bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association of rs5888 SNP in the scavenger receptor class B type 1 gene and serum lipid levels
Authors: Wu Dong-Feng , Yin Rui-Xing , Hu Xi-Jiang , Aung Lynn Htet Htet , Cao Xiao-Li , Miao Lin , Li Qing , Yan Ting-Ting , Wu Jin-Zhen , Pan Shang-Ling 
Published: May 2012

Abstract

Background
Bai Ku Yao is a special subgroup of the Yao minority in China. The present study was undertaken to detect the association of rs5888 single nucleotide polymorphism (SNP) in the scavenger receptor class B type 1 (SCARB1) gene and several environmental factors with serum lipid levels in the Guangxi Bai Ku Yao and Han populations.

Methods
A total of 598 subjects of Bai Ku Yao and 585 subjects of Han Chinese were randomly selected from our stratified randomized cluster samples. Genotypes of the SCARB1 rs5888 SNP were determined by polymerase chain reaction and restriction fragment length polymorphism combined with gel electrophoresis, and then confirmed by direct sequencing.

Results
The levels of total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), apolipoprotein (Apo) AI were lower but ApoB was higher in Bai Ku Yao than in Han (P < 0.05-0.001). The frequencies of C and T alleles were 78.3% and 21.7% in Bai Ku Yao, and 73.7% and 26.3% in Han (P < 0.01); respectively. The frequencies of CC, CT and TT genotypes were 60.0%, 36.6% and 3.4% in Bai Ku Yao, and 54.2%, 39.0% and 6.8% in Han (P < 0.01); respectively. The subjects with TT genotype in both ethnic groups had lower HDL-C and ApoAI levels than the subjects with CC or CT genotype (P < 0.05 for all). Subgroup analyses showed that the subjects with TT genotype in Bai Ku Yao had lower HDL-C and ApoAI levels in males than the subjects with CC or CT genotype (P < 0.05 for all), and the T allele carriers had higher TC, LDL-C and ApoB levels in females than the T allele noncarriers (P < 0.05 for all). The participants with TT genotype in Han also had a lower tendency of HDL-C and ApoAI levels in males than the participants with CC or CT genotype, but the difference did not reach statistically significant (P = 0.063 and P = 0.086; respectively). The association of serum HDL-C and ApoAI levels and genotypes was confirmed by the multiple linear regression analysis in both ethnic groups. Serum lipid parameters were also correlated with several environmental factors.

Conclusions
The differences in serum lipid levels between the two ethnic groups might partially attribute to the differences in the SCARB1 rs5888 SNP and several environmental factors.
The human proteome – a scientific opportunity for transforming diagnostics, therapeutics, and healthcare
Authors: Vidal Marc , Chan Daniel W , Gerstein Mark , Mann Matthias , Omenn Gilbert S , Tagle Danilo , Sechi Salvatore ,   Workshop Participants
Published: May 2012

Abstract
A National Institutes of Health (NIH) workshop was convened in Bethesda, MD on September 26–27, 2011, with representative scientific leaders in the field of proteomics and its applications to clinical settings. The main purpose of this workshop was to articulate ways in which the biomedical research community can capitalize on recent technology advances and synergize with ongoing efforts to advance the field of human proteomics. This executive summary and the following full report describe the main discussions and outcomes of the workshop.
A polarity comparison timing synchronization estimation for MB-OFDM-based UWB systems
Authors: Wang Xue , Qian Zhihong , Wang Yijun 
Published: May 2012

Abstract
We propose a new approach for timing synchronization estimation with polarity comparison for multi-band orthogonal frequency division multiplexing (MB-OFDM)-based UWB systems. We attempt to locate the start sample of frame sequences by calculating difference of the two cross-correlation functions, between received symbols, the successive received symbols, and predefined preamble sequence. It makes sense to propose polarity comparison and identification ideas to the scenario, the cross-correlation difference exceeding predefined threshold is not unique. If polarities of selected symbols are not all the same, the estimator is put forward to find out a peak of correlation summation to figure out the unique timing point and promote synchronization accuracy. Uniqueness and accuracy of timing synchronization, therefore, could be guaranteed. The performance of the proposed estimator is evaluated by mean square error (MSE) and synchronization probability. The proposed estimator could carry out timing synchronization for MB-OFDM-based UWB systems and make the uniqueness of timing index for sure. The MSEs of the proposed estimator are evidently lower than the reference method for a great deal. Total and exact synchronization probability could get as much as 100 and 96%.
Existence of positive solutions to a non-positive elastic beam equation with both ends fixed
Authors: Lu Haixia , Sun Li , Sun Jingxian 
Published: May 2012

Abstract
This article is concerned with the existence of nontrivial solutions for a non-positive fourth-order two-point boundary value problem (BVP) and the existence of positive solutions for a semipositive fourth-order two-point BVP. In mechanics, the problem describes the deflection of an elastic beam rigidly fixed at both ends. The method to show our main results is the topological degree and fixed point theory of nonlinear operator on lattice.

Mathematics Subject Classification 2010: 34B18; 34B16; 34B15.
T cell independent secondary antibody responses to the envelope protein of simian immunodeficiency virus
Authors: Nabi Ghulam , Temchura Vladimir , Großmann Claudius , Kuate Seraphin , Tenbusch Matthias , Überla Klaus 
Published: May 2012

AbstractBackgroundDuring human (HIV) and simian (SIV) immunodeficiency virus infection, loss of CD4+ T cells and progression to AIDS are associated with a decline in antibody titers to the viral Gag protein, while antibodies to the Env protein remain high, suggesting a T cell independent antibody response to Env.ResultsTo explore differential regulation of Gag and Env antibody responses, immunocompetent BALB/c and T cell deficient nude mice were immunized with virus like particles (VLP) of simian immunodeficiency virus or adenoviral vectors expressing SIV Gag and Env. High levels of antibodies against Gag and Env could only be induced in immunocompetent mice, but not in the immunodeficient mice. Thus, neither cells expressing Env after adenoviral gene transfer nor VLPs induce a T cell independent primary anti-Env antibody response. However, secondary B cell responses to Env, but not to Gag, were observed in immunodeficient mice after transfer of primed B cells and boosting with VLPs or adenoviral vectors expressing Gag and Env. This T cell independent secondary antibody response to Env was reduced after stimulation with VLPs modified to contain monomeric membrane bound gp130 surface subunit of Env and undetectable after injection of soluble gp130.ConclusionsMembrane-bound trimeric Env seems to be responsible for the maintenance of high levels of anti-Env antibodies during progression to AIDS. This T cell independent secondary antibody response may prevent T cell-dependent affinity maturation and thus contribute to viral immune escape by favoring persistence of non-protective antibodies.
The slow-scale linear noise approximation: an accurate, reduced stochastic description of biochemical networks under timescale separation conditions
Authors: Thomas Philipp , Straube Arthur V , Grima Ramon 
Published: May 2012

Abstract

Background
It is well known that the deterministic dynamics of biochemical reaction networks can be more easily studied if timescale separation conditions are invoked (the quasi-steady-state assumption). In this case the deterministic dynamics of a large network of elementary reactions are well described by the dynamics of a smaller network of effective reactions. Each of the latter represents a group of elementary reactions in the large network and has associated with it an effective macroscopic rate law. A popular method to achieve model reduction in the presence of intrinsic noise consists of using the effective macroscopic rate laws to heuristically deduce effective probabilities for the effective reactions which then enables simulation via the stochastic simulation algorithm (SSA). The validity of this heuristic SSA method is a priori doubtful because the reaction probabilities for the SSA have only been rigorously derived from microscopic physics arguments for elementary reactions.

Results
We here obtain, by rigorous means and in closed-form, a reduced linear Langevin equation description of the stochastic dynamics of monostable biochemical networks in conditions characterized by small intrinsic noise and timescale separation. The slow-scale linear noise approximation (ssLNA), as the new method is called, is used to calculate the intrinsic noise statistics of enzyme and gene networks. The results agree very well with SSA simulations of the non-reduced network of elementary reactions. In contrast the conventional heuristic SSA is shown to overestimate the size of noise for Michaelis-Menten kinetics, considerably under-estimate the size of noise for Hill-type kinetics and in some cases even miss the prediction of noise-induced oscillations.

Conclusions
A new general method, the ssLNA, is derived and shown to correctly describe the statistics of intrinsic noise about the macroscopic concentrations under timescale separation conditions. The ssLNA provides a simple and accurate means of performing stochastic model reduction and hence it is expected to be of widespread utility in studying the dynamics of large noisy reaction networks, as is common in computational and systems biology.
Spice: discovery of phenotype-determining component interplays
Authors: Chen Zhengzhang , Padmanabhan Kanchana , Rocha Andrea M , Shpanskaya Yekaterina , Mihelcic James R , Scott Kathleen , Samatova Nagiza F 
Published: May 2012

AbstractBackgroundA latent behavior of a biological cell is complex. Deriving the underlying simplicity, or the fundamental rules governing this behavior has been the Holy Grail of systems biology. Data-driven prediction of the system components and their component interplays that are responsible for the target system’s phenotype is a key and challenging step in this endeavor.ResultsThe proposed approach, which we call System Phenotype-related Interplaying Components Enumerator (Spice), iteratively enumerates statistically significant system components that are hypothesized (1) to play an important role in defining the specificity of the target system’s phenotype(s); (2) to exhibit a functionally coherent behavior, namely, act in a coordinated manner to perform the phenotype-specific function; and (3) to improve the predictive skill of the system’s phenotype(s) when used collectively in the ensemble of predictive models.Spicecan be applied to both instance-based data and network-based data. When validated,Spiceeffectively identified system components related to three target phenotypes: biohydrogen production, motility, and cancer. Manual results curation agreed with the known phenotype-related system components reported in literature. Additionally, using the identified system components as discriminatory features improved the prediction accuracy by 10% on the phenotype-classification task when compared to a number of state-of-the-art methods applied to eight benchmark microarray data sets.ConclusionWe formulate a problem—enumeration of phenotype-determining system component interplays—and propose an effective methodology (Spice) to address this problem.Spiceimproved identification of cancer-related groups of genes from various microarray data sets and detected groups of genes associated with microbial biohydrogen production and motility, many of which were reported in literature.Spicealso improved the predictive skill of the system’s phenotype determination compared to individual classifiers and/or other ensemble methods, such as bagging, boosting, random forest, nearest shrunken centroid, and random forest variable selection method.
Genome-scale modeling using flux ratio constraints to enable metabolic engineering of clostridial metabolism in silico
Authors: McAnulty Michael J , Yen Jiun Y , Freedman Benjamin G , Senger Ryan S 
Published: May 2012

Abstract

Background
Genome-scale metabolic networks and flux models are an effective platform for linking an organism genotype to its phenotype. However, few modeling approaches offer predictive capabilities to evaluate potential metabolic engineering strategies in silico.

Results
A new method called “f lux b alance a nalysis with flux ratio s (FBrAtio)” was developed in this research and applied to a new genome-scale model of Clostridium acetobutylicum ATCC 824 (i CAC490) that contains 707 metabolites and 794 reactions. FBrAtio was used to model wild-type metabolism and metabolically engineered strains of C. acetobutylicum where only flux ratio constraints and thermodynamic reversibility of reactions were required. The FBrAtio approach allowed solutions to be found through standard linear programming. Five flux ratio constraints were required to achieve a qualitative picture of wild-type metabolism for C. acetobutylicum for the production of: (i) acetate, (ii) lactate, (iii) butyrate, (iv) acetone, (v) butanol, (vi) ethanol, (vii) CO2 and (viii) H2. Results of this simulation study coincide with published experimental results and show the knockdown of the acetoacetyl-CoA transferase increases butanol to acetone selectivity, while the simultaneous over-expression of the aldehyde/alcohol dehydrogenase greatly increases ethanol production.

Conclusions
FBrAtio is a promising new method for constraining genome-scale models using internal flux ratios. The method was effective for modeling wild-type and engineered strains of C. acetobutylicum.
Oxidation of dibenzothiophene (DBT) by Serratia marcescens UCP 1549 formed biphenyl as final product
Authors: de Araújo HélviaW Casullo , de Freitas Siva Marta Cristina , Lins Clarissai Matos , do Nascimento Aline Elesbão , da Silva CarlosAlberto Alves , Campos-Takaki Galba M 
Published: May 2012

Abstract

Background
The desulphurization of dibenzothiophene (DBT), a recalcitrant thiophenic fossil fuel component by Serratia marcescens (UCP 1549) in order for reducing the Sulphur content was investigated. The Study was carried out establishing the growth profile using Luria Bertani medium to different concentrations of DBT during 120 hours at 28°C, and orbital Shaker at 150 rpm.

Results
The results indicated that concentrations of DBT 0.5, 1.0 and 2.0 mM do not affected the growth of the bacterium. The DBT showed similar Minimum Inhibitory Concentration (MIC) and Minimum Bactericidal Concentration (MCB) (3.68 mM). The desulphurization of DBT by S. marcescens was used with 96 hours of growth on 2 mM of DBT, and was determined by gas chromatography (GC) and GC-mass spectrometry. In order to study the desulphurization process by S. marcescens was observed the presence of a sulfur-free product at 16 hours of cultivation.

Conclusions
The data suggests the use of metabolic pathway “4S” by S. marcescens (UCP 1549) and formed biphenyl. The microbial desulphurization process by Serratia can be suggest significant reducing sulphur content in DBT, and showed promising potential for reduction of the sulfur content in diesel oil.
Increased type II collagen cleavage by cathepsin K and collagenase activities with aging and osteoarthritis in human articular cartilage
Authors: Dejica Valeria M , Mort John S , Laverty Sheila , Antoniou John , Zukor David J , Tanzer Michael , Poole A Robin 
Published: May 2012

Abstract

Introduction

The intra-helical cleavage of type II collagen by proteases, including collagenases and cathepsin K, is increased with aging and osteoarthritis (OA) in cartilage as determined by immunochemical assays. The distinct sites of collagen cleavage generated by collagenases and cathepsin K in healthy and OA human femoral condylar cartilages were identified and compared.

Methods

Fixed frozen cartilage sections were examined immunohistochemically, using antibodies that react with the collagenase-generated cleavage neoepitopes, C2C and C1,2C, and the primary cleavage neoepitope (C2K) generated in type II collagen by the action of cathepsin K and possibly by other proteases, but not by any collagenases studied to date.

Results

In most cases, the staining patterns for collagen cleavage were similar for all three epitopes: weak to moderate mainly pericellular staining in non-OA cartilage from younger individuals and stronger, more widespread staining in aging and OA cartilages that often extended from the superficial to the mid/deep zone of the tissue. In very degenerate OA specimens, with significant disruption of the articular surface, staining was distributed throughout most of the cartilage matrix.

Conclusions

Cleavage of collagen by proteases usually arises pericellularly around chondrocytes at and near the articular surface, subsequently becoming more intense and extending progressively deeper into the cartilage with aging and OA. The close correspondence between the distributions of these products suggests that both collagenases and cathepsin K, and other proteases that may generate this distinct cathepsin K cleavage site, are usually active in the same sites in the degradation of type II collagen.
Green tea drinking and subsequent risk of breast cancer in a population to based cohort of Japanese women
Authors: Iwasaki Motoki , Inoue Manami , Sasazuki Shizuka , Sawada Norie , Yamaji Taiki , Shimazu Taichi , Willett Walter C , Tsugane Shoichiro ,   Japan Public Health Center-based Prospective Study Group
Published: May 2012

Abstract
Introduction
Although many in vitro and animal studies have demonstrated a protective effect of green tea against breast cancer, findings from epidemiological studies have been inconsistent, and whether high green tea intake reduces the risk of breast cancer remains unclear.

Methods
In this Japan Public Health Center-based Prospective Study, 581 cases of breast cancer were newly diagnosed in 53,793 women during 13.6 years' follow-up from the baseline survey in 1990 to 1994. After the five-year follow-up survey in 1995 to 1998, 350 cases were newly diagnosed in 43,639 women during 9.5 years' follow-up. The baseline questionnaire assessed the frequency of total green tea drinking while the five-year follow-up questionnaire assessed that of two types of green tea, Sencha and Bancha/Genmaicha, separately.

Results
Compared with women who drank less than one cup of green tea per week, the adjusted hazard ratio (HR) for women who drank five or more cups per day was 1.12 (95% confidence interval (CI) 0.81 to 1.56; P for trend = 0.60) in the baseline data. Similarly, compared with women who drank less than one cup of Sencha or Bancha/Genmaicha per week, adjusted HRs for women who drank 10 or more cups per day were 1.02 (95% CI 0.55 to 1.89; P for trend = 0.48) for Sencha and 0.86 (0.34 to 2.17; P for trend = 0.66) for Bancha/Genmaicha. No inverse association was found regardless of hormone receptor-defined subtype or menopausal status.

Conclusions
In this population-based prospective cohort study in Japan we found no association between green tea drinking and risk of breast cancer.
Downregulation of the tumor-suppressor miR-16 via progestin-mediated oncogenic signaling contributes to breast cancer development
Authors: Rivas Martin A , Venturutti Leandro , Huang Yi-Wen , Schillaci Roxana , Huang Tim Hui-Ming , Elizalde Patricia V 
Published: May 2012

Abstract
Introduction
Experimental and clinical evidence points to a critical role of progesterone and the nuclear progesterone receptor (PR) in controlling mammary gland tumorigenesis. However, the molecular mechanisms of progesterone action in breast cancer still remain elusive. On the other hand, micro RNAs (miRNAs) are short ribonucleic acids which have also been found to play a pivotal role in cancer pathogenesis. The role of miRNA in progestin-induced breast cancer is poorly explored. In this study we explored progestin modulation of miRNA expression in mammary tumorigenesis.

Methods
We performed a genome-wide study to explore progestin-mediated regulation of miRNA expression in breast cancer. miR-16 expression was studied by RT-qPCR in cancer cell lines with silenced PR, signal transducer and activator of transcription 3 (Stat3) or c-Myc, treated or not with progestins. Breast cancer cells were transfected with the precursor of miR-16 and proliferation assays, Western blots or in vivo experiments were performed. Target genes of miR-16 were searched through a bioinformatical approach, and the study was focused on cyclin E. Reporter gene assays were performed to confirm that cyclin E 3'UTR is a direct target of miR-16.

Results
We found that nine miRNAs were upregulated and seven were downregulated by progestin in mammary tumor cells. miR-16, whose function as a tumor suppressor in leukemia has already been shown, was identified as one of the downregulated miRNAs in murine and human breast cancer cells. Progestin induced a decrease in miR-16 levels via the classical PR and through a hierarchical interplay between Stat3 and the oncogenic transcription factor c-Myc. A search for miR-16 targets showed that the CCNE1 gene, encoding the cell cycle regulator cyclin E, contains conserved putative miR-16 target sites in its mRNA 3' UTR region. We found that, similar to the molecular mechanism underlying progestin-modulated miR-16 expression, Stat3 and c-Myc participated in the induction of cyclin E expression by progestin. Moreover, overexpression of miR-16 abrogated the ability of progestin to induce cyclin E upregulation, revealing that cyclin E is a novel target of miR-16 in breast cancer. Overexpression of miR-16 also inhibited progestin-induced breast tumor growth in vitro and in vivo, demonstrating for the first time, a role for miR-16 as a tumor suppressor in mammary tumorigenesis. We also found that the ErbB ligand heregulin (HRG) downregulated the expression of miR-16, which then participates in the proliferative activity of HRG in breast tumor cells.

Conclusions
In this study, we reveal the first progestin-regulated miRNA expression profile and identify a novel role for miR-16 as a tumor suppressor in progestin- and growth factor-induced growth in breast cancer.