bluuebunny/crossref_metadata_2025 huggingface dataset:
Temperature Switch PCR (TSP): Robust assay design for reliable amplification and genotyping of SNPs
Authors: Tabone Tania , Mather Diane E , Hayden Matthew J
Published: December 2009

Background

Many research and diagnostic applications rely upon the assay of individual single nucleotide polymorphisms (SNPs). Thus, methods to improve the speed and efficiency for single-marker SNP genotyping are highly desirable. Here, we describe the method of temperature-switch PCR (TSP), a biphasic four-primer PCR system with a universal primer design that permits amplification of the target locus in the first phase of thermal cycling before switching to the detection of the alleles. TSP can simplify assay design for a range of commonly used single-marker SNP genotyping methods, and reduce the requirement for individual assay optimization and operator expertise in the deployment of SNP assays.

Results

We demonstrate the utility of TSP for the rapid construction of robust and convenient endpoint SNP genotyping assays based on allele-specific PCR and high resolution melt analysis by generating a total of 11,232 data points. The TSP assays were performed under standardised reaction conditions, requiring minimal optimization of individual assays. High genotyping accuracy was verified by 100% concordance of TSP genotypes in a blinded study with an independent genotyping method.

Conclusion

Theoretically, TSP can be directly incorporated into the design of assays for most current single-marker SNP genotyping methods. TSP provides several technological advances for single-marker SNP genotyping including simplified assay design and development, increased assay specificity and genotyping accuracy, and opportunities for assay automation. By reducing the requirement for operator expertise, TSP provides opportunities to deploy a wider range of single-marker SNP genotyping methods in the laboratory. TSP has broad applications and can be deployed in any animal and plant species.
Direct sequencing and expression analysis of a large number of miRNAs in Aedes aegypti and a multi-species survey of novel mosquito miRNAs
Authors: Li Song , Mead Edward A , Liang Shaohui , Tu Zhijian
Published: December 2009

Background

MicroRNAs (miRNAs) are a novel class of gene regulators whose biogenesis involves hairpin structures called precursor miRNAs, or pre-miRNAs. A pre-miRNA is processed to make a miRNA:miRNA* duplex, which is then separated to generate a mature miRNA and a miRNA*. The mature miRNAs play key regulatory roles during embryonic development as well as other cellular processes. They are also implicated in control of viral infection as well as innate immunity. Direct experimental evidence for mosquito miRNAs has been recently reported in anopheline mosquitoes based on small-scale cloning efforts.

Results

We obtained approximately 130, 000 small RNA sequences from the yellow fever mosquito, Aedes aegypti, by 454 sequencing of samples that were isolated from mixed-age embryos and midguts from sugar-fed and blood-fed females, respectively. We also performed bioinformatics analysis on the Ae. aegypti genome assembly to identify evidence for additional miRNAs. The combination of these approaches uncovered 98 different pre-miRNAs in Ae. aegypti which could produce 86 distinct miRNAs. Thirteen miRNAs, including eight novel miRNAs identified in this study, are currently only found in mosquitoes. We also identified five potential revisions to previously annotated miRNAs at the miRNA termini, two cases of highly abundant miRNA* sequences, 14 miRNA clusters, and 17 cases where more than one pre-miRNA hairpin produces the same or highly similar mature miRNAs. A number of miRNAs showed higher levels in midgut from blood-fed female than that from sugar-fed female, which was confirmed by northern blots on two of these miRNAs. Northern blots also revealed several miRNAs that showed stage-specific expression. Detailed expression analysis of eight of the 13 mosquito-specific miRNAs in four divergent mosquito genera identified cases of clearly conserved expression patterns and obvious differences. Four of the 13 miRNAs are specific to certain lineage(s) within mosquitoes.

Conclusion

This study provides the first systematic analysis of miRNAs in Ae. aegypti and offers a substantially expanded list of miRNAs for all mosquitoes. New insights were gained on the evolution of conserved and lineage-specific miRNAs in mosquitoes. The expression profiles of a few miRNAs suggest stage-specific functions and functions related to embryonic development or blood feeding. A better understanding of the functions of these miRNAs will offer new insights in mosquito biology and may lead to novel approaches to combat mosquito-borne infectious diseases.
Exercise-induced motor improvement after complete spinal cord transection and its relation to expression of brain-derived neurotrophic factor and presynaptic markers
Authors: Macias Matylda , Nowicka Dorota , Czupryn Artur , Sulejczak Dorota , Skup Małgorzata , Skangiel-Kramska Jolanta , Czarkowska-Bauch Julita
Published: December 2009

Background

It has been postulated that exercise-induced activation of brain-derived neurotrophic factor (BDNF) may account for improvement of stepping ability in animals after complete spinal cord transection. As we have shown previously, treadmill locomotor exercise leads to up-regulation of BDNF protein and mRNA in the entire neuronal network of intact spinal cord. The questions arise: (i) how the treadmill locomotor training, supplemented with tail stimulation, affects the expression of molecular correlates of synaptic plasticity in spinal rats, and (ii) if a response is related to BDNF protein level and distribution.

We investigated the effect of training in rats spinalized at low thoracic segments on the level and distribution of BDNF immunoreactivity (IR) in ventral quadrants of the lumbar segments, in conjunction with markers of presynaptic terminals, synaptophysin and synaptic zinc.

Results

Training improved hindlimb stepping in spinal animals evaluated with modified Basso-Beattie-Bresnahan scale. Grades of spinal trained animals ranged between 5 and 11, whereas those of spinal were between 2 and 4. Functional improvement was associated with changes in presynaptic markers and BDNF distribution. Six weeks after transection, synaptophysin IR was reduced by 18% around the large neurons of lamina IX and training elevated its expression by over 30%. The level of synaptic zinc staining in the ventral horn was unaltered, whereas in ventral funiculi it was decreased by 26% postlesion and tended to normalize after the training. Overall BDNF IR levels in the ventral horn, which were higher by 22% postlesion, were unchanged after the training. However, training modified distribution of BDNF in the processes with its predominance in the longer and thicker ones. It also caused selective up-regulation of BDNF in two classes of cells (soma ranging between 100-400 μm2 and over 1000 μm2) of the ventrolateral and laterodorsal motor nuclei.

Conclusion

Our results show that it is not BDNF deficit that determines lack of functional improvement in spinal animals. They indicate selectivity of up-regulation of BDNF in distinct subpopulations of cells in the motor nuclei which leads to changes of innervation targeting motoneurons, tuned up by locomotor activity as indicated by a region-specific increase of presynaptic markers.
Satisfaction with care after total hip or knee replacement predicts self-perceived health status after surgery
Authors: Baumann Cédric , Rat Anne Christine , Osnowycz Georges , Mainard Didier , Cuny Christian , Guillemin Francis
Published: December 2009

Background

Inpatient satisfaction with care is a standard indicator of the quality of care delivered during hospitalization. Total hip and knee replacement (THR/TKR) for osteoarthritis (OA) are among the most successful orthopaedic interventions having a positive impact on health-related quality of life (HRQoL). The aim was to evaluate the effect of satisfaction shortly after hospital discharge on 1-month, 6-month and 1-year Medical Outcomes Study 36-item Short Form (SF-36) scores for OA patients after THR and TKR, controlling for patient characteristics, clinical presentation and preoperative SF-36 scores.

Methods

A multicenter prospective cohort study recruited 231 patients with OA scheduled to receive THR or TKR. Satisfaction was assessed by the Patients Judgment of Hospital Quality (PJHQ) questionnaire and HRQoL by the SF-36 questionnaire. Linear models for repeated measures assessed the relation between satisfaction (scores were dichotomized) and postoperative SF-36 scores.

Results

Of 231 participants, 189 were followed up 12 months after discharge (mean age 69 SD = 8; 42.6% male). The mean length of hospital stay was 13.5 (SD = 4) days. After adjustment for preoperative SF-36 scores, sociodemographic and clinical patient characteristics, satisfied patients (PJHQ score > 70) had higher SF-36 scores 1 year after surgery than did less-satisfied patients. Admission, medical care, and nursing and daily care scores mainly predicted bodily pain, mental health, social functioning, vitality and general health scores of the SF-36.

Conclusion

Besides being a quality-of-care indicator, immediate postoperative patient satisfaction with care may bring a new insight into clinical practice, as a predictor of self-perceived health status after surgery.
Microbial production host selection for converting second-generation feedstocks into bioproducts
Authors: Rumbold Karl , van Buijsen Hugo JJ , Overkamp Karin M , van Groenestijn Johan W , Punt Peter J , Werf Mariët J van der
Published: December 2009

Background

Increasingly lignocellulosic biomass hydrolysates are used as the feedstock for industrial fermentations. These biomass hydrolysates are complex mixtures of different fermentable sugars, but also inhibitors and salts that affect the performance of the microbial production host. The performance of six industrially relevant microorganisms, i.e. two bacteria (Escherichia coli and Corynebacterium glutamicum), two yeasts (Saccharomyces cerevisiae and Pichia stipitis) and two fungi (Aspergillus niger and Trichoderma reesei) were compared for their (i) ability to utilize monosaccharides present in lignocellulosic hydrolysates, (ii) resistance against inhibitors present in lignocellulosic hydrolysates, (iii) their ability to utilize and grow on different feedstock hydrolysates (corn stover, wheat straw, sugar cane bagasse and willow wood). The feedstock hydrolysates were generated in two manners: (i) thermal pretreatment under mild acid conditions followed by enzymatic hydrolysis and (ii) a non-enzymatic method in which the lignocellulosic biomass is pretreated and hydrolyzed by concentrated sulfuric acid. Moreover, the ability of the selected hosts to utilize waste glycerol from the biodiesel industry was evaluated.

Results

Large differences in the performance of the six tested microbial production hosts were observed. Carbon source versatility and inhibitor resistance were the major discriminators between the performances of these microorganisms. Surprisingly all 6 organisms performed relatively well on pretreated crude feedstocks. P. stipitis and A. niger were found to give the overall best performance C. glutamicum and S. cerevisiae were shown to be the least adapted to renewable feedstocks.

Conclusion

Based on the results obtained we conclude that a substrate oriented instead of the more commonly used product oriented approach towards the selection of a microbial production host will avoid the requirement for extensive metabolic engineering. Instead of introducing multiple substrate utilization and detoxification routes to efficiently utilize lignocellulosic hydrolysates only one biosynthesis route forming the product of interest has to be engineered.
Determination of the Plasmodium vivax relapse pattern in Camopi, French Guiana
Authors: Hanf Matthieu , Stéphani Aurélia , Basurko Célia , Nacher Mathieu , Carme Bernard
Published: December 2009

Background

Malaria is a major public health problem in French Guiana, where Plasmodium vivax has become the dominant malaria species since 2000. As in others endemic areas, it is important to specify the pattern of vivax malaria relapses and to try to discriminate efficiently re-infections from relapses.

Methods

This study was conducted in children born between January 1, 2001 and December 31, 2008 in Camopi, an Amerindian village located in the Amazon forest (n = 325), using an open cohort design. Primary and secondary attack rates of P. vivax were calculated using survival analysis. With the difference between the primary and secondary rates, this study aimed to estimate indirectly P. vivax relapse rate and evaluate its time evolution.

Results

Of the 1042 malaria attacks recorded, 689 (66%) were due to P. vivax (without mixed infection). One hundred and fifty one children had their primary attack with P. vivax and 106 had their two first attacks with P. vivax. In the absence of primaquine treatment, it was shown that P. vivax relapses mainly occurred during the first three months after the first attack. Thirty percent of children never had a relapse, 42% had a relapse before the first month after primary attack, 59% before the second month and 63% before the third month.

Conclusion

This study confirmed that the relapse pattern in Camopi was compatible with the pattern described for the P. vivax Chesson (tropical) strain. In addition, due to the relapse rate time evolution, a simple arbitrary classification rule could be constructed: before 90 days after the primary attack, the secondary attack is a relapse; after 90 days, it is a re-infection. Adapted management of malaria cases based on these results could be devised.
Haemoglobin interference and increased sensitivity of fluorimetric assays for quantification of low-parasitaemia Plasmodium infected erythrocytes
Authors: Moneriz Carlos , Marín-García Patricia , Bautista José M , Diez Amalia , Puyet Antonio
Published: December 2009

Background

Improvements on malarial diagnostic methods are currently needed for the correct detection in low-density Plasmodium falciparum infections. Microfluorimetric DNA-based assays have been previously used for evaluation of anti-malarial drug efficacy on Plasmodium infected erythrocytes. Several factors affecting the sensitivity of these methods have been evaluated, and tested for the detection and quantification of the parasite in low parasitaemia conditions.

Methods

Parasitaemia was assessed by measuring SYBRGreen I® (SGI) and PicoGreen® (PG) fluorescence of P. falciparum Dd2 cultures on human red blood cells. Different modifications of standard methods were tested to improve the detection sensitivity. Calculation of IC50 for chloroquine was used to validate the method.

Results

Removal of haemoglobin from infected red-blood cells culture (IRBC) increased considerably the fluorescent signal obtained from both SGI and PG. Detergents used for cell lysis also showed to have an effect on the fluorescent signal. Upon depletion of haemoglobin and detergents the fluorescence emission of SGI and PG increased, respectively, 10- and 60-fold, extending notably the dynamic range of the assay. Under these conditions, a 20-fold higher PG vs. SGI fluorescent signal was observed. The estimated limits of detection and quantification for the PG haemoglobin/detergent-depleted method were 0.2% and 0.7% parasitaemia, respectively, which allow the detection of ~10 parasites per microliter. The method was validated on whole blood-infected samples, displaying similar results as those obtained using IRBC. Removal of white-blood cells prior to the assay allowed to increase the accuracy of the measurement, by reducing the relative uncertainty at the limit of detection from 0.5 to 0.1.

Conclusion

The use of PG microassays on detergent-free, haemoglobin-depleted samples appears as the best choice both for the detection of Plasmodium in low-density infections and anti-malarial drugs tests.
Involvement of cyclin B1 in progesterone-mediated cell growth inhibition, G2/M cell cycle arrest, and apoptosis in human endometrial cell
Authors: Tang Li , Zhang Yu , Pan Hong , Luo Qiong , Zhu Xiao-Ming , Dong Min-Yue , Leung Peter CK , Sheng Jian-Zhong , Huang He-Feng
Published: December 2009

Background

Progesterone plays an important role in the proliferation and differentiation of human endometrial cells (hECs). Large-dose treatment with progesterone has been used for treatment of endometrial proliferative disorders. However, the mechanisms behind remain unknown.

Methods

To investigate the role of cyclin B1 in proliferation and differentiation of hECs in menstrual cycle, the expression of cyclin B1 throughout the menstrual cycle was evaluated in hECs. To determine the effects of progesterone on the proliferation, cell cycle progression and apoptosis of hECs and to test if cyclin B1 is involved in these effects, progesterone and/or Alsterpaullone (Alp, a specific inhibitor of Cyclin B1/Cdc2) were added to primary hECs. Cellular proliferation was evaluated with MTT test, cell cycle with propidium iodide (PI) staining and flow cytometry, apoptosis with FITC-Annexin V and the expression of cyclin B1 with Western blotting.

Results

The expression level of cyclin B1 in secretory endometria was significantly lower than in proliferative endometria (p < 0.01). Progesterone significantly inhibited the growth of hECs in a concentration-dependent manner (P < 0.01). The treatment with progesterone significantly decreased the expression of cyclin B1, increased the proportions of cell in G2/M phase, and apoptotic cells (P < 0.05 for all). The presence of Alp significantly enhanced the effects of progesterone on cyclin B1 down-regulation, G2/M cell cycle arrest and induction of apoptosis (P < 0.01 for all).

Conclusion

Our findings suggest that cyclin B1 is a critical factor in proliferation and differentiation of hECs. Progesterone may inhibit cell proliferation, mediate G2/M cell cycle arrest and induce apoptosis in hECs via down-regulating Cyclin B1.
Initiation of the expression of peroxisome proliferator - activated receptor gamma (PPAR gamma) in the rat ovary and the role of FSH
Authors: Long Mary J , Sairam M Ram , Komar Carolyn M
Published: December 2009

PPARgamma is highly expressed in granulosa cells by 23 days post-partum (pp) and is down-regulated in response to the LH surge. We tested the hypothesis that high levels of FSH during the neonatal period trigger the expression of PPARgamma. To determine when PPARgamma expression is initiated, ovaries were collected from neonatal rats. Messenger RNA for PPARgamma was undetectable on day 1, low from days 5-14, and increased by day 19 pp (p < 0.05). PPARgamma was detected in select granulosa cells in primary/early secondary follicles. Messenger RNA for the FSH receptor was detected as early as day 1 and remained steady throughout day 19 pp. The FSH receptor was detected by immunoblot analysis in ovaries collected 1, 2, and 5-9 days pp. In a subsequent experiment, neonatal rats were treated with acyline (GnRH antagonist) which significantly reduced FSH (p < 0.05) but not levels of mRNA for PPARgamma. The role of FSH in the induction of PPARgamma expression was further assessed in ovarian tissue from FORKO mice. Both mRNA and protein for PPARgamma were identified in ovarian tissue from FORKO mice. In summary, the FSH/FSH receptor system is present in granulosa cells prior to the onset of expression of PPARgamma. Reducing FSH during the neonatal period, or the ability to respond to FSH, did not decrease expression of mRNA for PPARgamma. These data indicate that FSH is not a primary factor initiating the expression of PPARgamma and that other agents play a role in activating its expression in the ovary.
Multiple non-cell-autonomous defects underlie neocortical callosal dysgenesis in Nfib-deficient mice
Authors: Piper Michael , Moldrich Randal X , Lindwall Charlotta , Little Erica , Barry Guy , Mason Sharon , Sunn Nana , Kurniawan Nyoman Dana , Gronostajski Richard M , Richards Linda J
Published: December 2009

Background

Agenesis of the corpus callosum is associated with many human developmental syndromes. Key mechanisms regulating callosal formation include the guidance of axons arising from pioneering neurons in the cingulate cortex and the development of cortical midline glial populations, but their molecular regulation remains poorly characterised. Recent data have shown that mice lacking the transcription factor Nfib exhibit callosal agenesis, yet neocortical callosal neurons express only low levels of Nfib. Therefore, we investigate here how Nfib functions to regulate non-cell-autonomous mechanisms of callosal formation.

Results

Our investigations confirmed a reduction in glial cells at the midline in Nfib-/- mice. To determine how this occurs, we examined radial progenitors at the cortical midline and found that they were specified correctly in Nfib mutant mice, but did not differentiate into mature glia. Cellular proliferation and apoptosis occurred normally at the midline of Nfib mutant mice, indicating that the decrease in midline glia observed was due to deficits in differentiation rather than proliferation or apoptosis. Next we investigated the development of callosal pioneering axons in Nfib-/- mice. Using retrograde tracer labelling, we found that Nfib is expressed in cingulate neurons and hence may regulate their development. In Nfib-/- mice, neuropilin 1-positive axons fail to cross the midline and expression of neuropilin 1 is diminished. Tract tracing and immunohistochemistry further revealed that, in late gestation, a minor population of neocortical axons does cross the midline in Nfib mutants on a C57Bl/6J background, forming a rudimentary corpus callosum. Finally, the development of other forebrain commissures in Nfib-deficient mice is also aberrant.

Conclusion

The formation of the corpus callosum is severely delayed in the absence of Nfib, despite Nfib not being highly expressed in neocortical callosal neurons. Our results indicate that in addition to regulating the development of midline glial populations, Nfib also regulates the expression of neuropilin 1 within the cingulate cortex. Collectively, these data indicate that defects in midline glia and cingulate cortex neurons are associated with the callosal dysgenesis seen in Nfib-deficient mice, and provide insight into how the development of these cellular populations is controlled at a molecular level.
Altemeier operation associated with dynamic graciloplasty: a case report
Authors: Mongardini Massimo , Iachetta Roberto Paolo , Cola Alessandra , Effetti Eleonora Degli , Custureri Filippo
Published: December 2009

Introduction

More than 80% of patients with full-thickness rectal prolapse have co-existing fecal incontinence. Choosing the ideal surgical strategy is always a difficult task. We combined an Altemeier rectosigmoid resection with anal dynamic graciloplasty to provide a functional neosphincter. We found no published reports describing this surgical association.

Case presentation

We report the case of a 72-year-old Caucasian woman with full-thickness rectal prolapse associated with fecal incontinence from severe neuromuscular damage.

Conclusion

Combined dynamic graciloplasty and an Altemeier operation could be a valid therapeutic option in patients with severe rectal prolapse with fecal incontinence from severe neurogenic damage.
Antimicrobial effect of silver-impregnated cellulose: potential for antimicrobial therapy
Authors: Kim Juyoung , Kwon Soonjo , Ostler Erik
Published: December 2009

Background

Silver has long been known to have antimicrobial activity. To incorporate this property into multiple applications, a silver-impregnated cellulose (SIC) with low cytotoxicity to human cells was developed. SIC differs from other silver treatment methods in that the leaching of silver particles is non-existent and the release of ionic silver is highly controlled.

Results

Candida albicans, Micrococcus luteu, Pseudomonas putida, and Escherichia coli were used for antimicrobial testing. No microbial cells were able to grow in the presence of SIC at concentrations above 0.0035 Ag w/v %. Even at a concentration of 0.00035 Ag w/v %, P. putida and M. luteu failed to grow, and C. albicans and E. coli exhibited diminished growth. To determine the cytotoxic effect of silver on human cells, five different concentrations of SIC were tested on human fibroblasts. In SIC concentrations of 0.035 Ag w/v % and below, no cytotoxicity was observed.

Conclusion

The optimal concentration of SIC for a broad range of anti-microbial activity and low or negligible cytotoxicity was 0.0035 Ag w/v %. Although the highly controlled releasing characteristics of SIC would prove a substantial improvement over current technologies, further investigation for genotoxicity and other biocompatibility test will be required.
The impacts of pretreatment on the fermentability of pretreated lignocellulosic biomass: a comparative evaluation between ammonia fiber expansion and dilute acid pretreatment
Authors: Lau Ming W , Gunawan Christa , Dale Bruce E
Published: December 2009

Background

Pretreatment chemistry is of central importance due to its impacts on cellulosic biomass processing and biofuels conversion. Ammonia fiber expansion (AFEX) and dilute acid are two promising pretreatments using alkaline and acidic pH that have distinctive differences in pretreatment chemistries.

Results

Comparative evaluation on these two pretreatments reveal that (i) AFEX-pretreated corn stover is significantly more fermentable with respect to cell growth and sugar consumption, (ii) both pretreatments can achieve more than 80% of total sugar yield in the enzymatic hydrolysis of washed pretreated solids, and (iii) while AFEX completely preserves plant carbohydrates, dilute acid pretreatment at 5% solids loading degrades 13% of xylose to byproducts.

Conclusion

The selection of pretreatment will determine the biomass-processing configuration, requirements for hydrolysate conditioning (if any) and fermentation strategy. Through dilute acid pretreatment, the need for hemicellulase in biomass processing is negligible. AFEX-centered cellulosic technology can alleviate fermentation costs through reducing inoculum size and practically eliminating nutrient costs during bioconversion. However, AFEX requires supplemental xylanases as well as cellulase activity. As for long-term sustainability, AFEX has greater potential to diversify products from a cellulosic biorefinery due to lower levels of inhibitor generation and lignin loss.
3PFDB - A database of Best Representative PSSM Profiles (BRPs) of Protein Families generated using a novel data mining approach
Authors: Shameer Khader , Nagarajan Paramasivam , Gaurav Kumar , Sowdhamini Ramanathan
Published: December 2009

Background

Protein families could be related to each other at broad levels that group them as superfamilies. These relationships are harder to detect at the sequence level due to high evolutionary divergence. Sequence searches are strongly directed and influenced by the best representatives of families that are viewed as starting points. PSSMs are useful approximations and mathematical representations of protein alignments, with wide array of applications in bioinformatics approaches like remote homology detection, protein family analysis, detection of new members and evolutionary modelling. Computational intensive searches have been performed using the neural network based sensitive sequence search method called FASSM to identify the Best Representative PSSMs for families reported in Pfam database version 22.

Results

We designed a novel data mining approach for the assessment of individual sequences from a protein family to identify a single Best Representative PSSM profile (BRP) per protein family. Using the approach, a database of protein family-specific best representative PSSM profiles called 3PFDB has been developed. PSSM profiles in 3PFDB are curated using performance of individual sequence as a reference in a rigorous scoring and coverage analysis approach using FASSM. We have assessed the suitability of 10, 85,588 sequences derived from seed or full alignments reported in Pfam database (Version 22). Coverage analysis using FASSM method is used as the filtering step to identify the best representative sequence, starting from full length or domain sequences to generate the final profile for a given family. 3PFDB is a collection of best representative PSSM profiles of 8,524 protein families from Pfam database.

Conclusion

Availability of an approach to identify BRPs and a curated database of best representative PSI-BLAST derived PSSMs for 91.4% of current Pfam family will be a useful resource for the community to perform detailed and specific analysis using family-specific, best-representative PSSM profiles. 3PFDB can be accessed using the URL:http://caps.ncbs.res.in/3pfdb
Ectopic thymoma of the lung; a rare case report and review of the literature
Authors: Skoutelis Kostas , Nikolopoulos Dimitrios D , Markopoulos Kostas , Chabipi Katerina , Stoungioti Sofia , Papastamatiou Miltiadis
Published: December 2009

Introduction

Ectopic thymoma is a rare neoplasm, which can be developed in various sites, with the lung being amongst the rarest.

Case presentation

In this paper, we present the case of a woman with a slow-growing ectopic thymoma, stemming from the visceral pleura of the upper lobe of the left lung anteriorly, extending into the left lung and the cardiac wall, invading the fatty tissue near the pericardium, notably without infiltrating the lung or cardiac parenchyma. The thymoma was successfully removed via thoracotomy.

Conclusion

Ectopic thymoma is an uncommon neoplasm. To our knowledge, a case of an ectopic thymoma stemming from the visceral pleura of the lung is extremely rare.
Changes in stroke volume induced by passive leg raising in spontaneously breathing patients: comparison between echocardiography and Vigileo™/FloTrac™ device
Authors: Biais Matthieu , Vidil Lionel , Sarrabay Philippe , Cottenceau Vincent , Revel Philippe , Sztark François
Published: December 2009

Introduction

Passive leg raising (PLR) is a simple reversible maneuver that mimics rapid fluid loading and increases cardiac preload. The effects of this endogenous volume expansion on stroke volume enable the testing of fluid responsiveness with accuracy in spontaneously breathing patients. However, this maneuver requires the determination of stroke volume with a fast-response device, because the hemodynamic changes may be transient. The Vigileo™ monitor (Vigileo™; Flotrac™; Edwards Lifesciences, Irvine, CA, USA) analyzes systemic arterial pressure wave and allows continuous stroke volume monitoring. The aims of this study were (i) to compare changes in stroke volume induced by passive leg raising measured with the Vigileo™ device and with transthoracic echocardiography and (ii) to compare their ability to predict fluid responsiveness.

Methods

Thirty-four patients with spontaneous breathing activity and considered for volume expansion were included. Measurements of stroke volume were obtained with transthoracic echocardiography (SV-TTE) and with the Vigileo™ (SV-Flotrac) in a semi-recumbent position, during PLR and after volume expansion (500 ml saline). Patients were responders to volume expansion if SV-TTE increased ≥ 15%.

Results

Four patients were excluded. No patients received vasoactive drugs. Seven patients presented septic hypovolemia. PLR-induced changes in SV-TTE and in SV-Flotrac were correlated (r2 = 0.56, P < 0.0001). An increase in SV-TTE ≥ 13% during PLR was predictive of response to volume expansion with a sensitivity of 100% and a specificity of 80%. An increase in SV-Flotrac ≥16% during PLR was predictive of response to volume expansion with a sensitivity of 85% and a specificity of 90%. There was no difference between the area under the ROC curve for PLR-induced changes in SV-TTE (AUC = 0.96 ± 0.03) or SV-Flotrac (AUC = 0.92 ± 0.05). Volume expansion-induced changes in SV-TTE correlated with volume expansion-induced changes in SV-Flotrac (r2 = 0.77, P < 0.0001). In all patients, the highest plateau value of SV-TTE recorded during PLR was obtained within the first 90 s following leg elevation, whereas it was 120 s for SV-Flotrac.

Conclusions

PLR-induced changes in SV-Flotrac are able to predict the response to volume expansion in spontaneously breathing patients without vasoactive support.
An efficient multiscale method for time-domain waveform tomography
Authors: Boonyasiriwat Chaiwoot , Valasek Paul , Routh Partha , Cao Weiping , Schuster Gerard T. , Macy Brian
Published: December 2009

This efficient multiscale method for time-domain waveform tomography incorporates filters that are more efficient than Hamming-window filters. A strategy for choosing optimal frequency bands is proposed to achieve computational efficiency in the time domain. A staggered-grid, explicit finite-difference method with fourth-order accuracy in space and second-order accuracy in time is used for forward modeling and the adjoint calculation. The adjoint method is utilized in inverting for an efficient computation of the gradient directions. In the multiscale approach, multifrequency data and multiple grid sizes are used to overcome somewhat the severe local minima problem of waveform tomography. The method is applied successfully to 1D and 2D heterogeneous models; it can accurately recover low- and high-wavenumber components of the velocity models. The inversion result for the 2D model demonstrates that the multiscale method is computationally efficient and converges faster than a conventional, single-scale method.
Fast simulation of triaxial borehole induction measurements acquired in axially symmetrical and transversely isotropic media
Authors: Wang Gong Li , Torres-Verdín Carlos , Gianzero Stan
Published: December 2009

We introduce and successfully test an efficient method to simulate triaxial borehole electromagnetic (EM) induction measurements acquired in axially symmetrical and transversely isotropic (TI) media. The method uses a Fourier series expansion to express the azimuthal dependence of EM fields and the source term whereby the essentially 3D problem collapses to a series of independent 2D problems. Each 2D problem is solved with a semianalytic method that uses normalized Bessel functions and normalized Hankel functions to express the radial dependence of EM fields, thereby improving numerical stability. In addition, use is made of amplitude and slope basis functions to describe the longitudinal dependence of EM fields to avoid grid refinement in the vicinity of horizontal formation boundaries. For validation, we compare the new simulation method to two 1D analytic methods in horizontally and radially layered formations, and to one 3D finite-difference method (3DFD) in multilayered formations that include borehole and invasion zones. Numerical results indicate that the method is accurate in formations with high conductivity contrasts compared to 1D methods and is more than ten times more efficient than the 3DFD method in multilayer formations.
Solow's 1956 Contribution in the Context of the Harrod-Domar Model
Authors: Hagemann Harald
Published: December 2009

Shortly after World War II growth theory came to occupy a central position in modern economics. Two of the most important early contributions were made by Harrod and Domar. Both aimed to extend Keynes's analysis in the General Theory into the long run by considering under what conditions a growing economy could realize full capacity utilization and full employment. Solow's neoclassical model came into existence as a reaction to the approaches by Harrod and Domar and some problems associated with it, as in particular the enormous instability. Solow saw the main reason for this “knife-edge” problem in the absence of any adjustment mechanism and based his alternative model on substitution between capital and labor in production and flexibility of factor prices. This article focuses on Solow's motivation and the main content of his approach in reaction to Harrod and Domar's impulse. Furthermore, focus is on the reactions by Harrod and Domar et al. as well as on the distinction between two different instability problems, namely, the divergence between the warranted and the natural rates of growth that marked Solow's starting point, and the divergence between the warranted and the actual rates of growth creating a business-cycle problem.
James Tobin and Growth Theory: Financial Factors and Long-Run Growth
Authors: Dimand Robert W. , Durlauf Steven N.
Published: December 2009

Although Tobin 1955 was one of the founding papers of the neoclassical one-sector growth model with smooth substitution between capital and labor, James Tobin's contributions to long-run growth theory throughout his career stood apart from other neoclassical growth models because of his emphasis on portfolio substitution between money and capital as a possible source of the non-neutrality of money even in the long run. This paper examines Tobin's contributions to growth theory over more than four decades and the relationship of his work to the evolution of modern growth economics.
Solow in the Tropics
Authors: Toye John
Published: December 2009

Although Robert Solow never applied his neoclassical growth model to an underdeveloped country, neither did he ever exclude underdeveloped countries from its scope. For a generation, the model's use to predict worldwide convergence in levels of per capita income provided the main link from growth theory to development economics. In the last two decades, augmented Solow models, endogenous growth models, and exercises in development accounting have proliferated. Nevertheless, it is argued, the formalization of development economics and the post-1980 dominance of neoclassical development economics at the World Bank were driven as much by the theory of trade distortions as by the revival of interest in growth models and growth accounting.
Hotelling, Rawls, Solow: How Exhaustible Resources Came to Be Integrated into the Neoclassical Growth Model
Authors: Erreygers Guido
Published: December 2009

Exhaustible resources were integrated into the neoclassical growth model in the early 1970s. This happened partly as a reaction to various reports focusing on the limits to growth. At a deeper level, the debate on Rawls's theory of justice in an intergenerational context and Hotelling's economics of exhaustible resources were crucial inputs. This paper concentrates on Solow's contribution to the integration. It also traces its influence on the economics profession, focusing on the Hartwick rule and the way in which economists think about sustainability.
Solovian and New Growth Theory from the Perspective of Allyn Young on Macroeconomic Increasing Returns
Authors: Sandilands Roger J.
Published: December 2009

This paper evaluates Solow's neoclassical growth model and related empirical estimates of the sources of growth. Invoking Allyn Young, it is argued that the fundamental sources of growth cannot be measured by the value of factor inputs (including research inputs) without reference to the overall growth of product demand in the economy that both induces and limits increased specialization. What is attributed to the factors—the value of their marginal products—is not a measure of their contribution. Integration does not give the social picture. Young's theory of macroeconomic increasing returns reveals the limitations of models that assume an aggregate production function exhibiting constant returns to scale while “augmented” by exogenous technical progress. His endogenously self-sustaining growth paradigm is also shown to differ in important respects (including in its policy implications) from modern endogenous growth theory.
Endogenous Growth: Valuable Advance, Substantive Misnomer
Authors: Baumol William J.
Published: December 2009

Endogenous growth theory has made many valuable contributions, perhaps most notably in providing the tools that permit more effective empirical investigation of the growth process. Its one shortcoming, which is stressed here, is its inability to live up to its name, for where it has failed is in describing the wheels, the balance springs, and the interactions of the various other critical components of the mechanism that drives the growth process. This is no criticism because that is not the legitimate task of macroeconomics, one of whose prime virtues lies in judicious suppression of such complicating details in order to permit a better grasp of the overall workings of the economic machine. Such details are the task of the microeconomist, whose work must supplement the macro insights so that, together, we will obtain a fuller understanding of the growth process and how it may be improved.
The Rise and Fall of Cross-Country Growth Regressions
Authors: Durlauf Steven N.
Published: December 2009

This paper discusses the history of the use of cross-country regressions in modern growth economics. These regressions continue to be the workhorse of empirical growth analysis even though their meaning continues to be controversial. I argue that the early interpretations of these regressions have proven to be inappropriate and led to substantial exaggeration of the evidentiary support for various new growth theories. On the other hand, I argue that these regressions have a valuable role to play in identifying the modern analog of stylized facts for growth behavior.
Plasma dispositions of ivermectin, doramectin and moxidectin following subcutaneous administration in rabbits
Authors: Gokbulut C , Biligili A , Kart A , Turgut C
Published: December 2009

This study evaluated the comparative plasma dispositions of ivermectin (IVM), doramectin (DRM) and moxidectin (MXD) following subcutaneous administration in rabbits. Fifteen New Zealand white rabbits were allocated into three groups of five animals each. The animals in each group received IVM, DRM or MXD by subcutaneous injection at a single dose of 0.3 mg/kg. Blood samples were collected at various times between 1 h and 40 days after treatment and the plasma samples were analysed by high-performance liquid chromatography using fluorescence detection. Moxidectin was absorbed faster from the injection site and reached the peak plasma concentration ( Cmax) significantly earlier than IVM and DRM. There was no significant difference in Cmax values among the three molecules, whereas the area under the concentration–time curves of DRM (258.40 ng.d/mL) and IVM (191.62 ng.d/mL) was significantly higher than that of MXD (83.17 ng.d/mL). The mean plasma residence time and terminal half-life ( t1/2λ z) were longer for DRM (7.52 and 4.48 days, respectively) and MXD (8.97 and 8.16 days, respectively) compared with IVM (4.73 and 2.75 days, respectively). Considering the pharmacokinetic parameters for the parent molecules, the persistence of DRM and MXD are significantly longer than IVM and this may have a positive effect on their efficacy in rabbits following subcutaneous administration or utility relating to interdosing interval.
Risky Sexual Behaviors Among Hispanic Young Adults In South Florida: Nativity, Age at Immigration And Gender Differences
Authors: Weiss Ursula Keller , Tillman Kathryn Harker
Published: December 2009

CONTEXT: U.S. Hispanics are disadvantaged compared with whites in regard to sexual health, particularly early sexual initiation and contraceptive use. It is unclear whether differences in nativity and immigration are associated with risky sexual behaviors.

METHODS: Data collected between 1998 and 2000 from a community sample in South Florida were analyzed to examine sexual behaviors among 709 Hispanic individuals aged 18–23. Associations between nativity and age at immigration and sexual behaviors were assessed separately by gender using chi‐square tests and analyses of covariance.

RESULTS: Smaller proportions of sexually experienced women who had immigrated to the United States before age six than of similar U.S.‐born women reported having had vaginal sex (83% vs. 91%) and oral sex (71% vs. 86%) in the past year. Compared with U.S.‐born women, those who had immigrated at age six or older reported lower levels of oral sex (66% vs. 86% of those with sexual experience) and drug use in conjunction with sex in the past year (mean score, 1.2 vs. 1.6 on a scale of 1–5), and a lower average lifetime number of sexual partners (2.0 vs. 3.7 in the sample overall). Immigrant men were no less likely than U.S.‐born men to engage in risky sexual behavior.

CONCLUSIONS: Given the diversity of nativity and immigration histories among Hispanics in the United States, it is important that research examine both factors. An understanding of their joint association with sexual activity, plus the conditioning effects of gender, could help professionals to develop effective education and prevention programs for young people who are at risk for engaging in potentially dangerous sexual behavior.
A Little Thing Called Love: Condom Use in High‐Risk Primary Heterosexual Relationships
Authors: Corbett A. Michelle , Dickson‐Gómez Julia , Hilario Helena , Weeks Margaret R.
Published: December 2009

CONTEXT:Condoms are less likely to be used in primary relationships than in other relationship types. An understanding of what women and men expect when entering into these relationships, as well as how they make decisions about condom use and other prevention behaviors, is essential to eff orts to curb the spread of HIV.

METHODS:Qualitative in‐depth interviews were conducted with 25 high‐risk heterosexual couples, including HIV‐serodiscordant couples, participating in a trial of the female condom in Hartford in 2004–2007. Data were codedand analyzed in an iterative inductive and deductive process.

RESULTS:Participants described nonuse of condoms as a strategy to fi nd and maintain a primary relationship, establish trust and increase intimacy. Many had unprotected intercourse while recognizing their risk of HIV and other STDs, placing their love for their partner and other emotional needs over concerns about their health. Several couples reduced their STD risk by practicing negotiated safety (i.e., using condoms until their serostatus had been determined) or similar strategies, including sharing sexual or drug use history, disclosing HIV test results and using condoms until they decided that their relationship would be monogamous.

CONCLUSIONS:HIV prevention approaches must recognize the importance of love and the needs that primary relationships satisfy if they are to be considered relevant by those at greatest risk. Negotiated safety and similar strategies may be an important risk reduction tool for heterosexuals, particularly those in HIV‐aff ected relationships, but their potential eff ectiveness may vary.