bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNA secondary structure prediction using stochastic context-free grammars and evolutionary history.
Authors: Knudsen B , Hein J 
Published: July 2002

Abstract
MOTIVATION: Many computerized methods for RNA secondary structure prediction have been developed. Few of these methods, however, employ an evolutionary model, thus relevant information is often left out from the structure determination. This paper introduces a method which incorporates evolutionary history into RNA secondary structure prediction. The method reported here is based on stochastic context-free grammars (SCFGs) to give a prior probability distribution of structures. RESULTS: The phylogenetic tree relating the sequences can be found by maximum likelihood (ML) estimation from the model introduced here. The tree is shown to reveal information about the structure, due to mutation patterns. The inclusion of a prior distribution of RNA structures ensures good structure predictions even for a small number of related sequences. Prediction is carried out using maximum a posteriori estimation (MAP) estimation in a Bayesian approach. For small sequence sets, the method performs very well compared to current automated methods.
BIND—a data specification for storing and describing
biomolecular interactions, molecular complexes and pathways
Authors: Bader Gary D. , Hogue Christopher W. V. 
Published: July 2002

Abstract
* To whom correspondence should be addressed.
Motivation: Proteomics is gearing up towards high-throughput methods for identifying and characterizing all of the proteins, protein domains and protein interactions in a cell and will eventually create more recorded biological information than the Human Genome Project. Each protein expressed in a cell can interact with various other proteins and molecules in the course of its function. A standard data specification is required that can describe and store this information in all its detail and allow efficient cross-platform transfer of data. A complete specification must be the basis for any database or tool for managing and analysing this information.
Results: We have defined a complete data specification in ASN.1 that can describe information about biomolecular interactions, complexes and pathways. Our group is using this data specification in our database, the Biomolecular Interaction Network Database (BIND). An interaction record is based on the interaction between two objects. An object can be a protein, DNA, RNA, ligand, molecular complex or an interaction. Interaction description encompasses cellular location, experimental conditions used to observe the interaction, conserved sequence, molecular location, chemical action, kinetics, thermodynamics, and chemical state. Molecular complexes are defined as collections of more than two interactions that form a complex, with extra descriptive information such as complex topology. Pathways are defined as collections of more than two interactions that form a pathway, with additional descriptive information such as cell cycle stage. A request for proposal of a human readable flat-file format that mirrors the BIND data specification is also tendered for interested parties.
Availability: The ASN.1 data specification for biomolecular interaction, molecular complex and pathway data is available at ftp://bioinfo.mshri.on.ca/pub/BIND/Spec/bind.asn. An interactive browser for this document is available through our homepage at http://bioinfo.mshri.on.ca/BIND/asn-browser/.
Contact: hogue@mshri.on.ca
Phylogenetically enhanced statistical tools for RNA structure
prediction
Authors: Akmaev Viatcheslav R. , Kelley Scott T. , Stormo Gary D. 
Published: July 2002

Abstract
Motivation: Methods that predict the structure of molecules by looking for statistical correlation have been quite effective. Unfortunately, these methods often disregard phylogenetic information in the sequences they analyze. Here, we present a number of statistics for RNA molecular-structure prediction. Besides common pair-wise comparisons, we consider a few reasonable statistics for base-triple predictions, and present an elaborate analysis of these methods. All these statistics incorporate phylogenetic relationships of the sequences in the analysis to varying degrees, and the different nature of these tests gives a wide choice of statistical tools for RNA structure prediction.
Results: Starting from statistics that incorporate phylogenetic information only as independent sequence evolution models for each position of a multiple alignment, and extending this idea to a joint evolution model of two positions, we enhance the usual purely statistical methods (e.g. methods based on the Mutual Information statistic) with the use of phylogenetic information available in the sequences. In particular, we present a joint model based on the HKY evolution model, and consequently a \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \({\chi}^{2}\) \end{document}test of independence for two positions. A significant part of this work is devoted to some mathematical analysis of these methods. We tested these statistics on regions of 16S and 23S rRNA, and tRNA.
Availability: The programs are available upon request.
Contact: slava@colorado.edu
Visualizing large hierarchical clusters in hyperbolic space
Authors: Bingham Jonathan , Sudarsanam Sucha 
Published: July 2002

Abstract
Summary: HyperTree is an application to visualize and navigate large trees in hyperbolic space. It includes color-coding, search mechanisms and navigational aids, as well as focus+context viewing, allowing enormous trees to fit within the fixed space of a computer screen or printed page.
Availability: A demo is available online at http://www.kinase.com/tools/HyperTree.html
Contact: sucha-sudarsanam@sugen.com
Nucleosome formation potential of eukaryotic DNA: calculation
and promoters analysis
Authors: Levitsky Victor G. , Podkolodnaya Olga A. , Kolchanov Nikolay A. , Podkolodny Nikolay L. 
Published: July 2002

Abstract
Motivation: A rapid growth in the number of genes with known sequences calls for developing automated tools for their classification and analysis. It became clear that nucleosome packaging of eukaryotic DNA is very important for gene functioning. Automated computer tools for characterization of nucleosome packaging density could be useful for studying of gene regulation and genome annotation.
Results: A program for constructing nucleosome formation potential profiles of eukaryotic DNA sequences was developed. Nucleosome packaging density was analyzed for different functional types of human promoters. It was found that in promoters of tissue-specific genes, the nucleosome formation potential was essentially higher than in genes expressed in many tissues, or housekeeping genes. Hence, capability of nucleosome positioning in the promoter region may serve as a factor regulating gene expression.
Availability: The program for nucleosome sites recognition is included into the GeneExpress system; section ‘DNA Nucleosomal Organization’, http://wwwmgs.bionet.nsc.ru/mgs/programs/recon/.
Contact: levitsky@bionet.nsc.ru
* To whom correspondence should be addressed.
A probabilistic method for identifying start codons in
bacterial genomes
Authors: Suzek Baris E. , Ermolaeva Maria D. , Schreiber Mark , Salzberg Steven L. 
Published: July 2002

Abstract
As the pace of genome sequencing has accelerated, the need for highly accurate gene prediction systems has grown. Computational systems for identifying genes in prokaryotic genomes have sensitivities of 98–99% or higher (Delcher et al. , Nucleic Acids Res. , 27, 4636–4641, 1999). These accuracy figures are calculated by comparing the locations of verified stop codons to the predictions. Determining the accuracy of start codon prediction is more problematic, however, due to the relatively small number of start sites that have been confirmed by independent, non-computational methods. Nonetheless, the accuracy of gene finders at predicting the exact gene boundaries at both the 5′ and 3′ ends of genes is of critical importance for microbial genome annotation, especially in light of the important signaling information that is sometimes found on the 5′ end of a protein coding region. In this paper we propose a probabilistic method to improve the accuracy of gene identification systems at finding precise translation start sites. The new system, RBSfinder, is tested on a validated set of genes from Escherichia coli , for which it improves the accuracy of start site locations predicted by computational gene finding systems from the range 67–77% to 90% correct.
* To whom correspondence should be addressed.
Conformational model for binding site recognition by the
E.coli MetJ transcription factor
Authors: Liu Rongxiang , Blackwell Thomas W. , States David J. 
Published: July 2002

Abstract
Motivation: Current methods for identifying sequence specific binding sites in DNA sequence using position specific weight matrices are limited in both sensitivity and specificity. Double strand DNA helix exhibits sequence dependent variations in conformation. Interactions between macromolecules result from complementarity of the two tertiary structures. We hypothesize that this conformational variation plays a role in transcription factor binding site recognition, and that the use of this structure information will improve the predictive power of transcription factor binding site models.
Results: Conformation models for the sequence dependence of DNA helix distortion have been developed. Using our conformational models, we defined a tertiary structure template for the met operon repressor MetJ binding site. Both naturally occurring sites and precursor binding sites identified through in vitro selection were used as the basis for template definition. The conformational model appears to recognize features of protein binding sites that are distinct from the features recognized by primary sequence based profiles. Combining the conformational model and primary sequence profile yields a hybrid model with improved discriminatory power compared with either the conformational model or sequence profile alone. Using our hybrid model, we searched the E.coli genome. We are able to identify the documented MetJ sites in the promoter regions of metA, metB, metC, metR and metF. In addition, we find several novel loci with characteristics suggesting that they are functional MetJ repressor binding sites. Novel MetJ binding sites are found upstream of the metK gene, as well as upstream of a gene, abc, a gene that encodes for a component of a multifunction transporter which may transport amino acids across the membrane. The false positive rate is significantly lower than the sequence profile method.
Availability: The programs of implementation of this algorithm are available upon request. The list of crystal structures used for compiling the mean base step parameters of DNA is available by anonymous ftp at http://stateslab.wustl.edu/pub/helix/StructureList.
Contact: states@ccb.wustl.edu
* To whom correspondence should be addressed.
PAL: an object-oriented programming library for molecular
evolution and phylogenetics
Authors: Drummond Alexei , Strimmer Korbinian 
Published: July 2002

Abstract
Summary: Phylogenetic Analysis Library (PAL) is a collection of Java classes for use in molecular evolution and phylogenetics. PAL provides a modular environment for the rapid construction of both special-purpose and general analysis programs. PAL version 1.1 consists of 145 public classes or interfaces in 13 packages, including classes for models of character evolution, maximum-likelihood estimation, and the coalescent, with a total of more than 27000 lines of code. The PAL project is set up as a collaborative project to facilitate contributions from other researchers.
Availability: The program is free and is available at http://www.pal-project.org. It requires Java 1.1 or later. PAL is licensed under the GNU General Public License.
Contact: a.drummond@auckland.ac.nz; korbinian.strimmer@zoo.ox.ac.uk
Supplementary information: An online description of the Application Programming Interface (API) of all public classes in PAL is available at http://www.pal-project.org/api/.
* To whom correspondence should be addressed.
Evaluation of protein multiple alignments by SAM-T99 using the
BAliBASE multiple alignment test set
Authors: Karplus Kevin , Hu Birong 
Published: July 2002

Abstract
Motivation: SAM-T99 is an iterative hidden Markov model-based method for finding proteins similar to a single target sequence and aligning them. One of its main uses is to produce multiple alignments of homologs of the target sequence. Previous tests of SAM-T99 and its predecessors have concentrated on the quality of the searches performed, not on the quality of the multiple alignment. In this paper we report on tests of multiple alignment quality, comparing SAM-T99 to the standard multiple aligner, CLUSTALW.
Results: The paper evaluates the multiple-alignment aspect of the SAM-T99 protocol, using the BAliBASE benchmark alignment database. On these benchmarks, SAM-T99 is comparable in accuracy with ClustalW.
Availability: The SAM-T99 protocol can be run on the web at http://www.cse.ucsc.edu/research/compbio/HMM-apps/T99-query.html and the alignment tune-up option described here can be run at http://www.cse.ucsc.edu/research/compbio/HMM-apps/T99-tuneup.html. The protocol is also part of the standard SAM suite of tools. http://www.cse.ucsc.edu/research/compbio/sam/
The Bioinformatics Template Library—generic components
for biocomputing
Authors: Pitt W. R. , Williams M. A. , Steven M. , Sweeney B. , Bleasby A. J. , Moss D. S. 
Published: July 2002

Abstract
Motivation: The efficiency of bioinformatics programmers can be greatly increased through the provision of ready-made software components that can be rapidly combined, with additional bespoke components where necessary, to create finished programs. The new standard for C++ includes an efficient and easy to use library of generic algorithms and data-structures, designed to facilitate low-level component programming. The extension of this library to include functionality that is specifically useful in compute-intensive tasks in bioinformatics and molecular modelling could provide an effective standard for the design of reusable software components within the biocomputing community.
Results: A novel application of generic programming techniques in the form of a library of C++ components called the Bioinformatics Template Library (BTL) is presented. This library will facilitate the rapid development of efficient programs by providing efficient code for many algorithms and data-structures that are commonly used in biocomputing, in a generic form that allows them to be flexibly combined with application specific object-oriented class libraries.
Availability: The BTL is available free of charge from our web site http://www.cryst.bbk.ac.uk/~classlib/ and the EMBL file server http://www.embl-ebi.ac.uk/FTP/index.html
Contact: d.moss@mail.cryst.bbk.ac.uk; m.williams@biochemistry.ucl.ac.uk
* To whom correspondence should be addressed.
3 Present address: Celltech Chiroscience, Granta Park, Great Abingdon, Cambridge CB1 6GS, UK.
4 Present address: Department of Biochemistry & Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK.
Preclinical safety evaluation of moxifloxacin, a novel fluoroquinolone
Authors: von Keutz Eckhard , Schlüter Gerhard 
Published: July 2002

Abstract
The toxicity of moxifloxacin (BAY 12-8039), a novel fluoroquinolone with a broad spectrum of antibacterial activity, was evaluated in a comprehensive programme of toxicological studies that included single and multiple dose toxicity studies in rats, mice, dogs and monkeys, reproductive system toxicity studies in rats and monkeys and in-vitro and in-vivo mutagenicity assays. Although moxifloxacin is not intended for long-term clinical use, an accelerated bioassay in target organs to assess carcinogenesis was performed in rats. In addition to the routine toxicological programme required for the development of a drug intended for short-term administration, a major part of the preclinical programme for moxifloxacin comprised studies designed specifically to address the safety issues known to be features of fluoroquinolones, i.e. adverse effects on the central nervous and cardiovascular systems, phototoxicity, arthrotoxicity and oculotoxicity. The results of the toxicological investigations confirmed that the safety profile of moxifloxacin is comparable to those of other fluoroquinolones.
The Legacy Sketch Machine: From Artificial to Architectural Intelligence
Authors: dPrix Wolf , Schmidbaur Karolin , Bolojan Daniel , Baseta Efilena 
Published: April 2022

AbstractIn the office of Coop Himme(l)blau in Vienna, a series of software machine‐learning protocols and practices continually reinterpret the   firm's past and future projects, unleashing new work and possibilities for architectures yet to exist. Here Wolf dPrix, Karolin Schmidbaur, Daniel Bolojan and Efilena Baseta explain the uses and some of the outputs of this suite of tools.
Sequential Masterplanning: Using Urban‐GANs
Authors: He Wanyu 
Published: April 2022

AbstractAI, and particularly the use of generative adversarial networks (GANs), can provide a more dynamic urban‐planning visual tool allowing the development potential of specific sites to be explored. Wanyu He – founder and CEO of XKool Technology, co‐founder of Future Architecture Lab and University of Hong Kong academic – explains how.
A “Two‐in‐One” Strategy for Flexible Aqueous Batteries Operated at −80 °C
Authors: Hu Yin , Shi Rongwei , Ren Yongyuan , Peng Wansu , Feng Chengdong , Zhao Yan , Zheng Sijie , Li Weizheng , Sun Zhe , Guo Jiangna , Guo Siyu , Wang Xiaoliang , Yan Feng 
Published: April 2022

AbstractThe development of aqueous metal‐ion batteries has attracted great attention due to their relatively low cost and high safety levels. However, their practical applications are hindered by the ease at which their aqueous electrolytes freeze. Inspired by the antifreezing properties of salts and alcohol cryoprotective agents, a “two‐in‐one” cryoprotective agent, hydroxyl‐functionalized poly(ionic liquid) (PIL‐OH)‐based hydrogel electrolyte for aqueous lithium‐ion batteries (ALIBs) is developed. The synergy of both ionic hydration and hydrogen bond interactions between the PIL‐OH and water molecules impairs the hydrogen‐bond networks of water and depresses the freezing point of water below −80 °C. Benefiting from exceptional ultralow temperature tolerance, the prepared PIL‐OH hydrogel exhibits a highly enhanced low temperature adaptability and a high ionic conductivity of 0.08 mS cm−1 at −80 °C. The PIL‐OH hydrogel‐based flexible ALIBs exhibit high flexible durability and good cycling stability with 93% capacity retention over 200 cycles at −80 °C. The PIL‐OH hydrogel report herein opens up new opportunities for practical applications of wearable and flexible aqueous batteries at ultralow temperature environments, such as the North and South Poles.
Intelligent Micro‐/Nanorobots for Cancer Theragnostic
Authors: Wang Jie , Dong Yue , Ma Peng , Wang Yu , Zhang Fangyu , Cai Bocheng , Chen Peng , Liu Bi‐Feng 
Published: April 2022

AbstractCancer is one of the most intractable diseases owing to its high mortality rate and lack of effective diagnostic and treatment tools. Advancements in micro‐/nanorobot (MNR)‐assisted sensing, imaging, and therapeutics offer unprecedented opportunities to develop MNR‐based cancer theragnostic platforms. Unlike ordinary nanoparticles, which exhibit Brownian motion in biofluids, MNRs overcome viscous resistance in an ultralow Reynolds number (Re << 1) environment by effective self‐propulsion. This unique locomotion property has motivated the advanced design and functionalization of MNRs as a basis for next‐generation cancer‐therapy platforms, which offer the potential for precise distribution and improved permeation of therapeutic agents. Enhanced barrier penetration, imaging‐guided operation, and biosensing are additionally studied to enable the promising cancer‐related applications of MNRs. Herein, the recent advances in MNR‐based cancer therapy are comprehensively addresses, including actuation engines, diagnostics, medical imaging, and targeted drug delivery; promising research opportunities that can have a profound impact on cancer therapy over the next decade is highlighted.
Polyhedral Carbon Anchored on Carbon Nanosheet with Abundant Atomic Fe‐Nx Moieties for Oxygen Reduction
Authors: Liu Dong , Huyan Chenxi , Zhao Yuanyuan , Liu Terence Xiaoteng , Wang Ding , Sun Jining , Dai Sheng , Chen Fei , Xu Ben Bin 
Published: April 2022

AbstractCarbon‐based single‐atom iron electrocatalysts with nitrogen coordination (CSAIN) have recently shown enormous promise to replace the costly Pt for boosting the cathodic oxygen reduction reaction (ORR) in fuel cells. However, there remains a great challenge to achieve highly efficient CSAIN catalysts for the ORR in acidic electrolytes. Herein, a novel CSAIN catalyst is synthesized by pyrolyzing a precursor mixture consisting of metal–organic framework and conductive polymer hybrid. After pyrolysis at a high temperature, the CSAIN with a structure of carbon nanosheet supported polyhedral carbon is achieved, where the unique structure endows CSAIN with expediting electron transfer and mass transport, as well as largely exposed surface to host atomically dispersed iron active sites. As a result, the optimal CSAIN catalyst shows a high ORR activity with its half‐wave potential of 0.77 V (vs RHE) and a Tafel slope of 74.1 mV dec–1, which are comparable to that of commercial Pt/C catalyst (0.80 V and 81.9 mV dec–1).
Magnetic Actuator with Programmable Force Distribution and Self‐Sensing for Bidirectional Deformation Control
Authors: Gao Yinduan , Deng Huaxia , Zhang Jingyi , Shu Quan , Xu Zhenbang , Cao Xufeng , Wang Bochao , Gong Xinglong 
Published: April 2022

AbstractThe realization of bidirectional deformation function is an important symbol of most natural creatures and intelligent flexible robots. Currently, most soft actuators are developed on the basis of transition between two different states, which means difficulties of control during the whole movement. In this work, variable distribution positions of hard magnetorheological elastomers (H‐MREs) in the matrix are used to achieve different magnetic force distributions. The programmable force distribution promotes different deformations of the magnetic actuators, which enlarges the deformation range by 51.69% under the same magnetic field. Pre‐magnetizing the H‐MREs makes them have a certain residual magnetization. Due to the residual magnetization property of H‐MREs, the magnetized actuator can not only be attracted but also be repelled by the applied magnetic field. This bidirectional deformation capability gives the actuators a wider deformation range and greater clamping force, such as the smart gripper for pinching up object. In addition, the actuators are integrated with a flexible sensing layer with high resolution and strong stability for self‐sensing. This kind of force distribution programmable technology and self‐sensing performance have the potential to broaden the application of actuators in medical equipment requiring high control accuracy.