bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clustalnet: the joining of Clustal and CORBA
Authors: Campagne F. 
Published: July 2002

Abstract
Motivation: Performing sequence alignment operations from a different program than the original sequence alignment code, and/or through a network connection, is often required. Interactive alignment editors and large-scale biological data analysis are common examples where such a flexibility is important. Interoperability between the alignment engine and the client should be obtained regardless of the architectures and programming languages of the server and client.
Results: Clustalnet, a Clustal alignment CORBA server is described, which was developed on the basis of Clustalw. This server brings the robustness of the algorithms and implementations of Clustal to a new level of reuse. A Clustalnet server object can be accessed from a program, transparently through the network. We present interfaces to perform the alignment operations and to control these operations via immutable contexts. The interfaces that select the contexts do not depend on the nature of the operation to be performed, making the design modular. The IDL interfaces presented here are not specific to Clustal and can be implemented on top of different sequence alignment algorithm implementations.
Availability: This implementation is freely available for non-commercial use for a variety of architectures. Clustalnet can be downloaded from http://transport.physbio.mssm.edu/clustalnet.
Contact: campagne@inka.mssm.edu
Supplementary Information: Alignment encoding description and full IDL in the documentation, with the distribution.
Digital reviews in molecular biology: approaches to structured
digital publication
Authors: Steffen D. L. , Levine A. E. , Yarus S. , Baasiri R. A. , Wheeler D. A. 
Published: July 2002

Abstract
Motivation: It is widely appreciated that it is no longer possible for biomedical research scientists to keep up with as much of what is published in their field as they ought. One solution to this problem is to increase the efficiency of information use by moving away from the classical browsing model for scientific information dissemination towards an information on demand model which would allow researchers to access information quickly and efficiently only as they need it. The most common approach to this goal has been to use information retrieval technology to improve access to text databases of biomedical information. We are interested in exploring an alternative; encoding this information for storage in structured databases for efficient retrieval.
Results: Two small databases described here are test beds for development of structured digital publication software; the Tumor Gene Database, containing information about genes which are the sites for cancer-causing mutations, and the Mammary Transgene Database, containing information about expression of transgenes in agriculturally important animals. Both have been successfully searched by users and edited by curators via the World Wide Web.
Availability: These databases can be accessed at http://www.tumor-gene.org/drmb.html
Contact: For further information on these databases, contact the individual database owners, listed on the page above, or David Steffen, Biomedical Computing, Inc., 6626 Westchester, Houston, Texas 77005, steffen@biomedcomp.com
Combining frequency and positional information to predict
transcription factor binding sites
Authors: Kiełbasa Szymon
   M. , Korbel Jan O. , Beule Dieter , Schuchhardt Johannes , Herzel Hanspeter 
Published: July 2002

Abstract
Motivation: Even though a number of genome projects have been finished on the sequence level, still only a small proportion of DNA regulatory elements have been identified. Growing amounts of gene expression data provide the possibility of finding coregulated genes by clustering methods. By analysis of the promoter regions of those genes, rather weak signals of transcription factor binding sites may be detected.
Results: We introduce the new algorithm ITB, an Integrated Tool for Box finding, which combines frequency and positional information to predict transcription factor binding sites in upstream regions of coregulated genes. Motifs are extracted by exhaustive analysis of regular expression-like patterns and by estimating probabilities of positional clusters of motifs. ITB detects consensus sequences of experimentally verified transcription factor binding sites of the yeast Saccharomyces cerevisiae. Moreover, a number of new binding site candidates with significant scores are predicted. Besides applying ITB on yeast upstream regions, the program is run on human promoter sequences.
Availability: ITB is available upon request.
Contact: s.kielbasa@itb.biologie.hu-berlin.de
* Both authors contributed equally.
Using clusters of computers for large QU-GENE simulation

experiments
Authors: Micallef Kevin P. , Cooper Mark , Podlich Dean W. 
Published: July 2002

Abstract
Summary: The QU-GENE Computing Cluster (QCC) is a hardware and software solution to the automation and speedup of large QU-GENE (QUantitative GENEtics) simulation experiments that are designed to examine the properties of genetic models, particularly those that involve factorial combinations of treatment levels. QCC automates the management of the distribution of components of the simulation experiments among the networked single-processor computers to achieve the speedup.
Contact: k.micallef@mailbox.uq.edu.au
Supplementary information: http://pig.ag.uq.edu.au/qu-gene/cluster.htm
* To whom correspondence should be addressed.
Dynamic simulation of the human red blood cell metabolic

network
Authors: Jamshidi Neema , Edwards Jeremy S. , Fahland Tom , Church George M. , Palsson Bernhard O. 
Published: July 2002

Abstract
Summary: We have developed a Mathematica®application package to perform dynamic simulations of the red blood cell (RBC) metabolic network. The package relies on, and integrates, many years of mathematical modeling and biochemical work on red blood cell metabolism. The extensive data regarding the red blood cell metabolic network and the previous kinetic analysis of all the individual components makes the human RBC an ideal ‘model’ system for mathematical metabolic models. The Mathematica package can be used to understand the dynamics and regulatory characteristics of the red blood cell.
Availability: The Mathematica package and an example file can be downloaded from http://gcrg.ucsd.edu
ProDDO: a database of disordered proteins from the Protein Data

Bank (PDB)
Authors: Sim Kim Lan , Uchida Tomoyuki , Miyano Satoru 
Published: July 2002

Abstract
Summary: ProDDO represents a ‘pre-screened’ database that denotes disorder (or possible disorder) in proteins from the PDB.
Availability: ProDDO is available at http://bonsai.ims.u-tokyo.ac.jp/~klsim/database.html
Contact: klsim@plato.gws.uky.edu
* To whom correspondence should be addressed. Present address: Kentucky Center for Structural Biology, Department of Biochemistry, University of Kentucky, 800 Rose Street, Lexington, KY 40536-0298, USA.
ADAPTSITE: detecting natural selection at single amino acid

sites
Authors: Suzuki Yoshiyuki , Gojobori Takashi , Nei Masatoshi 
Published: July 2002

Abstract
Summary: ADAPTSITE is a program package for detecting natural selection at single amino acid sites, using a multiple alignment of protein-coding sequences for a given phylogenetic tree. The program infers ancestral codons at all interior nodes, and computes the total numbers of synonymous (cS) and nonsynonymous (cN) substitutions as well as the average numbers of synonymous (sS) and nonsynonymous (sN) sites for each codon site. The probabilities of occurrence of synonymous and nonsynonymous substitutions are approximated by sS / (sS + sN) and sN / (sS + sN), respectively. The null hypothesis of selective neutrality is tested for each codon site, assuming a binomial distribution for the probability of obtaining cS and cN.
Availability: ADAPTSITE is available free of charge at the World-Wide Web sites http://mep.bio.psu.edu/adaptivevol.html and http://www.cib.nig.ac.jp/dda/yossuzuk/welcome.html. The package includes the source code written in C, binary files for UNIX operating systems, manual, and example files.
Contact: yis1@psu.edu
* To whom correspondence should be addressed.
Generation of a database containing discordant intron positions
in eukaryotic genes (MIDB)
Authors: Sakharkar Meena K. , Tan Tin Wee , de Souza Sandro J. 
Published: July 2002

Abstract
Motivation: Intron sliding is the relocation of intron–exon boundaries over short distances and is often also referred to as intron slippage or intron migration or intron drift. We have generated a database containing discordant intron positions in homologous genes (MIDB—Mismatched Intron DataBase). Discordant intron positions are those that are either closely located in homologous genes (within a window of 10 nucleotides) or an intron position that is present in one gene but not in any of its homologs. The MIDB database aims at systematically collecting information about mismatched introns in the genes from GenBank and organizing it into a form useful for understanding the genomics and dynamics of introns thereby helping understand the evolution of genes.
Results: Intron displacement or sliding is critically important for explaining the present distribution of introns among orthologous and paralogous genes. MIDB allows examining of intron movements and allows mapping of intron positions from homologous proteins onto a single sequence. The database is of potential use for molecular biologists in general and for researchers who are interested in gene evolution and eukaryotic gene structure. Partial analysis of this database allowed us to identify a few putative cases of intron sliding.
Availability: http://intron.bic.nus.edu.sg/midb/midb.html
Contact: meena@bic.nus.edu.sg
* To whom correspondence should be addressed.
Identification of characteristic oligonucleotides in the
bacterial 16S ribosomal RNA sequence dataset
Authors: Zhang Zhengdong , Willson Richard C. , Fox George E. 
Published: July 2002

Abstract
Motivation: The phylogenetic structure of the bacterial world has been intensively studied by comparing sequences of 16S ribosomal RNA (16S rRNA). This database of sequences is now widely used to design probes for the detection of specific bacteria or groups of bacteria one at a time. The success of such methods reflects the fact that there are local sequence segments that are highly characteristic of particular organisms or groups of organisms. It is not clear, however, the extent to which such signature sequences exist in the 16S rRNA dataset. A better understanding of the numbers and distribution of highly informative oligonucleotide sequences may facilitate the design of hybridization arrays that can characterize the phylogenetic position of an unknown organism or serve as the basis for the development of novel approaches for use in bacterial identification.
Results: A computer-based algorithm that characterizes the extent to which any individual oligonucleotide sequence in 16S rRNA is characteristic of any particular bacterial grouping was developed. A measure of signature quality, Qs, was formulated and subsequently calculated for every individual oligonucleotide sequence in the size range of 5–11 nucleotides and for 15mers with reference to each cluster and subcluster in a 929 organism representative phylogenetic tree. Subsequently, the perfect signature sequences were compared to the full set of 7322 sequences to see how common false positives were. The work completed here establishes beyond any doubt that highly characteristic oligonucleotides exist in the bacterial 16S rRNA sequence dataset in large numbers. Over 16000 15mers were identified that might be useful as signatures. Signature oligonucleotides are available for over 80% of the nodes in the representative tree.
Availability: The programs described herein are available at http://prion.bchs.uh.edu/16S_signatures/programs/. A preliminary database of signature sequences identified in this paper is available at: http://prion.bchs.uh.edu/16S_signatures/.
Contact: zzhang@bayou.uh.edu; fox@uh.edu
* To whom correspondence should be addressed.
PATRI—paternity inference using genetic data
Authors: Signorovitch J. , Nielsen R. 
Published: July 2002

Abstract
Summary: PATRI is a new application for paternity analysis using genetic data that accounts for the sampling fraction of potential fathers.
Availability: Executables are available at www.biom.cornell.edu/Homepages/Rasmus_Nielsen/
Contact: jes48@cornell.edu
* To whom correspondence should be addressed.
Microarray data warehouse allowing for inclusion of experiment
annotations in statistical analysis
Authors: Fellenberg Kurt , Hauser Nicole C. , Brors Benedikt , Hoheisel Jörg
   D. , Vingron Martin 
Published: July 2002

Abstract
Motivation: Microarray technology provides access to expression levels of thousands of genes at once, producing large amounts of data. These datasets are valuable only if they are annotated by sufficiently detailed experiment descriptions. However, in many databases a substantial number of these annotations is in free-text format and not readily accessible to computer-aided analysis.
Results: The Multi-Conditional Hybridization Intensity Processing System (M-CHIPS), a data warehousing concept, focuses on providing both structure and algorithms suitable for statistical analysis of a microarray database’s entire contents including the experiment annotations. It addresses the rapid growth of the amount of hybridization data, more detailed experimental descriptions, and new kinds of experiments in the future. We have developed a storage concept , a particular instance of which is an organism-specific database. Although these databases may contain different ontologies of experiment annotations, they share the same structure and therefore can be accessed by the very same statistical algorithms. Experiment ontologies have not yet reached their final shape, and standards are reduced to minimal conventions that do not yet warrant extensive description. An ontology-independent structure enables updates of annotation hierarchies during normal database operation without altering the structure.
Availability and supplementary information: http://www.dkfz.de/tbi/services/mchips
Contact: k.fellenberg@dkfz.de
* To whom correspondence should be addressed.
3 Present address: Max-Planck-Institute for Molecular Genetics, Ihnestr. 73, D-14195 Berlin, Germany.
BetaTPred: prediction of β-TURNS in a protein
using statistical algorithms
Authors: Kaur Harpreet , Raghava G. P. S. 
Published: July 2002

Abstract
Motivation: β-turns play an important role from a structural and functional point of view. β-turns are the most common type of non-repetitive structures in proteins and comprise on average, 25% of the residues. In the past numerous methods have been developed to predict β-turns in a protein. Most of these prediction methods are based on statistical approaches. In order to utilize the full potential of these methods, there is a need to develop a web server.
Results: This paper describes a web server called BetaTPred, developed for predicting β-TURNS in a protein from its amino acid sequence. BetaTPred allows the user to predict turns in a protein using existing statistical algorithms. It also allows to predict different types of β-TURNS e.g. type I, I′, II, II′, VI, VIII and non-specific. This server assists the users in predicting the consensus β-TURNS in a protein.
Availability: The server is accessible from http://imtech.res.in/raghava/betatpred/
Contact: raghava@imtech.res.in
Supplementary information: http://imtech.res.in/raghava/betatpred/intro.html
* To whom correspondence should be addressed.
Construction of optimal quality control for oligo arrays
Authors: Colbourn Charles J. , Ling Alan C. H. , Tompa Martin 
Published: July 2002

Abstract
Motivation: Oligo arrays are important experimental tools for the high throughput measurement of gene expression levels. During production of oligo arrays, it is important to identify any faulty manufacturing step.
Results: We describe a practical algorithm for the construction of optimal quality control designs that identify any faulty manufacturing step. The algorithm uses hillclimbing, a search technique from combinatorial optimization. We also present the results of using this algorithm on all practical quality control design sizes.
Availability: On request from the authors.
Contact: tompa@cs.washington.edu
* To whom correspondence should be addressed.
TranScout: prediction of gene expression regulatory proteins
from their sequences
Authors: Aguilar Daniel , Oliva Baldomero , Aviles Francesc X. , Querol Enrique 
Published: July 2002

Abstract
Motivation: The advent of genomics yields thousands of reading frames in search of function. Identification of conserved functional motifs in protein sequences can be helpful for function prediction.
Results: A database and a classification of reported DNA-binding protein motifs has been designed. A program (‘TranScout’) has been developed for the detection and evaluation of conserved motifs in prokaryotic and eukaryotic sequences of proteins with a gene regulatory function. The efficiency of the program is shown in a benchmark against a database obtained from SWISS-PROT without the protein sequences used to train the program. All motifs were detected with a mean average sensitivity of 0.98 and a mean average specificity of 0.92.
Availability: The program is freely available for use on the internet at http://luz.uab.es/transcout/. The user can find additional information at this site.
Contact: Enric.Querol@uab.es; boliva@imim.es
* To whom correspondence should be addressed.
2 Present address: Laboratorio de Biologı́a Estructural Computacional (GRIB), Universitat Pompeu Fabra, C/Doctor Aiguader, Barcelona 08003, Spain.
PATH: a task for the inference of phylogenies
Authors: del Val Coral , Ernst Peter , Bräuning Rüdiger , Glatting Karl-Heinz , Suhai Sandor 
Published: July 2002

Abstract
Summary: Phylogenetic Analysis Task in Husar (PATH) is a task for the inference of phylogenies. It executes three phylogenetic methods and automatically chooses the evolutionary model for each set of data. The output of the tasks shows the consensus trees together with full results obtained from all executed methods.
Availability: PATH is available at the German EMBnet node after registration via www at http://genome.dkfz-heidelberg.de
Contact: genome@dkfz.de
Recyclable 2D Colloid Surfactants with High Catalytic Activities at Pickering Emulsion Interfaces
Authors: Seo Bokgi , Sung Minchul , Park Bum Jun , Kim Jin Woong 
Published: February 2022

AbstractThis study introduces a novel 2D colloid surfactant system that exhibits catalytic activity at the interface of a reactant‐containing water‐in‐oil Pickering emulsion microreactor. To this end, amphiphilic nanoplatelets (ANPLs) are fabricated with hydrophobic poly (n‐butyl methacrylate) brushes on one face, and hydrophilic poly (2‐aminoethyl methacrylate) brushes on the other face via surface‐induced activators regenerated by electron transfer atom transfer radical polymerization (SI‐ARGET ATRP) on zirconium hydrogen phosphate (ZrHP) nanoplatelets. Subsequently, in situ reduction of metal precursors on the primary amine reaction sites on the hydrophilic face of ANPLs is conducted, thus enabling the production of ANPL catalysts (ANPLcat): ANPLAg, ANPLPd, and ANPLAu. Owing to the platelet geometry and catalytic functionalization, the ANPLcat demonstrates excellent ability to stabilize the Pickering emulsion reactant drops, while exhibiting its own catalytic activity at the interface. It is demonstrated that this ANPLcat system has a high catalytic activity that requires a short reduction reaction time with the speed of which is 750% higher compared with the spherical colloidal surfactant catalyst. In addition, ANPLcat is easily recoverable and recyclable. These results highlight that the ANPLcat‐based emulsion microreactor system is expected to be widely applied as a high‐performance catalyst for various organic chemical reactions.
A “Closed‐Loop” Therapeutic Strategy Based on Mutually Reinforced Ferroptosis and Immunotherapy
Authors: Du Yaqian , Zhang Rui , Yang Jiani , Liu Shikai , Zhou Jialing , Zhao Ruoxi , He Fei , Zhang Yanqiao , Yang Piaoping , Lin Jun 
Published: February 2022

AbstractThe immunosuppression and immune escape of current immunotherapy result in low efficacy, and ferroptosis is greatly restricted by the low reactive oxygen species (ROS) production efficiency. Here, for the first time a “closed‐loop” therapy based on photothermal enhancement of ferroptosis and immunotherapy stimulated by each other on a multifunctional nanoplatform is reported. This platform is composed of copper silicate and iron silicate mesoporous hollow nanospheres, followed by in situ growth of Au nanoparticles and loading of an immune adjuvant resiquimod R848. The laser irradiation‐mediated heat and the introduction of copper ions significantly enhance ROS generation, leading to the simultaneous depletion of glutathione peroxidase 4 (GPX4) and glutathione (GSH). The onset of ferroptosis in tumor cells is thus enhanced and an immune response with immunogenic cell death (ICD) is triggered, promoting the dendritic cells (DCs) maturation and T cell infiltration. Interferon γ (IFN‐γ) released from CD8+ T cells downregulates the expression of SLC7A11 and GPX4, which in turn enhances ferroptosis expression, thus constituting a “closed‐Loop” therapy. Importantly, this system is effective in both killing the primary tumor and inhibiting tumor metastasis. The proposed “closed‐loop” therapeutic strategy may provide a guidance for the design of future antitumor nanoplatforms.
Band Alignment at Heterointerface with Rapid Charge Transfer Supporting Excellent Photocatalytic Degradation of Methylene Blue under Sunlight
Authors: Talukdar Meenakshi , Behera Sushant Kumar , Jana Subrata , Samal Prasanjit , Deb Pritam 
Published: February 2022

AbstractEngineering 2D heterostructure using proximitized interfaces is an effective approach to attain high efficiency photocatalytic performance toward dye degradation. Strong interfacial interaction and abundant coupled interfaces and 2D/2D face‐to‐face contact heterostructure facilitate efficient charge separation contributing to high photocatalytic activity. In this aspect, for the first time the authors have analyzed the band alignment of the 2D/2D heterojunction, using Perdew–Burke–Ernzerhof semilocal meta‐generalized‐gradient approximation case and Heyd–Scuseria–Ernzerhof hybrid functional approach in density functional theory stimulation. Close proximity of CuSe nanoflakes with carbon nitride sheets facilitate electron transfer process leading to more proficient photocatalytic degradation, which is confirmed from the inverse participation ratio of individual atoms on the proximitized hetero interface and electrostatic potential line‐ups. The results demonstrate that this 2D/2D heterostructure has desired type‐II band alignment, which is facilitating rapid separation of photogenerated carriers in support of experimental findings. The face‐to‐face contact heterostructure with effective separation and low recombination rate of photogenerated electron–hole pairs helps in complete degradation of dye within 15 min. Further, the brilliance in photocatalytic performance of the developed type II heterostructure correlating with experimental results has introduced this system as a new class of material for wastewater treatment.