bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stability analysis of yield and capsaicinoids content in chili (Capsicum spp.) grown across six environments
Authors: Gurung Tulsi , Techawongstien Suchila , Suriharn Bhalang , Techawongstien Sungcom 
Published: March 2012

AbstractThere is a need for identifying chili cultivars with stable amounts of capsaicinoids so that the amount of pungency in the final product can be controlled. Therefore, six cultivars were evaluated for yield and capsaicinoid contents across six environments, four in Thailand and two in Bhutan, ranging from 200 to 1,630 m above mean sea level. Combined analyses showed significant differences among cultivars, environments, and for cultivar by environment interactions for fruit yields, individual capsaicinoid and total capsaicinoid contents. A large proportion (46.1 %) of variation on yield was attributed to environments; however, for total capsaicinoid contents, genotype effect accounted for 74.2 % of variation. Variation due to environment was 5.8 %, while for cultivar by environment interaction was 15.8 %. Cultivar Dallay khorsaney had high capsaicin, dihydrocapsaicin and total capsaicinoids but was very sensitive to environmental changes, and therefore good for specific adaptation. Cultivar KKU-P-11003 with total capsaicinoid contents of 78,721 Scoville heat unit was stable for dry fruit yield, capsaicin, dihydrocapsaicin, and total capsaicinoids with regression coefficients b = 1.06, 1.06, 0.78, and 0.96 respectively. Therefore, KKU-P-11003 was considered suitable for diverse environments. In addition, this result indicates that it is possible to select stable cultivar for capsaicinoid contents.
Outcome of unintended pregnancy after ultrasound‐guided high‐intensity focused ultrasound ablation of uterine fibroids
Authors: Qin Juan , Chen Jin‐Yun , Zhao Wen‐Peng , Hu Liang , Chen Wen‐Zhi , Wang Zhi‐Biao 
Published: March 2012

AbstractObjectiveTo evaluate the safety of ultrasound‐guided high‐intensity focused ultrasound (USgHIFU) ablation of uterine fibroids among women with unintentional pregnancy within 1 year of therapy.MethodsA retrospective analysis was conducted of 435 women who underwent USgHIFU therapy at Chongqing Medical University, China, between October 1, 2006, and October 1, 2009.ResultsUnplanned pregnancy was reported by 24 women within 1 year of USgHIFU ablation; 8 of these women had desired pregnancy before undergoing treatment. A total of 27 fibroids were detected, 24 of which were treated (mean volume 65.9 ± 58.8 cm3). Pregnancy was continued by 7 women without any complications. One pregnant woman who had desired pregnancy before therapy underwent an induced abortion owing to concerns about the effects of USgHIFU on the fetus. Fourteen women without pregnancy intention before USgHIFU therapy chose to undergo induced abortion; 2 women experienced spontaneous abortion. No adhesion occurred after USgHIFU therapy. Furthermore, USgHIFU, labor, and abortion had no effect on subsequent menstruation or sexual activities.ConclusionPregnancy within 1 year after USgHIFU ablation of uterine fibroids appears safe; however, large scale studies are required to confirm these data.
The role of serum testosterone to prostate‐specific antigen ratio as a predictor of prostate cancer risk
Authors: Gurbuz Cenk , Canat Lutfi , Atis Gokhan , Guner Bayram , Caskurlu Turhan 
Published: March 2012

AbstractWe analyzed the ratio of serum total testosterone (sTT) to prostate‐specific antigen (PSA) as a predictor of prostate cancer risk. One‐hundred‐four consecutive men with a normal digital rectal examination and a serum PSA level of 2.5–10 ng/ml underwent transrectal ultrasonography‐guided biopsy using a 10‐core scheme. The sTT level was determined before the procedure using a chemiluminescent assay, and the ratio of sTT to PSA (sTT/PSA) was calculated after transforming sTT measurements from ng/dL to ng/mL. The overall cancer detection rate was 17.3%. The median sTT level was 332 ng/dl in men with cancer and 413 ng/dL in those without (p = 0.032). The median sTT/PSA ratio in these groups was 0.55 and 0.74, respectively (p = 0.035). The receiver operator characteristic (ROC) method was used to evaluate the properties of the sTT/PSA ratio, with testosterone and PSA as predictors of prostate cancer risk. The accuracy of the sTT/PSA ratio in prostate cancer diagnosis, represented by the area under the curve (AUC), was 0.739 (95% CI 0.640–0.823, p < 0.05). Optimizing the sensitivity and specificity of the sTT/PSA ratio using the ROC provided a cutoff point of 0.60, which corresponded to 82% sensitivity and 62% specificity. When the patients were divided into normal‐ and low‐sTT level groups according to testosterone value (300 ng/dl), the probability of detecting prostate cancer was 3.3‐fold higher in hypogonadal men as compared with eugonadal men. These results support the use of the sTT‐to‐PSA ratio for predicting the risk of prostate cancer and increasing the specificity of PSA measurement.
Effect of antiangiogenic therapy on tumor growth, vasculature and kinase activity in basal‐ and luminal‐like breast cancer xenografts
Authors: Lindholm Evita M. , Kristian Alexandr , Nalwoga Hawa , Krüger Kristi , Nygård Ståle , Akslen Lars A. , Mælandsmo Gunhild M. , Engebraaten Olav 
Published: March 2012

Several clinical trials have investigated the efficacy of bevacizumab in breast cancer, and even if growth inhibiting effects have been registered when antiangiogenic treatment is given in combination with chemotherapy no gain in overall survival has been observed. One reason for the lack of overall survival benefit might be that appropriate criteria for selection of patients likely to respond to antiangiogenic therapy in combination with chemotherapy, are not available.To determine factors of importance for antiangiogenic treatment response and/or resistance, two representative human basal‐ and luminal‐like breast cancer xenografts were treated with bevacizumab and doxorubicin alone or in combination. In vivo growth inhibition, microvessel density (MVD) and proliferating tumor vessels (pMVD = proliferative microvessel density) were analysed, while kinase activity was determined using the PamChip Tyrosine kinase microarray system.Results showed that both doxorubicin and bevacizumab inhibited basal‐like tumor growth significantly, but with a superior effect when given in combination. In contrast, doxorubicin inhibited luminal‐like tumor growth most effectively, and with no additional benefit of adding antiangiogenic therapy. In agreement with the growth inhibition data, vascular characterization verified a more pronounced effect of the antiangiogenic treatment in the basal‐like compared to the luminal‐like tumors, demonstrating total inhibition of pMVD and a significant reduction in MVD at early time points (three days after treatment) and sustained inhibitory effects until the end of the experiment (day 18). In contrast, luminal‐like tumors only showed significant effect on the vasculature at day 10 in the tumors having received both doxorubicin and bevacizumab.Kinase activity profiling in both tumor models demonstrated that the most effective treatment in vivo was accompanied with increased phosphorylation of kinase substrates of growth control and angiogenesis, like EGFR, VEGFR2 and PLCγ1. This may be a result of regulatory feedback mechanisms contributing to treatment resistance, and may suggest response markers of value for the prediction of antiangiogenic treatment efficacy.
Sustained Improvements in Peripheral Venous Catheter Care in Non–Intensive Care Units: A Quasi-Experimental Controlled Study of Education and Feedback
Authors: Fakih Mohamad G. , Jones Karen , Rey Janice E. , Berriel-Cass Dorine , Kalinicheva Tatyana , Szpunar Susanna , Saravolatz Louis D. 
Published: April 2012

Background and Objectives.Peripheral venous catheters (PVCs) can be associated with serious infectious complications. We evaluated the effect of education and feedback on process measures to improve PVC care and infectious complications.Design.Quasi-experimental controlled crossover study with sampling before and after education.Setting.An 804-bed tertiary care teaching hospital.Participants.Nurses and patients in 10 non-intensive care units.Methods.We implemented a process to improve PVC care in 10 non-intensive care units. The 4 periods (each 3 months in duration) included a preintervention period and a staggered educational intervention among nurses. During intervention period 1, 5 units participated in the intervention (group A), and 5 units served as a control group (group B). Group B underwent the intervention during intervention period 2, and both groups A and B received feedback on performance during intervention period 3. Process measures were evaluated twice monthly, and feedback was given to nurses directly and to the unit manager on a monthly basis.Results.During the preintervention period, there were no significant differences between groups A and B. Of 4,904 intravascular catheters evaluated, 4,434 (90.4%) were peripheral. By the end of the study, there were significant improvements in processes, compared with the preintervention period, including accurate documentation of dressing (from 442 cases [38%] to 718 cases [59%]; P<.0001), catheter dressing being intact (from 968 cases [88.5%] to 1,024 cases [95.2%]; P<.0001), and correct demonstration of scrubbing the hub before infusion (from 161 demonstrations [54%] to 316 demonstrations [95%]; P <.0001). There was a significant reduction in PVC-associated bloodstream infection, from 2.2 cases per 10,000 patient-days during the preintervention period (5 cases) to 0.44 cases per 10,000 patient days during the 3 intervention periods (3 cases; P = .016).Conclusions.Education and real-time feedback to nurses increases and sustains compliance with processes to reduce the risk of infection from PVCs.
DADP: the database of anuran defense peptides
Authors: Novković Mario , Simunić Juraj , Bojović Viktor , Tossi Alessandro , Juretić Davor 
Published: March 2012

Abstract
Summary: Anuran tissues, and especially skin, are a rich source of bioactive peptides and their precursors. We here present a manually curated database of antimicrobial and other defense peptides with a total of 2571 entries, most of them in the precursor form with demarcated signal peptide (SP), acidic proregion(s) and bioactive moiety(s) corresponding to 1923 non-identical bioactive sequences. Search functions on the corresponding web server facilitate the extraction of six distinct SP classes. The more conserved of these can be used for searching cDNA and UniProtKB databases for potential bioactive peptides, for creating PROSITE search patterns, and for phylogenetic analysis.
Availability: DADP is accessible at http://split4.pmfst.hr/dadp/
Contact: juretic@pmfst.hr
Supplementary information: Supplementary data are available at Bioinformatics online.
Inferring gene regulatory networks by ANOVA
Authors: Küffner Robert , Petri Tobias , Tavakkolkhah Pegah , Windhager Lukas , Zimmer Ralf 
Published: March 2012

Abstract
Motivation: To improve the understanding of molecular regulation events, various approaches have been developed for deducing gene regulatory networks from mRNA expression data.
Results: We present a new score for network inference, η2, that is derived from an analysis of variance. Candidate transcription factor:target gene (TF:TG) relationships are assumed more likely if the expression of TF and TG are mutually dependent in at least a subset of the examined experiments. We evaluate this dependency by η2, a non-parametric, non-linear correlation coefficient. It is fast, easy to apply and does not require the discretization of the input data. In the recent DREAM5 blind assessment, the arguably most comprehensive evaluation of inference methods, our approach based on η2 was rated the best performer on real expression compendia. It also performs better than methods tested in other recently published comparative assessments. About half of our predicted novel predictions are true interactions as estimated from qPCR experiments performed for DREAM5.
Conclusions: The score η2 has a number of interesting features that enable the efficient detection of gene regulatory interactions. For most experimental setups, it is an interesting alternative to other measures of dependency such as Pearson's correlation or mutual information.
Availability: See http://www2.bio.ifi.lmu.de/˜kueffner/anova.tar.gz for code and example data.
Contact: kueffner@bio.ifi.lmu.de
Supplementary information: Supplementary data are available at Bioinformatics online.
A subspace method for the detection of transcription factor binding sites
Authors: Pairó Erola , Maynou Joan , Marco Santiago , Perera Alexandre 
Published: March 2012

Abstract
Motivation: The identification of the sites at which transcription factors (TFs) bind to Deoxyribonucleic acid (DNA) is an important problem in molecular biology. Many computational methods have been developed for motif finding, most of them based on position-specific scoring matrices (PSSMs) which assume the independence of positions within a binding site. However, some experimental and computational studies demonstrate that interdependences within the positions exist.
Results: In this article, we introduce a novel motif finding method which constructs a subspace based on the covariance of numerical DNA sequences. When a candidate sequence is projected into the modeled subspace, a threshold in the Q-residuals confidence allows us to predict whether this sequence is a binding site. Using the TRANSFAC and JASPAR databases, we compared our Q-residuals detector with existing PSSM methods. In most of the studied TF binding sites, the Q-residuals detector performs significantly better and faster than MATCH and MAST. As compared with Motifscan, a method which takes into account interdependences, the performance of the Q-residuals detector is better when the number of available sequences is small.
Availability: http://r-forge.r-project.org/projects/meet
Contact: epairo@ibecbarcelona.eu; alexandre.perera@upc.edu
Supplementary information: Supplementary data (1, 2, 3 and 4) are available at Bioinformatics online.
Large-scale analysis of conserved rare codon clusters suggests an involvement in co-translational molecular recognition events
Authors: Chartier Matthieu , Gaudreault Francis , Najmanovich Rafael 
Published: March 2012

Abstract
Motivation: An increasing amount of evidence from experimental and computational analysis suggests that rare codon clusters are functionally important for protein activity. Most of the studies on rare codon clusters were performed on a limited number of proteins or protein families. In the present study, we present the Sherlocc program and how it can be used for large scale protein family analysis of evolutionarily conserved rare codon clusters and their relation to protein function and structure. This large-scale analysis was performed using the whole Pfam database covering over 70% of the known protein sequence universe. Our program Sherlocc, detects statistically relevant conserved rare codon clusters and produces a user-friendly HTML output.
Results: Statistically significant rare codon clusters were detected in a multitude of Pfam protein families. The most statistically significant rare codon clusters were predominantly identified in N-terminal Pfam families. Many of the longest rare codon clusters are found in membrane-related proteins which are required to interact with other proteins as part of their function, for example in targeting or insertion. We identified some cases where rare codon clusters can play a regulating role in the folding of catalytically important domains. Our results support the existence of a widespread functional role for rare codon clusters across species. Finally, we developed an online filter-based search interface that provides access to Sherlocc results for all Pfam families.
Availability: The Sherlocc program and search interface are open access and are available at http://bcb.med.usherbrooke.ca
Contact: rafael.najmanovich@usherbrooke.ca
Supplementary information: Supplementary data are available at Bioinformatics online.
OCAP: an open comprehensive analysis pipeline for iTRAQ
Authors: Wang Penghao , Yang Pengyi , Yang Jean Yee Hwa 
Published: March 2012

Abstract
Motivation: Mass spectrometry-based iTRAQ protein quantification is a high-throughput assay for determining relative protein expressions and identifying disease biomarkers. Processing and analysis of these large and complex data involves a number of distinct components and it is desirable to have a pipeline to efficiently integrate these together. To date, there are limited public available comprehensive analysis pipelines for iTRAQ data and many of these existing pipelines have limited visualization tools and no convenient interfaces with downstream analyses. We have developed a new open source comprehensive iTRAQ analysis pipeline, OCAP, integrating a wavelet-based preprocessing algorithm which provides better peak picking, a new quantification algorithm and a suite of visualizsation tools. OCAP is mainly developed in C++ and is provided as a standalone version (OCAP_standalone) as well as an R package. The R package (OCAP) provides the necessary interfaces with downstream statistical analysis.
Availability: OCAP is freely available and can be downloaded at http://www.maths.usyd.edu.au/u/penghao
Contact: penghao.wang@sydney.edu.au
Predicting giant transmembrane β-barrel architecture
Authors: Reboul Cyril F. , Mahmood Khalid , Whisstock James C. , Dunstone Michelle A. 
Published: March 2012

Abstract
Motivation: The β-barrel is a ubiquitous fold that is deployed to accomplish a wide variety of biological functions including membrane-embedded pores. Key influences of β-barrel lumen diameter include the number of β-strands (n) and the degree of shear (S), the latter value measuring the extent to which the β-sheet is tilted within the β-barrel. Notably, it has previously been reported that the shear value for small antiparallel β-barrels (n≤24) typically ranges between n and 2n. Conversely, it has been suggested that the β-strands in giant antiparallel β-barrels, such as those formed by pore forming cholesterol-dependent cytolysins (CDC), are parallel relative to the axis of the β-barrel, i.e. S=0. The S=0 arrangement, however, has never been observed in crystal structures of small β-barrels. Therefore, the structural basis for how CDCs form a β-barrel and span a membrane remains to be understood.
Results: Through comparison of molecular models with experimental data, we are able to identify how giant CDC β-barrels utilize a ‘near parallel’ arrangement of β-strands where S=n/2. Furthermore, we show how side-chain packing within the β-barrel lumen is an important limiting factor with respect to the possible shear values for small β-barrels (n≤24 β-strands). In contrast, our models reveal no such limitation restricts the shear value of giant β-barrels (n&gt;24 β-strands). Giant β-barrels can thus access a different architecture compared with smaller β-barrels.
Contact: michelle.dunstone@monash.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
GECA: a fast tool for gene evolution and conservation analysis in eukaryotic protein families
Authors: Fawal Nizar , Savelli Bruno , Dunand Christophe , Mathé Catherine 
Published: March 2012

Abstract
Summary: GECA is a fast, user-friendly and freely-available tool for representing gene exon/intron organization and highlighting changes in gene structure among members of a gene family. It relies on protein alignment, completed with the identification of common introns in the corresponding genes using CIWOG. GECA produces a main graphical representation showing the resulting aligned set of gene structures, where exons are to scale. The important and original feature of GECA is that it combines these gene structures with a symbolic display highlighting sequence similarity between subsequent genes. It is worth noting that this combination of gene structure with the indications of similarities between related genes allows rapid identification of possible events of gain or loss of introns, or points to erroneous structural annotations. The output image is generated in a portable network graphics format which can be used for scientific publications.
Availability and implementation: Web-implemented version and source code are freely available at https://peroxibase.toulouse.inra.fr/geca_input_demo.php and a detailed example can be found at https://peroxibase.toulouse.inra.fr/geca_instructions.php
Contact: mathe@lrsv.ups-tlse.fr
Supplementary information: Supplementary data are available at Bioinformatics online.
Design for manufacture and assembly: background, capabilities and applications
Authors: Bogue Robert 
Published: March 2012

PurposeThe purpose of this paper is to describe the design for manufacture (DFM) and design for assembly (DFA) concepts and illustrate their benefits and applications.Design/methodology/approachFollowing an introduction, this paper provides an historical background to DFM and DFA. It then describes these techniques, highlights their capabilities and benefits and provides some examples of their applications. Finally, brief conclusions are drawn.FindingsSoftware implementations of DFM and DFA are shown to yield significant financial savings by allowing products to be designed with enhanced manufacturing and assembly characteristics.Originality/valueThe paper provides an introduction to the DFM and DFA concepts which play a critical role in today's highly competitive markets.
Complexity mapping of the product and assembly system
Authors: Samy S.N. , ElMaraghy H.A. 
Published: March 2012

PurposeThe purpose of this paper is to present methods for assessing and mapping the complexity of products and their assembly. In cases of complexity of assembly it is important to consider and model at the product design stages when only data about individual parts/products and their assembly attributes are known. Assessing the complexity of assembly systems, based on the attributes of their components, is an essential step towards designing them for the least complexity.Design/methodology/approachThis paper presents a mapping method between the complexity of products and their variants and complexity of the system needed to assemble them. A method has also been developed to assess and compare the complexity of assembly systems based on the characteristics of their physical components for comparison and re‐design to reduce complexity.FindingsThe complexity dependency matrix estimates the average assembly equipment complexity for a certain product based on the interactions between parts handling, insertion and assembly attributes and assembly system functions. An automobile engine piston, domestic appliance drive, car fan motor and a three‐pin electric power plug products were used to demonstrate the application of the developed methodology.Originality/valueThe developed methods can be used by products and assembly systems designers to identify and alleviate major sources of complexity.