bluuebunny/crossref_metadata_2025_split huggingface dataset:
Remote state preparation with unit success probability
Authors: Nguyen Ba An , Cao Thi Bich , Nung Van Don , Kim Jaewan 
Published: July 2011

Abstract
Remote state preparation is a secure and faithful method for transmitting known quantum states by means of local operation and classical communication. Existing protocols in the general case succeed just with probabilities of less than 100%. In this paper, we design a protocol to remotely prepare the most general single-qubit state that always succeeds. To achieve unit success probability, the preparer is allowed to use additional local resources and implement adaptive measurements. Our protocol is meaningful because the most expensive resource, i.e. the quantum channel previously shared between the preparer and the receiver, remains the same as in the original protocol (Pati 2000 Phys. Rev. A 63 014302), which, however, succeeds only half the time.
Annotation concept synthesis and enrichment analysis: a logic-based approach to the interpretation of high-throughput experiments
Authors: Jiline Mikhail , Matwin Stan , Turcotte Marcel 
Published: July 2011

AbstractMotivation: Annotation Enrichment Analysis (AEA) is a widely used analytical approach to process data generated by high-throughput genomic and proteomic experiments such as gene expression microarrays. The analysis uncovers and summarizes discriminating background information (e.g. GO annotations) for sets of genes identified by experiments (e.g. a set of differentially expressed genes, a cluster). The discovered information is utilized by human experts to find biological interpretations of the experiments.However, AEA isolates and tests for overrepresentation only individual annotation terms or groups of similar terms and is limited in its ability to uncover complex phenomena involving relationship between multiple annotation terms from various knowledge bases. Also, AEA assumes that annotations describe the whole object of interest, which makes it difficult to apply it to sets of compound objects (e.g. sets of protein–protein interactions) and to sets of objects having an internal structure (e.g. protein complexes).Results: We propose a novel logic-based Annotation Concept Synthesis and Enrichment Analysis (ACSEA) approach. ACSEA fuses inductive logic reasoning with statistical inference to uncover more complex phenomena captured by the experiments. We evaluate our approach on large-scale datasets from several microarray experiments and on a clustered genome-wide genetic interaction network using different biological knowledge bases. The discovered interpretations have lower P-values than the interpretations found by AEA, are highly integrative in nature, and include analysis of quantitative and structured information present in the knowledge bases. The results suggest that ACSEA can boost effectiveness of the processing of high-throughput experiments.Contact: mjiline@site.uottawa.ca
CSO validator: improving manual curation workflow for biological pathways
Authors: Jeong Euna , Nagasaki Masao , Ikeda Emi , Sekiya Yayoi , Saito Ayumu , Miyano Satoru 
Published: July 2011

Abstract
Summary: Manual curation and validation of large-scale biological pathways are required to obtain high-quality pathway databases. In a typical curation process, model validation and model update based on appropriate feedback are repeated and requires considerable cooperation of scientists. We have developed a CSO (Cell System Ontology) validator to reduce the repetition and time during the curation process. This tool assists in quickly obtaining agreement among curators and domain experts and in providing a consistent and accurate pathway database.
Availability: The tool is available on http://csovalidator.csml.org.
Contact: masao@hgc.jp
A Lasso regression model for the construction of microRNA-target regulatory networks
Authors: Lu Yiming , Zhou Yang , Qu Wubin , Deng Minghua , Zhang Chenggang 
Published: July 2011

Abstract
Motivation: MicroRNAs have recently emerged as a major class of regulatory molecules involved in a broad range of biological processes and complex diseases. Construction of miRNA-target regulatory networks can provide useful information for the study and diagnosis of complex diseases. Many sequence-based and evolutionary information-based methods have been developed to identify miRNA–mRNA targeting relationships. However, as the amount of available miRNA and gene expression data grows, a more statistical and systematic method combining sequence-based binding predictions and expression-based correlation data becomes necessary for the accurate identification of miRNA–mRNA pairs.
Results: We propose a Lasso regression model for the identification of miRNA–mRNA targeting relationships that combines sequence-based prediction information, miRNA co-regulation, RISC availability and miRNA/mRNA abundance data. By comparing this modelling approach with two other known methods applied to three different datasets, we found that the Lasso regression model has considerable advantages in both sensitivity and specificity. The regression coefficients in the model can be used to determine the true regulatory efficacies in tissues and was demonstrated using the miRNA target site type data. Finally, by constructing the miRNA regulatory networks in two stages of prostate cancer (PCa), we found the several significant miRNA-hubbed network modules associated with PCa metastasis. In conclusion, the Lasso regression model is a robust and informative tool for constructing the miRNA regulatory networks for diagnosis and treatment of complex diseases.
Availability: The R program for predicting miRNA–mRNA targeting relationships using the Lasso regression model is freely available, along with the described datasets and resulting regulatory network, at http://biocompute.bmi.ac.cn/CZlab/alarmnet/. The source code is open for modification and application to other miRNA/mRNA expression datasets.
Contact: zhangcg@bmi.ac.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
Using fishery-dependent data to inform the development and operation of a co-management initiative to reduce cod mortality and cut discards
Authors: Holmes S. J. , Bailey N. , Campbell N. , Catarino R. , Barratt K. , Gibb A. , Fernandes P. G. 
Published: July 2011

Abstract
Holmes, S. J., Bailey, N., Campbell, N., Catarino, R., Barratt, K., and Gibb, A., and Fernandes, P. G. 2011. Using fishery-dependent data to inform the development and operation of a co-management initiative to reduce cod mortality and cut discards. – ICES Journal of Marine Science, 68: 1679–1688. The Scottish conservation credits scheme is a voluntary programme introduced in 2008, designed to reduce mortality and discarding of cod in line with EU Common Fisheries Policy management objectives. The scheme was expanded in 2009, building on the initial elements of real-time closures (RTCs) and gear requirements. Various measures were agreed in a co-management framework involving fishers, non-governmental organizations, government officials, and scientists. The main objective was to encourage cod avoidance and the reduction of cod discards using spatial tools such as RTCs and seasonal closures, along with gear options that reduce cod capture. The scheme was incentivized by rewarding participation with additional days at sea. Real-time monitoring was carried out with extensive use of fishery-dependent information, allowing management to be adapted as required and to address emerging problems. The use of vessel monitoring system data, logbook records, fishers’ knowledge, and observer data is described in terms of implementing and assessing the scheme. Compliance with the closure elements of the scheme was judged to have been good, and estimated catch rates by the Scottish fleet met target criteria, but the assessed catch savings of cod from RTCs were less than predicted. Modifications to the scheme were introduced for 2010, reflecting improved knowledge and experience.
Adrenergic and cardiac dysfunction in primary hyperparathyroidism
Authors: Birgander Mats , Juul‐Möller Steen , Bondeson Anne‐Greth , Bondeson Lennart , Rydberg Erik 
Published: July 2011

SummaryObjective  Primary hyperparathyroidism (PHPT) is associated with cardiovascular morbidity and premature death, but the underlying mechanisms are incompletely understood. The aim of this study was to investigate whether adrenergic dysfunction may be a contributing factor.Patients and methods  Forty‐nine patients with mild PHPT (serum calcium 2·7 ± 0·1 mm) and 48 control subjects, matched for age and sex, were examined; patients within 1 month before parathyroidectomy (PTX) and 6 months postoperatively; control subjects at inclusion. Heart rate variability (HRV) was analysed in 24‐h electrocardiograms, and plasma concentrations of epinephrine and norepinephrine were measured at rest and immediately after standardized physical tests.Results  At baseline, the patients showed, compared to the controls, reduced stress‐related increase of circulating epinephrine (P < 0·05) and norepinephrine (P < 0·05). No significant change was observed 6 months after PTX. At baseline, there were no significant differences between patients and controls in HRV or heart rate, but 6 months after curative PTX, the patients showed significantly reduced HRV in both frequency and time domain, and their maximum and average heart rate had decreased (P = 0·011 and P = 0·018, respectively). The patients with the highest preoperative levels of circulating parathyroid hormone showed the greatest changes in heart rate and HRV postoperatively.Conclusions  This study demonstrates a previously unknown impairment of catecholamine response to physical stress in PHPT along with changes of HRV, also indicating adrenergic dysfunction. These factors should be considered in the ongoing controversy regarding the management of patients with mild ‘asymptomatic’ PHPT.
Evidence for visfatin as an independent predictor of endothelial dysfunction in polycystic ovary syndrome
Authors: Pepene Carmen E. 
Published: July 2011

SummaryObjective  Emerging evidence links adipocyte‐secreted hormones, in particular adiponectin and visfatin, to cardiovascular pathology. Although adipocytokines dysregulation is common in polycystic ovary syndrome (PCOS) within the context of obesity and insulin resistance, their participation in the process of vascular injury remains elusive.Design and Methods  This prospective, case–control study enrolled 102 young women (69 patients with PCOS and 33 eumenorrheic age‐matched controls); serum adiponectin, resistin and visfatin, testosterone, SHBG, lipids, glucose, insulin, the homeostasis model assessment of insulin resistance (HOMA‐IR) and high‐sensitivity C‐reactive protein (hs‐CRP) were simultaneously measured in all participants. Body composition analysis was performed using dual X‐ray absorptiometry. Endothelium impairment was assessed by carotid artery intimae‐media thickness (CIMT) and brachial artery flow‐mediated vasodilatation (FMD), respectively.Results  In PCOS, both univariate and multivariate analyses evidenced that circulating visfatin was significantly related to free testosterone (P = 0·024) and brachial artery FMD (P = 0·008; P < 0·01 in multivariate analyses). By every visfatin tertile, a stepwise decrease in FMD was observed in all and PCOS only (P = 0·036), not confounded by age, body mass index, total body fat mass, testosterone, SHBG or HOMA‐IR. Multiple regression analysis retained visfatin and free testosterone as independent predictors of FMD, explaining about 20% of FMD variability. Adiponectin correlated with CIMT and hs‐CRP, but the association was driven by age, body mass and body fat. No relationship between resistin and endothelial markers was found.Conclusion  Visfatin may be a candidate to play a role in the pathogenesis of endothelial dysfunction in PCOS, independently of additional risk factors.
Effectiveness of photodynamic therapy in Bowen’s disease: an observational and descriptive study in 51 lesions
Authors: Truchuelo M. , Fernández‐Guarino M. , Fleta B. , Alcántara J. , Jaén P. 
Published: July 2011

AbstractIntroduction  Bowen disease (BD) or squamous cell carcinoma (SCC) in situ affects both skin and mucous membranes and has the potential to progress to invasive SCC. Photodynamic therapy (PDT) has been approved recently for the treatment of BD. Some studies have demonstrated its efficacy and good cosmetic outcome.Objective  To assess the efficacy of PDT in the treatment of BD.Patients and methods  We carried out an observational, retrospective and descriptive study. A total of 47 patients with 51 lesions of BD were included. All the lesions were confirmed with previous cutaneous biopsy. All patients were treated with the standard protocol. Topical methyl‐aminolaevulinic acid was occluded during 3 h and followed by illumination with red‐light (630 nm, 38 J/cm2, 7.5 min). Clinical and fluorescence photographs images were taken before each session. All patients received two sessions one week apart. Clinical response was classified in partial or complete response. Fluorescence response was classified in negative, intermediate or intense. The follow‐up period and the adverse events observed including pain were also collected.Results  A total of 20 men and 27 women with a mean age of 75.57 years old were treated with PDT. Lesions were most frequently located in the lower limbs. Globally, 76.09% of the lesions achieved complete response after 2 sessions with a medium follow‐up of 16.61 months. Fluorescence of the lesions disappeared when clinical response was achieved, but not always. The most common adverse effect was an immediate burning sensation. All lesions showed an excellent cosmetic result.Conclusion  Photodynamic therapy is an effective treatment for BD in terms of both clinical remission and cosmetic results, with good tolerance and minimal adverse effects.
Neuronal tryptophan hydroxylase expression in BALB/cJ and C57Bl/6J mice
Authors: Bach Helene , Arango Victoria , Huang Yung‐Yu , Leong Sharlene , John Mann J. , Underwood Mark D. 
Published: July 2011

J. Neurochem. (2011) 118, 1067–1074.AbstractBALB/c is an inbred stress‐sensitive mouse strain exhibiting low brain serotonin (5‐HT) content and a 5‐HT biosynthetic enzyme tryptophan hydroxylase (Tph2) variant reported to have lower catalytic activity compared with other inbred base strains. To evaluate other mechanisms that may explain low 5‐HT, we compared BALB/cJ mice and a control inbred strain C57Bl/6J mice, for expression of Tph2 mRNA, TPH2 protein and regional levels of 5‐HT and its metabolite 5‐hydroxyindoleacetic acid. Tph2 mRNA and TPH2 protein in brainstem dorsal raphe nuclei was assayed by in situ hybridization and immunocytochemistry respectively. 5‐HT and 5‐hydroxyindoleacetic acid were determined by HPLC. BALB/cJ mice had 20% less Tph2 mRNA and 28% fewer TPH2 immunolabeled neurons than C57Bl/6J mice (t = −2.59, p = 0.02). The largest difference in Tph2 transcript expression was in rostral dorsal raphe nuclei (t = 2.731, p = 0.008). 5‐HT was 15% lower in the midbrain and 18% lower in the cerebral cortex of BALB/cJ compared with C57Bl/6J mice (p < 0.05). The behavioral differences in BALB/cJ mice relative to the C57Bl/6J strain may be due in part, to fewer 5‐HT neurons and lower Tph2 gene expression resulting in less 5‐HT neurotransmission. Future studies quantifying expression per neuron are needed to determine whether less expression is explained by fewer neurons or also less expression per neuron, or both.
Mutants of β‐strand β3 and the loop B in the interface between α7 subunits of a homomeric acetylcholine receptor show functional and pharmacological alterations
Authors: Criado Manuel , Mulet José , Gerber Susana , Sala Salvador , Sala Francisco 
Published: July 2011

J. Neurochem. (2011) 118, 968–978.AbstractActivation of nicotinic acetylcholine receptors (nAChR) requires a global conformational change involving a number of domains of the protein. Structural data from Torpedo nAChR suggest that adjacent subunits might be functionally coupled at the interface between the β‐strand β3 and the loop B through a salt bridge between α1Asp152 and γArg78. We have checked this hypothesis in homomeric α7 nAChRs by mutating residues at these (Gly152 and Arg79) and neighboring locations and analyzing the results obtained after expression of single and double mutants in Xenopus oocytes. We found that Arg79 mutants showed a decreased gating function when challenged with different agonists, being the reduction more important for dimethylphenylpiperazinium. EC50 values in these mutants were also increased up to 30‐fold. In contrast, mutating Gly152 only showed significant higher EC50 values for ACh. However, all Gly153 mutants presented increased gating function and lower EC50 values with no significant differences among them. When analyzing several mutant cycles it is concluded that Arg79 is functionally coupled to Gly152, but neither to Gly153 nor to Asp157. These data suggest an involvement of the minus side of homomeric α7 nAChRs in their gating function, reinforcing the significance of complementary subunits in the gating of neuronal nAChRs.
Net Production and Consumption of Fluorescent Colored Dissolved Organic Matter by Natural Bacterial Assemblages Growing on Marine Phytoplankton Exudates
Authors: Romera-Castillo Cristina , Sarmento Hugo , Álvarez-Salgado Xosé Antón , Gasol Josep M. , Marrasé Celia 
Published: July 2011

ABSTRACT

An understanding of the distribution of colored dissolved organic matter (CDOM) in the oceans and its role in the global carbon cycle requires a better knowledge of the colored materials produced and consumed by marine phytoplankton and bacteria. In this work, we examined the net uptake and release of CDOM by a natural bacterial community growing on DOM derived from four phytoplankton species cultured under axenic conditions. Fluorescent humic-like substances exuded by phytoplankton (excitation/emission [Ex/Em] wavelength, 310 nm/392 nm; Coble's peak M) were utilized by bacteria in different proportions depending on the phytoplankton species of origin. Furthermore, bacteria produced humic-like substances that fluoresce at an Ex/Em wavelength of 340 nm/440 nm (Coble's peak C). Differences were also observed in the Ex/Em wavelengths of the protein-like materials (Coble's peak T) produced by phytoplankton and bacteria. The induced fluorescent emission of CDOM produced by prokaryotes was an order of magnitude higher than that of CDOM produced by eukaryotes. We have also examined the final compositions of the bacterial communities growing on the exudates, which differed markedly depending on the phytoplankton species of origin.
Alteromonas
and
Roseobacter
were dominant during all the incubations on
Chaetoceros
sp. and
Prorocentrum minimum
exudates, respectively.
Alteromonas
was the dominant group growing on
Skeletonema costatum
exudates during the exponential growth phase, but it was replaced by
Roseobacter
afterwards. On
Micromonas pusilla
exudates,
Roseobacter
was replaced by
Bacteroidetes
after the exponential growth phase. Our work shows that fluorescence excitation-emission matrices of CDOM can be a helpful tool for the identification of microbial sources of DOM in the marine environment, but further studies are necessary to explore the association of particular bacterial groups with specific fluorophores.
Comparison of the Host Specificities of Two Bacteroidales Quantitative PCR Assays Used for Tracking Human Fecal Contamination
Authors: Van De Werfhorst Laurie C. , Sercu Bram , Holden Patricia A. 
Published: July 2011

ABSTRACT
The sewage-associated real-time quantitative PCR (qPCR) assays BacHum and HF183 SYBR were compared for specificity against local fecal sources. Both assays were equally sensitive to sewage, but BacHum showed substantially more false-positive results for cat, dog, gull, and raccoon feces.
Volatile Compound Fingerprinting of Mixed-Culture Fermentations
Authors: de Bok Frank A. M. , Janssen Patrick W. M. , Bayjanov Jumamurat R. , Sieuwerts Sander , Lommen Arjen , van Hylckama Vlieg Johan E. T. , Molenaar Douwe 
Published: July 2011

ABSTRACT
With the advent of the -omics era, classical technology platforms, such as hyphenated mass spectrometry, are currently undergoing a transformation toward high-throughput application. These novel platforms yield highly detailed metabolite profiles in large numbers of samples. Such profiles can be used as fingerprints for the accurate identification and classification of samples as well as for the study of effects of experimental conditions on the concentrations of specific metabolites. Challenges for the application of these methods lie in the acquisition of high-quality data, data normalization, and data mining. Here, a high-throughput fingerprinting approach based on analysis of headspace volatiles using ultrafast gas chromatography coupled to time of flight mass spectrometry (ultrafast GC/TOF-MS) was developed and evaluated for classification and screening purposes in food fermentation. GC-MS mass spectra of headspace samples of milk fermented by different mixed cultures of lactic acid bacteria (LAB) were collected and preprocessed in MetAlign, a dedicated software package for the preprocessing and comparison of liquid chromatography (LC)-MS and GC-MS data. The Random Forest algorithm was used to detect mass peaks that discriminated combinations of species or strains used in fermentations. Many of these mass peaks originated from key flavor compounds, indicating that the presence or absence of individual strains or combinations of strains significantly influenced the concentrations of these components. We demonstrate that the approach can be used for purposes like the selection of strains from collections based on flavor characteristics and the screening of (mixed) cultures for the presence or absence of strains. In addition, we show that strain-specific flavor characteristics can be traced back to genetic markers when comparative genome hybridization (CGH) data are available.
Novel Antiphytopathogenic Compound 2-Heptyl-5-Hexylfuran-3-Carboxylic Acid, Produced by Newly Isolated Pseudomonas sp. Strain SJT25
Authors: Wang Xiao-Ying , Xu Yu-Quan , Lin Shuang-Jun , Liu Zhen-Zhen , Zhong Jian-Jiang 
Published: July 2011

ABSTRACTPseudomonassp. strain SJT25, which strongly antagonizes plant pathogens, was isolated from rice rhizosphere soil by a bioactivity-guided approach. A novel antiphytopathogenic compound was isolated from the fermentation broth ofPseudomonassp. SJT25 and identified as 2-heptyl-5-hexylfuran-3-carboxylic acid. This compound showed antimicrobial activities bothin vitroandin vivo.
Creation of a Cellooligosaccharide-Assimilating Escherichia coli Strain by Displaying Active Beta-Glucosidase on the Cell Surface via a Novel Anchor Protein
Authors: Tanaka Tsutomu , Kawabata Hitomi , Ogino Chiaki , Kondo Akihiko 
Published: July 2011

ABSTRACT

We demonstrated direct assimilation of cellooligosaccharide using
Escherichia coli
displaying beta-glucosidase (BGL). BGL from
Thermobifida fusca
YX (Tfu0937) was displayed on the
E. coli
cell surface using a novel anchor protein named Blc. This strain was grown successfully on 0.2% cellobiose, and the optical density at 600 nm (OD
600
) was 1.05 after 20 h.