bluuebunny/crossref_metadata_2025_split huggingface dataset:
Large-scale dynamic gene regulatory network inference combining differential equation models with local dynamic Bayesian network analysis
Authors: Li Zheng , Li Ping , Krishnan Arun , Liu Jingdong 
Published: August 2011

Abstract
Motivation: Reverse engineering gene regulatory networks, especially large size networks from time series gene expression data, remain a challenge to the systems biology community. In this article, a new hybrid algorithm integrating ordinary differential equation models with dynamic Bayesian network analysis, called Differential Equation-based Local Dynamic Bayesian Network (DELDBN), was proposed and implemented for gene regulatory network inference.
Results: The performance of DELDBN was benchmarked with an in vivo dataset from yeast. DELDBN significantly improved the accuracy and sensitivity of network inference compared with other approaches. The local causal discovery algorithm implemented in DELDBN also reduced the complexity of the network inference algorithm and improved its scalability to infer larger networks. We have demonstrated the applicability of the approach to a network containing thousands of genes with a dataset from human HeLa cell time series experiments. The local network around BRCA1 was particularly investigated and validated with independent published studies. BRAC1 network was significantly enriched with the known BRCA1-relevant interactions, indicating that DELDBN can effectively infer large size gene regulatory network from time series data.
Availability: The R scripts are provided in File 3 in Supplementary Material.
Contact: zheng.li@monsanto.com; jingdong.liu@monsanto.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Positive impact of hepatitis C virus (HCV) treatment on antiretroviral treatment adherence in human immunodeficiency virus–HCV coinfected patients: one more argument for expanded access to HCV treatment for injecting drug users
Authors: Roux Perrine , Fugon Lionel , Winnock Maria , Salmon‐Céron Dominique , Lacombe Karine , Sogni Philippe , Spire Bruno , Dabis François , Carrieri Maria Patrizia ,   for the ANRS‐CO‐13‐HEPAVIH Study Group
Published: August 2011

ABSTRACTAims  Treatment for the hepatitis C virus (HCV) may be delayed significantly in human immunodeficiency virus (HIV)/HCV coinfected patients on antiretroviral treatment (ART) for fear that its burden could compromise ART adherence. However, the effect such treatment has on ART adherence in observational settings remains largely unknown. Longitudinal data were used to investigate the relationship between initiating HCV treatment and adherence to ART in HIV/HCV coinfected patients.Design  The French national prospective cohort of patients coinfected with HIV and HCV (ANRS‐CO‐13‐HEPAVIH) is a multi‐centre cohort.Setting  Seventeen out‐patient hospital services delivering HIV and HCV care in France.Participants  HIV/HCV coinfected patients on ART (n = 593 patients, 976 visits).Measurements  Self‐administered questionnaires and medical records. A mixed logistic regression model based on generalized estimates equations (GEE) to identify factors associated with non‐adherence to ART.Findings  Among the 593 patients, 36% were classified as non‐adherent to ART at the enrolment visit and 12% started HCV treatment during follow‐up. ART adherence was not associated statistically with HCV treatment initiation. The proportion of patients maintaining adherence or becoming adherent to ART for those starting HCV treatment was higher than in the rest of the sample (P = 0.07). After multiple adjustment for known correlates, such as poor housing conditions, binge drinking, recent drug use and depressive symptoms, patients who initiated HCV treatment were less likely to be non‐adherent to ART [odds ratio (95% confidence interval) = 0.41 (0.24–0.71)].Conclusions  Engaging human immunodeficiency virus/hepatitis C virus coinfected individuals in hepatitis C virus treatment is associated with high adherence to antiretroviral treatment. Physicians should prioritize hepatitis C virus treatment as part of a multi‐disciplinary approach.
Prevention of mother‐to‐child transmission of human immunodeficiency virus among pregnant women using injecting drugs in Ukraine, 2000–10
Authors: Thorne Claire , Semenenko Igor , Malyuta Ruslan ,   Ukraine European Collaborative Study Group in EuroCoord
Published: August 2011

ABSTRACTAims  To compare clinical status, mother‐to‐child transmission (MTCT) rates, use of prevention of (PMTCT) interventions and pregnancy outcomes between HIV‐infected injecting drug users (IDUs) and non‐IDUs.Design and setting  Prospective cohort study conducted in seven human immunodeficiency virus/acquired immune deficiency syndrome (HIV/AIDS) Centres in Ukraine, 2000–10.Participants  Pregnant HIV‐infected women, identified before/during pregnancy or intrapartum, and their live‐born infants (n = 6200); 1028 women followed post‐partum.Measurements  Maternal and delivery characteristics, PMTCT prophylaxis, MTCT rates, preterm delivery (PTD) and low birth weight (LBW).Findings  Of 6200 women, 1111 (18%) reported current/previous IDU. The proportion of IDUs diagnosed with HIV before conception increased from 31% in 2000/01 to 60% in 2008/09 (P < 0.01). Among women with undiagnosed HIV at conception, 20% of IDUs were diagnosed intrapartum versus 4% of non‐IDUs (P < 0.01). At enrolment, 14% of IDUs had severe/advanced HIV symptoms versus 6% of non‐IDUs (P < 0.001). IDUs had higher rates of PTD and LBW infants than non‐IDUs, respectively, 16% versus 7% and 22% versus 10% (P < 0.001). IDUs were more likely to receive no neonatal or intrapartum PMTCT prophylaxis compared with non‐IDUs (OR 2.81, p < 0.001). MTCT rates were 10.8% in IDUs versus 5.9% in non‐IDUs; IDUs had increased MTCT risk (adjusted odds ratio 1.32, P = 0.049). Fewer IDUs with treatment indications received HAART compared with non‐IDUs (58% versus 68%, P = 0.03).Conclusions  Pregnant human immunodeficiency virus‐infected injecting drug users in Ukraine have worse clinical status, poorer access to prevention of mother‐to‐child transmission prophylaxis and highly active antiretroviral therapy, more adverse pregnancy outcomes and higher risk of mother‐to‐child transmission than non‐injecting drug user women.
Reduced growth hormone secretion in obesity is associated with smaller LDL and HDL particle size
Authors: Makimura Hideo , Feldpausch Meghan N. , Stanley Takara L. , Sun Noelle , Grinspoon Steven K. 
Published: August 2011

SummaryObjective  Reduced growth hormone (GH) secretion is observed in obesity and may contribute to increases in cardiovascular disease (CVD) risk. Lipoprotein characteristics including increased small dense low‐density lipoprotein (LDL) particles are known independent risk factors for CVD. We hypothesized that reduced GH secretion in obesity would be associated with a more atherogenic lipid profile including increased small dense LDL particles.Design  To evaluate this hypothesis, we studied 102 normal weight and obese men and women using standard GH stimulation testing to assess GH secretory capacity and performed comprehensive lipoprotein analyses including determination of lipoprotein particle size and subclass concentrations using proton NMR spectroscopy.Results  Obese subjects were stratified into reduced or sufficient GH secretion based on the median peak‐stimulated GH (≤6·25 μg/l). Obese subjects with reduced GH secretion (n = 35) demonstrated a smaller mean LDL and HDL particle size in comparison to normal weight subjects (n = 33) or obese subjects with sufficient GH (n = 34) by anova (P < 0·0001). Univariate analyses demonstrated peak‐stimulated GH was positively associated with LDL (r = 0·50; P < 0·0001) and HDL (r = 0·57; P < 0·0001), but not VLDL (P = 0·06) particle size. Multivariate regression analysis controlling for age, gender, race, ethnicity, tobacco, use of lipid‐lowering medication, BMI and HOMA demonstrated peak‐stimulated GH remained significantly associated with LDL particle size (β = 0·01; P = 0·01; R2 = 0·42; P < 0·0001 for overall model) and HDL particle size (β = 0·008; P = 0·001; R2 = 0·44; P < 0·0001 for overall model).Conclusions  These results suggest reduced peak‐stimulated GH in obesity is independently associated with a more atherogenic lipoprotein profile defined in terms of particle size.
Elevated E‐selectin and diastolic blood pressure in diabetic children
Authors: Maggio Albane B. R. , Farpour‐Lambert Nathalie J. , Montecucco Fabrizio , Pelli Graziano , Marchand Laetitia M. , Schwitzgebel Valérie , Mach François , Aggoun Yacine , Beghetti Maurice 
Published: August 2011

Eur J Clin Invest 2012; 42 (3): 303–309AbstractBackground  Cardiovascular risk markers are related to micro‐angiopathy in children with type 1 diabetes (T1DM), but there is no information about their relationship with blood pressure (BP) and endothelial function.Materials and methods  This was a case–control study including 29 children with T1DM (mean age 10·5 ± 2·7 years, disease duration: 3·8 ± 2·2 years) and 39 healthy controls (mean age: 9·8 ± 2·7 years). We assessed 24‐h ambulatory BP, vascular function and serum level of lipids, vascular cell adhesion molecule‐1 (VCAM‐1; ICAM) and selectins (E‐selectin; P‐selectin).Results  The subject groups had similar physical characteristics and lipids level, except body mass index (BMI) which was higher in T1DM than in healthy children (18·6 ± 2·6 vs. 16·7 ± 2·5 kg/m2, P = 0·003). Children with T1DM had increased 24 h diastolic BP z‐score (0·62 ± 0·9 vs. −0·65 ± 0·8, P < 0·001), even after adjustment for BMI, as well as higher VCAM‐1 concentration (492 ± 346 vs. 340 ± 225 ng/mL, P = 0·039) compared to healthy subjects. Diastolic BP z‐scores were associated with disease duration, E‐selectin and triglyceride levels in the T1DM group (P < 0·05). E‐selectin was also related to triglycerides, otherwise there were no relationships between vascular function, markers and BP.Conclusion  E‐selectin, an early atherosclerosis biomarker, is positively associated with diastolic BP values in children with T1DM, despite relatively short disease duration.
Insertion of an intact CR1 retrotransposon in a cadherin gene linked with Bt resistance in the pink bollworm, Pectinophora gossypiella
Authors: Fabrick J. A. , Mathew L. G. , Tabashnik B. E. , Li X. 
Published: August 2011

AbstractThree mutations in the Pectinophora gossypiella cadherin gene PgCad1 are linked with resistance to Bacillus thuringiensis (Bt) toxin Cry1Ac. Here we show that the r3 mutation entails recent insertion into PgCad1 of an active chicken repeat (CR1) retrotransposon, designated CR1‐1_Pg. Unlike most other CR1 elements, CR1‐1_Pg is intact, transcribed by a flanking promoter, contains target site duplications and has a relatively low number of copies. Examination of transcripts from the PgCad1 locus revealed that CR1‐1_Pg disrupts both the cadherin protein and a long noncoding RNA of unknown function. Together with previously reported data, these findings show that transposable elements disrupt eight of 12 cadherin alleles linked with resistance to Cry1Ac in three lepidopteran species, indicating that the cadherin locus is a common target for disruption by transposable elements.
Shelf life of alginate beads containing lactobacilli and bifidobacteria: characterisation of microspheres containing Lactobacillus delbrueckii subsp. bulgaricus
Authors: Corbo Maria Rosaria , Bevilacqua Antonio , Sinigaglia Milena 
Published: August 2011

SummaryCapsules, containing different microorganisms (Lactobacillus plantarum, L. casei, L. delbrueckii subsp. bulgaricus, L. delbrueckii subsp. delbrueckii, L. reuteri, L. rhamnosus, Bifidobacterium breve and B. animalis subsp. lactis), were produced through a simple extrusion protocol and dipped in a CaCl2 solution (0.5% or 8%). Beads were characterised, to assess the encapsulation yield (EY) and the shelf life at 4 °C (defined as the time to retain inside a cell count of 6 log CFU g−1); then, L. delbrueckii subsp. bulgaricus was used as target for system optimisation, through the study of the kinetic of cell release, as a function of the concentration of CaCl2 solution, agitation (150 rpm) and recycling. The EY was 50% or higher, and the shelf life was at least 30 days. Concerning beads containing L. delbrueckii subsp. bulgaricus, the release of cells from capsules followed a biphasic (diauxic) trend and the microsphere could be used successfully for two times, as only after third reuse, the amount of release cells decreased.
Assessment of cavitated and active non‐cavitated caries lesions in 3‐ to 4‐year‐old preschool children: a field study
Authors: PARISOTTO THAÍS M. , STEINER‐OLIVEIRA CAROLINA , De SOUZA‐e‐SILVA CÍNTIA M. , PERES REGINA C. R. , RODRIGUES LIDIANY K. A. , NOBRE‐DOS‐SANTOS MARINÊS 
Published: August 2011

International Journal of Paediatric Dentistry 2012; 22: 92–99Background.  The prevalence of early childhood caries (ECC) is high in developing countries; thus, sensitive methods for the early diagnosis of ECC are of prime importance to implement the appropriate preventive measures.Aim.  To investigate the effects of the addition of early caries lesions (ECL) into WHO threshold caries detection methods on the prevalence of caries in primary teeth and the epidemiological profile of the studied population.Design.  In total, 351 3‐ to 4‐year‐old preschoolers participated in this cross‐sectional study. Clinical exams were conducted by one calibrated examiner using WHO and WHO + ECL criteria. During the exams, a mirror, a ball‐ended probe, gauze, and an artificial light were used. The data were analysed by Wilcoxon and Mc‐Nemar’s tests (α = 0.05).Results.  Good intra‐examiner Kappa values at tooth/surface levels were obtained for WHO and WHO + ECL criteria (0.93/0.87 and 0.75/0.78, respectively). The dmfs scores were significantly higher (P < 0.05) when WHO + ECL criteria were used. ECLs were the predominant caries lesions in the majority of teeth.Conclusions.  The results strongly suggest that the WHO + ECL diagnosis method could be used to identify ECL in young children under field conditions, increasing the prevalence and classification of caries activity and providing valuable information for the early establishment of preventive measures.
A predictive model of avian natal dispersal distance provides prior information for investigating response to landscape change
Authors: Garrard Georgia E. , McCarthy Michael A. , Vesk Peter A. , Radford James Q. , Bennett Andrew F. 
Published: August 2011

Summary1. Informative Bayesian priors can improve the precision of estimates in ecological studies or estimate parameters for which little or no information is available. While Bayesian analyses are becoming more popular in ecology, the use of strongly informative priors remains rare, perhaps because examples of informative priors are not readily available in the published literature.2. Dispersal distance is an important ecological parameter, but is difficult to measure and estimates are scarce. General models that provide informative prior estimates of dispersal distances will therefore be valuable.3. Using a world‐wide data set on birds, we develop a predictive model of median natal dispersal distance that includes body mass, wingspan, sex and feeding guild. This model predicts median dispersal distance well when using the fitted data and an independent test data set, explaining up to 53% of the variation.4. Using this model, we predict a priori estimates of median dispersal distance for 57 woodland‐dependent bird species in northern Victoria, Australia. These estimates are then used to investigate the relationship between dispersal ability and vulnerability to landscape‐scale changes in habitat cover and fragmentation.5. We find evidence that woodland bird species with poor predicted dispersal ability are more vulnerable to habitat fragmentation than those species with longer predicted dispersal distances, thus improving the understanding of this important phenomenon.6. The value of constructing informative priors from existing information is also demonstrated. When used as informative priors for four example species, predicted dispersal distances reduced the 95% credible intervals of posterior estimates of dispersal distance by 8–19%. Further, should we have wished to collect information on avian dispersal distances and relate it to species’ responses to habitat loss and fragmentation, data from 221 individuals across 57 species would have been required to obtain estimates with the same precision as those provided by the general model.
No evidence of senescence in a 300‐year‐old mountain herb
Authors: Garcia Maria B. , Dahlgren Johan P. , Ehrlén Johan 
Published: August 2011

Summary1. Understanding how vital rates and reproductive value change with age is fundamental to demography, life history evolution and population genetics. The universality of organism senescence has been questioned on both theoretical and empirical grounds, and the prevalence and strength of senescence remain a controversial issue. Plants are particularly interesting for studies of senescence since individuals of many species have been reported to reach very high ages.2. In this study, we examined whether the herb Borderea pyrenaica, known to reach ages of more than 300 years, experiences senescence. We collected detailed demographic information from male and female individuals in two populations over 5 years. An unusual morphological feature in this species enabled us to obtain exact age estimates for each of the individuals at the end of the demographic study.3. We used restricted cubic regression splines and generalized linear models to determine nonlinear effects of age and size on vital rates. We then incorporated the effects of age and size in integral projection models of demography for determining the relationship between age and reproductive value. As the species is dioecious, we performed analyses separately for males and females and examined also the hypothesis that a larger reproductive effort in females comes at a senescence cost.4. We found no evidence for senescence. Recorded individuals reached 260 years, but growth and fecundity of female and male individuals did not decrease at high ages, and survival and reproductive value increased with age. The results were qualitatively similar also when accounting for size and among‐individual vital rate heterogeneity, with the exception that male flowering probability decreased with age when accounting for size increases.5.
Synthesis. Overall, our results show that performance of both male and female plants of B. pyrenaica may increase rather than decrease at ages up to several centuries, and they support the notion that senescence may be negligible in long‐lived modular organisms. This highlights the need to explore mechanisms that enable some species to maintain high reproductive values also at very high ages and to identify the evolutionary reasons why some organisms appear to experience no or negligible senescence.
Tropical tree species assemblages in topographical habitats change in time and with life stage
Authors: Kanagaraj Rajapandian , Wiegand Thorsten , Comita Liza S. , Huth Andreas 
Published: August 2011

Summary1.Recent studies have documented shifts in habitat associations of single tropical tree species from one life stage to the next. However, the community‐level consequences of such shifts have not been investigated, and it is not clear whether they would amplify, neutralize or completely alter habitat structuring during the transitions to the adult community.2.We compared habitat‐driven species assemblages at three life stages (i.e. recruitment, juvenile and reproductive stages) and six censuses for tree and shrub species in a fully censused 50‐ha plot of Panamanian lowland forest. Habitat types were determined using multivariate regression trees that group areas with similar species composition (i.e. species assemblages) according to their topographical characteristics.3.Three topographical variables (a topographical wetness index, slope and elevation) were major determinants of species assemblages. When analysing individuals of all life stages together, we found a distinct and temporally consistent structuring of the plot into four dominant habitat types (low and high plateaus, slope and swamp) which was consistent with previous classifications. Basically, the same habitat structuring emerged for the juvenile communities of individual censuses. However, recruits showed a weak and temporally inconsistent habitat structuring.4.A notable homogenization in species assemblages occurred during the transition from juvenile to reproductive, through both a reduction in the number of species assemblages (in 3 censuses, one large reproductive assemblage covered 93% of the plot, and in others, an additional slope habitat emerged) and a reduction in the classification error. Overall, habitat structuring became noisier and weaker over the 25 years of the study.5.Synthesis.Our results suggest that mortality processes during the transition from recruits to juveniles must enhance the signal of habitat structuring. However, during the transition to the reproductive stage, species may have lost the advantage of being in the habitat with which they had become associated, or the quality of habitat changed during their life span because of larger climatic changes. The homogeneous assemblages of the reproductive stage could be interpreted as support for neutral theories, but further research is required to unravel the mechanisms behind these intriguing observations.
Evidence‐based medicine and epistemological imperialism: narrowing the divide between evidence and illness
Authors: Crowther Helen , Lipworth Wendy , Kerridge Ian 
Published: August 2011

AbstractEvidence‐based medicine (EBM) has been rapidly and widely adopted because it claims to provide a method for determining the safety and efficacy of medical therapies and public health interventions more generally. However, as others have noted, EBM may be riven through with cultural bias, both in the generation of evidence and in its translation. We suggest that technological and scientific advances in medicine accentuate and entrench these cultural biases, to the extent that they may invalidate the evidence we have about disease and its treatment. This creates a significant ethical, epistemological and ontological challenge for medicine.
Mere anecdote: evidence and stories in medicine
Authors: Nunn Robin 
Published: August 2011

AbstractIn evidence‐based medicine, randomized controlled trials are said to be the highest evidence of what works, while anecdotes have low value or are not even considered to be medical evidence. Similar hierarchical views of evidence have infected other disciplines, including evidence‐based education and evidence‐based government. Here, I explore the artificial divisions of acceptable from unacceptable evidence, numbers from narrative and sciences from humanities. I challenge the deprecation of stories in medicine. Some stories are based on experiments while others are based on more or less plausible theories. Some stories offer vast and impressive statistics gathered from many observations while others present one noteworthy event. Published reports are themselves stories of what experimenters did. Systematic reviewers generate their own observations of collected stories of experiments. Reviewers of systematic reviews in turn report their observations of systematic reviews. All of these stories become evidence of what works in medicine.