bluuebunny/crossref_metadata_2025_split huggingface dataset:
A comparison study on feature selection of DNA structural properties for promoter prediction
Authors: Gan Yanglan , Guan Jihong , Zhou Shuigeng 
Published: January 2012

AbstractBackgroundPromoter prediction is an integrant step for understanding gene regulation and annotating genomes. Traditional promoter analysis is mainly based on sequence compositional features. Recently, many kinds of structural features have been employed in promoter prediction. However, considering the high-dimensionality and overfitting problems, it is unfeasible to utilize all available features for promoter prediction. Thus it is necessary to choose some appropriate features for the prediction task.ResultsThis paper conducts an extensive comparison study on feature selection of DNA structural properties for promoter prediction. Firstly, to examine whether promoters possess some special structures, we carry out a systematical comparison among the profiles of thirteen structural features on promoter and non-promoter sequences. Secondly, we investigate the correlations between these structural features and promoter sequences. Thirdly, both filter and wrapper methods are utilized to select appropriate feature subsets from thirteen different kinds of structural features for promoter prediction, and the predictive power of the selected feature subsets is evaluated. Finally, we compare the prediction performance of the feature subsets selected in this paper with nine existing promoter prediction approaches.ConclusionsExperimental results show that the structural features are differentially correlated to promoters. Specifically, DNA-bending stiffness, DNA denaturation and energy-related features are highly correlated with promoters. The predictive power for promoter sequences differentiates greatly among different structural features. Selecting the relevant features can significantly improve the accuracy of promoter prediction.
Prevalence of diabetes among Han, Manchu and Korean ethnicities in the Mudanjiang area of China: a cross-sectional survey
Authors: Feng Yan , Yang Yumei , Ma Xuesong , Chen Kaiting , Wu Nannan , Wang Dongmei , Li Pengjie , Wang Minnan , Li Qiang , Zhang Jinchao 
Published: January 2012

Abstract

Background
Rapid socioeconomic development resulting in changing lifestyles and life expectancy appears to be accompanied by an increasing prevalence of type 2 diabetes. Genetic predisposition related to ethnicity is a major determinant of diabetes risk. This study investigates the prevalences of diabetes and prediabetes in different ethnic populations residing in the Mudanjiang area located in the northeast of China.

Methods
A cross-sectional survey was carried out among Han, Manchu and Korean Chinese aged 20 years or older. Diabetes and prediabetes were diagnosed using standard oral glucose tolerance tests.

Results
The prevalence of diabetes in Manchu (8.39%) and Korean Chinese (9.42%) was significantly lower than that in Han (12.10%). The prevalence of prediabetes was 18.96%, 19.36% and 20.47% in Han, Manchu and Korean populations, respectively. Korean Chinese had a lower prevalence of isolated impaired fasting glucose and higher prevalence of isolated impaired glucose tolerance than the other two ethnic groups. Most patients with diabetes, especially ethnic minority patients, were undiagnosed. A multiple logistic regression analysis showed that age, family history of diabetes, control of diet, self-monitoring of weight, central obesity, increased heart rate, hypertension, elevated plasma triglyceride level, elevated plasma low-density lipoprotein cholesterol, and Han ethnicity were significantly associated with an increased risk of diabetes. Further, Manchu Chinese were found to have the lowest risk of diabetes.

Conclusions
Our study indicates that diabetes is a major public health problem in the Mudanjiang area of China. Ethnicity plays a role in the different prevalences of diabetes and prediabetes among the three ethnic groups. Diabetes is less prevalent among Manchu Chinese compared with Han and Korean Chinese.
Fluoride bioavailability in saliva and plaque
Authors: Naumova Ella A , Kuehnl Phillip , Hertenstein Philipp , Markovic Ljubisa , Jordan Rainer A , Gaengler Peter , Arnold Wolfgang H 
Published: January 2012

Abstract

Background
Different fluoride formulations may have different effects on caries prevention. It was the aim of this clinical study to assess the fluoride content, provided by NaF compared to amine fluoride, in saliva and plaque.

Methods
Eight trained volunteers brushed their teeth in the morning for 3 minutes with either NaF or amine fluoride, and saliva and 3-day-plaque-regrowth was collected at 5 time intervals during 6 hours after tooth brushing. The amount of collected saliva and plaque was measured, and the fluoride content was analysed using a fluoride sensitive electrode. All subjects repeated all study cycles 5 times, and 3 cycles per subject underwent statistical analysis using the Wilcoxon-Mann-Whitney test.

Results
Immediately after brushing the fluoride concentration in saliva increased rapidly and dropped to the baseline level after 360 minutes. No difference was found between NaF and amine fluoride. All plaque fluoride levels were elevated after 30 minutes until 120 minutes after tooth brushing, and decreasing after 360 minutes to baseline. According to the highly individual profile of fluoride in saliva and plaque, both levels of bioavailability correlated for the first 30 minutes, and the fluoride content of saliva and plaque was back to baseline after 6 hours.

Conclusions
Fluoride levels in saliva and plaque are interindividually highly variable. However, no significant difference in bioavailability between NaF and amine fluoride, in saliva, or in plaque was found.
Engineered Trx2p industrial yeast strain protects glycolysis and fermentation proteins from oxidative carbonylation during biomass propagation
Authors: Gómez-Pastor Rocío , Pérez-Torrado Roberto , Cabiscol Elisa , Ros Joaquim , Matallana Emilia 
Published: January 2012

Abstract

Background
In the yeast biomass production process, protein carbonylation has severe adverse effects since it diminishes biomass yield and profitability of industrial production plants. However, this significant detriment of yeast performance can be alleviated by increasing thioredoxins levels. Thioredoxins are important antioxidant defenses implicated in many functions in cells, and their primordial functions include scavenging of reactive oxygen species that produce dramatic and irreversible alterations such as protein carbonylation.

Results
In this work we have found several proteins specifically protected by yeast Thioredoxin 2 (Trx2p). Bidimensional electrophoresis and carbonylated protein identification from TRX-deficient and TRX-overexpressing cells revealed that glycolysis and fermentation-related proteins are specific targets of Trx2p protection. Indeed, the TRX2 overexpressing strain presented increased activity of the central carbon metabolism enzymes. Interestingly, Trx2p specifically preserved alcohol dehydrogenase I (Adh1p) from carbonylation, decreased oligomer aggregates and increased its enzymatic activity.

Conclusions
The identified proteins suggest that the fermentative capacity detriment observed under industrial conditions in T73 wine commercial strain results from the oxidative carbonylation of specific glycolytic and fermentation enzymes. Indeed, increased thioredoxin levels enhance the performance of key fermentation enzymes such as Adh1p, which consequently increases fermentative capacity.
Casein phosphopeptides drastically increase the secretion of extracellular proteins in Aspergillus awamori. Proteomics studies reveal changes in the secretory pathway
Authors: Kosalková Katarina , García-Estrada Carlos , Barreiro Carlos , Flórez Martha G , Jami Mohammad S , Paniagua Miguel A , Martín Juan F 
Published: January 2012

Abstract

Background
The secretion of heterologous animal proteins in filamentous fungi is usually limited by bottlenecks in the vesicle-mediated secretory pathway.

Results
Using the secretion of bovine chymosin in Aspergillus awamori as a model, we found a drastic increase (40 to 80-fold) in cells grown with casein or casein phosphopeptides (CPPs). CPPs are rich in phosphoserine, but phosphoserine itself did not increase the secretion of chymosin. The stimulatory effect is reduced about 50% using partially dephosphorylated casein and is not exerted by casamino acids. The phosphopeptides effect was not exerted at transcriptional level, but instead, it was clearly observed on the secretion of chymosin by immunodetection analysis. Proteomics studies revealed very interesting metabolic changes in response to phosphopeptides supplementation. The oxidative metabolism was reduced, since enzymes involved in fermentative processes were overrepresented. An oxygen-binding hemoglobin-like protein was overrepresented in the proteome following phosphopeptides addition. Most interestingly, the intracellular pre-protein enzymes, including pre-prochymosin, were depleted (most of them are underrepresented in the intracellular proteome after the addition of CPPs), whereas the extracellular mature form of several of these secretable proteins and cell-wall biosynthetic enzymes was greatly overrepresented in the secretome of phosphopeptides-supplemented cells. Another important 'moonlighting' protein (glyceraldehyde-3-phosphate dehydrogenase), which has been described to have vesicle fusogenic and cytoskeleton formation modulating activities, was clearly overrepresented in phosphopeptides-supplemented cells.

Conclusions
In summary, CPPs cause the reprogramming of cellular metabolism, which leads to massive secretion of extracellular proteins.
Community and household socioeconomic factors associated with pesticide-using, small farm household members' health: a multi-level, longitudinal analysis
Authors: Cole Donald C , Orozco Fadya A , Ibrahim Selahadin , Wanigaratne Susitha 
Published: January 2012

Abstract

Background
Longitudinal studies using multi-level models to examine health inequalities in lower and middle income countries (LMICs) are rare. We explored socio-economic gradients in health among small farm members participating in a pesticide-related health and agriculture program in highland Ecuador.

Methods
We profiled 24 communities through key informant interviews, secondary data (percent of population with unsatisfied basic needs), and intervention implementation indicators. Pre (2005) and post (2007) surveys of the primary household and crop managers included common questions (education, age, and the health outcome - digit span scaled 0-10)) and pesticide-related practice questions specific to each. Household assets and pesticide use variables were shared across managers. We constructed multi-level models predicting 2007 digit span for each manager type, with staged introduction of predictor variables.

Results
376 household managers (79% of 2005 participants) and 380 crop managers (76% of 2005 participants) had complete data for analysis. The most important predictor of 2007 digit span was 2005 digit span: β (Standard Error) of 0.31(0.05) per unit for household and 0.17(0.04) for crop managers. Household asset score was next most important: 0.14(0.06) per unit for household and 0.14(0.05) for crop managers. Community percent with unsatisfied basic needs was associated with reductions in 2007 digit span: -0.04(0.01) per percent for household and -0.03(0.01) for crop managers.

Conclusions
The important roles of life endowments and/or persistent neurotoxicity were exemplified by limited change in the health outcome. Gradients by household assets and community deprivation were indicative of ongoing, structural inequities within this LMIC.
Studies on the antihypertensive and antidyslipidemic activities of Viola odorata leaves extract
Authors: Siddiqi Hasan S , Mehmood Malik H , Rehman Najeeb U , Gilani Anwar H 
Published: January 2012

Abstract

Background
This study was undertaken to provide pharmacological basis for the medicinal use of Viola odorata Linn. in hypertension and dyslipidemia using the in vivo and in vitro assays.

Results

Viola odorata leaves extract (Vo.Cr), which tested positive for alkaloids, saponins, tannins, phenolics, coumarins and flavonoids, caused a dose-dependent (0.1-1.0 mg/kg) decrease in mean arterial blood pressure in anaesthetized rats. In isolated guinea-pig atria, Vo.Cr equally inhibited force and rate of spontaneous atrial contractions. On the baseline of rat thoracic aortae (endothelium-intact and denuded), the plant extract caused phentolamine-sensitive vasoconstriction. When tested on phenylephrine (PE, 1 μM) and K+ (80 mM)-induced vasoconstriction, Vo.Cr caused a concentration-dependent relaxation and also caused a rightward shift of Ca++ concentration-response curves as well as suppression of PE (1 μM) control peaks in Ca++-free medium, similar to that caused by verapamil. In the presence of L-NAME, the relaxation curve of Vo.Cr was partially inhibited showing involvement of Nitric oxide (NO) mediated pathway. In Tyloxapol-induced dyslipidemia, Vo.Cr caused reduction in total cholesterol and triglyceride levels. In high-fat diet-induced dyslipidemia model, the plant extract caused a significant decrease in total cholesterol, LDL-C, atherogenic index and prevented the increase in average body weights, while it increased HDL-C.

Conclusions
These data indicate that the vasodilator effect of the plant extract is mediated through multiple pathways like inhibition of Ca++ influx via membranous Ca++ channels, its release from intracellular stores and NO-mediated pathways, which possibly explain the fall in BP. The plant also showed reduction in body weight and antidyslipidemic effect which may be due to the inhibition of synthesis and absorption of lipids and antioxidant activities. Thus, this study provides a pharmacologic rationale to the medicinal use of Viola odorata in hypertension and dyslipidemia.
SMTP (Stachybotrys microspora triprenyl phenol) enhances clot clearance in a pulmonary embolism model in rats
Authors: Hu Weimin , Narasaki Ritsuko , Nishimura Naoko , Hasumi Keiji 
Published: January 2012

Abstract

Background

Stachybotrys microspora triprenyl phenols (SMTPs) are a novel family of small molecules that enhance both activation and fibrin-binding of plasminogen. While their effects on fibrinolysis have been characterized in vitro, little is known about their activity in vivo with respect to plasminogen activation and blood clot clearance.

Results
To select a potent SMTP congener for the evaluation of its action in vitro and in vivo, we tested several SMTP congeners with distinct structural properties for their effects on plasminogen activation. As a result, SMTP-7 (orniplabin) was found to have distinguished activity. Several lines of biochemical evidence supported the idea that SMTP-7 acted as a plasminogen modulator. SMTP-7 elevated plasma level of plasmin-α2-antiplasmin complex, an index of plasmin formation in vivo, 1.5-fold in mice after the intravenous injections at doses of 5 and 10 mg kg-1. In a rat pulmonary embolism model, SMTP-7 (5 mg kg-1) enhanced the rate of clot clearance ~3-fold in the absence of exogenous plasminogen activator. Clot clearance was enhanced further by 5 mg kg-1 of SMTP-7 in combination with single-chain urokinase-type plasminogen activator.

Conclusions
Our results show that SMTP-7 is a superior plasminogen modulator among the SMTP family compounds and suggest that the agent enhances plasmin generation in vivo, leading to clearance of thrombi in a model of pulmonary embolism.
Highly pathogenic avian influenza virus H5N1 controls type I IFN induction in chicken macrophage HD-11 cells: a polygenic trait that involves NS1 and the polymerase complex
Authors: Liniger Matthias , Moulin Hervé R , Sakoda Yoshihiro , Ruggli Nicolas , Summerfield Artur 
Published: January 2012

Abstract

Background
Influenza A viruses are well characterized to antagonize type I IFN induction in infected mammalian cells. However, limited information is available for avian cells. It was hypothesised that avian influenza viruses (AIV) with distinct virulence may interact differently with the avian innate immune system. Therefore, the type I IFN responses induced by highly virulent and low virulent H5N1 AIV and reassortants thereof were analysed in chicken cells.

Results
The highly pathogenic (HP) AIV A/chicken/Yamaguchi/7/04 (H5N1) (Yama) did not induce type I IFN in infected chicken HD-11 macrophage-like cells. This contrasted with an NS1 mutant Yama virus (Yama-NS1A144V) and with the attenuated H5N1 AIV A/duck/Hokkaido/Vac-1/04 (Vac) carrying the haemagglutinin (HA) of the Yama virus (Vac-Yama/HA), that both induced type I IFN in these cells. The substitution of the NS segment from Yama with that from Vac in the Yama backbone resulted in induction of type I IFN secretion in HD-11 cells. However, vice versa, the Yama NS segment did not prevent type I IFN induction by the Vac-Yama/HA virus. This was different with the PB1/PB2/PA segment reassortant Yama and Vac-Yama/HA viruses. Whereas the Yama virus with the Vac PB1/PB2/PA segments induced type I IFN in HD-11 cells, the Vac-Yama/HA virus with the Yama PB1/PB2/PA segments did not. As reported for mammalian cells, the expression of H5N1 PB2 inhibited the activation of the IFN-β promoter in chicken DF-1 fibroblast cells. Importantly, the Yama PB2 was more potent at inhibiting the IFN-β promoter than the Vac PB2.

Conclusions
The present study demonstrates that the NS1 protein and the polymerase complex of the HPAIV Yama act in concert to antagonize chicken type I IFN secretion in HD-11 cells. PB2 alone can also exert a partial inhibitory effect on type I IFN induction. In conclusion, the control of type I IFN induction by H5N1 HPAIV represents a complex phenotype that involves a particular viral gene constellation rather than a single viral protein. Collectively, these findings contribute to understand the high virulence of HPAIV H5N1 viruses observed in the chicken host.
Distribution of enteroviruses in hospitalized children with hand, foot and mouth disease and relationship between pathogens and nervous system complications
Authors: Xu Wei , Liu Chun-feng , Yan Li , Li Jiu-jun , Wang Li-jie , Qi Ying , Cheng Rui-bo , Xiong Xiao-yu 
Published: January 2012

AbstractBackgroundTo explore the relationship between enteroviruses and hospitalized children with hand, foot and mouth disease (HFMD) complicated with nervous system disease. 234 hospitalized HFMD patients treated in Shengjing Hospital, Liaoning Province were analyzed retrospectively. Based on the presence and severity of nervous system disease, the patients were grouped as follows: general patients, severely ill patients, critically ill patients and fatal patients. Based on the detected pathogen, the patients were grouped as follows: Enterovirus 71 (EV71) infection, coxsackie A16 (CA16) infection and other enterovirus (OE) infection.ResultsOf the 423 hospitalized patients, most were admitted in July 2010(129/423, 30.5%). Enteroviruses were detected in 177(41.8%). 272/423 patients were male (64.3%), and fatal patients had the greatest proportion of male patients (p< 0.05). EV71 infection was found in 89/423 patients (21%). CA16 infection was detected in 8/423 patients (16.1%). Compared to group CA16, patients in group EV71 were hospitalized earlier, and the duration of hospitalization was longer (p< 0.05). Of the 92 patients with nervous system damage, 65 were infected with EV71 and 19 were infected with CA16. Among these CA16 infected patients, 2 had brainstem encephalitis and 1 had AFP. There were more patients with nervous system dysfunction in group EV71 than in groups CA16 or OE (p< 0.05). The 5 fatalities all occurred in group EV71 patients (p< 0.05). Infection with EV71 was most likely to cause neurogenic pulmonary edema (p< 0.05). Patients in group EV71 had a higher rate of suffering from coma and limb movement disorder than patients in groups CA16 or OE (p< 0.05).ConclusionThe disease progresses faster in EV71-infected HFMD patients. These patients are more likely to suffer nervous system damage, neurogenic pulmonary edema, severe sequelae or death. CA16 and other enteroviruses can also cause HFMD with severe nervous system complications.
On the molecular mechanism of GC content variation among eubacterial genomes
Authors: Wu Hao , Zhang Zhang , Hu Songnian , Yu Jun 
Published: January 2012

Abstract

Background
As a key parameter of genome sequence variation, the GC content of bacterial genomes has been investigated for over half a century, and many hypotheses have been put forward to explain this GC content variation and its relationship to other fundamental processes. Previously, we classified eubacteria into dnaE-based groups (the dimeric combination of DNA polymerase III alpha subunits), according to a hypothesis where GC content variation is essentially governed by genome replication and DNA repair mechanisms. Further investigation led to the discovery that two major mutator genes, polC and dnaE2, may be responsible for genomic GC content variation. Consequently, an in-depth analysis was conducted to evaluate various potential intrinsic and extrinsic factors in association with GC content variation among eubacterial genomes.

Results
Mutator genes, especially those with dominant effects on the mutation spectra, are biased towards either GC or AT richness, and they alter genomic GC content in the two opposite directions. Increased bacterial genome size (or gene number) appears to rely on increased genomic GC content; however, it is unclear whether the changes are directly related to certain environmental pressures. Certain environmental and bacteriological features are related to GC content variation, but their trends are more obvious when analyzed under the dnaE-based grouping scheme. Most terrestrial, plant-associated, and nitrogen-fixing bacteria are members of the dnaE1|dnaE2 group, whereas most pathogenic or symbiotic bacteria in insects, and those dwelling in aquatic environments, are largely members of the dnaE1|polV group.

Conclusion
Our studies provide several lines of evidence indicating that DNA polymerase III α subunit and its isoforms participating in either replication (such as polC) or SOS mutagenesis/translesion synthesis (such as dnaE2), play dominant roles in determining GC variability. Other environmental or bacteriological factors, such as genome size, temperature, oxygen requirement, and habitat, either play subsidiary roles or rely indirectly on different mutator genes to fine-tune the GC content. These results provide a comprehensive insight into mechanisms of GC content variation and the robustness of eubacterial genomes in adapting their ever-changing environments over billions of years.

Reviewers
This paper was reviewed by Nicolas Galtier, Adam Eyre-Walker, and Eugene Koonin.