bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparative analysis of haplotype association mapping algorithms
Authors: McClurg Phillip , Pletcher Mathew T , Wiltshire Tim , Su Andrew I
Published: February 2006

Background

Finding the genetic causes of quantitative traits is a complex and difficult task. Classical methods for mapping quantitative trail loci (QTL) in miceuse an F2 cross between two strains with substantially different phenotype and an interval mapping method to compute confidence intervals at each position in the genome. This process requires significant resources for breeding and genotyping, and the data generated are usually only applicable to one phenotype of interest. Recently, we reported the application of a haplotype association mapping method which utilizes dense genotyping data across a diverse panel of inbred mouse strains and a marker association algorithm that is independent of any specific phenotype. As the availability of genotyping data grows in size and density, analysis of these haplotype association mapping methods should be of increasing value to the statistical genetics community.

Results

We describe a detailed comparative analysis of variations on our marker association method. In particular, we describe the use of inferred haplotypes from adjacent SNPs, parametric and nonparametric statistics, and control of multiple testing error. These results show that nonparametric methods are slightly better in the test cases we study, although the choice of test statistic may often be dependent on the specific phenotype and haplotype structure being studied. The use of multi-SNP windows to infer local haplotype structure is critical to the use of a diverse panel of inbred strains for QTL mapping. Finally, because the marginal effect of any single gene in a complex disease is often relatively small, these methods require the use of sensitive methods for controlling family-wise error. We also report our initial application of this method to phenotypes cataloged in the Mouse Phenome Database.

Conclusion

The use of inbred strains of mice for QTL mapping has many advantages over traditional methods. However, there are also limitations in comparison to the traditional linkage analysis from F2 and RI lines. Application of these methods requires careful consideration of algorithmic choices based on both theoretical and practical factors. Our findings suggest general guidelines, though a complete evaluation of these methods can only be performed as more genetic data in complex diseases becomes available.
Bayesian detection of periodic mRNA time profiles without use of training examples
Authors: Andersson Claes R , Isaksson Anders , Gustafsson Mats G
Published: February 2006

Background

Detection of periodically expressed genes from microarray data without use of known periodic and non-periodic training examples is an important problem, e.g. for identifying genes regulated by the cell-cycle in poorly characterised organisms. Commonly the investigator is only interested in genes expressed at a particular frequency that characterizes the process under study but this frequency is seldom exactly known. Previously proposed detector designs require access to labelled training examples and do not allow systematic incorporation of diffuse prior knowledge available about the period time.

Results

A learning-free Bayesian detector that does not rely on labelled training examples and allows incorporation of prior knowledge about the period time is introduced. It is shown to outperform two recently proposed alternative learning-free detectors on simulated data generated with models that are different from the one used for detector design. Results from applying the detector to mRNA expression time profiles fromS. cerevisiaeshowsthat the genes detected as periodically expressed only contain a small fraction of the cell-cycle genes inferred from mutant phenotype. For example, when the probability of false alarm was equal to 7%, only 12% of the cell-cycle genes were detected. The genes detected as periodically expressed were found to have a statistically significant overrepresentation of known cell-cycle regulated sequence motifs. One known sequence motif and 18 putative motifs, previously not associated with periodic expression, were also over represented.

Conclusion

In comparison with recently proposed alternative learning-free detectors for periodic gene expression, Bayesian inference allows systematic incorporation of diffusea prioriknowledge about, e.g. the period time. This results in relative performance improvements due to increased robustness against errors in the underlying assumptions. Results from applying the detector to mRNA expression time profiles fromS. cerevisiaeinclude several new findings that deserve further experimental studies.
The complete mitochondrial genome of the enigmatic bigheaded turtle (Platysternon): description of unusual genomic features and the reconciliation of phylogenetic hypotheses based on mitochondrial and nuclear DNA
Authors: Parham James F , Feldman Chris R , Boore Jeffrey L
Published: February 2006

Background

The big-headed turtle (Platysternon megacephalum) from east Asia is the sole living representative of a poorly-studied turtle lineage (Platysternidae). It has no close living relatives, and its phylogenetic position within turtles is one of the outstanding controversies in turtle systematics.Platysternonwas traditionally considered to be close to snapping turtles (Chelydridae) based on some studies of its morphology and mitochondrial (mt) DNA, however, other studies of morphology and nuclear (nu) DNA do not support that hypothesis.

Results

We sequenced the complete mt genome ofPlatysternonand the nearly complete mt genomes of two other relevant turtles and compared them to turtle mt genomes from the literature to form the largest molecular dataset used to date to address this issue. The resulting phylogeny robustly rejects the placement ofPlatysternonwith Chelydridae, but instead shows that it is a member of the Testudinoidea, a diverse, nearly globally-distributed group that includes pond turtles and tortoises. We also discovered thatPlatysternonmtDNA has large-scale gene rearrangements and possesses two, nearly identical, control regions, features that distinguish it from all other studied turtles.

Conclusion

Our study robustly determines the phylogenetic placement ofPlatysternonand provides a well-resolved outline of major turtle lineages, while demonstrating the significantly greater resolving power of comparing large amounts of mt sequence over that of short fragments. Earlier phylogenies placingPlatysternonwith chelydrids required a temporal gap in the fossil record that is now unnecessary. The duplicated control regions and gene rearrangements of thePlatysternonmtDNA probably resulted from the duplication of part of the genome and then the subsequent loss of redundant genes. Although it is possible that having two control regions may provide some advantage, explaining why the control regions would be maintained while some of the duplicated genes were eroded, examples of this are rare. So far, duplicated control regions have been reported for mt genomes from just 12 clades of metazoans, includingPlatysternon.
Complete association between a retroviral insertion in the tyrosinase gene and the recessive white mutation in chickens
Authors: Chang Chung-Ming , Coville Jean-Luc , Coquerelle Gérard , Gourichon David , Oulmouden Ahmad , Tixier-Boichard Michèle
Published: February 2006

Background

In chickens, three mutant alleles have been reported at the C locus, including the albino mutation, and the recessive white mutation, which is characterized by white plumage and pigmented eyes. The albino mutation was found to be a 6 bp deletion in the tyrosinase (TYR) gene. The present work describes an approach to identify the structural rearrangement in the TYR gene associated with the recessive white mutation.

Results

Molecular analysis of the chicken TYR gene has revealed a major structural difference (Restriction Fragment Length Polymorphism, RFLP) in the genomic DNA of the recessive white chicken. A major size difference of 7.7 kb was found in intron 4 of the TYR gene by long-range PCR. Molecular cloning and sequencing results showed the insertion of a complete avian retroviral sequence of the Avian Leukosis Virus (ALV) family. Several aberrant transcripts of the tyrosinase gene were found in 10 week old recessive white chickens but not in the homozygous wild type colored chicken. We established a rapid genotyping diagnostic test based on the discovery of this retroviral insertion. It shows that all homozygous carriers of this insertion had a white plumage in various chicken strains. Furthermore, it was possible to distinguish heterozygous carriers from homozygous normal chickens in a segregating line.

Conclusion

In this study, we conclude that the insertion of a complete avian retroviral sequence in intron 4 of the tyrosinase gene is diagnostic of the recessive white mutation in chickens. This insertion causes aberrant transcripts lacking exon 5, and we propose that this insertion is the causal mutation for the recessive white allele in the chicken.
The DtxR protein acting as dual transcriptional regulator directs a global regulatory network involved in iron metabolism of Corynebacterium glutamicum
Authors: Brune Iris , Werner Hendrikje , Hüser Andrea T , Kalinowski Jörn , Pühler Alfred , Tauch Andreas
Published: February 2006

Background

The knowledge about complete bacterial genome sequences opens the way to reconstruct the qualitative topology and global connectivity of transcriptional regulatory networks. Since iron is essential for a variety of cellular processes but also poses problems in biological systems due to its high toxicity, bacteria have evolved complex transcriptional regulatory networks to achieve an effective iron homeostasis. Here, we apply a combination of transcriptomics, bioinformatics, in vitro assays, and comparative genomics to decipher the regulatory network of the iron-dependent transcriptional regulator DtxR of Corynebacterium glutamicum.

Results

A deletion of the dtxR gene of C. glutamicum ATCC 13032 led to the mutant strain C. glutamicum IB2103 that was able to grow in minimal medium only under low-iron conditions. By performing genome-wide DNA microarray hybridizations, differentially expressed genes involved in iron metabolism of C. glutamicum were detected in the dtxR mutant. Bioinformatics analysis of the genome sequence identified a common 19-bp motif within the upstream region of 31 genes, whose differential expression in C. glutamicum IB2103 was verified by real-time reverse transcription PCR. Binding of a His-tagged DtxR protein to oligonucleotides containing the 19-bp motifs was demonstrated in vitro by DNA band shift assays. At least 64 genes encoding a variety of physiological functions in iron transport and utilization, in central carbohydrate metabolism and in transcriptional regulation are controlled directly by the DtxR protein. A comparison with the bioinformatically predicted networks of C. efficiens, C. diphtheriae and C. jeikeium identified evolutionary conserved elements of the DtxR network.

Conclusion

This work adds considerably to our currrent understanding of the transcriptional regulatory network of C. glutamicum genes that are controlled by DtxR. The DtxR protein has a major role in controlling the expression of genes involved in iron metabolism and exerts a dual regulatory function as repressor of genes participating in iron uptake and utilization and as activator of genes responsible for iron storage and DNA protection. The data suggest that the DtxR protein acts as global regulator by controlling the expression of other regulatory proteins that might take care of an iron-dependent regulation of a broader transcriptional network of C. glutamicum genes.
Evaluation and selection of tandem repeat loci for a Brucella MLVA typing assay
Authors: Le Flèche Philippe , Jacques Isabelle , Grayon Maggy , Al Dahouk Sascha , Bouchon Patrick , Denoeud France , Nöckler Karsten , Neubauer Heinrich , Guilloteau Laurence A , Vergnaud Gilles
Published: February 2006

Background

The classification of Brucella into species and biovars relies on phenotypic characteristics and sometimes raises difficulties in the interpretation of the results due to an absence of standardization of the typing reagents. In addition, the resolution of this biotyping is moderate and requires the manipulation of the living agent. More efficient DNA-based methods are needed, and this work explores the suitability of multiple locus variable number tandem repeats analysis (MLVA) for both typing and species identification.

Results

Eighty tandem repeat loci predicted to be polymorphic by genome sequence analysis of three available Brucella genome sequences were tested for polymorphism by genotyping 21 Brucella strains (18 reference strains representing the six 'classical' species and all biovars as well as 3 marine mammal strains currently recognized as members of two new species). The MLVA data efficiently cluster the strains as expected according to their species and biovar. For practical use, a subset of 15 loci preserving this clustering was selected and applied to the typing of 236 isolates. Using this MLVA-15 assay, the clusters generated correspond to the classical biotyping scheme of Brucella spp. The 15 markers have been divided into two groups, one comprising 8 user-friendly minisatellite markers with a good species identification capability (panel 1) and another complementary group of 7 microsatellite markers with higher discriminatory power (panel 2).

Conclusion

The MLVA-15 assay can be applied to large collections of Brucella strains with automated or manual procedures, and can be proposed as a complement, or even a substitute, of classical biotyping methods. This is facilitated by the fact that MLVA is based on non-infectious material (DNA) whereas the biotyping procedure itself requires the manipulation of the living agent. The data produced can be queried on a dedicated MLVA web service site.
Are osteoporotic fractures being adequately investigated?: A questionnaire of GP & orthopaedic surgeons
Authors: Chami George , Jeys Lee , Freudmann Mathew , Connor Louise , Siddiqi Mashood
Published: February 2006

Background

To investigate the current practice of Orthopaedic Surgeons & General Practitioners (GP) when presented with patients who have a fracture, with possible underlying Osteoporosis.

Methods

Questionnaires were sent to 140 GPs and 140 Orthopaedic Surgeons. The participants were asked their routine clinical practice with regard to investigation of underlying osteoporosis in 3 clinical scenarios.

55 year old lady with a low trauma Colles fracture

60 year old lady with a vertebral wedge fracture

70 year old lady with a low trauma neck of femur fracture.

Results

Most doctors agreed that patients over 50 years old with low trauma fractures required investigation for osteoporosis, however, most surgeons (56%, n = 66) would discharge patients with low trauma Colles fracture without requesting or initiating investigation for osteoporosis. Most GPs (67%, n = 76) would not investigate a similar patient for osteoporosis, unless prompted by the Orthopaedic Surgeon or patient.

More surgeons (71%, n= 83) and GPs (64%, n = 72) would initiate investigations for osteoporosis in a vertebral wedge fracture, but few surgeons (35%, n = 23) would investigate a neck of femur fracture patient after orthopaedic treatment.

Conclusion

Most doctors know that fragility fractures in patients over 50 years old require investigation for Osteoporosis; however, a large population of patients with osteoporotic fractures are not being given the advantages of secondary prevention.
Gene expression profiles in developing nephrons using Lim1 metanephric mesenchyme-specific conditional mutant mice
Authors: Chen You-Tzung , Kobayashi Akio , Kwan Kin Ming , Johnson Randy L , Behringer Richard R
Published: February 2006

Background

Lim1 is a homeobox gene that is essential for nephrogenesis. During metanephric kidney development, Lim1 is expressed in the nephric duct, ureteric buds, and the induced metanephric mesenchyme. Conditional ablation of Lim1 in the metanephric mesenchyme blocks the formation of nephrons at the nephric vesicle stage, leading to the production of small, non-functional kidneys that lack nephrons.

Methods

In the present study, we used Affymetrix probe arrays to screen for nephron-specific genes by comparing the expression profiles of control and Lim1 conditional mutant kidneys. Kidneys from two developmental stages, embryonic day 14.5 (E14.5) and 18.5 (E18.5), were examined.

Results

Comparison of E18.5 kidney expression profiles generated a list of 465 nephron-specific gene candidates that showed a more than 2-fold increase in their expression level in control kidney versus the Lim1 conditional mutant kidney. Computational analysis confirmed that this screen enriched for kidney-specific genes. Furthermore, at least twenty-eight of the top fifty (56%) candidates (or their vertebrate orthologs) were previously reported to have a nephron-specific expression pattern. Our analysis of E14.5 expression data yielded 41 candidate genes that are up-regulated in the control kidneys compared to the conditional mutants. Three of them are related to the Notch signaling pathway that is known to be important in cell fate determination and nephron patterning.

Conclusion

Therefore, we demonstrate that Lim1 conditional mutant kidneys serve as a novel tissue source for comprehensive expression studies and provide a means to identify nephron-specific genes.
Study protocol to investigate the effect of a lifestyle intervention on body weight, psychological health status and risk factors associated with disease recurrence in women recovering from breast cancer treatment [ISRCTN08045231]
Authors: Saxton John M , Daley Amanda , Woodroofe Nicola , Coleman Robert , Powers Hilary , Mutrie Nanette , Siddall Vanessa , Crank Helen
Published: February 2006

Background

Breast cancer survivors often encounter physiological and psychological problems related to their diagnosis and treatment that can influence long-term prognosis. The aim of this research is to investigate the effects of a lifestyle intervention on body weight and psychological well-being in women recovering from breast cancer treatment, and to determine the relationship between changes in these variables and biomarkers associated with disease recurrence and survival.

Methods/design

Following ethical approval, a total of 100 patients will be randomly assigned to a lifestyle intervention (incorporating dietary energy restriction in conjunction with aerobic exercise training) or normal care control group. Patients randomised to the dietary and exercise intervention will be given individualised healthy eating dietary advice and written information and attend moderate intensity aerobic exercise sessions on three to five days per week for a period of 24 weeks. The aim of this strategy is to induce a steady weight loss of up to 0.5 Kg each week. In addition, the overall quality of the diet will be examined with a view to (i) reducing the dietary intake of fat to ~25% of the total calories, (ii) eating at least 5 portions of fruit and vegetables a day, (iii) increasing the intake of fibre and reducing refined carbohydrates, and (iv) taking moderate amounts of alcohol. Outcome measures will include body weight and body composition, psychological health status (stress and depression), cardiorespiratory fitness and quality of life. In addition, biomarkers associated with disease recurrence, including stress hormones, estrogen status, inflammatory markers and indices of innate and adaptive immune function will be monitored.

Discussion

This research will provide valuable information on the effectiveness of a practical, easily implemented lifestyle intervention for evoking positive effects on body weight and psychological well-being, two important factors that can influence long-term prognosis in breast cancer survivors. However, the added value of the study is that it will also evaluate the effects of the lifestyle intervention on a range of biomarkers associated with disease recurrence and survival. Considered together, the results should improve our understanding of the potential role that lifestyle-modifiable factors could play in saving or prolonging lives.
Signs of positive selection of somatic mutations in human cancers detected by EST sequence analysis
Authors: Babenko Vladimir N , Basu Malay K , Kondrashov Fyodor A , Rogozin Igor B , Koonin Eugene V
Published: February 2006

Background

Carcinogenesis typically involves multiple somatic mutations in caretaker (DNA repair) and gatekeeper (tumor suppressors and oncogenes) genes. Analysis of mutation spectra of the tumor suppressor that is most commonly mutated in human cancers, p53, unexpectedly suggested that somatic evolution of the p53 gene during tumorigenesis is dominated by positive selection for gain of function. This conclusion is supported by accumulating experimental evidence of evolution of new functions of p53 in tumors. These findings prompted a genome-wide analysis of possible positive selection during tumor evolution.

Methods

A comprehensive analysis of probable somatic mutations in the sequences of Expressed Sequence Tags (ESTs) from malignant tumors and normal tissues was performed in order to access the prevalence of positive selection in cancer evolution. For each EST, the numbers of synonymous and non-synonymous substitutions were calculated. In order to identify genes with a signature of positive selection in cancers, these numbers were compared to: i) expected numbers and ii) the numbers for the respective genes in the ESTs from normal tissues.

Results

We identified 112 genes with a signature of positive selection in cancers, i.e., a significantly elevated ratio of non-synonymous to synonymous substitutions, in tumors as compared to 37 such genes in an approximately equal-sized EST collection from normal tissues. A substantial fraction of the tumor-specific positive-selection candidates have experimentally demonstrated or strongly predicted links to cancer.

Conclusion

The results of EST analysis should be interpreted with extreme caution given the noise introduced by sequencing errors and undetected polymorphisms. Furthermore, an inherent limitation of EST analysis is that multiple mutations amenable to statistical analysis can be detected only in relatively highly expressed genes. Nevertheless, the present results suggest that positive selection might affect a substantial number of genes during tumorigenic somatic evolution.
Inflammation and enhanced nociceptive responses to bladder distension produced by intravesical zymosan in the rat
Authors: Randich Alan , Uzzell Tyler , Cannon Ronda , Ness Timothy J
Published: February 2006

Background

Mycotic infections of the bladder produce pain and inflammatory changes. The present study examined the inflammatory and nociceptive effects of the yeast cell wall component, zymosan, when admininstered into the urinary bladder in order to characterize this form of bladder sensitization.

Methods

Parametric analyses of the time-course (0–48 hr) and concentration (0–2% solutions) variables associated with intravesical zymosan-induced bladder inflammation were performed in female rats. Plasma extravasation of Evan's Blue dye was used as a measure of tissue inflammation. Cardiovascular and visceromotor responses to urinary bladder distension were used as measures of nociception.

Results

Zymosan-induced bladder inflammation, as indexed by plasma extravasation of Evan's Blue, was significantly greater in rats treated with either 1 or 2% solutions as compared to either 0.1 or 0.5% zymosan solutions. In time-course studies (1 – 48 hr post-treatment), 1% zymosan-induced inflammation progressively increased with time following administration, was greatest at 24 hr and began to normalize by 48 hr. In the studies of inflammation-induced changes in nociception, arterial blood pressure (ABP) and visceromotor responses to graded distension of the urinary bladder were significantly increased relative to controls 24 hr after zymosan administration.

Conclusion

These studies provide important time-course and solution concentration parameters for studies of zymosan-induced inflammation of the bladder and suggest utility of this model for the study of bladder-related pain.
Uncharged isocoumarin-based inhibitors of urokinase-type plasminogen activator
Authors: Heynekamp Justin J , Hunsaker Lucy A , Vander Jagt Thomas A , Deck Lorraine M , Vander Jagt David L
Published: February 2006

Background

Urokinase-type plasminogen activator (uPA) plays a major role in extracellular proteolytic events associated with tumor cell growth, migration and angiogenesis. Consequently, uPA is an attractive target for the development of small molecule active site inhibitors. Most of the recent drug development programs aimed at nonpeptidic inhibitors targeted at uPA have focused on arginino mimetics containing amidine or guanidine functional groups attached to aromatic or heterocyclic scaffolds. There is a general problem of limited bioavailability of these charged inhibitors. In the present study, uPA inhibitors were designed on an isocoumarin scaffold containing uncharged substituents.

Results

4-Chloro-3-alkoxyisocoumarins were synthesized in which the 3-alkoxy group contained a terminal bromine; these were compared with similar inhibitors that contained a charged terminal functional group. Additional variations included functional groups attached to the seven position of the isocoumarin scaffold. N- [3-(3-Bromopropoxy)-4-chloro-1-oxo-1H-isochromen-7-yl]benzamide was identified as an uncharged lead inhibitor of uPA, Ki = 0.034 μM. Molecular modeling of human uPA with these uncharged inhibitors suggests that the bromine occupies the same position as positively charged arginino mimetic groups.

Conclusion

This study demonstrates that potent uncharged inhibitors of uPA can be developed based upon the isocoumarin scaffold. A tethered bromine in the three position and an aromatic group in the seven position are important contributors to binding. Although the aim was to develop compounds that act as mechanism-based inactivators, these inhibitors are competitive reversible inhibitors.
Nurses' perceptions and experiences of communication in the operating theatre: a focus group interview
Authors: Nestel Debra , Kidd Jane
Published: February 2006

Nurses' perceptions and experiences of communication in the operating theatre: a focus group interview

Background

Communication programmes are well established in nurse education. The focus of programmes is most often on communicating with patients with less attention paid to inter-professional communication or skills essential for working in specialised settings. Although there are many anecdotal reports of communication within the operating theatre, there are few empirical studies. This paper explores communication behaviours for effective practice in the operating theatre as perceived by nurses and serves as a basis for developing training.

Methods

A focus group interview was conducted with seven experienced theatre nurses from a large London teaching hospital. The interview explored their perceptions of the key as well as unique features of effective communication skills in the operating theatre. Data was transcribed and thematically analysed until agreement was achieved by the two authors.

Results

There was largely consensus on the skills deemed necessary for effective practice including listening, clarity of speech and being polite. Significant influences on the nature of communication included conflict in role perception and organisational issues. Nurses were often expected to work outside of their role which either directly or indirectly created barriers for effective communication. Perceptions of a lack of collaborative team effort also influenced communication.

Conclusion

Although fundamental communication skills were identified for effective practice in the operating theatre, there were significant barriers to their use because of confusion over clarity of roles (especially nurses' roles) and the implications for teamwork. Nurses were dissatisfied with several aspects of communication. Future studies should explore the breadth and depth of this dissatisfaction in other operating theatres, its impact on morale and importantly on patient safety. Interprofessional communication training for operating theatre staff based in part on the key issues identified in this study may help to create clarity in roles and focus attention on effective teamwork and promote clinical safety.
Influence of head models on EEG simulations and inverse source localizations
Authors: Ramon Ceon , Schimpf Paul H , Haueisen Jens
Published: February 2006

Background

The structure of the anatomical surfaces, e.g., CSF and gray and white matter, could severely influence the flow of volume currents in a head model. This, in turn, will also influence the scalp potentials and the inverse source localizations. This was examined in detail with four different human head models.

Methods

Four finite element head models constructed from segmented MR images of an adult male subject were used for this study. These models were: (1) Model 1: full model with eleven tissues that included detailed structure of the scalp, hard and soft skull bone, CSF, gray and white matter and other prominent tissues, (2) the Model 2 was derived from the Model 1 in which the conductivity of gray matter was set equal to the white matter, i.e., a ten tissue-type model, (3) the Model 3 was derived from the Model 1 in which the conductivities of gray matter and CSF were set equal to the white matter, i.e., a nine tissue-type model, (4) the Model 4 consisted of scalp, hard skull bone, CSF, gray and white matter, i.e., a five tissue-type model. How model complexity influences the EEG source localizations was also studied with the above four finite element models of the head. The lead fields and scalp potentials due to dipolar sources in the motor cortex were computed for all four models. The inverse source localizations were performed with an exhaustive search pattern in the motor cortex area. The inverse analysis was performed by adding uncorrelated Gaussian noise to the scalp potentials to achieve a signal to noise ratio (SNR) of -10 to 30 dB. The Model 1 was used as a reference model.

Results

The reference model, as expected, performed the best. The Model 3, which did not have the CSF layer, performed the worst. The mean source localization errors (MLEs) of the Model 3 were larger than the Model 1 or 2. The scalp potentials were also most affected by the lack of CSF geometry in the Model 3. The MLEs for the Model 4 were also larger than the Model 1 and 2. The Model 4 and the Model 3 had similar MLEs in the SNR range of -10 dB to 0 dB. However, in the SNR range of 5 dB to 30 dB, the Model 4 has lower MLEs as compared with the Model 3.

Discussion

These results indicate that the complexity of head models strongly influences the scalp potentials and the inverse source localizations. A more complex head model performs better in inverse source localizations as compared to a model with lesser tissue surfaces. The CSF layer plays an important role in modifying the scalp potentials and also influences the inverse source localizations. In summary, for best results one needs to have highly heterogeneous models of the head for accurate simulations of scalp potentials and for inverse source localizations.
Electrical impedance tomography imaging using a priori ultrasound data
Authors: Soleimani Manuchehr
Published: February 2006

Background

Different imaging systems (e.g. electrical, magnetic, and ultrasound) rely on a wide variety of physical properties, and the datasets obtained from such systems provide only partial information about the unknown true state. One approach is to choose complementary imaging systems, and to combine the information to achieve a better representation.

Methods

This paper discusses the combination of ultrasound and electrical impedance tomography (EIT) information. Ultrasound reflection signals are good at locating sharp acoustic density changes associated with the boundaries of objects. Some boundaries, however, may be indeterminable due to masking from intermediate boundaries or because they are outside the ultrasound beam. Conversely, the EIT data contains relatively low-quality information, but it includes the whole region enclosed by the electrodes.

Results

Results are shown from a narrowband level-set method applied to 2D and 3D EIT incorporating limited angle ultrasound time of flight data.

Conclusion

The EIT reconstruction is shown to be faster and more accurate using the additional edge information from both one and four transducer ultrasound systems.
Merkel cell carcinoma
Authors: Koljonen Virve
Published: February 2006

Background

Merkel cell carcinoma (MCC) is an unusual primary neuroendocrine carcinoma of the skin. MCC is a fatal disease, and patients have a poor chance of survival. Moreover, MCC lacks distinguishing clinical features, and thus by the time the diagnosis is made, the tumour usually have metastasized. MCC mainly affects sun-exposed areas of elderly persons. Half of the tumours are located in the head and neck region.

Methods

MCC was first described in 1972. Since then, most of the cases reported, have been in small series of patients. Most of the reports concern single cases or epidemiological studies. The present study reviews the world literature on MCC. The purpose of this article is to shed light on this unknown neuroendocrine carcinoma and provide the latest information on prognostic markers and treatment options.

Results

The epidemiological studies have revealed that large tumour size, male sex, truncal site, nodal/distant disease at presentation, and duration of disease before presentation, are poor prognostic factors. The recommended initial treatment is extensive local excision. Adjuvant radiation therapy has recently been shown to improve survival. Thus far, no chemotherapy protocol have achieved the same objective.

Conclusion

Although rare, the fatality of this malignancy makes is important to understand the etiology and pathophysiology. During the last few years, the research on MCC has produced prognostic markers, which can be translated into clinical patient care.
Expression of early transcription factors Oct-4, Sox-2 and Nanog by porcine umbilical cord (PUC) matrix cells
Authors: Carlin Ryan , Davis Duane , Weiss Mark , Schultz Bruce , Troyer Deryl
Published: February 2006

Background

Three transcription factors that are expressed at high levels in embryonic stem cells (ESCs) are Nanog, Oct-4 and Sox-2. These transcription factors regulate the expression of other genes during development and are found at high levels in the pluripotent cells of the inner cell mass. The downregulation of these three transcription factors correlates with the loss of pluripotency and self-renewal, and the beginning of subsequent differentiation steps. The roles of Nanog, Oct-4 and Sox-2 have not been fully elucidated. They are important in embryonic development and maintenance of pluripotency in ESCs. We studied the expression of these transcription factors in porcine umbilical cord (PUC) matrix cells.

Methods

Cells were isolated from Wharton's jelly of porcine umbilical cords (PUC) and histochemically assayed for the presence of alkaline phosphatase and the presence of Nanog, Oct-4 and Sox-2 mRNA and protein. PCR amplicons were sequenced and compared with known sequences. The synthesis of Oct-4 and Nanog protein was analyzed using immunocytochemistry. FACS analysis was utilized to evaluate Hoechst 33342 dye-stained cells.

Results

PUC isolates were maintained in culture and formed colonies that express alkaline phosphatase. FACS analysis revealed a side population of Hoechst dye-excluding cells, the Hoechst exclusion was verapamil sensitive. Quantitative and non-quantitative RT-PCR reactions revealed expression of Nanog, Oct-4 and Sox-2 in day 15 embryonic discs, PUC cell isolates and porcine fibroblasts. Immunocytochemical analysis detected Nanog immunoreactivity in PUC cell nuclei, and faint labeling in fibroblasts. Oct-4 immunoreactivity was detected in the nuclei of some PUC cells, but not in fibroblasts.

Conclusion

Cells isolated from PUC express three transcription factors found in pluripotent stem cell markers both at the mRNA and protein level. The presence of these transcription factors, along with the other characteristics of PUC cells such as their colony-forming ability, Hoechst dye-excluding side population and alkaline phosphatase expression, suggests that PUC cells have properties of primitive pluripotent stem cells. Furthermore, PUC cells are an easily and inexpensively obtained source of stem cells that are not hampered by the ethical or legal issues associated with ESCs. In addition, these cells can be cryogenically stored and expanded.
Antimicrobial resistance of Escherichia coliisolates from broiler chickens and humans
Authors: Miles Tricia D , McLaughlin Wayne , Brown Paul D
Published: February 2006

Background

Antimicrobial usage is considered the most important factor promoting the emergence, selection and dissemination of antimicrobial-resistant microorganisms in both veterinary and human medicine. The aim of this study was to investigate the prevalence and genetic basis of tetracycline resistance in faecal Escherichia coli isolates from healthy broiler chickens and compare these data with isolates obtained from hospitalized patients in Jamaica.

Results

Eighty-two E. coli strains isolated from faecal samples of broiler chickens and urine and wound specimens of hospitalized patients were analyzed by agar disc diffusion to determine their susceptibility patterns to 11 antimicrobial agents. Tetracycline resistance determinants were investigated by plasmid profiling, transformations, and amplification of plasmid-borne resistance genes. Tetracycline resistance occurred at a frequency of 82.4% in avian isolates compared to 43.8% in human isolates. In addition, among avian isolates there was a trend towards higher resistance frequencies to kanamycin and nalidixic acid (p < 0.05), while a greater percentage of human isolates were resistant to chloramphenicol and gentamicin (p < 0.05). Multiple drug resistance was found in isolates from both sources and was usually associated with tetracycline resistance. Tetracycline-resistant isolates from both avian and human sources contained one or several plasmids, which were transmissible by transformation of chemically-competent E. coli. Tetracycline resistance was mediated by efflux genes tetB and/or tetD.

Conclusion

The present study highlights the prevalence of multiple drug resistant E. coli among healthy broiler chickens in Jamaica, possibly associated with expression of tetracycline resistance. While there did not appear to be a common source for multiple drug resistance in the strains from avian or human origin, the genes encoding resistance are similar. These results suggest that genes are disseminated in the environment and warrant further investigation of the possibility for avian sources acting as reservoirs for tetracycline resistance.
Importance of Uterine Cell Death, Renewal, and Their Hormonal Regulation in Hamsters that Show Progesterone-Dependent Implantation
Authors: Zhang Qian , Paria Bibhash C.
Published: February 2006

This study was initiated to investigate the significance of uterine cell death and proliferation during the estrous cycle and early pregnancy and their correlation with sex steroids in hamsters where blastocyst implantation occurs in only progesterone-primed uteri. The results obtained in hamsters were also compared with mice where blastocyst implantation occurs in progesterone-primed uteri if estrogen is provided. Apoptotic cells in the uterus were detected by using terminal deoxynucleotide transferase-mediated deoxyuridine triphosphate nick end labeling (TUNEL) technique. Uterine cell proliferation was determined by 5-bromo-2′-deoxyuridine labeling followed by immunohistochemistry and methyl-tritiated [3H]thymidine labeling. Active caspase-3, an executor protein of cell death, expression was assayed by immunohistochemistry/immunofluorescence. Our results demonstrate that epithelial proliferation on the second day after mating marks the initiation of pregnancy-related uterine changes in both species despite their differences in hormonal requirements. Hamsters and mice showed subtle differences in uterine proliferative and apoptotic patterns during early pregnancy and in response to steroids. There existed almost a direct correlation between apoptosis and caspase-3 expression, suggesting uterine cell death mostly involves the caspase pathway. Consistent with these findings, we showed, for the first time, that execution of uterine epithelial cell apoptosis by caspase-3 is important for blastocyst implantation because a caspsase-3 inhibitor N-acetyl-DEVD-CHO when instilled inside the uterine lumen on d 3 of pregnancy inhibits implantation in hamsters and mice. The overall results indicate that uterine cell apoptosis and proliferation patterns are highly ordered cell-specific phenomena that play an important role in maintaining the sexual cycle and pregnancy-associated uterine changes.
Gastric Inhibitory Polypeptide as an Endogenous Factor Promoting New Bone Formation after Food Ingestion
Authors: Tsukiyama Katsushi , Yamada Yuichiro , Yamada Chizumi , Harada Norio , Kawasaki Yukiko , Ogura Masahito , Bessho Kazuhisa , Li Minqi , Amizuka Norio , Sato Masahiro , Udagawa Nobuyuki , Takahashi Naoyuki , Tanaka Kiyoshi , Oiso Yutaka , Seino Yutaka
Published: February 2006

Calcium plays a fundamental role as second messenger in intracellular signaling and bone serves as the body’s calcium reserve to tightly maintain blood calcium levels. Calcium in ingested meal is the main supply and inadequate calcium intake causes osteoporosis and bone fracture. Here, we describe a novel mechanism of how ingested calcium is deposited on bone. Meal ingestion elicits secretion of the gut hormone gastric inhibitory polypeptide (GIP) from endocrine K cells in the duodenum. Bone histomorphometrical analyses revealed that bone formation parameters in the mice lacking GIP receptor (GIPR−/−) were significantly lower than those of wild-type (GIPR+/+) mice, and that the number of osteoclasts, especially multinuclear osteoclasts, was significantly increased in GIPR−/− mice, indicating that GIPR−/− mice have high-turnover osteoporosis. In vitro examination showed the percentage of osteoblastic cells undergoing apoptosis to be significantly decreased in the presence of GIP. Because GIPR−/− mice exhibited an increased plasma calcium concentration after meal ingestion, GIP directly links calcium contained in meal to calcium deposition on bone.
Sex-Dependent Liver Gene Expression Is Extensive and Largely Dependent upon Signal Transducer and Activator of Transcription 5b (STAT5b): STAT5b-Dependent Activation of Male Genes and Repression of Female Genes Revealed by Microarray Analysis
Authors: Clodfelter Karl H. , Holloway Minita G. , Hodor Paul , Park Soo-Hee , Ray William J. , Waxman David J.
Published: February 2006

Sexual dimorphism in mammalian liver contributes to sex differences in physiology, homeostasis, and steroid and foreign compound metabolism. Many sex-dependent liver genes are regulated by sex differences in pituitary GH secretion, with the transcription factor, signal transducer and activator of transcription (STAT5b), proposed to mediate signaling by the pulsatile, male plasma GH profile. Presently, a large-scale gene expression study was conducted using male and female mice, wild type and Stat5b inactivated, to characterize sex differences in liver gene expression and their dependence on STAT5b. The relative abundance of individual liver RNAs was determined for each sex-genotype combination by competitive hybridization to 23,574-feature oligonucleotide microarrays. Significant sex differences in hepatic expression were seen for 1603 mouse genes. Of 850 genes showing higher expression in males, 767 (90%) were down-regulated in STAT5b-deficient males. Moreover, of 753 genes showing female-predominant expression, 461 (61%) were up-regulated in STAT5b-deficient males. In contrast, approximately 90% of the sex-dependent genes were unaffected by STAT5b deficiency in females. Thus: 1) STAT5b is essential for sex-dependent liver gene expression, a characteristic of approximately 1600 mouse genes (4% of the genome); 2) male-predominant liver gene expression requires STAT5b, or STAT5b-dependent factors, which act in a positive manner; and 3) many female-predominant liver genes are repressed in males in a STAT5b-dependent manner. Several of the STAT5b-dependent male genes encode transcriptional repressors; these may include direct STAT5b targets that repress female-predominant genes in male liver. Several female-predominant repressors are elevated in STAT5b-deficient males; these may contribute to the major loss of male gene expression seen in the absence of STAT5b.
The Poet's Toys: Christopher Marlowe and the Liberties of Erotic Elegy
Authors: James Heather
Published: February 2006

Heather James is associate professor of English and comparative literature at the University of Southern California. She is author of Shakespeare's Troy: Drama, Politics, and the Translation of Empire (1997) and numerous essays on such topics as the politics of sympathy, absolutist jests and games, what Shakespeare's heroines want, and the political status of Ovid in the early modern period. She is also coeditor of the Norton Anthology of World Literature. Her essay “Royal Jokes and Sovereign Mystery in Castiglione and Marguerite de Navarre” appeared in the December 2003 issue of MLQ.
Democracy and Economics in Afghanistan: Is the Cart Before the Horse?
Authors: Frank Kevin K.
Published: February 2006

Kevin K. Frank is a captain in the US Navy. He served as the senior military intelligence officer in Afghanistan in 2004 and returned to Afghanistan for the elections of September 2005.
Bioinspired Electron-Transfer Systems and Applications
Authors: Fukuzumi Shunichi
Published: February 2006

Bioinspired electron-transfer systems including artificial photosynthesis and respiration are presented herein together with some of their applications. First, multi-step electron-transfer systems composed of electron donor–acceptor ensembles have been developed, mimicking functions of the photosynthetic reaction center. However, a significant amount of energy is lost during the multi-step electron-transfer processes. Then, as an alternative to conventional charge-separation functional molecular models based on multi-step long-range electron transfer within redox cascades, simple donor–acceptor dyads have been developed to attain a long-lived and high energy charge-separated state without significant loss of excitation energy, by fine control of the redox potentials and of the geometry of donor–acceptor dyads that have small reorganization energies of electron transfer. Such simple molecular dyads, capable of fast charge separation but extremely slow charge recombination, have significant advantages with regard to synthetic feasibility, providing a variety of applications including construction of organic solar cells and development of efficient photocatalytic systems for the solar energy conversion. An efficient four-electron reduction of dioxygen to water by one-electron reductants such as ferrocene derivatives as well as by an NADH analog has also been achieved as a respiration model by using a cofacial dicobalt porphyrin that can form the μ-peroxo Co(III)–O2–Co(III) complex. The catalytic mechanism of the four-electron reduction of dioxygen has been clarified based on the detailed kinetic study and the detection of the intermediate.