bluuebunny/crossref_metadata_2025_split huggingface dataset:
Contemporary divergence in early life history in grayling (Thymallus thymallus)
Authors: Thomassen Gaute , Barson Nicola J , Haugen Thrond O , Vøllestad L Asbjørn 
Published: December 2011

Abstract

Background
Following colonization of new habitats and subsequent selection, adaptation to environmental conditions might be expected to be rapid. In a mountain lake in Norway, Lesjaskogsvatnet, more than 20 distinct spawning demes of grayling have been established since the lake was colonized, some 20-25 generations ago. The demes spawn in tributaries consistently exhibiting either colder or warmer temperature conditions during spawning in spring and subsequent early development during early summer. In order to explore the degree of temperature-related divergence in early development, a multi-temperature common-garden experiment was performed on embryos from four different demes experiencing different spring temperatures.

Results
Early developmental characters were measured to test if individuals from the four demes respond differently to the treatment temperatures. There was clear evidence of among-deme differences (genotype - environment interactions) in larval growth and yolk-to-body-size conversion efficiency. Under the cold treatment regime, larval growth rates were highest for individuals belonging to cold streams. Individuals from warm streams had the highest yolk-consumption rate under cold conditions. As a consequence, yolk-to-body-mass conversion efficiency was highest for cold-deme individuals under cold conditions. As we observed response parallelism between individuals from demes belonging to similar thermal groups for these traits, some of the differentiation seems likely to result from local adaptation

Conclusion
The observed differences in length at age during early larval development most likely have a genetic component, even though both directional and random processes are likely to have influenced evolutionary change in the demes under study.
Sequencing by ligation variation with endonuclease V digestion and deoxyinosine-containing query oligonucleotides
Authors: Ho Antoine , Murphy Maurice , Wilson Susan , Atlas Susan R , Edwards Jeremy S 
Published: December 2011

Abstract

Background
Sequencing-by-ligation (SBL) is one of several next-generation sequencing methods that has been developed for massive sequencing of DNA immobilized on arrayed beads (or other clonal amplicons). SBL has the advantage of being easy to implement and accessible to all because it can be performed with off-the-shelf reagents. However, SBL has the limitation of very short read lengths.

Results
To overcome the read length limitation, research groups have developed complex library preparation processes, which can be time-consuming, difficult, and result in low complexity libraries. Herein we describe a variation on traditional SBL protocols that extends the number of sequential bases that can be sequenced by using Endonuclease V to nick a query primer, thus leaving a ligatable end extended into the unknown sequence for further SBL cycles. To demonstrate the protocol, we constructed a known DNA sequence and utilized our SBL variation, cyclic SBL (cSBL), to resequence this region. Using our method, we were able to read thirteen contiguous bases in the 3' - 5' direction.

Conclusions
Combining this read length with sequencing in the 5' - 3' direction would allow a read length of over twenty bases on a single tage. Implementing mate-paired tags and this SBL variation could enable > 95% coverage of the genome.
Chromatin-driven de novo discovery of DNA binding motifs in the human malaria parasite
Authors: Harris Elena Y , Ponts Nadia , Le Roch Karine G , Lonardi Stefano 
Published: December 2011

Abstract

Background
Despite extensive efforts to discover transcription factors and their binding sites in the human malaria parasite Plasmodium falciparum, only a few transcription factor binding motifs have been experimentally validated to date. As a consequence, gene regulation in P. falciparum is still poorly understood. There is now evidence that the chromatin architecture plays an important role in transcriptional control in malaria.

Results
We propose a methodology for discovering cis-regulatory elements that uses for the first time exclusively dynamic chromatin remodeling data. Our method employs nucleosome positioning data collected at seven time points during the erythrocytic cycle of P. falciparum to discover putative DNA binding motifs and their transcription factor binding sites along with their associated clusters of target genes. Our approach results in 129 putative binding motifs within the promoter region of known genes. About 75% of those are novel, the remaining being highly similar to experimentally validated binding motifs. About half of the binding motifs reported show statistically significant enrichment in functional gene sets and strong positional bias in the promoter region.

Conclusion
Experimental results establish the principle that dynamic chromatin remodeling data can be used in lieu of gene expression data to discover binding motifs and their transcription factor binding sites. Our approach can be applied using only dynamic nucleosome positioning data, independent from any knowledge of gene function or expression.
Resistance to topoisomerase cleavage complex induced lethality in Escherichia coli via titration of transcription regulators PurR and FNR
Authors: Liu I-Fen , Aedo Sandra , Tse-Dinh Yuk-Ching 
Published: December 2011

Abstract

Background
Accumulation of gyrase cleavage complex in Escherichia coli from the action of quinolone antibiotics induces an oxidative damage cell death pathway. The oxidative cell death pathway has also been shown to be involved in the lethality following accumulation of cleavage complex formed by bacterial topoisomerase I with mutations that result in defective DNA religation.

Methods
A high copy number plasmid clone spanning the upp-purMN region was isolated from screening of an E. coli genomic library and analyzed for conferring increased survival rates following accumulation of mutant topoisomerase I proteins as well as treatment with the gyrase inhibitor norfloxacin.

Results
Analysis of the intergenic region upstream of purM demonstrated a novel mechanism of resistance to the covalent protein-DNA cleavage complex through titration of the cellular transcription regulators FNR and PurR responsible for oxygen sensing and repression of purine nucleotide synthesis respectively. Addition of adenine to defined growth medium had similar protective effect for survival following accumulation of topoisomerase cleavage complex, suggesting that increase in purine level can protect against cell death.

Conclusions
Perturbation of the global regulator FNR and PurR functions as well as increase in purine nucleotide availability could affect the oxidative damage cell death pathway initiated by topoisomerase cleavage complex.
Exposure to and opinions towards sex education among adolescent students in Mumbai: A cross-sectional survey
Authors: Benzaken Tami , Palep Ashutosh H , Gill Paramjit S 
Published: December 2011

Abstract

Background
The aim of this study was to determine students' exposure to sex education and identify students' perceptions of accessibility to sexual health advice and their preferences in implementing sex education.

Methods
A cross-sectional study was carried out in junior colleges in Mumbai in 2010. The self-administered questionnaire investigated male and female students' (aged 15-17) exposure and opinions towards sex education. Data was entered into and analysed using SPSS version 17.0.

Results
The questionnaire was completed by 427 students. Almost 90% of students believed it important to have sex education as part of school curriculum; over 60% reported prior exposure to sex education in school. However, only 45% were satisfied they had good access to advice about contraception and sexual health, particularly, females reported more limited access.

Conclusions
The majority responding indicated a desire for more widespread implementation of school-based sex education, particularly amongst female respondents.
Predictors of adherence to isoniazid preventive therapy among HIV positive adults in Addis Ababa, Ethiopia
Authors: Mindachew Mesele , Deribew Amare , Tessema Fasil , Biadgilign Sibhatu 
Published: December 2011

Abstract

Background
Isoniazide preventive therapy (IPT) is given to individuals with latent infection of tuberculosis (TB) to prevent the progression to active disease. One of the primary reasons for failure of IPT is poor adherence.

Methods
A cross sectional study was conducted in four hospitals in Addis Ababa. Data were collected using a pre-tested interviewer-administered structured questionnaire. Bivariate and multivariate analysis was done to identify predictors of IPT.

Results
A total of 319 (97.5%) individual participated in this study. Within seven days recall period, self-reported dose adherence rate was 86.5%. Individual who received explanation about IPT from health care providers (OR = 7.74; 95%CI: 3.144, 19.058); who had good feeling/comfortable to take IPT in front of other people [OR = 5.981, 95%CI (2.308, 15.502)] and who attended clinical appointment regularly (OR = 4.0; 95%CI: 1.062, 15.073) were more likely to adhere to IPT. Participants who developed IPT related adverse effect were 93% less likely to adhere to the prescribed doses (OR = 0.065; 95%CI: 0.024, 0.179).

Conclusion
The prevalence of self reported dose adherence over the past 7 days was higher. Non-adherence was observed among respondent who were not provided with sufficient information about IPT. The health care providers need to strengthen their educational and counseling efforts to convince the patient before putting them on IPT. To enhance adherence, health education efforts should focus on the importance of IPT, the details of the regimen and adverse effects.
Prevalence of overweight and obesity among Chinese Yi nationality: a cross-sectional study
Authors: Gao Yun , Ran Xing-Wu , Xie Xiao-Hua , Lu Hua-Lin , Chen Tao , Ren Yan , Long Yang , Tian Hao-Ming 
Published: December 2011

Abstract

Background
Overweight and obesity are considered a serious health problem. There are little data on the prevalence of overweight and obesity among the Yi ethnic group in China. This study aimed to investigate the epidemiologic features of overweight/obesity among Chinese Yi nationality.

Methods
A cross-sectional study, including 1255 subjects aged 20-75 years, was carried out in Liangshan Yi Autonomous Prefecture of Sichuan province from 2007 to 2008. Overweight/overall obesity was defined by World Health Organization (WHO) or the Working Group on Obesity in China.

Results
Overall, the prevalence of overweight and obesity was 19.0% and 2.9%, respectively, based on the WHO definition, while it was 21.0% and 7.4%, respectively, according to the Working Group on Obesity in China, which is similar to data reported in the 2002 Chinese National Nutrition and Health Survey. Urban residents had a significantly higher prevalence of obesity (WHO criteria: 4.3% vs 1.7% p = 0.008; China criteria: 11.4% vs 3.7%, p < 0.001) and overweight (WHO criteria: 28.9% vs 8.9% p < 0.001; China criteria: 31.2% vs 10.4%, p < 0.001) than that in rural residents. Older age, a family history of obesity, higher income, drinking and urban residence were significantly associated with an increased risk of overweight/obesity.

Conclusions
The prevalence of overweight/obesity in the Yi nationality is similar to that in Chinese adults 5 years ago. However, urban residents have a much higher prevalence of overweight/obesity than their rural counterparts. Lifestyle and diet patterns associated with socioeconomic status may explain the difference between urban and rural residents. The prevention of overweight/obesity among urban inhabitants deserves more attention in national health education programs.
Ecological Niche Modelling of the Bacillus anthracis A1.a sub-lineage in Kazakhstan
Authors: Mullins Jocelyn , Lukhnova Larissa , Aikimbayev Alim , Pazilov Yerlan , Van Ert Matthew , Blackburn Jason K 
Published: December 2011

Abstract

Background

Bacillus anthracis, the causative agent of anthrax, is a globally distributed zoonotic pathogen that continues to be a veterinary and human health problem in Central Asia. We used a database of anthrax outbreak locations in Kazakhstan and a subset of genotyped isolates to model the geographic distribution and ecological associations of B. anthracis in Kazakhstan. The aims of the study were to test the influence of soil variables on a previous ecological niche based prediction of B. anthracis in Kazakhstan and to determine if a single sub-lineage of B. anthracis occupies a unique ecological niche.

Results
The addition of soil variables to the previously developed ecological niche model did not appreciably alter the limits of the predicted geographic or ecological distribution of B. anthracis in Kazakhstan. The A1.a experiment predicted the sub-lineage to be present over a larger geographic area than did the outbreak based experiment containing multiple lineages. Within the geographic area predicted to be suitable for B. anthracis by all ten best subset models, the A1.a sub-lineage was associated with a wider range of ecological tolerances than the outbreak-soil experiment. Analysis of rule types showed that logit rules predominate in the outbreak-soil experiment and range rules in the A1.a sub-lineage experiment. Random sub-setting of locality points suggests that models of B. anthracis distribution may be sensitive to sample size.

Conclusions
Our analysis supports careful consideration of the taxonomic resolution of data used to create ecological niche models. Further investigations into the environmental affinities of individual lineages and sub-lineages of B. anthracis will be useful in understanding the ecology of the disease at large and small scales. With model based predictions serving as approximations of disease risk, these efforts will improve the efficacy of public health interventions for anthrax prevention and control.
Heterologous overexpression of Glomerella cingulata FAD-dependent glucose dehydrogenase in Escherichia coli and Pichia pastoris
Authors: Sygmund Christoph , Staudigl Petra , Klausberger Miriam , Pinotsis Nikos , Djinović-Carugo Kristina , Gorton Lo , Haltrich Dietmar , Ludwig Roland 
Published: December 2011

Abstract

Background
FAD dependent glucose dehydrogenase (GDH) currently raises enormous interest in the field of glucose biosensors. Due to its superior properties such as high turnover rate, substrate specificity and oxygen independence, GDH makes its way into glucose biosensing. The recently discovered GDH from the ascomycete Glomerella cingulata is a novel candidate for such an electrochemical application, but also of interest to study the plant-pathogen interaction of a family of wide-spread, crop destroying fungi. Heterologous expression is a necessity to facilitate the production of GDH for biotechnological applications and to study its physiological role in the outbreak of anthracnose caused by Glomerella (anamorph Colletotrichum) spp.

Results
Heterologous expression of active G. cingulata GDH has been achieved in both Escherichia coli and Pichia pastoris, however, the expressed volumetric activity was about 4800-fold higher in P. pastoris. Expression in E. coli resulted mainly in the formation of inclusion bodies and only after co-expression with molecular chaperones enzymatic activity was detected. The fed-batch cultivation of a P. pastoris transformant resulted in an expression of 48,000 U L-1 of GDH activity (57 mg L-1). Recombinant GDH was purified by a two-step purification procedure with a yield of 71%. Comparative characterization of molecular and catalytic properties shows identical features for the GDH expressed in P. pastoris and the wild-type enzyme from its natural fungal source.

Conclusions
The heterologous expression of active GDH was greatly favoured in the eukaryotic host. The efficient expression in P. pastoris facilitates the production of genetically engineered GDH variants for electrochemical-, physiological- and structural studies.
A novel cold-active β-D-galactosidase from the Paracoccus sp. 32d - gene cloning, purification and characterization
Authors: Wierzbicka-Woś Anna , Cieśliński Hubert , Wanarska Marta , Kozłowska-Tylingo Katarzyna , Hildebrandt Piotr , Kur Józef 
Published: December 2011

Abstract

Background
β-D-Galactosidases (EC 3.2.1.23) catalyze the hydrolysis of terminal non-reducing β-D-galactose residues in β-D-galactosides. Cold-active β-D-galactosidases have recently become a focus of attention of researchers and dairy product manufactures owing to theirs ability to: (i) eliminate of lactose from refrigerated milk for people afflicted with lactose intolerance, (ii) convert lactose to glucose and galactose which increase the sweetness of milk and decreases its hydroscopicity, and (iii) eliminate lactose from dairy industry pollutants associated with environmental problems. Moreover, in contrast to commercially available mesophilic β-D-galactosidase from Kluyveromyces lactis the cold-active counterparts could make it possible both to reduce the risk of mesophiles contamination and save energy during the industrial process connected with lactose hydrolysis.

Results
A genomic DNA library was constructed from soil bacterium Paracoccus sp. 32d. Through screening of the genomic DNA library on LB agar plates supplemented with X-Gal, a novel gene encoding a cold-active β-D-galactosidase was isolated. The in silico analysis of the enzyme amino acid sequence revealed that the β-D-galactosidase Paracoccus sp. 32d is a novel member of Glycoside Hydrolase Family 2. However, owing to the lack of a BGal_small_N domain, the domain characteristic for the LacZ enzymes of the GH2 family, it was decided to call the enzyme under study 'BgaL'. The bgaL gene was cloned and expressed in Escherichia coli using the pBAD Expression System. The purified recombinant BgaL consists of two identical subunits with a combined molecular weight of about 160 kDa. The BgaL was optimally active at 40°C and pH 7.5. Moreover, BgaL was able to hydrolyze both lactose and o-nitrophenyl-β-D-galactopyranoside at 10°C with K
m values of 2.94 and 1.17 mM and k
cat values 43.23 and 71.81 s-1, respectively. One U of the recombinant BgaL would thus be capable hydrolyzing about 97% of the lactose in 1 ml of milk in 24 h at 10°C.

Conclusions
A novel bgaL gene was isolated from Paracoccus sp. 32d encoded a novel cold-active β-D-galactosidase. An E. coli expression system has enabled efficient production of soluble form of BgaL Paracoccus sp. 32d. The amino acid sequence analysis of the BgaL enzyme revealed notable differences in comparison to the result of the amino acid sequences analysis of well-characterized cold-active β-D-galactosidases belonging to Glycoside Hydrolase Family 2. Finally, the enzymatic properties of Paracoccus sp. 32d β-D-galactosidase shows its potential for being applied to development of a new industrial biocatalyst for efficient lactose hydrolysis in milk.
Cross-linking cellulose nanofibrils for potential elastic cryo-structured gels
Authors: Syverud Kristin , Kirsebom Harald , Hajizadeh Solmaz , Chinga-Carrasco Gary 
Published: December 2011

AbstractCellulose nanofibrils were produced from P. radiata kraft pulp fibers. The nanofibrillation was facilitated by applying 2,2,6,6-tetramethylpiperidinyl-1-oxyl-mediated oxidation as pretreatment. The oxidized nanofibrils were cross-linked with polyethyleneimine and poly N-isopropylacrylamide-co-allylamine-co-methylenebisacrylamide particles and were frozen to form cryo-structured gels. Samples of the gels were critical-point dried, and the corresponding structures were assessed with scanning electron microscopy. It appears that the aldehyde groups in the oxidized nanofibrils are suitable reaction sites for cross-linking. The cryo-structured materials were spongy, elastic, and thus capable of regaining their shape after a given pressure was released, indicating a successful cross-linking. These novel types of gels are considered potential candidates in biomedical and biotechnological applications.
Improving network energy efficiency through cooperative idling in the multi-cell systems
Authors: Xu Jie , Qiu Ling , Yu Chengwen 
Published: December 2011

Abstract
Network energy efficiency (NEE) is considered as the metric to address the energy efficiency problem in the cooperative multi-cell systems in this article. At first, three typical schemes with different levels of cooperation, i.e., interference aware game theory, inter-cell interference cancellation, and multi-cell joint processing, are discussed. For both unconstrained and constrained case, efficient power control strategies are developed to maximize the NEE. During the optimization, both the optimization objects and strategies are distinct because of different levels of data and channel state information at the transmitter sharing. In order to further improve NEE, a novel cooperative idling (CI) scheme is proposed through cooperatively switching some BSs into micro-sleep and guaranteeing the data transmission with the other active BSs' cooperative transmission. Simulation results indicate that cooperation can improve both NEE and network capacity and demonstrate that CI can further improve the NEE significantly.
Biomarkers of acute lung injury: worth their salt?
Authors: Proudfoot Alastair G , Hind Matthew , Griffiths Mark JD 
Published: December 2011

Abstract
The validation of biomarkers has become a key goal of translational biomedical research. The purpose of this article is to discuss the role of biomarkers in the management of acute lung injury (ALI) and related research. Biomarkers should be sensitive and specific indicators of clinically important processes and should change in a relevant timeframe to affect recruitment to trials or clinical management. We do not believe that they necessarily need to reflect pathogenic processes. We critically examined current strategies used to identify biomarkers and which, owing to expedience, have been dominated by reanalysis of blood derived markers from large multicenter Phase 3 studies. Combining new and existing validated biomarkers with physiological and other data may add predictive power and facilitate the development of important aids to research and therapy.