bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract

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

Abstract

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

Abstract

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

Abstract

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

Abstract

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

Abstract

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

Abstract

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

AbstractBackgroundThe 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.ResultsBy 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.ConclusionsMammalian 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

Abstract

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

AbstractBackgroundThe 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.ResultsWe 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.ConclusionThe 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

BackgroundThe 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.MethodsIn 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.ResultsThe 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.ConclusionsHIV‐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.