bluuebunny/crossref_metadata_2025 huggingface dataset:
Rehabilitation and acute exacerbations
Authors: Burtin C. , Decramer M. , Gosselink R. , Janssens W. , Troosters T.
Published: July 2011

Recent evidence indicates that acute exacerbations of chronic obstructive pulmonary disease aggravate the extrapulmonary consequences of the disease. Skeletal muscle dysfunction, a sustained decrease in exercise tolerance, enhanced symptoms of depression and fatigue are reported. Avoidance of physical activities is likely to be a key underlying mechanism and increases the risk of new exacerbations. Pulmonary rehabilitation is an intervention targeting these systemic consequences. Exercise strategies need to be adapted to the increased feelings of dyspnoea and fatigue.

This review aims to describe the systemic consequences of acute exacerbations and compiles evidence for the feasibility and effectiveness of different rehabilitation strategies to counteract these consequences during and/or immediately after the acute phase of the exacerbation. Resistance training and neuromuscular electrical stimulation have been applied safely in frail, hospitalised patients and have the potential to prevent muscle atrophy. Comprehensive pulmonary rehabilitation, including general exercise training, can be implemented immediately after the exacerbation, leading to a reduction in hospital admissions and an increase in exercise tolerance and quality of life. Self-management strategies play a crucial role in changing disease-related health behaviour and preventing hospital admissions.
DNACLUST: accurate and efficient clustering of phylogenetic marker genes
Authors: Ghodsi Mohammadreza , Liu Bo , Pop Mihai
Published: July 2011

Background

Clustering is a fundamental operation in the analysis of biological sequence data. New DNA sequencing technologies have dramatically increased the rate at which we can generate data, resulting in datasets that cannot be efficiently analyzed by traditional clustering methods.

This is particularly true in the context of taxonomic profiling of microbial communities through direct sequencing of phylogenetic markers (e.g. 16S rRNA) - the domain that motivated the work described in this paper. Many analysis approaches rely on an initial clustering step aimed at identifying sequences that belong to the same operational taxonomic unit (OTU). When defining OTUs (which have no universally accepted definition), scientists must balance a trade-off between computational efficiency and biological accuracy, as accurately estimating an environment's phylogenetic composition requires computationally-intensive analyses. We propose that efficient and mathematically well defined clustering methods can benefit existing taxonomic profiling approaches in two ways: (i) the resulting clusters can be substituted for OTUs in certain applications; and (ii) the clustering effectively reduces the size of the data-sets that need to be analyzed by complex phylogenetic pipelines (e.g., only one sequence per cluster needs to be provided to downstream analyses).

Results

To address the challenges outlined above, we developed DNACLUST, a fast clustering tool specifically designed for clustering highly-similar DNA sequences.

Given a set of sequences and a sequence similarity threshold, DNACLUST creates clusters whose radius is guaranteed not to exceed the specified threshold. Underlying DNACLUST is a greedy clustering strategy that owes its performance to novel sequence alignment and k- mer based filtering algorithms.

DNACLUST can also produce multiple sequence alignments for every cluster, allowing users to manually inspect clustering results, and enabling more detailed analyses of the clustered data.

Conclusions

We compare DNACLUST to two popular clustering tools: CD-HIT and UCLUST. We show that DNACLUST is about an order of magnitude faster than CD-HIT and UCLUST (exact mode) and comparable in speed to UCLUST (approximate mode). The performance of DNACLUST improves as the similarity threshold is increased (tight clusters) making it well suited for rapidly removing duplicates and near-duplicates from a dataset, thereby reducing the size of the data being analyzed through more elaborate approaches.
InterMitoBase: An annotated database and analysis platform of protein-protein interactions for human mitochondria
Authors: Gu Zuguang , Li Jie , Gao Song , Gong Ming , Wang Junling , Xu Hua , Zhang Chenyu , Wang Jin
Published: July 2011

Background

The mitochondrion is an essential organelle which plays important roles in diverse biological processes, such as metabolism, apoptosis, signal transduction and cell cycle. Characterizing protein-protein interactions (PPIs) that execute mitochondrial functions is fundamental in understanding the mechanisms underlying biological functions and diseases associated with mitochondria. Investigations examining mitochondria are expanding to the system level because of the accumulation of mitochondrial proteomes and human interactome. Consequently, the development of a database that provides the entire protein interaction map of the human mitochondrion is urgently required.

Results

InterMitoBase provides a comprehensive interactome of human mitochondria. It contains the PPIs in biological pathways mediated by mitochondrial proteins, the PPIs between mitochondrial proteins and non-mitochondrial proteins as well as the PPIs between mitochondrial proteins. The current version of InterMitoBase covers 5,883 non-redundant PPIs of 2,813 proteins integrated from a wide range of resources including PubMed, KEGG, BioGRID, HPRD, DIP and IntAct. Comprehensive curations have been made on the interactions derived from PubMed. All the interactions in InterMitoBase are annotated according to the information collected from their original sources, GenBank and GO. Additionally, InterMitoBase features a user-friendly graphic visualization platform to present functional and topological analysis of PPI networks identified. This should aid researchers in the study of underlying biological properties.

Conclusions

InterMitoBase is designed as an integrated PPI database which provides the most up-to-date PPI information for human mitochondria. It also works as a platform by integrating several on-line tools for the PPI analysis. As an analysis platform and as a PPI database, InterMitoBase will be an important database for the study of mitochondria biochemistry, and should be particularly helpful in comprehensive analyses of complex biological mechanisms underlying mitochondrial functions.
Genome-wide expression quantitative trait loci (eQTL) analysis in maize
Authors: Holloway Beth , Luck Stanley , Beatty Mary , Rafalski J-Antoni , Li Bailin
Published: July 2011

Background

Expression QTL analyses have shed light on transcriptional regulation in numerous species of plants, animals, and yeasts. These microarray-based analyses identify regulators of gene expression as either cis-acting factors that regulate proximal genes, or trans-acting factors that function through a variety of mechanisms to affect transcript abundance of unlinked genes.

Results

A hydroponics-based genetical genomics study in roots of a Zea mays IBM2 Syn10 double haploid population identified tens of thousands of cis-acting and trans-acting eQTL. Cases of false-positive eQTL, which results from the lack of complete genomic sequences from both parental genomes, were described. A candidate gene for a trans-acting regulatory factor was identified through positional cloning. The unexpected regulatory function of a class I glutamine amidotransferase controls the expression of an ABA 8'-hydroxylase pseudogene.

Conclusions

Identification of a candidate gene underlying a trans-eQTL demonstrated the feasibility of eQTL cloning in maize and could help to understand the mechanism of gene expression regulation. Lack of complete genome sequences from both parents could cause the identification of false-positive cis- and trans-acting eQTL.
Identification and characterization of microRNAs from Phaeodactylum tricornutum by high-throughput sequencing and bioinformatics analysis
Authors: Huang Aiyou , He Linwen , Wang Guangce
Published: July 2011

Background

Diatoms, which are important planktons widespread in various aquatic environments, are believed to play a vital role in primary production as well as silica cycling. The genomes of the pennate diatom Phaeodactylum tricornutum and the centric diatom Thalassiosira pseudonana have been sequenced, revealing some characteristics of the diatoms' mosaic genome as well as some features of their fatty acid metabolism and urea cycle, and indicating their unusual properties. To identify microRNAs (miRNAs) from P. tricornutum and to study their probable roles in nitrogen and silicon metabolism, we constructed and sequenced small RNA (sRNA) libraries from P. tricornutum under normal (PT1), nitrogen-limited (PT2) and silicon-limited (PT3) conditions.

Results

A total of 13 miRNAs were identified. They were probable P. tricornutum-specific novel miRNAs. These miRNAs were sequenced from P. tricornutum under normal, nitrogen-limited and/or silicon-limited conditions, and their potential targets were involved in various processes, such as signal transduction, protein amino acid phosphorylation, fatty acid biosynthetic process, regulation of transcription and so on.

Conclusions

Our results indicated that P. tricornutum contained novel miRNAs that have no identifiable homologs in other organisms and that they might play important regulator roles in P. tricornutum metabolism.
Evaluation of direct inoculation of the BD PHOENIX system from positive BACTEC blood cultures for both Gram-positive cocci and Gram-negative rods
Authors: Beuving Judith , van der Donk Christina FM , Linssen Catharina FM , Wolffs Petra FG , Verbon Annelies
Published: July 2011

Background

Rapid identification (ID) and antibiotic susceptibility testing (AST) of the causative micro-organism of bloodstream infections result in earlier targeting of antibiotic therapy.

In order to obtain results of ID and AST up to 24 hours earlier, we evaluated the accuracy of direct inoculation of the Phoenix system from positive blood cultures (BACTEC) by using Serum Separator Tubes to harvest bacteria from positive blood cultures. Results were compared to those of standard Phoenix procedure. Discrepancies between the two methods were resolved by using the API system, E-test or microbroth dilution.

Results

ID with the direct method was correct for 95.2% of all tested Enterobacteriaceae (n = 42) and 71.4% of Pseudomonas aeruginosa strains (n = 7).

AST with the direct method showed a categorical agreement for Gram-negative rods (GNR) of 99.0%, with 0.7% minor errors, 0.3% very major errors and no major errors. All antibiotics showed an agreement of >95%.

The direct method for AST of Staphylococcus (n = 81) and Enterococcus (n = 3) species showed a categorical agreement of 95.4%, with a minor error rate of 1.1%, a major error rate of 3.1% and a very major error rate of 0.4%. All antibiotics showed an agreement of >90%, except for trimethoprim-sulfamethoxazole and erythromycin.

Conclusions

Inoculation of Phoenix panels directly from positive blood cultures can be used to report reliable results of AST of GNR a day earlier, as well as ID-results of Enterobacteriaceae. For Staphylococcus and Enterococcus species, results of AST can also be reported a day earlier for all antibiotics, except for erythromycin and trimethoprim-sulfamethoxazole.
Rural-to-urban migration and its implication for new cooperative medical scheme coverage and utilization in China
Authors: Qiu Peiyuan , Yang Yang , Zhang Juying , Ma Xiao
Published: July 2011

Background

China has been experiencing the largest rural to urban migration in history. Rural-to-urban migrants are those who leave their hometown for another place in order to work or live without changing their hukou status, which is a household registration system in China, categorizing people as either rural residents or urban residents. Rural-to-urban migrants typically find better job opportunities in destination cities, and these pay higher salaries than available in their home regions. This has served to improve the enrollment rates in the New Cooperative Medical Scheme (NCMS) of rural families, protecting households from falling into poverty due to diseases. However, current regulations stipulate that people who are registered in China's rural hukou can only participate in their local NCMS, which in turn poses barriers when migrants seek medical services in the health facilities of their destination cities. To examine this issue in greater depth, this study examined the associations between migration, economic status of rural households, and NCMS enrollment rate, as well as NCMS utilization of rural-to-urban migrants.

Methods

A multistage cluster sampling procedure was adopted. Our sample included 9,097 households and 36,720 individuals. Chi-square test and T-test were used to examine differences between the two populations of migrants and non-migrants based on age, gender, marriage status, and highest level of education. Ordinal logistic regression was used to examine the association between migration and household economic status. Binary logistic regression was used to examine the associations between household economic status, migration and enrollment in the NCMS.

Results

Migration was positively associated with improved household economic status. In households with no migrants, only 11.3% of the population was in the richest quintile, whereas the percentage was more than doubled in households with family members who migrated in 2006. Among those using in-patient medical services, 54.3% of migrants in comparison with 17.5% of non-migrants used out-of-county hospitals, many of which were not designated hospitals (Designated hospitals refer to hospitals where, if people use in patient health care, could receive reimbursement from the NCMS.); and 55.2% of migrants in comparison with 24.6% of non-migrants, who had the NCMS in 2006, received no reimbursement from the NCMS. The three main reasons of not receiving reimbursement were: staying in a hospital not designated by the NCMS, lack of knowledge of NCMS policies, and encountering difficulties obtaining reimbursement.

Conclusion

Migrants to urban centers improve the economic status of their rural household economic of origin. However, obtaining reimbursement under the current NCMS for the cost of hospital services provided by undesignated providers in urban centers is limited. Addressing this challenge is an emerging policy priority.
Antibacterial activity of some selected medicinal plants of Pakistan
Authors: Bibi Yamin , Nisa Sobia , Chaudhary Fayyaz M , Zia Muhammad
Published: July 2011

Background

Screening of the ethnobotenical plants is a pre-requisite to evaluate their therapeutic potential and it can lead to the isolation of new bioactive compounds.

Methods

The crude extracts and fractions of six medicinal important plants (Arisaema flavum, Debregeasia salicifolia, Carissa opaca, Pistacia integerrima, Aesculus indica, and Toona ciliata) were tested against three Gram positive and two Gram negative ATCC bacterial species using the agar well diffusion method.

Results

The crude extract of P. integerrima and A. indica were active against all tested bacterial strains (12-23 mm zone of inhibition). Other four plant's crude extracts (Arisaema flavum, Debregeasia salicifolia, Carissa opaca, and Toona ciliata) were active against different bacterial strains. The crude extracts showed varying level of bactericidal activity. The aqueous fractions of A. indica and P. integerrima crude extract showed maximum activity (19.66 and 16 mm, respectively) against B. subtilis, while the chloroform fractions of T. ciliata and D. salicifolia presented good antibacterial activities (13-17 mm zone of inhibition) against all the bacterial cultures tested.

Conclusion

The methanol fraction of Pistacia integerrima, chloroform fractions of Debregeasia salicifolia & Toona ciliata and aqueous fraction of Aesculus indica are suitable candidates for the development of novel antibacterial compounds.
The role of Cra in regulating acetate excretion and osmotic tolerance in E. coli K-12 and E. coli B at high density growth
Authors: Son Young-Jin , Phue Je-Nie , Trinh Loc B , Lee SangJun , Shiloach Joseph
Published: July 2011

Background

E. coli B (BL21), unlike E.coli K-12 (JM109) is insensitive to glucose concentration and, therefore, grows faster and produces less acetate than E. coli K-12, especially when growing to high cell densities at high glucose concentration. By performing genomic analysis, it was demonstrated that the cause of this difference in sensitivity to the glucose concentration is the result of the differences in the central carbon metabolism activity. We hypothesized that the global transcription regulator Cra (FruR) is constitutively expressed in E. coli B and may be responsible for the different behaviour of the two strains. To investigate this possibility and better understand the function of Cra in the two strains, cra - negative E. coli B (BL21) and E. coli K-12 (JM109) were prepared and their growth behaviour and gene expression at high glucose were evaluated using microarray and real-time PCR.

Results

The deletion of the cra gene in E. coli B (BL21) minimally affected the growth and maximal acetate accumulation, while the deletion of the same gene in E.coli K-12 (JM109) caused the cells to stop growing as soon as acetate concentration reached 6.6 g/L and the media conductivity reached 21 mS/cm. ppsA (gluconeogenesis gene), aceBA (the glyoxylate shunt genes) and poxB (the acetate producing gene) were down-regulated in both strains, while acs (acetate uptake gene) was down-regulated only in E.coli B (BL21). These transcriptional differences had little effect on acetate and pyruvate production. Additionally, it was found that the lower growth of E. coli K-12 (JM109) strain was the result of transcription inhibition of the osmoprotectant producing bet operon (betABT).

Conclusions

The transcriptional changes caused by the deletion of cra gene did not affect the activity of the central carbon metabolism, suggesting that Cra does not act alone; rather it interacts with other pleiotropic regulators to create a network of metabolic effects. An unexpected outcome of this work is the finding that cra deletion caused transcription inhibition of the bet operon in E. coli K-12 (JM109) but did not affect this operon transcription in E. coli B (BL21). This property, together with the insensitivity to high glucose concentrations, makes this the E. coli B (BL21) strain more resistant to environmental changes.
Optimizing HIV-1 protease production in Escherichia coli as fusion protein
Authors: Volontè Federica , Piubelli Luciano , Pollegioni Loredano
Published: July 2011

Background

Human immunodeficiency virus (HIV) is the etiological agent in AIDS and related diseases. The aspartyl protease encoded by the 5' portion of the pol gene is responsible for proteolytic processing of the gag-pol polyprotein precursor to yield the mature capsid protein and the reverse transcriptase and integrase enzymes. The HIV protease (HIV-1Pr) is considered an attractive target for designing inhibitors which could be used to tackle AIDS and therefore it is still the object of a number of investigations.

Results

A recombinant human immunodeficiency virus type 1 protease (HIV-1Pr) was overexpressed in Escherichia coli cells as a fusion protein with bacterial periplasmic protein dithiol oxidase (DsbA) or glutathione S-transferase (GST), also containing a six-histidine tag sequence. Protein expression was optimized by designing a suitable HIV-1Pr cDNA (for E. coli expression and to avoid autoproteolysis) and by screening six different E. coli strains and five growth media. The best expression yields were achieved in E. coli BL21-Codon Plus(DE3)-RIL host and in TB or M9 medium to which 1% (w/v) glucose was added to minimize basal expression. Among the different parameters assayed, the presence of a buffer system (based on phosphate salts) and a growth temperature of 37°C after adding IPTG played the main role in enhancing protease expression (up to 10 mg of chimeric DsbA:HIV-1Pr/L fermentation broth). GST:HIVPr was in part (50%) produced as soluble protein while the overexpressed DsbA:HIV-1Pr chimeric protein largely accumulated in inclusion bodies as unprocessed fusion protein. A simple refolding procedure was developed on HiTrap Chelating column that yielded a refolded DsbA:HIV-1Pr with a > 80% recovery. Finally, enterokinase digestion of resolubilized DsbA:HIV-1Pr gave more than 2 mg of HIV-1Pr per liter of fermentation broth with a purity ≤ 80%, while PreScission protease cleavage of soluble GST:HIVPr yielded ~ 0.15 mg of pure HIV-1Pr per liter.

Conclusions

By using this optimized expression and purification procedure fairly large amounts of good-quality HIV-1Pr recombinant enzyme can be produced at the lab-scale and thus used for further biochemical studies.
Inflammatory stress exacerbates ectopic lipid deposition in C57BL/6J mice
Authors: Mei Mei , Zhao Lei , Li Qing , Chen Yaxi , Huang Ailong , Varghese Zac , Moorhead John F , Zhang Suhua , Powis Stephen H , Li Qifu , Ruan Xiong Z
Published: July 2011

Background

Chronic systemic inflammation and abnormal free fatty acid metabolism are closely related to ectopic lipid deposition. In this study, we investigate if inflammation tissue-specifically disrupts lipogenesis and lipolysis in nonadipose tissues and adipose tissue, resulting in ectopic lipid deposition in C57BL/6J mice.

Methods

We used casein injection in C57BL/6J mice to induce a chronic systemic inflammatory stress in vivo. Serum was analyzed for free fatty acid and cytokines. Insulin sensitivities were evaluated by glucose and insulin tolerance tests. Liver, muscle, adipose tissues were taken for lipid analysis. Real-time polymerase chain reaction and western blotting were used to examine the gene and protein expression of molecules involved in adipogenesis and lipolysis in tissues.

Results

Casein injection elevated serum levels of IL-6 and SAA in mice, which are associated with increased lipid accumulation in liver and muscle, suggesting that chronic systemic inflammation induces ectopic lipid deposition in nonadipose tissues. The inflammatory stress upregulated mRNA and protein expression of sterol regulatory element binding protein 1, fatty acid synthase, and acetyl CoA carboxylase alpha, while inhibited these molecules expression in adipose. Interestingly, in the same experimental setting, inflammation increased triglyceride lipase and hormone-sensitive lipase expression in white adipose tissue. Inflammation also induced insulin resistance and increased serum free fatty acid levels in C57BL/6J mice.

Conclusions

Chronic systemic inflammation increased lipogenesis in nonadipose tissues and lipolysis in white adipose tissue, resulting in ectopic lipid deposition in nonadipose tissues. This disturbed free fatty acid homeostasis and caused insulin resistance in C57BL/6J mice.
Fractalkine is expressed in the human ovary and increases progesterone biosynthesis in human luteinised granulosa cells
Authors: Huang Shuo , Zhao Ping , Yang Liying , Chen Yuan , Yan Jie , Duan Enkui , Qiao Jie
Published: July 2011

Background

Recent evidence from rodent ovaries has demonstrated expression of fractalkine and the existence of fractalkine receptor, and showed that there is a significant increase in steroidogenesis in response to fractalkine, yet the role of fractalkine and CX3CR1 in the human ovary is still unknown. This study aimed to determine the expression levels of fractalkine and CX3CR1 in the human ovary and to investigate their roles in sexual hormone biosynthesis by human luteinising granulosa cells. This is the first detailed report of fractalkine and CX3CR1 expression and function in the human ovary.

Methods

Fractalkine and CX3CR1 expression levels were measured by immunohistochemistry using ovarian tissue from pathological specimens from five individuals. Granulosa cells were obtained from patients during IVF treatment. They were cultured and treated with increasing doses of hCG with or without fractalkine. Media were collected to detect estradiol and progesterone by chemiluminescence. StAR, 3-βHSD and CYP11A expression were determined in granulosa cells treated with or without fractalkine by real-time RT-PCR.

Results

Fractalkine and CX3CR1 were expressed in the human ovary and in luteinising granulosa cells. However, fractalkine expression was stronger in luteinising granulosa cells. Treatment with fractalkine augmented hCG stimulation of progesterone production in a dose-dependent manner with concomitant increases in transcript levels for key steroidogenic enzymes (StAR, 3-βHSD and CYP11A) but had no effect on estradiol biosynthesis(P < 0.05).

Conclusions

Fractalkine and CX3CR1 were found to express in human ovary and luteinising granulosa cells. Fractalkine can increase the biosynthesis of progesterone in a dose-dependent manner by enhancing transcript levels of key steroidogenic enzymes.
Vaccination with dengue virus-like particles induces humoral and cellular immune responses in mice
Authors: Zhang Shuo , Liang Mifang , Gu Wen , Li Chuan , Miao Fang , Wang Xiaofang , Jin Cong , Zhang Li , Zhang Fushun , Zhang Quanfu , Jiang Lifang , Li Mengfeng , Li Dexin
Published: July 2011

Background

The incidence of dengue, an infectious disease caused by dengue virus (DENV), has dramatically increased around the world in recent decades and is becoming a severe public health threat. However, there is currently no specific treatment for dengue fever, and licensed vaccine against dengue is not available. Vaccination with virus-like particles (VLPs) has shown considerable promise for many viral diseases, but the effect of DENV VLPs to induce specific immune responses has not been adequately investigated.

Results

By optimizing the expression plasmids, recombinant VLPs of four antigenically different DENV serotypes DENV1-4 were successfully produced in 293T cells. The vaccination effect of dengue VLPs in mice showed that monovalent VLPs of each serotype stimulated specific IgG responses and potent neutralizing antibodies against homotypic virus. Tetravalent VLPs efficiently enhanced specific IgG and neutralizing antibodies against all four serotypes of DENV. Moreover, vaccination with monovalent or tetravalent VLPs resulted in the induction of specific cytotoxic T cell responses.

Conclusions

Mammalian cell expressed dengue VLPs are capable to induce VLP-specific humoral and cellular immune responses in mice, and being a promising subunit vaccine candidate for prevention of dengue virus infection.
Safety and Efficacy of miltefosine alone and in combination with sodium stibogluconate and liposomal amphotericin B for the treatment of primary visceral leishmaniasis in East Africa: study protocol for a randomized controlled trial
Authors: Omollo Raymond , Alexander Neal , Edwards Tansy , Khalil Eltahir AG , Younis Brima M , Abuzaid Abuzaid A , Wasunna Monique , Njoroge Njenga , Kinoti Dedan , Kirigi George , Dorlo Thomas PC , Ellis Sally , Balasegaram Manica , Musa Ahmed M
Published: July 2011

Background

Treatment options for Visceral Leishmaniasis (VL) in East Africa are far from satisfactory due to cost, toxicity, prolonged treatment duration or emergence of parasite resistance. Hence there is a need to explore alternative treatment protocols such as miltefosine alone or in combinations including miltefosine, sodium stibogluconate (SSG) or liposomal amphotericin B. The aim of this trial is to identify regimen(s) which are sufficiently promising for future trials in East Africa.

Methods/Design

A phase II randomized, parallel arm, open-labelled trial is being conducted to assess the efficacy of each of the three regimens: liposomal amphotericin B with SSG, Liposomal amphotericin B with miltefosine and miltefosine alone. The primary endpoint is cure at day 28 with secondary endpoint at day 210 (6 months). Initial cure is a single composite measure based on parasitologic evaluation (bone marrow, spleen or lymph node aspirate) and clinical assessment. Repeated interim analyses have been planned after recruitment of 15 patients in each arm with a maximum sample size of 63 for each. These will follow group-sequential methods (the triangular test) to identify when a regimen is inadequate (<75% efficacy) or adequate (>90% efficacy). We describe a method to ensure consistency of the sequential analysis of day 28 cure with the non-sequential analysis of day 210 cure.

Discussion

A regimen with adequate efficacy would be a candidate for treatment of VL with reasonable costs. The design allows repeated testing throughout the trial recruitment period while maintaining good statistical properties (Type I & II error rates) and reducing the expected sample sizes.

Trial Registration

ClinicalTrials.gov: NCT01067443
A novel procedure for the quantitative analysis of metabolites, storage products and transcripts of laser microdissected seed tissues of Brassica napus
Authors: Schiebold Silke , Tschiersch Henning , Borisjuk Ljudmilla , Heinzel Nicolas , Radchuk Ruslana , Rolletschek Hardy
Published: July 2011

Background

The biology of the seed is complicated by the extensive non-homogeneity (spatial gradients) in gene expression, metabolic conversions and storage product accumulation. The detailed understanding of the mechanisms underlying seed growth and storage therefore requires the development of means to obtain tissue-specific analyses. This approach also represents an important priority in the context of seed biotechnology.

Results

We provide a guideline and detailed procedures towards the quantitative analysis of laser micro-dissected (LM) tissues in oilseed rape (Brassica napus). This includes protocols for laser microdissection of the seed, and the subsequent extraction and quantitative analysis of lipids, starch and metabolites (sugars, sugar phosphates, nucleotides, amino acids, intermediates of glycolysis and citric acid cycle). We have also developed a protocol allowing the parallel analysis of the transcriptome usingBrassica-specific microarrays. Some data are presented regarding the compartmentation of metabolites within the oilseed rape embryo.

Conclusion

The described methodology allows for the rapid, combined analysis of metabolic intermediates, major storage products and transcripts in a tissue-specific manner. The protocols are robust for oilseed rape, and should be readily adjustable for other crop species. The suite of methods applied to LM tissues represents an important step in the context of both the systems biology and the biotechnology of oilseeds.
Prevalence of Helicobacter pylori in HIV‐infected, HAART‐naïve Ugandan children: a hospital‐based survey
Authors: Hestvik Elin , Tylleskar Thorkild , Ndeezi Grace , Grahnquist Lena , Olafsdottir Edda , Tumwine James K , Kaddu‐Mulindwa Deogratias H
Published: July 2011

Background

The aim of this survey was to determine the prevalence of and factors associated with Helicobacter pylori (H. pylori) colonization in HIV‐infected, highly active antiretroviral therapy‐naïve Ugandan children aged 0‐12 years.

Methods

In a hospital‐based survey, 236 HIV‐infected children were tested for H. pylori colonization using a faecal antigen test. A standardized interview with socio‐demographic information and medical history was used to assess risk factors. A cluster of differentiation 4 (CD4) cell percentage was prevalent in most children.

Results

The overall prevalence of H. pylori in the HIV‐infected children was 22.5%. Age‐specific prevalence was as follows: up to one year, 14.7%; 1‐3 years, 30.9%; and 3‐12 years, 20.7%. HIV‐infected children who were more seriously affected by their disease (low CD4 cell percentage or WHO clinical stage II‐IV) were less likely to be colonized with H. pylori. There was a trend for a lower prevalence of H. pylori in children who had taken antibiotics for the preceding two weeks (21.6%) than in those who had not taken antibiotics (35.7%). There was no statistically significant difference in prevalence by gender, housing, congested living, education of the female caretaker, drinking water or toilet facilities.

Conclusions

HIV‐infected, HAART‐naïve Ugandan children had a lower prevalence of H. pylori colonization compared with apparently healthy Ugandan children (44.3%). Children with a low CD4 cell percentage and an advanced clinical stage of HIV had an even lower risk of H. pylori colonization. Treatment with antibiotics due to co‐morbidity with infectious diseases is a possible explanation for the relatively low prevalence.
Enhancement of β-xylosidase productivity in cellulase producing fungus Acremonium cellulolyticus
Authors: Kanna Machi , Yano Shinichi , Inoue Hiroyuki , Fujii Tatsuya , Sawayama Shigeki
Published: July 2011

Enzymatic hydrolysis is one of the most important processes in bioethanol production from lignocellulosic biomass. Acremonium cellulolyticus is a filamentous fungus with high cellulase production but productivity of hemicellulase, especially β-xylosidase, is lower than other filamentous fungi. We identified 2.4 Kb β-xylosidase gene in the A. cellulolyticus genome sequence information and it encoded 798 amino acids without introns. To enhance hemicellulase productivity in A. cellulolyticus, we transformed this fungus with the identified β-xylosidase gene driven by the cellobiohydrolase Ι (cbh1) promoter, using the protoplast-polyethyleneglycol (PEG) method, and obtained a transformant, YKX1. Hydrolysis rate of xylooligosaccharides was more than 50-fold higher using culture supernatant from YKX1 than that from the parental strain, Y-94. Total cellulase activity (measured by filter paper assay) in YKX1 was not affected by the cbh1 promoter used for expression of β-xylosidase, and induced by cellulose. Since YKX1 can produce larger amount of β-xylosidase without affecting cellulase productivity, it is considered to be beneficial for practical monosaccharide recoveries from lignocellulosic biomass.
Evaluation of the Bcl-2 family antagonist ABT-737 in collagen-induced arthritis
Authors: Lawlor Kate E , Smith Scott D , van Nieuwenhuijze Annemarie , Huang David C S , Wicks Ian P
Published: July 2011

Therapeutic manipulation of cellular apoptosis holds great promise for malignant and potentially nonmalignant diseases. A relative resistance to apoptosis in RA synovium is associated with increased expression of prosurvival Bcl-2 family members. In this study, we demonstrate that treatment of DBA/1 mice, prior to the onset of CIA with ABT-737, a BH3 mimetic targeting Bcl-2, Bcl-w, and Bcl-xL, ameliorated disease development. In contrast, treatment of mice with ABT-737 in established CIA did not alter the course of disease. ABT-737 induced lymphopenia, however pathogenic lymphoid populations in CIA mice were less affected, as shown by relatively normal T and B cell responses to CII. Naïve lymphocytes were highly sensitive to apoptosis after culture with ABT-737, but synovial macrophages and neutrophils were not. Mcl-1 was detected in synovial monocyte/macrophages and neutrophils and strikingly, its expression, rather than Bcl-2 and Bcl-xL, increased in the affected paws and lymphoid organs of mice with CIA. These observations implicate Mcl-1, which is not targeted by ABT-737, in the survival of inflammatory cells in established CIA and suggest that antagonism of Mcl-1 may be more effective in diseases such as RA.
PAK1-Nck Regulates Cyclin D1 Promoter Activity in Response to Prolactin
Authors: Tao Jing , Oladimeji Peter , Rider Leah , Diakonova Maria
Published: July 2011

Prolactin (PRL) is critical for alveolar proliferation and differentiation in normal mammary development and is also implicated in breast cancer. PRL influences cell proliferation and growth by altering the expression of cyclin D1. Cyclin D1 expression is directly regulated by PRL through the Janus kinase 2 (JAK2)/signal transducer and activator of transcription 5-mediated transcriptional activation of the cyclin D1 promoter. A p21-activated serine-threonine kinase (PAK)1 has also been implicated in the regulation of cyclin D1 gene expression. We have previously demonstrated that JAK2 directly phosphorylates PAK1 and extend these data here to demonstrate that PAK1 activates the cyclin D1 promoter in response to PRL. We show that mutation of PAK1 Tyr 153, 201, and 285 (sites of JAK2 phosphorylation; PAK1 Y3F) decreases both PAK1 nuclear translocation in response to PRL and PRL-induced cyclin D1 promoter activity by 55%. Mutation of the PAK1 nuclear localization signals decreases PRL-induced cyclin D1 promoter activity by 46%. A PAK1 Y3F mutant lacking functional nuclear localization signals decreases PRL-induced cyclin D1 activity by 68%, suggesting that there is another PAK1-dependent mechanism to activate the cyclin D1 promoter. We have found that adapter protein Nck sequesters PAK1 in the cytoplasm and that coexpression of both PAK1 and Nck inhibits the amplifying effect of PRL-induced PAK1 on cyclin D1 promoter activity (95% inhibition). This inhibition is partially abolished by disruption of PAK1-Nck binding. We propose two PAK1-dependent mechanisms to activate cyclin D1 promoter activity in response to PRL: via nuclear translocation of tyrosyl-phosphorylated PAK1 and via formation of a Nck-PAK1 complex that sequesters PAK1 in the cytoplasm.
Genetic activation of Nrf2 signaling is sufficient to ameliorate neurodegenerative phenotypes in aDrosophilamodel of Parkinson’s disease
Authors: Barone Maria Cecilia , Sykiotis Gerasimos P. , Bohmann Dirk
Published: July 2011

Parkinson’s disease (PD) is the most common neurodegenerative movement disorder. Oxidative stress has been associated with the etiology of both sporadic and monogenic forms of PD. The transcription factor Nrf2, a conserved global regulator of cellular antioxidant responses, has been implicated in neuroprotection against PD pathology. However, direct evidence that upregulation of the Nrf2 pathway is sufficient to confer neuroprotection in genetic models of PD is lacking. Expression of the PD-linked gene encoding α-synuclein in dopaminergic neurons of Drosophila results in decreased locomotor activity and selective neuron loss in a progressive age-dependent manner, providing a genetically accessible model of PD. Here we show that upregulation of the Nrf2 pathway by overexpressing Nrf2 or its DNA-binding dimerization partner, Maf-S, restores the locomotor activity of α-synuclein-expressing flies. Similar benefits are observed upon RNA-interference-mediated downregulation of the prime Nrf2 inhibitor, Keap1, as well as in conditions of keap1 heterozygosity. Consistently, the α-synuclein-induced dopaminergic neuron loss is suppressed by Maf-S overexpression or keap1 heterozygosity. Our data validate the sustained upregulation of the Nrf2 pathway as a neuroprotective strategy against PD. This model provides a genetically accessible in vivo system in which to evaluate the potential of additional Nrf2 pathway components and regulators as therapeutic targets.
A high-sugar diet produces obesity and insulin resistance in wild-typeDrosophila
Authors: Palanker Musselman Laura , Fink Jill L. , Narzinski Kirk , Ramachandran Prasanna Venkatesh , Sukumar Hathiramani Sumitha , Cagan Ross L. , Baranski Thomas J.
Published: July 2011

Insulin-resistant, ‘type 2’ diabetes (T2D) results from a complex interplay between genes and environment. In particular, both caloric excess and obesity are strongly associated with T2D across many genetic backgrounds. To gain insights into how dietary excess affects insulin resistance, we studied the simple model organism Drosophila melanogaster. Larvae reared on a high-sugar diet were hyperglycemic, insulin resistant and accumulated fat – hallmarks of T2D – compared with those reared on control diets. Excess dietary sugars, but not fats or proteins, elicited insulin-resistant phenotypes. Expression of genes involved in lipogenesis, gluconeogenesis and β-oxidation was upregulated in high-sugar-fed larvae, as were FOXO targets, consistent with known mechanisms of insulin resistance in humans. These data establish a novel Drosophila model of diet-induced insulin resistance that bears strong similarity to the pathophysiology of T2D in humans.
Identification of Amino Acid Phosphorodiamidates of Antiviral Nucleosides Using Electrospray Ionisation Tandem Mass Spectrometry
Authors: Cui Juntao , Gao Xiang , Fan Aiting , Zhang Shuangyan , Liu Yan , Xu Pengxiang , Zhao Yufen
Published: July 2011

Several amino acid phosphorodiamidate derivatives of d4T as anti-HIV prodrugs were synthesised and investigated using electrospray ionisation multistage tandem mass spectrometry (ESI-MS n). A novel methyl group migration in the gas phase was observed in ESI-MS2 of the sodium adducts of amino acid methyl ester of phosphorodiamidates of 2′,3′-didehydro-2′,3′-dideox y thymidine (d4T). The proposed structures of the rearrangement ions were confirmed by high-resolution tandem mass spectrometry. A possible mechanism involving the pentacoordinate phosphoric–carboxylic phosphate anhydride was proposed, in which a seven-membered ring intermediate was formed by coordination with the metal ion between the phosphoryl group and carbonyl oxygen atom. Thus, the intrinsic properties of phosphoryl group might be the key factors responsible for this migration.
Intercluster Reactions Show That (CH3)2S+CH2CO2H is a Better Methyl Cation Donor Than (CH3)3N+CH2CO2H
Authors: Yoo Ellie Jung Hwa , Feketeová Linda , Khairallah George N. , O'Hair Richard A.J.
Published: July 2011

The intrinsic methylating abilities of the known biological methylating zwitterionic agents, dimethylsulfonioacetate (DMSA), (CH3)2S+CH2CO2− (1) and glycine betaine (GB), (CH3)3N+CH2CO2− (2), have been examined via a range of gas phase experiments involving collision-induced dissociation (CID) of their proton-bound homo- and heterodimers, including those containing the amino acid arginine. The relative yields of the products of methyl cation transfer are consistent in all cases and show that protonated DMSA is a more potent methylating agent than protonated GB. Since methylation can occur at more than one site in arginine, the [M + CH3]+ ion of arginine, formed from the heterocluster [DMSA + Arg + H]+, was subject to an additional stage of CID. The resultant CID spectrum is virtually identical to that of an authentic sample of protonated arginine- O-methyl ester but is significantly different to that of an authentic sample of protonated NG-methyl arginine. This suggests that methylation has occurred within a salt bridge complex of [DMSA + Arg + H]+, in which the arginine exists in the zwitterionic form. Finally, density functional theory calculations on the model salts, (CH3CO2−)[(CH3)3S+] and (CH3CO2−)[(CH3)4N+], show that methylation of CH3CO2− by (CH3)3S+ is both kinetically and thermodynamically preferred over methylation by (CH3)4N+.
Immunoglobulin E deficiency: a forgotten clue pointing to possible immunodeficiency?
Authors: Unsworth David J , Virgo Paul F , Lock Robert J
Published: July 2011

Background

Patients with primary antibody deficiency often have delayed diagnosis. Very low IgE, found during investigations for allergy, may be a marker for other immunodeficiency.

Methods

We introduced a new laboratory policy of testing cases with very low IgE levels for possible linked antibody deficiency. The data represent an audit of routine results collected over two years.

Results

Very low IgE (≤2 IU/mL) was identified in 85/2622 (3.2%) routine patient samples. Two children and four adult patients were found to have one or more classes of immunoglobulin below the reference range for age. In 2/6, the initiative of the laboratory led to a new unsuspected diagnosis of antibody immunodeficiency.

Conclusions

Common variable immunodeficiency continues to be overlooked as a primary cause of lung disease in adults. Very low serum IgE should trigger appropriate investigation (immunoglobulin quantification and serum electrophoresis).
Restoring the seal of an anatomical face mask
Authors: Singhal Suresh , Lal Jatin
Published: July 2011

The face mask is a device to facilitate the delivery of gases from a breathing system to a patient by creating an airtight seal around the face. Of the many types of face masks available, the anatomical face mask is most commonly used for anaesthesia. With repeated usage, the seal of the anatomical face mask becomes flattened due to the loss of air in the cushion, leading to a poor fit on the patient's face. This results in air dilution during spontaneous respiration and inadequate gas exchange during controlled ventilation. A simple solution to restore this seal has been provided.
Comparative analysis of tuberculous and brucellar spondylodiscitis
Authors: Çelik Ali Kutta , Aypak Adalet , Aypak Cenk
Published: July 2011

Our aim was to compare the clinical, radiological and prognostic features of spontaneous spondylodiscitis secondary to tuberculosis (TS) and brucellosis (BS). This prospective study involved 41 patients diagnosed with spondylodiscitis. Of these, 18 (43.1%) had BS and 23 (56.1%) had TS. The mean age of TS patients was 52 ± 13.43 years and older than BS patients ( P < 0.001). A prolonged clinical course of the disease, constitutional symptoms, lymphocytosis, increased erythrocyte sedimentation rate (ESR), presence of posterior vertebrae lesions and psoas abscesses were significantly more frequent in the TS group. There are significant clinical, biological and radiological differences between TS and BS. These differences permit a presumptive aetiological diagnosis and orient the initial empirical medical treatment while awaiting a final microbiological diagnosis.
Scrub typhus presenting as acute abdomen
Authors: Mahajan Sanjay K , Babu Sharath , Sharma Dhruv , Singh Digvijay , Kanga Anil , Kaushal Satinder S
Published: July 2011

Scrub typhus, a zoonosis, is a systemic febrile illness with diverse clinical manifestations. It may also present with signs and symptoms of acute abdomen. We present two serologically confirmed cases of scrub typhus presenting with acute abdomen that were managed conservatively with antibiotics.
Group Buying: A New Mechanism for Selling Through Social Interactions
Authors: Jing Xiaoqing , Xie Jinhong
Published: July 2011

This paper examines a unique selling strategy, Group Buying, under which consumers enjoy a discounted group price if they are willing and able to achieve a required group size and coordinate their transaction time. We argue that Group Buying allows a seller to gain from facilitating consumer social interaction, i.e., using a group discount to motivate informed customers to work as “sales agents” to acquire less-informed customers through interpersonal information/knowledge sharing. We formally model such an information-sharing effect and examine if and when Group Buying is more profitable than (1) traditional individual-selling strategies, and (2) another popular social interaction scheme, Referral Rewards programs. We show that Group Buying dominates traditional individual-selling strategies when the information/knowledge gap between expert and novice consumers is neither too high nor too low (e.g., for products in the midstage of their life cycle) and when interpersonal information sharing is very efficient (e.g., in cultures that emphasize trust and group conformity, or when implemented through existing online social networks). We also show that, unlike Referral Rewards programs, Group Buying requires information sharing before any transaction takes place, thereby increasing the scale of social interaction but also incurring a higher cost. As a result, Group Buying is optimal when interpersonal communication is very efficient or when the product valuation of the less-informed consumer segment is high.

This paper was accepted by Preyas Desai, marketing.