bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biological phenotypes associated with individuals at high risk for developing alcohol‐related disorders. Part 2
Authors: Schuckit Marc A. 
Published: July 2002

AbstractThis paper reviews comparisons of populations at higher and lower risk for alcoholism on biological phenotypes. The results of studies must be considered in the context of the research methods used including the need for large, carefully defined samples and longitudinal designs. Comparisons of children of alcoholics and controls have revealed potentially important differences on level of response to alcohol, cognitive attributes and differences in alcohol‐metabolizing and other enzyme systems responsible for various aspects of the body's reaction to alcohol. Many opportunities for future research in this area exist, including large‐scale, longitudinal studies that simultaneously evaluate multiple domains of influence, and searches for candidate genes or other biological material that will simplify procedures and increase the accuracy of measurement.
Possessions and the Extended Self
Authors: Belk Russell W. 
Published: July 2002

Abstract
Our possessions are a major contributor to and reflection of our identities. A variety of evidence is presented supporting this simple and compelling premise. Related streams of research are identified and drawn upon in developing this concept and implications are derived for consumer behavior. Because the construct of extended self involves consumer behavior rather than buyer behavior, it appears to be a much richer construct than previous formulations positing a relationship between self-concept and consumer brand choice.
Algorithms and software for support of gene identification experiments.
Authors: Sze S H , Roytberg M A , Gelfand M S , Mironov A A , Astakhova T V , Pevzner P A 
Published: July 2002

Abstract
MOTIVATION: Gene annotation is the final goal of gene prediction algorithms. However, these algorithms frequently make mistakes and therefore the use of gene predictions for sequence annotation is hardly possible. As a result, biologists are forced to conduct time-consuming gene identification experiments by designing appropriate PCR primers to test cDNA libraries or applying RT-PCR, exon trapping/amplification, or other techniques. This process frequently amounts to 'guessing' PCR primers on top of unreliable gene predictions and frequently leads to wasting of experimental efforts. RESULTS: The present paper proposes a simple and reliable algorithm for experimental gene identification which bypasses the unreliable gene prediction step. Studies of the performance of the algorithm on a sample of human genes indicate that an experimental protocol based on the algorithm's predictions achieves an accurate gene identification with relatively few PCR primers. Predictions of PCR primers may be used for exon amplification in preliminary mutation analysis during an attempt to identify a gene responsible for a disease. We propose a simple approach to find a short region from a genomic sequence that with high probability overlaps with some exon of the gene. The algorithm is enhanced to find one or more segments that are probably contained in the translated region of the gene and can be used as PCR primers to select appropriate clones in cDNA libraries by selective amplification. The algorithm is further extended to locate a set of PCR primers that uniformly cover all translated regions and can be used for RT-PCR and further sequencing of (unknown) mRNA.
SALSA: improved protein database searching by a new algorithm for assembly of sequence fragments into gapped alignments.
Authors: Rognes T , Seeberg E 
Published: July 2002

Abstract
MOTIVATION: Optimal sequence alignment based on the Smith-Waterman algorithm is usually too computationally demanding to be practical for searching large sequence databases. Heuristic programs like FASTA and BLAST have been developed which run much faster, but at the expense of sensitivity. RESULTS: In an effort to approximate the sensitivity of an optimal alignment algorithm, a new algorithm has been devised for the computation of a gapped alignment of two sequences. After scanning for high-scoring words and extensions of these to form fragments of similarity, the algorithm uses dynamic programming to build an accurate alignment based on the fragments initially identified. The algorithm has been implemented in a program called SALSA and the performance has been evaluated on a set of test sequences. The sensitivity was found to be close to the Smith-Waterman algorithm, while the speed was similar to FASTA (ktup = 2). AVAILABILITY: Searches can be performed from the SALSA homepage at http://dna.uio.no/salsa/ using a wide range of databases. Source code and precompiled executables are also available. CONTACT: torbjorn.rognes@labmed.uio.no
JavaShade: multiple sequence alignment box-and-shading on the World Wide Web.
Authors: Southern M R , Lewis A P 
Published: July 2002

Abstract
RESULTS: JavaShade is a multiple sequence alignment box-and-shade tool for generating high quality printed output that uses a variety of methods for boxing and shading, allowing the most appropriate functions to be chosen for displaying the most meaningful positions in an alignment. AVAILABILITY: JavaShade is available from the WWW at http://industry.ebi.ac.uk/JavaShade
SECOST: sequence-conformation-structure database for amino acid residues in proteins.
Authors: Shats O , Vaisman I I , Shats A , Sherman S 
Published: July 2002

Abstract
The sequence-conformation-structure database for amino acid residues contains information on 114 828 individual residues derived from the spatial structures of 473 high-quality non-homologous proteins. The information in the database is obtained using a variety of different methods and can be used in various protein modeling applications.
A brief history of genome research and bioinformatics in France
Authors: Danchin Antoine 
Published: July 2002

Abstract
The development of in silico genomics has progressed slowly in France for a number of political reasons. Two administrative organizations, the Groupement de Recherche sur les Génomes (GREG) and the Groupement de Recherche 1029 (GDR 1029) of the Centre National de la Recherche Scientifique (CNRS) have been established. These organizations have created the dynamics that hopefully will place France (which coordinated consortia that completed several of the first large microbial genomes) among the developed nations that support Large-Scale Biology.
Contact: adanchin@pasteur.fr
GABAagent: a system for integrating data on GABA receptors
Authors: Rachedi Abdelkrim , Rebhan Michael , Xue Hong 
Published: July 2002

Abstract
Motivation: Scientific data pertaining to GABA receptors, which are of medical importance, are widely scattered throughout numerous heterogeneous Internet resources. This situation has made the integrated acquisition of such data difficult and substantially time consuming even for researchers who are Internet aficionados. Thus, there exists a genuine need for the development of Internet applications, such as GABAagent, which provide efficient and timely access to concise and integrated information.
Results: We report here the establishment of a novel server (GABAagent) which has been written in Perl script, and which is freely accessible through the Internet. GABAagent is designed to assist researchers in retrieving focused and integrated information related to GABA receptors from various public domain databases.
GABAagent relies on server-side flat-file databases that have been created through data mining from Internet sources such as the PubMed, DDBJ, SWISS-PROT and TrEMBL, in addition to the many World Wide Web (Web) sites which are accessible through Excite (E-Web). These warehouse databases are regularly updated and contain among other things, information concerning: (i) GABA receptor publications, (ii) DNA and protein sequences and (iii) the contents of related E-Web sites along with their addresses. Our system also provides hard links to the above-mentioned Web sites and E-Web sites; the feature which adds to it the character of virtual federation type of database.
The current version of GABAagent provides two user-friendly services. The first is a search engine possessing intelligent query reformulation support (GABAengine), the second an elaborate email alert service was designed into the system (GABAalert). The GABAengine allows the user to search server-side databases exclusively for GABA receptor-related queries. Whereas, GABAalert allows the user, by means of subscription, to receive immediate and/or monthly updates automatically.
Availability: GABAagent is freely accessible at the following Web address http://www.ust.hk/gaba.
Contact: gaba@ust.hk
Quick selection of representative protein chain sets based on
customizable requirements
Authors: Noguchi Tamotsu , Onizuka Kentaro , Ando Makoto , Matsuda Hideo , Akiyama Yutaka 
Published: July 2002

Abstract
Motivation: Protein structure classification has been recognized as one of the most important research issues in protein structure analysis. A substantial number of methods for the classification have been proposed, and several databases have been constructed using these methods. Since some proteins with very similar sequences may exhibit structural diversities, we have proposed PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB), which strategy of selection is based not only on sequence similarity but also on structural similarity. Forty-eight representative sets whose similarity criteria were predetermined were made available over the World Wide Web (WWW). However, the sets were insufficient in number to satisfy users researching protein structures by various methods.
Result: We have improved the system for PDB-REPRDB so that the user may obtain a quick selection of representative chains from PDB. The selection of representative chains can be dynamically configured according to the user’s requirement. The WWW interface provides a large degree of freedom in setting parameters, such as cut-off scores of sequence and structural similarity. This paper describes the method we use to classify chains and select the representatives in the system. We also describe the interface used to set the parameters.
Availability: The system for PDB-REPRDB is available at the PAPIA WWW server (http://www.rwcp.or.jp/papia/).
Contact: noguchi@trc.rwcp.or.jp
* To whom correspondence should be addressed.
3 Present address: Information Processing Systems Department, NKK Corporation, 1-1-2 Marunouchi, Chiyoda-ku, Tokyo 100-8202, Japan
In silico identification of transcripts and SNPs from

a region of 4p linked with bipolar affective disorder
Authors: Semple C. A. M. , Morris S. W. , Porteous D. J. , Evans K. L. 
Published: July 2002

Abstract
Contact: c.semple@hgu.mrc.ac.uk
Availability: Files containing the accession numbers of all EST clusters and SNPs from this study are available at ftp://ftp.hgu.mrc.ac.uk/pub/colins.
To whom correspondence should be addressed.
Visualizing plant metabolomic correlation networks using
clique–metabolite matrices
Authors: Kose Frank , Weckwerth Wolfram , Linke Thomas , Fiehn Oliver 
Published: July 2002

Abstract
Motivation: Today, metabolite levels in biological samples can be determined using multiparallel, fast, and precise metabolomic approaches. Correlations between the levels of various metabolites can be searched to gain information about metabolic links. Such correlations are the net result of direct enzymatic conversions and of indirect cellular regulation over transcriptional or biochemical processes. In order to visualize metabolic networks derived from correlation lists graphically, each metabolite pair may be represented as vertices connected by an edge. However, graph complexity rapidly increases with the number of edges and vertices. To gain structural information from metabolite correlation networks, improvements in clarity are needed.
Results: To achieve this clarity, three algorithms are combined. First, a list of linear metabolite correlations is generated that can be regarded as a set of pairs of edges (or as 2-cliques). Next, a branch-and-bound algorithm was developed to find all maximal cliques by combining submaximal cliques. Due to a clique assignment procedure, the generation of unnecessary submaximal cliques is avoided in order to maintain high efficiency. Differences and similarities to the Bron–Kerbosch algorithm are pointed out. Lastly, metabolite correlation networks are visualized by clique–metabolite matrices that are sorted to minimize the length of lines that connect different cliques and metabolites. Examples of biochemical hypotheses are given that can be built from interpretation of such clique matrices.
Availability: The algorithms are implemented in Visual Basic and can be downloaded from our web site along with a test data set (http://www.mpimp-golm.mpg.de/fiehn/projekte/data-mining-e.html).
Contact: kose@mpimp-golm.mpg.de
* To whom correspondence should be addressed.
Clustering of highly homologous sequences to reduce the size of

large protein databases
Authors: Li Weizhong , Jaroszewski Lukasz , Godzik Adam 
Published: July 2002

Abstract
Summary: We present a fast and flexible program for clustering large protein databases at different sequence identity levels. It takes less than 2 h for the all-against-all sequence comparison and clustering of the non-redundant protein database of over 560000 sequences on a high-end PC. The output database, including only the representative sequences, can be used for more efficient and sensitive database searches.
Availability: The program is available from http://bioinformatics.burnham-inst.org/cd-hi
Contact: liwz@sdsc.edu or adam@burnham-inst.org
* To whom correspondence should be addressed.
Cladogramer: incorporating haplotype frequency into cladogram
analysis
Authors: Zhang Louxin , Heng Chew-Kiat , Tan Tin Wee 
Published: July 2002

Abstract
Summary: We implement a program that incorporates polymorphic sites data, haplotype frequency arrays, and other factors, into cladogram estimation.
Availability: It is available at http://sdmc.krdl.org.sg:8080/~lxzhang/cladogramer
Contact: lxzhang@krdl.org.sg
Missing value estimation methods for DNA microarrays
Authors: Troyanskaya Olga , Cantor Michael , Sherlock Gavin , Brown Pat , Hastie Trevor , Tibshirani Robert , Botstein David , Altman Russ B. 
Published: July 2002

Abstract
Motivation: Gene expression microarray experiments can generate data sets with multiple missing expression values. Unfortunately, many algorithms for gene expression analysis require a complete matrix of gene array values as input. For example, methods such as hierarchical clustering and K-means clustering are not robust to missing data, and may lose effectiveness even with a few missing values. Methods for imputing missing data are needed, therefore, to minimize the effect of incomplete data sets on analyses, and to increase the range of data sets to which these algorithms can be applied. In this report, we investigate automated methods for estimating missing data.
Results: We present a comparative study of several methods for the estimation of missing values in gene microarray data. We implemented and evaluated three methods: a Singular Value Decomposition (SVD) based method (SVDimpute), weighted K-nearest neighbors (KNNimpute), and row average. We evaluated the methods using a variety of parameter settings and over different real data sets, and assessed the robustness of the imputation methods to the amount of missing data over the range of 1–20% missing values. We show that KNNimpute appears to provide a more robust and sensitive method for missing value estimation than SVDimpute, and both SVDimpute and KNNimpute surpass the commonly used row average method (as well as filling missing values with zeros). We report results of the comparative experiments and provide recommendations and tools for accurate estimation of missing microarray data under a variety of conditions.
Availability: The software is available at http://smi-web.stanford.edu/projects/helix/pubs/impute/
Contact: russ.altman@stanford.edu
* To whom correspondence should be addressed.
An HMM model for coiled-coil domains and a comparison with
PSSM-based predictions
Authors: Delorenzi Mauro , Speed Terry 
Published: July 2002

Abstract
Motivation: Large-scale sequence data require methods for the automated annotation of protein domains. Many of the predictive methods are based either on a Position Specific Scoring Matrix (PSSM) of fixed length or on a window-less Hidden Markov Model (HMM). The performance of the two approaches is tested for Coiled-Coil Domains (CCDs). The prediction of CCDs is used frequently, and its optimization seems worthwhile.
Results: We have conceived MARCOIL, an HMM for the recognition of proteins with a CCD on a genomic scale. A cross-validated study suggests that MARCOIL improves predictions compared to the traditional PSSM algorithm, especially for some protein families and for short CCDs. The study was designed to reveal differences inherent in the two methods. Potential confounding factors such as differences in the dimension of parameter space and in the parameter values were avoided by using the same amino acid propensities and by keeping the transition probabilities of the HMM constant during cross-validation.
Availability: The prediction program and the databases are available at http://www.wehi.edu.au/bioweb/Mauro/Marcoil
Contact: delorenzi@wehi.edu.au
* To whom correspondence should be addressed.
Self–assembly of tobacco mosaic virus: the role of an intermediate aggregate in generating both specificity and speed
Authors: Butler P. J. G. 
Published: July 2002

The tobacco mosaic virus (TMV) particle was the first macromolecular structure to be shown to self–assemble
in vitro
, allowing detailed studies of the mechanism.

Nucleation of TMV self–assembly is by the binding of a specific stem–loop of the single–stranded viral RNA into the central hole of a two–ring sub–assembly of the coat protein, known as the ‘disk’. Binding of the loop onto its specific binding site, between the two rings of the disk, leads to melting of the stem so more RNA is available to bind. The interaction of the RNA with the protein subunits in the disk cause this to dislocate into a proto–helix, rearranging the protein subunits in such a way that the axial gap between the rings at inner radii closes, entrapping the RNA.
Assembly starts at an internal site on TMV RNA, about 1 kb from its 3′–terminus, and the elongation in the two directions is different. Elongation of the nucleated rods towards the 5′–terminus occurs on a ‘travelling loop’ of the RNA and, predominantly, still uses the disk sub–assembly of protein subunits, consequently incorporating approximately 100 further nucleotides as each disk is added, while elongation towards the 3′–terminus uses smaller protein aggregates and does not show this ’quantized‘ incorporation.
Factors Associated With Patients Not Receiving Oral Anticancer Drugs
Authors: Doshi Sahil D. , Lichtenstein Morgan R. L. , Beauchemin Melissa P. , Raghunathan Rohit , Lee Shing , Law Cynthia , Accordino Melissa K. , Elkin Elena B. , Wright Jason D. , Hershman Dawn L. 
Published: October 2022

ImportanceOral anticancer drugs (OACDs) are increasingly prescribed for cancer treatment and require significant coordination of care. Retrospective studies suggest that 10% to 20% of OACD prescriptions are never received by the patients, but the reasons behind this are poorly understood.ObjectivesTo estimate the rate of failure to receive OACD prescriptions among patients with cancer and to examine the underlying reasons for this failure.Design, Setting, and ParticipantsA prospective cohort study was conducted among patients with cancer who were prescribed a new OACD from January 1, 2018, to December 31, 2019, at an urban academic medical center. Data analysis was conducted between 2021 and 2022.Main Outcomes and MeasuresPatient demographic, clinical, and insurance data and OACD delivery dates were collected. The reasons for a failure to receive a prescribed OACD within 3 months were confirmed by manual review of medical records and were classified into 7 categories: clinical deterioration, financial access, clinician-directed change in decision-making, patient-directed change in decision-making, transfer of care, loss to follow-up, and unknown or other. A multivariable random-effects model was developed to identify factors associated with failure to receive a prescribed OACD.ResultsThe cohort included 1024 patients (538 men [53%]; mean [SD] age, 66.2 [13.9] years; 463 non-Hispanic White patients [45%], 140 non-Hispanic Black patients [14%], and 300 Hispanic patients [29%]), representing 1197 new OACD prescriptions. Of the 1197 prescriptions, 158 (13%) were categorized as having not been received by the patient. The most common reason for the failure to receive a prescribed OACD was due to patient and clinician decision-making (73 of 158 [46%]), and 20 cases (13%) in which prescriptions were not received were associated with financial access issues. In multivariable analysis, patients with a nonmetastatic solid malignant neoplasm were significantly less likely to not receive their OACDs than those with a hematologic malignant neoplasm (odds ratio, 0.57 [95% CI, 0.33-1.00]; P = .048).Conclusions and RelevanceThis cohort study of patients prescribed a new OACD found that 13% of prescriptions were not received. The failure to receive a prescribed OACD was most frequently due to a change in clinical decision-making or patient choice. Ultimately, the reasons for the failure to receive a prescribed OACD were multifactorial and may have been appropriate in some cases.
Hierarchically Assembled Counter Electrode for Fiber Solar Cell Showing Record Power Conversion Efficiency
Authors: Kang Xinyue , Zhu Zhengfeng , Zhao Tiancheng , Zhai Weijie , Xu Jianchen , Lin Zhengmeng , Zeng Kaiwen , Wang Bingjie , Sun Xuemei , Chen Peining , Peng Huisheng 
Published: October 2022

AbstractFiber solar cells have attracted significant interest as a promising wearable power supply solution for their merits of high flexibility, lightweight, and good compatibility with textile configuration and weaving process. However, because of the limited ion diffusion and charge transfer in the fiber counter electrode, the poor photovoltaic performances have long been one obstacle to hinder their real applications. Herein, in mimicking the efficient mass transport and exchange through the vascular tissue of plants like pine needle, a hierarchically assembled carbon nanotube (HCNT) fiber counter electrode is fabricated by a scalable process. The designed hierarchically aligned channels with large sizes of micrometers and small sizes of tens of nanometers in the HCNT fiber offers high‐flux pathways for rapid ion diffusion and abundant active area for charge transport, thus endowing the fiber dye‐sensitized solar cell with a record power conversion efficiency of 11.94%. By weaving such fiber solar cells in a scalable way, a flexible and breathable large photovoltaic textile (17 cm × 22 cm) is made to present a power output of 22.7 mW. These fiber solar cells are further integrated with fiber lithium‐ion batteries to efficiently power wearable electronics.