bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel approach for determining environment-specific protein costs: the case of Arabidopsis thaliana
Authors: Sajitz-Hermstein Max , Nikoloski Zoran 
Published: September 2010

Abstract
Motivation: Comprehensive understanding of cellular processes requires development of approaches which consider the energetic balances in the cell. The existing approaches that address this problem are based on defining energy-equivalent costs which do not include the effects of a changing environment. By incorporating these effects, one could provide a framework for integrating ‘omics’ data from various levels of the system in order to provide interpretations with respect to the energy state and to elicit conclusions about putative global energy-related response mechanisms in the cell.
Results: Here we define a cost measure for amino acid synthesis based on flux balance analysis of a genome-scale metabolic network, and develop methods for its integration with proteomics and metabolomics data. This is a first measure which accounts for the effect of different environmental conditions. We applied this approach to a genome-scale network of Arabidopsis thaliana and calculated the costs for all amino acids and proteins present in the network under light and dark conditions. Integration of function and process ontology terms in the analysis of protein abundances and their costs indicates that, during the night, the cell favors cheaper proteins compared with the light environment. However, this does not imply that there is squandering of resources during the day. The results from the association analysis between the costs, levels and well-defined expenses of amino acid synthesis, indicate that our approach not only captures the adjustment made at the switch of conditions, but also could explain the anticipation of resource usage via a global energy-related regulatory mechanism of amino acid and protein synthesis.
Contact: nikoloski@mpimp-golm.mpg.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Inferring cancer subnetwork markers using density-constrained biclustering
Authors: Dao Phuong , Colak Recep , Salari Raheleh , Moser Flavia , Davicioni Elai , Schönhuth Alexander , Ester Martin 
Published: September 2010

Abstract
Motivation: Recent genomic studies have confirmed that cancer is of utmost phenotypical complexity, varying greatly in terms of subtypes and evolutionary stages. When classifying cancer tissue samples, subnetwork marker approaches have proven to be superior over single gene marker approaches, most importantly in cross-platform evaluation schemes. However, prior subnetwork-based approaches do not explicitly address the great phenotypical complexity of cancer.
Results: We explicitly address this and employ density-constrained biclustering to compute subnetwork markers, which reflect pathways being dysregulated in many, but not necessarily all samples under consideration. In breast cancer we achieve substantial improvements over all cross-platform applicable approaches when predicting TP53 mutation status in a well-established non-cross-platform setting. In colon cancer, we raise prediction accuracy in the most difficult instances from 87% to 93% for cancer versus non−cancer and from 83% to (astonishing) 92%, for with versus without liver metastasis, in well-established cross-platform evaluation schemes.
Availability: Software is available on request.
Contact: alexsch@math.berkeley.edu; ester@cs.sfu.ca
Supplementary information: Supplementary data are available at Bioinformatics online.
Prediction of a gene regulatory network linked to prostate cancer from gene expression, microRNA and clinical data
Authors: Bonnet Eric , Michoel Tom , Van de Peer Yves 
Published: September 2010

Abstract
Motivation: Cancer is a complex disease, triggered by mutations in multiple genes and pathways. There is a growing interest in the application of systems biology approaches to analyze various types of cancer-related data to understand the overwhelming complexity of changes induced by the disease.
Results: We reconstructed a regulatory module network using gene expression, microRNA expression and a clinical parameter, all measured in lymphoblastoid cell lines derived from patients having aggressive or non-aggressive forms of prostate cancer. Our analysis identified several modules enriched in cell cycle-related genes as well as novel functional categories that might be linked to prostate cancer. Almost one-third of the regulators predicted to control the expression levels of the modules are microRNAs. Several of them have already been characterized as causal in various diseases, including cancer. We also predicted novel microRNAs that have never been associated to this type of tumor. Furthermore, the condition-dependent expression of several modules could be linked to the value of a clinical parameter characterizing the aggressiveness of the prostate cancer. Taken together, our results help to shed light on the consequences of aggressive and non-aggressive forms of prostate cancer.
Availability: The complete regulatory network is available as an interactive supplementary web site at the following URL: http://bioinformatics.psb.ugent.be/webtools/pronet/
Contact: yves.vandepeer@psb.vib-ugent.be
Mass spectrometry data processing using zero-crossing lines in multi-scale of Gaussian derivative wavelet
Authors: Nguyen Nha , Huang Heng , Oraintara Soontorn , Vo An 
Published: September 2010

Abstract
Motivation: Peaks are the key information in mass spectrometry (MS) which has been increasingly used to discover diseases-related proteomic patterns. Peak detection is an essential step for MS-based proteomic data analysis. Recently, several peak detection algorithms have been proposed. However, in these algorithms, there are three major deficiencies: (i) because the noise is often removed, the true signal could also be removed; (ii) baseline removal step may get rid of true peaks and create new false peaks; (iii) in peak quantification step, a threshold of signal-to-noise ratio (SNR) is usually used to remove false peaks; however, noise estimations in SNR calculation are often inaccurate in either time or wavelet domain. In this article, we propose new algorithms to solve these problems. First, we use bivariate shrinkage estimator in stationary wavelet domain to avoid removing true peaks in denoising step. Second, without baseline removal, zero-crossing lines in multi-scale of derivative Gaussian wavelets are investigated with mixture of Gaussian to estimate discriminative parameters of peaks. Third, in quantification step, the frequency, SD, height and rank of peaks are used to detect both high and small energy peaks with robustness to noise.
Results: We propose a novel Gaussian Derivative Wavelet (GDWavelet) method to more accurately detect true peaks with a lower false discovery rate than existing methods. The proposed GDWavelet method has been performed on the real Surface-Enhanced Laser Desorption/Ionization Time-Of-Flight (SELDI-TOF) spectrum with known polypeptide positions and on two synthetic data with Gaussian and real noise. All experimental results demonstrate that our method outperforms other commonly used methods. The standard receiver operating characteristic (ROC) curves are used to evaluate the experimental results.
Availability: http://ranger.uta.edu/∼heng/MS/GDWavelet.html or http://www.naaan.org/nhanguyen/archive.htm
Contact: heng@uta.edu
Identification of protein binding surfaces using surface triplet propensities
Authors: Mehio Wissam , Kemp Graham J.L. , Taylor Paul , Walkinshaw Malcolm D. 
Published: September 2010

Abstract
Motivation: The ability to reliably predict protein–protein and protein–ligand interactions is important for identifying druggable binding sites and for understanding how proteins communicate. Most currently available algorithms identify cavities on the protein surface as potential ligand recognition sites. The method described here does not explicitly look for cavities but uses small surface patches consisting of triplets of adjacent surface atomic groups that can be touched simultaneously by a probe sphere representing a solvent molecule. A total of 455 different types of triplets can be identified. A training set of 309 protein–ligand protein X-ray structures has been used to generate interface propensities for the triplets, which can be used to predict their involvement in ligand–binding interactions.
Results: The success rate for locating protein–ligand binding sites on protein surfaces using this new surface triplet propensities (STP) algorithm is 88% which compares well with currently available grid-based and energy-based approaches. Q-SiteFinder's dataset (Laurie and Jackson, 2005. Bioinformatics, 21, 1908–1916) was used to show the favorable performance of STP. An analysis of the different triplet types showed that higher ligand binding propensity is related to more polarizable surfaces. The interaction statistics between triplet atoms on the protein surface and ligand atoms have been used to estimate statistical free energies of interaction. The ΔGstat for halogen atoms interacting with hydrophobic triplets is −0.6 kcal/mol and an estimate of the maximal ΔGstat for a ligand atom interacting with a triplet in a binding pocket is −1.45 kcal/mol.
Availability: Freely available online at http://opus.bch.ed.ac.uk/stp. Website implemented in Php, with all major browsers supported.
Contact: m.walkinshaw@ed.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
The mRNA landscape at yeast translation initiation sites
Authors: Robbins-Pianka A. , Rice M. D. , Weir M. P. 
Published: September 2010

Abstract
Summary: Although translation initiation has been well studied, many questions remain in elucidating its mechanisms. An ongoing challenge is to understand how ribosomes choose a translation initiation site (TIS). To gain new insights, we analyzed large sets of TISs with the aim of identifying common characteristics that are potentially of functional importance. Nucleotide sequence context has previously been demonstrated to play an important role in the ribosome's selection of a TIS, and mRNA secondary structure is also emerging as a contributing factor.
Here, we analyze mRNA secondary structure using the folding predictions of the RNAfold algorithm. We present a method for analyzing these results using a rank-ordering approach to assess the overall degree of predicted secondary structure in a given region of mRNA. In addition, we used a modified version of the algorithm that makes use of only a subset of the standard version's output to incorporate base-pairing polarity constraints suggested by the ribosome scanning process. These methods were employed to study the TISs of 1735 genes in Saccharomyces cerevisiae.
Trends in base composition and base-pairing probabilities suggest that efficient translation initiation and high protein expression are aided by reduced secondary structure upstream and downstream of the TIS. However, the downstream reduction is not observed for sets of TISs with nucleotide sequence contexts unfavorable for translation initiation, consistent with previous suggestions that secondary structure downstream of the ribosome can facilitate TIS recognition.
Contact: mweir@wesleyan.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
A combined Gadget/FLR model for management strategy evaluations of the Barents Sea fisheries
Authors: Howell Daniel , Bogstad Bjarte 
Published: September 2010

Abstract
Howell, D., and Bogstad, B. 2010. A combined Gadget/FLR model for management strategy evaluations of the Barents Sea fisheries. – ICES Journal of Marine Science, 67: 1998–2004. A biologically sensible age–length structured multispecies Gadget model (incorporating minke whales, cod, herring, and capelin) for the Barents Sea—acting as the operating model—has been linked to Fisheries Library in R—acting as the management procedure—to perform management strategy evaluations. Assessments may be run using either XSA, survey-based methods, or by taking modelled stock numbers directly. Total allowable catches are based on the assessment and harvest control rules (HCRs). The tool can be used for assessing a wide variety of sources of uncertainties within the assessment process. Model structure and linkages are described and a fit to the historical data is presented. A base case of future dynamic (non-steady state) stock trends, based on the existing HCRs, is compared with alternative management and environmental scenarios. The relative differences for each scenario in terms of stock size and catches highlight a number of uncertainties within the biological and fisheries system. The results indicate that the current management rules are robust to the range of scenarios examined so far.
Integrating vessel monitoring systems (VMS) data with daily catch data from logbooks to explore the spatial distribution of catch and effort at high resolution
Authors: Gerritsen Hans , Lordan Colm 
Published: September 2010

Abstract
Gerritsen, H., and Lordan, C. 2011. Integrating vessel monitoring systems (VMS) data with daily catch data from logbooks to explore the spatial distribution of catch and effort at high resolution. – ICES Journal of Marine Science, 68: 245–252. Vessel monitoring systems (VMS) automatically collect positional data from fishing vessels, and the data can be linked to catch data from logbooks to provide a census of spatially resolved catch-and-effort data. The most appropriate and practical method for integrating Irish VMS and logbook data is explored and validated. A simple speed rule is applied to identify VMS records that correspond to fishing activity. The VMS data are then integrated with the catch data from logbooks using date and vessel identifier. Several assumptions were investigated, and the resulting distribution maps of catch and effort appear to be unbiased. The method is illustrated with an example of a time-series of spatially explicit estimates of catch per unit effort. The proposed method is relatively simple and does not require specialist software or computationally intensive methods. It will be possible to generalize this approach to similar datasets that are available within the EU and many other regions. Analysis of integrated VMS and logbook data will allow fisheries data to be analysed on a considerably finer spatial scale than was possible previously, opening up a range of potential applications.
Analysis of the CYP1A1 mRNA Dose-Response in Human Keratinocytes Indicates that Relative Potencies of Dioxins, Furans, and PCBs Are Species and Congener Specific
Authors: Sutter Carrie H. , Bodreddigari Sridevi , Sutter Thomas R. , Carlson Erik A. , Silkworth Jay B. 
Published: September 2010

AbstractReports indicate that toxic equivalency factors (TEFs) based primarily on rodent data do not accurately predict in vitro human responsiveness to certain dioxin-like chemicals (DLCs). To investigate this in cells responsive to dioxins and relevant to chloracne, normal human epidermal keratinocytes were treated with 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and several DLCs, each with a TEF value of 0.1, representing three classes of congeners. We estimated half maximal effective concentration (EC50)–based donor-specific relative potency (REP) values for cytochrome P450 1A1 (CYP1A1) messenger RNA (mRNA) induction for TCDD, 1,2,3,6,7,8-hexachlorodibenzo-p-dioxin (HxCDD), 2,3,7,8-tetrachlorodibenzofuran (TCDF), 1,2,3,6,7,8-hexachlorodibenzofuran (HxCDF), and 3,3′,4,4′,5-pentachlorobiphenyl (PCB 126). We also determined EC50-based population-level REP values (n = 4) for CYP1A1 mRNA induction for TCDD, HxCDF, and PCB 126. Furthermore, an alternative factor, the relative threshold factor (RTF) based on the low end (threshold) of the dose-response curve, was calculated. Our results demonstrated that HxCDF had a population-based REP value of 0.98, 9.8-fold higher than its assigned TEF value of 0.1. Conversely, PCB 126 had an REP value of 0.0027 and an RTF of 0.0022, 37-fold and 45-fold less than its assigned TEF of 0.1, respectively. The REP values for HxCDD and TCDF were 0.24 and 0.10, respectively, similar to their assigned value of 0.1. Therefore, although the DLCs tested in the current study all possessed the same assigned TEF value of 0.1, congener-specific differences in REPs and RTFs were observed for human keratinocytes. These congener-specific discrepancies are likely because of differences in interspecies factors that have yet to be defined.
Storage Stability of Flour‐Blasted Brown Rice
Authors: Guraya Harmeet S. , Patindol James A. 
Published: September 2010

ABSTRACTBrown rice was blasted with rice flour rather than sand in a sand blaster to make microperforations so that water could easily penetrate the brown rice endosperm and cook the rice in a shorter time. The flour‐blasted American Basmati brown rice, long‐grain brown rice, and parboiled long‐grain brown rice samples were stored in Ziploc storage bags under atmospheric conditions and in vacuum‐packed bags. They were periodically tested for over 10 months for changes in water absorption, free fatty acid (FFA), peroxide value (POV), viscosity changes of flour using the Rapid ViscoAnalyser (RVA), and texture of whole cooked kernel using a texture analyzer during cooking. Flour‐blasted brown rice absorbed less water but needed less cooking time than its counterpart that was not flour‐blasted. There was an increase in FFA, POV, peak viscosity (PV), final viscosity (FV), breakdown viscosity (BD), and setback viscosity (SB) during storage of flour‐blasted brown rice for 300 days, but no change was observed in texture (hardness, gumminess) and water absorption. The combined coefficient of correlation (including all types of rice) between FFA and FV is r = 0.86 and between FFA and SB is r = 0.90 at P < 0.0001.
Non‐tuberculous mycobacterial infections of the skin: A retrospective study of 29 cases
Authors: LEE Woo J. , KANG Seong M. , SUNG Heungsup , WON Chong H. , CHANG Sung E. , LEE Mi W. , KIM Mi N. , CHOI Jee H. , MOON Kee C. 
Published: September 2010

AbstractThe incidence of infections caused by non‐tuberculous mycobacteria has increased in recent years, due to a rise in dermatological procedures and a greater prevalence of immunosuppression in the general population. This study investigated the clinical and microbiological findings of non‐tuberculous mycobacterial skin infections. The study population included 29 patients from whom non‐tuberculous mycobacteria were cultured after isolation from skin biopsy materials, cutaneous abscesses or exudates. Clinical, microbiological and epidemiological data were collected from each patient. Eight patients were immunocompromised while 21 were not. Precipitating factors such as acupuncture, filler injection, surgical procedures and other traumatic events preceded infection in 13 (including 11 normal hosts and two immunocompromised hosts) of the 29 patients. Multiple skin lesions were present in eight patients (including three normal hosts and five immunocompromised hosts). In eight patients (including four immunocompromised hosts), symptoms were accompanied by tenosynovitis, osteomyelitis and myositis. Mycobacterium abscessus was isolated from nine patients, Mycobacterium fortuitum was isolated from nine patients, Mycobacterium chelonae was isolated from six patients, Mycobacterium marinum was isolated from two patients, a Mycobacterium avium complex member was isolated from two patients, and Mycobacterium haemophilum was isolated from one patient. Ten of the 24 cases caused by rapidly growing organisms (i.e. M. chelonae, M. abscessus and M. fortuitum groups) were precipitated by skin injuries such as acupuncture, filler infection and other medical procedures. Increases in skin medical procedures, including both acupuncture and esthetic interventions, explain the increasing incidence of these organisms. Immunocompromised patients tended to develop multiple skin lesions and deep tissue infections.
Screening of marine algae for potential tyrosinase inhibitor: Those inhibitors reduced tyrosinase activity and melanin synthesis in zebrafish
Authors: CHA Seon‐Heui , KO Seok‐Chun , KIM Daekyung , JEON You‐Jin 
Published: September 2010

AbstractIn order to find new anti‐browning and whitening agents in this study, we investigated 43 indigenous marine algae for tyrosinase inhibitory activity. The extracts from Endarachne binghamiae, Schizymenia dubyi, Ecklonia cava (EC) and Sargassum silquastrum (SS) evidenced potent tyrosinase inhibitory activity similar to that of positive control, kojic acid. Among those marine algae, EC and SS are distributed abundantly on Jeju Island. Therefore, we selected those two species for further studies. Our results evidenced that both species reduced cellular melanin synthesis and tyrosinase activity. On the other hand, we utilized zebrafish as an alternative in vivo model. All the tested samples evidenced excellent inhibitory effects on the pigmentation of zebrafish, most likely due to their potential tyrosinase inhibitory activity. In simultaneous in vivo toxicity tests, no toxicity was observed in either algal species, on the other hand, toxicity was observed in positive controls. These results provided that EC and SS extract could be used as an ingredient for whiting cosmetics and that zebrafish is an alternative in vivo model.
Characterization of long-term mixed donor–donor chimerism after double cord blood transplantation
Authors: Gertow J , Berglund S , Okas M , Uzunel M , Berg L , Kärre K , Mattsson J , Uhlin M 
Published: September 2010

SummaryDouble cord blood transplantation (DCBT) with two matched or partially matched cord blood units has been implemented successfully to circumvent the limitations of graft cell dose associated with single CBT. After DCBT, sustained haematopoiesis is derived almost exclusively from only one of the donated units. None the less, we previously observed two of six evaluable DCBT patients still having mixed donor–donor chimerism at 28 and 45 months post-transplantation, respectively. In the present study we utilize flow cytometry techniques to perform the first thorough analysis of phenotype and functionality of cord blood units in patients with mixed donor–donor chimerism. Our results suggest that the two stable cord blood units are different phenotypically and functionally: one unit shows more naive T cells, lower T cell cytokine production and higher frequencies of natural killer cells, the other shows higher frequencies of well-differentiated and functional lymphocytes. Additionally, in comparison with control patients having a single prevailing cord blood unit, the patients with donor–donor chimerism exhibit less overall T cell cytokine production and a smaller fraction of memory T cells. Furthermore, our results indicate that human leucocyte antigen-C match of donor units may partly explain the development of a donor–donor mixed chimerism.