bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coalgebraic description of generalised binary methods
Authors: HONSELL FURIO , LENISA MARINA , REDAMALLA REKHA 
Published: August 2007

We extend the coalgebraic account of specification and refinement of objects and classes in object-oriented programming given by Reichel and Jacobs to(generalised) binary methods. These are methods that take more than one parameter of a class type. Class types include products, sums and powerset type constructors. To allow for classconstructors, we model classes asbialgebras. We study and compare two solutions for modelling generalised binary methods, which use purely covariant functors.In the first solution, which applies when we already have a class implementation, we reduce the behaviour of a generalised binary method to that of a bunch of unary methods. These are obtained byfreezingthe types of the extra class parameters to constant types. If all parameter types arefinitary, thebisimilarity equivalenceinduced on objects by this model yields thegreatest congruencewith respect to method application.In the second solution, we treat binary methods asgraphsinstead of functions, thus turning contravariant occurrences in the functor into covariant ones.We show the existence offinal coalgebrasin both cases.
Boxed ambients with communication interfaces
Authors: GARRALDA PABLO , BONELLI EDUARDO , COMPAGNONI ADRIANA , DEZANI-CIANCAGLINI MARIANGIOLA 
Published: August 2007

We defineBACI(Boxed Ambients with Communication Interfaces), an ambient calculus with a flexible communication policy. Traditionally, typed ambient calculi have a fixed communication policy determining the kind of information that can be exchanged with a parent ambient, even though mobility changes the parent.BACIlifts that restriction, allowing different communication policies with different parents during computation. Furthermore,BACIseparates communication and mobility by making the channels of communication between ambients explicit. In contrast with other typed ambient calculi where communication policies are global, each ambient inBACIis equipped with a description of the communication policies ruling its information exchange with parent and child ambients. The communication policies of ambients increase when they move: more precisely, when an ambient enters another ambient, the entering ambient and the host ambient can exchange their communication ports and agree on the kind of information to be exchanged. This information is recorded locally in both ambients.We show the type-soundness ofBACI, proving that it satisfies the subject reduction property, and we study its behavioural semantics by means of a labelled transition system.
Comparison of percentages of tissues and nutrients between parents and F3offspring ofOreochromis aurea×Siniperca chuatsi
Authors: Jin-Long Wang , Hong Yang , Ting-Ting Wu 
Published: August 2007

AbstractThis research focused on the effect of distant hybridization to improve the flesh quality of offspring fromOreochromis aurea(♀)×Siniperca chuatsi(♂). The proportions of different tissues and percentages of nutrient components were compared between fish of the F3generation andO. aureaandS. chuatsi. The results showed that the proportion of flesh in F3hybrids was significantly lower than that inO. aurea. Crude lipid content was lower and crude protein content significantly higher in the F3generation. Concentrations of four kinds of amino acids important for flavour (DAA) were higher in the F3generation than inO. aurea, and the total DAA was significantly higher. Furthermore, the other amino acid contents and essential amino acid index of the F3generation were intermediate betweenO. aureaandS. chuatsi. We conclude that some effects of hybridization have induced flesh quality improvement.
Cloning and sequence analysis of complete cDNA of chitin deacetylase from Mucor racemosus
Authors: Xia-Yun Jiang , Shu-Ming Zou , Pei-Gen Zhou 
Published: August 2007

AbstractA complete chitin deacetylase (CDA) complementary DNA (cDNA) from Mucor racemosus was cloned and sequenced by reverse transcription-polymerase chain reaction (RT-PCR) and rapid amplification cDNA end (RACE) with gene special conserved primers. The cDNA sequence was submitted to GenBank (DQ538514). The complete cDNA with full-length of 1506 bp contained a 67 bp 5′-untranslated region, an open reading frame of 1344 bp and 95 bp 3′-untranslated region including tailing site AATAAA. The gene encoded a sequence of 448 amino acid residues and consisted of core nucleotides encoding a polysaccharide deacetylase domain covering 32% of the entire sequence. The CDA gene shared sequence homology with those of several fungi. The corresponding homology of the deduced amino acid sequences varied from 21 to 69%. Phylogenetic analysis according to the deduced amino acid sequences matched the classical fungi taxonomy. The three-dimensional structure of this protein was predicted. The protein had a whole CDA functional domain and a polysaccharide deacetylase domain.
Environmental impact and risk management strategies of Bt cotton commercialization in China
Authors: Kong-Ming Wu 
Published: August 2007

AbstractTransgenic cotton expressing the Cry1Ac toxin from Bacillus thuringiensis has been planted widely in China since 1997, and reached 70% of the total cotton area in 2006. The results of monitoring the environmental impact of Bt cotton commercialization indicated that the target pests, cotton bollworm (Helicoverpa armigera) and pink bollworm (Pectinophora gossypiella), were effectively controlled while the mirids (Hemiptera: Miridae) evolved to be key pests in the cotton system. There were no significant changes in resistance gene frequency of field populations of cotton bollworm, but a shift toward increased tolerance was apparent in the area of intensive planting of Bt cotton, indicating that the potential risk of resistance of the target pest has become a major threat for sustainable planting of Bt cotton. Considering the factors associated with the evolution of resistance, risk management strategies are discussed in this paper.
Tomato yellow leaf curl disease in Guangdong is caused by Tomato leaf curl Taiwan virus
Authors: Zi-Fu He , Hao Yu , Ming-Jie Mao , Fang-Fang Luo , Yi-Han Lin , Sui-Tao Wang 
Published: August 2007

AbstractA yellow leaf curl disease with chlorotic and yellowish leaves, upward leaf curling and stunting symptoms was observed on tomato in Shantou city of Guangdong province. A virus isolate BS was obtained from a diseased tomato plant. The complete DNA-A sequence of the virus isolate BS was determined to be 2740 nucleotides long, with all the characteristic features of begomovirus genome organization. BS DNA-A encoded six potential open reading frames (ORFs), with two (AV1 and AV2) in virus sense and four (AC1, AC2, AC3 and AC4) in complementary sense, and contained an intergenic region of 269 nucleotides. The results of BLAST searches showed that BS DNA-A had higher sequence identity with reported begomoviruses in Asia than with those in America and Africa. Further sequence comparisons indicated that BS was most closely related to the isolate of Tomato leaf curl Taiwan virus (ToLCTWV-[Taiwan]) with a sequence identity of 97.7%. Nucleotide sequence identities of AV1, AV2, AC1, AC2, AC3, AC4 and intergenic region (IR) between BS and ToLCTWV-[Taiwan] were 98.6, 98.0, 98.0, 97.5, 96.3, 98.6 and 96.6%, respectively, while that of the six ORF-encoded proteins between BS and ToLCTWV-[Taiwan] were 97.7, 99.1, 97.5, 95.6, 91.8 and 99.0%, respectively. Phylogenetic analysis based on the DNA-A sequences has also indicated that BS is most closely related to ToLCTWV-[Taiwan], forming a branch with ToLCTWV-[Taiwan], Tomato leaf curl Guangdong virus and Tomato yellow leaf curl Guangdong virus. The above results demonstrate that BS is an isolate of ToLCTWV.
Links between bacterial production, amino-acid utilization and community composition in productive lakes
Authors: Bertilsson Stefan , Eiler Alexander , Nordqvist Anneli , Jørgensen Niels Ole Gerslev 
Published: August 2007

Abstract
Influence of distribution and abundance of bacterial taxa on ecosystem function are poorly understood for natural microbial communities. We related 16S rRNA-based terminal restriction fragment length polymorphism to bacterial production and arginine uptake kinetics to test if functional features of bacterioplankton in four lakes could be predicted from community composition. Maximum arginine uptake rate (arginine Vmax) ranged from 10% to 100% of bacterial production. Owing to high growth efficiencies on arginine (63–77%), the bacterial community could potentially saturate its carbon demand using this single organic substrate, for example, during sudden surges of free amino acids. However, due to low in situ concentrations of arginine in these lakes (&lt;0.9 μg l−1), actual uptake rates at ambient concentrations rarely exceeded 10% of Vmax. Bacterial production and arginine Vmax could be predicted from a subset of bacterial ribotypes, tentatively affiliated with several bacterial divisions (Cyanobacteria, Actinobacteria, Bacteroidetes and Proteobacteria). Multivariate statistical analysis indicates that there were both highly important and less important ribotypes for the prediction of bacterial production and arginine Vmax. These populations were either negatively or positively related to the respective functional feature, indicating contrasting ecological roles. Our study provides a statistically robust demonstration that, apart from environmental conditions, patterns in bacterial community composition can also be used to predict lake ecosystem function.
Monitored Naltrexone without Counseling for Alcohol Abuse/Dependence in Schizophrenia‐Spectrum Disorders
Authors: Batki Steven L. , Dimmock Jacqueline A. , Wade Michael , Gately Paul W. , Cornell Martha , Maisto Stephen A. , Carey Kate B. , Ploutz‐Snyder Robert 
Published: July 2007

This clinical trial assessed the effects of monitored naltrexone treatment in 19 subjects with schizophrenia spectrum and alcohol use disorders in an eight‐week prospective open pilot study. Naltrexone was directly administered to subjects in oral doses of 100 mg on Mondays and Wednesdays, and 150 mg on Fridays. Subjects received reimbursement for attending the three weekly study visits. Subjects continued to receive their usual psychiatric care with no added alcohol counseling provided. Alcohol use was assessed by self‐report and biomarkers. Psychosis severity was measured by the Positive and Negative Syndrome Scale (PANSS). Subjects reported significant reductions in their number of drinks per week, drinks per drinking day, days of drinking to intoxication, and alcohol craving. Subjects also showed significant reductions in Addiction Severity Index (ASI) alcohol composite scores and in PANSS positive, negative and general psychopathology scores.
Early Abstinence in Cocaine Dependence: Influence of Comorbid Major Depression
Authors: Rubin Eric , Aharonovich Efrat , Bisaga Adam , Levin Frances R. , Raby Wilfrid N. , Nunes Edward V. 
Published: July 2007

Cocaine dependence (CD) is often accompanied by major depressive disorder (MDD). The comorbid condition (CD + MDD) is especially difficult to treat, with relapse possibly made more likely by intensified dysphoria during abstinence in the setting of MDD. We studied treatment‐seeking CD + MDD volunteers, currently depressed, and a comparison CD group over three days of inpatient monitored abstinence. At admission, Beck Depression Inventory (BDI) and anxiety scores differed significantly between groups. By Day 3, BDI scores improved for both CD and CD + MDD groups. The mood response to cocaine cessation among CD + MDD individuals resembled that of CD participants, contrary to some expectations.
Robust smooth segmentation approach for array CGH data analysis
Authors: Huang Jian , Gusnanto Arief , O'Sullivan Kathleen , Staaf Johan , Borg Åke , Pawitan Yudi 
Published: July 2007

AbstractMotivation: Array comparative genomic hybridization (aCGH) provides a genome-wide technique to screen for copy number alteration. The existing segmentation approaches for analyzing aCGH data are based on modeling data as a series of discrete segments with unknown boundaries and unknown heights. Although the biological process of copy number alteration is discrete, in reality a variety of biological and experimental factors can cause the signal to deviate from a stepwise function. To take this into account, we propose a smooth segmentation (smoothseg) approach.Methods: To achieve a robust segmentation, we use a doubly heavy-tailed random-effect model. The first heavy-tailed structure on the errors deals with outliers in the observations, and the second deals with possible jumps in the underlying pattern associated with different segments. We develop a fast and reliable computational procedure based on the iterative weighted least-squares algorithm with band-limited matrix inversion.Results: Using simulated and real data sets, we demonstrate how smoothseg can aid in identification of regions with genomic alteration and in classification of samples. For the real data sets, smoothseg leads to smaller false discovery rate and classification error rate than the circular binary segmentation (CBS) algorithm. In a realistic simulation setting, smoothseg is better than wavelet smoothing and CBS in identification of regions with genomic alterations and better than CBS in classification of samples. For comparative analyses, we demonstrate that segmenting the t-statistics performs better than segmenting the data.Availability: The R package smoothseg to perform smooth segmentation is available from http://www.meb.ki.se/~yudpawContact: yudi.pawitan@ki.se
AffyProbeMiner: a web resource for computing or retrieving accurately redefined Affymetrix probe sets
Authors: Liu Hongfang , Zeeberg Barry R. , Qu Gang , Koru A. Gunes , Ferrucci Alessandro , Kahn Ari , Ryan Michael C. , Nuhanovic Antej , Munson Peter J. , Reinhold William C. , Kane David W. , Weinstein John N. 
Published: July 2007

AbstractMotivation: Affymetrix microarrays are widely used to measure global expression of mRNA transcripts. That technology is based on the concept of a probe set. Individual probes within a probe set were originally designated by Affymetrix to hybridize with the same unique mRNA transcript. Because of increasing accuracy in knowledge of genomic sequences, however, a substantial number of the manufacturer's original probe groupings and mappings are now known to be inaccurate and must be corrected. Otherwise, analysis and interpretation of an Affymetrix microarray experiment will be in error.Results: AffyProbeMiner is a computationally efficient platform-independent tool that uses all RefSeq mature RNA protein coding transcripts and validated complete coding sequences in GenBank to (1) regroup the individual probes into consistent probe sets and (2) remap the probe sets to the correct sets of mRNA transcripts. The individual probes are grouped into probe sets that are ‘transcript-consistent’ in that they hybridize to the same mRNA transcript (or transcripts) and, therefore, measure the same entity (or entities). About 65.6 % of the probe sets on the HG-U133A chip were affected by the remapping. Pre-computed regrouped and remapped probe sets for many Affymetrix microarrays are made freely available at the AffyProbeMiner web site. Alternatively, we provide a web service that enables the user to perform the remapping for any type of short-oligo commercial or custom array that has an Affymetrix-format Chip Definition File (CDF). Important features that differentiate AffyProbeMiner from other approaches are flexibility in the handling of splice variants, computational efficiency, extensibility, customizability and user-friendliness of the interface.Availability: The web interface and software (GPL open source license), are publicly-accessible at http://discover.nci.nih.gov/affyprobeminer.Contact: hl224@georgetown.edu or barry@discover.nci.nih.gov
sMOL Explorer: an open source, web-enabled database and exploration tool for Small MOLecules datasets
Authors: Ingsriswang Supawadee , Pacharawongsakda Eakasit 
Published: July 2007

AbstractSummary: sMOL Explorer is a 2D ligand-based computational tool that provides three major functionalities: data management, information retrieval and extraction and statistical analysis and data mining through Web interface. With sMOL Explorer, users can create personal databases by adding each small molecule via a drawing interface or uploading the data files from internal and external projects into the sMOL database. Then, the database can be browsed and queried with textual and structural similarity search. The molecule can also be submitted to search against external public databases including PubChem, KEGG, DrugBank and eMolecules. Moreover, users can easily access a variety of data mining tools from Weka and R packages to perform analysis including (1) finding the frequent substructure, (2) clustering the molecular fingerprints, (3) identifying and removing irrelevant attributes from the data and (4) building the classification model of biological activity.Availability: sMOL Explorer is an Open Source project and is freely available to all interested users at http://www.biotec.or.th/ISL/SMOL/Contact: supawadee@biotec.or.th
BLISS 2.0: a web-based tool for predicting conserved regulatory modules in distantly-related orthologous sequences
Authors: Meng Hailong , Banerjee Arunava , Zhou Lei 
Published: July 2007

AbstractSummary: BLISS 2.0 is a web-based application for identifying conserved regulatory modules in distantly related orthologous sequences. Unlike existing approaches, it performs the cross-genome comparison at the binding site level. Experimental results on simulated and real world data indicate that BLISS 2.0 can identify conserved regulatory modules from sequences with little overall similarity at the DNA sequence level.Availability: http://www.blisstool.org/Contact: leizhou@ufl.edu
Modular decomposition of metabolic reaction networks based on flux analysis and pathway projection
Authors: Yoon Jeongah , Si Yaguang , Nolan Ryan , Lee Kyongbum 
Published: July 2007

AbstractMotivation: The rational decomposition of biochemical networks into sub-structures has emerged as a useful approach to study the design of these complex systems. A biochemical network is characterized by an inhomogeneous connectivity distribution, which gives rise to several organizational features, including modularity. To what extent the connectivity-based modules reflect the functional organization of the network remains to be further explored. In this work, we examine the influence of physiological perturbations on the modular organization of cellular metabolism.Results: Modules were characterized for two model systems, liver and adipocyte primary metabolism, by applying an algorithm for top–down partition of directed graphs with non-uniform edge weights. The weights were set by the engagement of the corresponding reactions as expressed by the flux distribution. For the base case of the fasted rat liver, three modules were found, carrying out the following biochemical transformations: ketone body production, glucose synthesis and transamination. This basic organization was further modified when different flux distributions were applied that describe the liver's metabolic response to whole body inflammation. For the fully mature adipocyte, only a single module was observed, integrating all of the major pathways needed for lipid storage. Weaker levels of integration between the pathways were found for the early stages of adipocyte differentiation. Our results underscore the inhomogeneous distribution of both connectivity and connection strengths, and suggest that global activity data such as the flux distribution can be used to study the organizational flexibility of cellular metabolism.Contact: kyongbum.lee@tufts.eduSupplementary information: Supplementary data are available at Bioinformatics online.
AssociationDB: web-based exploration of genomic association
Authors: Seelow Dominik , Hoffmann Katrin , Lindner Tom H. 
Published: July 2007

AbstractSummary: Genome-wide association studies use hundreds of thousands of markers making it challenging to present and finally interpret the results. We developed a graphical, web-based solution for an interactive exploration of the results of case-control studies, with a tight integration of related gene information and tissue-specific expression data. Association results are presented as physical position-based vertical bars with known genes included as horizontal bars at their respective physical positions. The interface allows the specification of filtering criteria for the association data and highlights potentially interesting genes with user-specified terms occurring in their reports or with relevant expression patterns. Pop-up windows and hyperlinks provide drill-down capabilities and quick access to relevant data AssociationDB can either be used as a stand-alone solution or as a front-end joining association results obtained by other software with genomic information.Availability: http://genetik.charite.de/AssociationDBContact: dominik.seelow@charite.deSupplementary information: The source code, a web-based demo, a step-by-step manual, and an installation guide are available at http://genetik.charite.de/AssociationDB.
Consensus Data Mining (CDM) Protein Secondary Structure Prediction Server: Combining GOR V and Fragment Database Mining (FDM)
Authors: Cheng Haitao , Sen Taner Z. , Jernigan Robert L. , Kloczkowski Andrzej 
Published: July 2007

AbstractSummary: One of the challenges in protein secondary structure prediction is to overcome the cross-validated 80% prediction accuracy barrier. Here, we propose a novel approach to surpass this barrier. Instead of using a single algorithm that relies on a limited data set for training, we combine two complementary methods having different strengths: Fragment Database Mining (FDM) and GOR V. FDM harnesses the availability of the known protein structures in the Protein Data Bank and provides highly accurate secondary structure predictions when sequentially similar structural fragments are identified. In contrast, the GOR V algorithm is based on information theory, Bayesian statistics, and PSI-BLAST multiple sequence alignments to predict the secondary structure of residues inside a sliding window along a protein chain. A combination of these two different methods benefits from the large number of structures in the PDB and significantly improves the secondary structure prediction accuracy, resulting in Q3 ranging from 67.5 to 93.2%, depending on the availability of highly similar fragments in the Protein Data Bank.Availability: The CDM server is freely accessible by public users and private institutions at http://gor.bb.iastate.edu/cdmContact: taner@iastate.edu