permeability barrier and decidual cell differentiation of three of the artificial models were quite different from that of pregnant uteri. One artificial model of decidualization, namely pseudopregnant animals receiving concanavalin A-coated Sepharose bead transfers on d 2.5 of pseudopregnancy, better recapitulated the decidual changes that occur in the pregnant uterus undergoing decidualization. This included the formation of a primary decidual zone-like permeability barrier and decidual growth. This model also exhibited similar temporal changes of the expression of genes involved in decidualization that are markers of decidual cell differentiation. Overall, the results of this study indicate that some models of inducing decidualization artificially produce responses that are more similar to those occurring in the pregnant uterus, whereas others are quite different. More importantly, the results suggest that concanavalin A-coated Sepharose beads can provide an equivalent stimulus as the trophectoderm to cause the formation of the primary decidual zone permeability barrier.
Adiponectin Attenuation of Endocrine Function within Human Term Trophoblast Cells
Authors: McDonald E. A. , Wolfe M. W. 
Published: June 2009

Abstract
The hormone adiponectin has been shown to be important in maintaining insulin sensitivity throughout the body, whereas potential effects on the placenta have not been assessed. Pregnancy constitutes a unique physiological environment in which metabolism has a profound effect on the health of both the mother and the developing fetus. It is imperative that a delicate balance in glucose delivery be maintained between maternal tissues and the fetal/placental unit. Adiponectin’s role in regulating peripheral insulin responsiveness suggests it may be a factor in maintaining this balance during gestation as well. Examination of human cytotrophoblast cells revealed that mRNA for both adiponectin receptors, adipoR1 and adipoR2, are abundantly expressed at term. We were, however, unable to reliably detect mRNA for adiponectin in primary cytotrophoblasts. Expression of both receptors was maintained after induction of syncytium formation by exogenous epidermal growth factor treatment. Treatment of cytotrophoblasts with adiponectin resulted in a significant drop, as assessed by quantitative RT-PCR, in expression for a number of genes involved in the endocrine function of the placenta, including the chorionic gonadotropin subunits, placental lactogen, and some steroidogenic enzymes. Immunofluorescent staining for connexin 43 and desmoplakin in primary trophoblasts revealed that adiponectin does not inhibit syncytialization of trophoblast cells in culture. Taken together, these data describe a novel role for maternal adiponectin in regulating the placental environment. Determination of the effects of such adipokines on the maternal-fetal interface is increasingly important, because the incidence of pregnancies complicated by gestational diabetes remains a significant health problem in developed countries.
Matrix Extracellular Phosphoglycoprotein (MEPE) Is a New Bone Renal Hormone and Vascularization Modulator
Authors: David Valentin , Martin Aline , Hedge Anne-Marie , Rowe Peter S. N. 
Published: June 2009

AbstractIncreased matrix extracellular phosphoglycoprotein (MEPE) expression occurs in several phosphate and bone-mineral metabolic disorders. To resolve whether MEPE plays a role, we created a murine model overexpressing MEPE protein (MEPE tgn) in bone. MEPE tgn mice displayed a growth and mineralization defect with altered bone-renal vascularization that persisted to adulthood. The growth mineralization defect was due to a decrease in bone remodeling, and MEPE tgn mice were resistant to diet-induced renal calcification. MEPE protein-derived urinary ASARM peptides and reduced urinary Ca X PO4 product mediated the suppressed renal calcification. Osteoblastic cells displayed reduced activity but normal differentiation. Osteoclastic precursors were unable to differentiate in the presence of osteoblasts. In the kidney, NPT2a up-regulation induced an increase in phosphate renal reabsorption, leading to hyperphosphatemia. We conclude MEPE and MEPE-phosphate-regulating gene with homologies to endopeptidases on the X chromosome (MEPE-PHEX) interactions are components to an age-diet-dependent pathway that regulates bone turnover and mineralization and suppresses renal calcification. This novel pathway also modulates bone-renal vascularization and bone turnover.