bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene selection and clustering for time-course
and dose–response microarray experiments using order-restricted inference
Authors: Peddada Shyamal D. , Lobenhofer Edward K. , Li Leping , Afshari Cynthia A. , Weinberg Clarice R. , Umbach David M. 
Published: April 2003

Abstract
We propose an algorithm for selecting and clustering genes according to their time-course or dose–response profiles using gene expression data. The proposed algorithm is based on the order-restricted inference methodology developed in statistics. We describe the methodology for time-course experiments although it is applicable to any ordered set of treatments. Candidate temporal profiles are defined in terms of inequalities among mean expression levels at the time points. The proposed algorithm selects genes when they meet a bootstrap-based criterion for statistical significance and assigns each selected gene to the best fitting candidate profile. We illustrate the methodology using data from a cDNA microarray experiment in which a breast cancer cell line was stimulated with estrogen for different time intervals. In this example, our method was able to identify several biologically interesting genes that previous analyses failed to reveal.
Contact: peddada@embryo.niehs.nih.gov
* To whom correspondence should be addressed.
† Present address: Amgen Inc. Thousand Oaks, CA 91320, USA.
GeneMerge—post-genomic analysis, data
mining, and hypothesis testing
Authors: Castillo-Davis Cristian I. , Hartl Daniel L. 
Published: April 2003

Abstract
Summary: GeneMerge is a web-based and standalone program written in PERL that returns a range of functional and genomic data for a given set of study genes and provides statistical rank scores for over-representation of particular functions or categories in the data set. Functional or categorical data of all kinds can be analyzed with GeneMerge, facilitating regulatory and metabolic pathway analysis, tests of population genetic hypotheses, cross-experiment comparisons, and tests of chromosomal clustering, among others. GeneMerge can perform analyses on a wide variety of genomic data quickly and easily and facilitates both data mining and hypothesis testing.
Availability: GeneMerge is available free of charge for academic use over the web and for download from: http://www.oeb.harvard.edu/hartl/lab/publications/GeneMerge.html.
Contact: ccastillo-davis@oeb.harvard.edu
Supplementary information: http://www.oeb.harvard.edu/hartl/lab/publications/GeneMerge.html
* To whom correspondence should be addressed.
A SYNERGISTIC MODEL FOR REPRESENTING AND INTERPRETING HUMAN ACTIVITIES AND EVENTS FROM VIDEO
Authors: BOURBAKIS NIKOLAOS , GATTIKER JIM R. , BEBIS GEORGE 
Published: April 2003

This paper describes a new and innovative and approach for representing, recognizing and interpreting human activity from video, contributing to an automated system capable of recognition of complex human behaviors. This technology is directly applicable for monitoring public safety and law enforcement, and capturing of activities is crucial for supporting virtual collaborations between citizens, and between citizens and government. Digital video stores of terabytes are now common, and will continue to increase until they dominate stored data. The government of the future will have to manage, organize, recall, and interpret information from this resource, This paper addresses one important facet of this. The approach presented here is a model based on the hierarchical synergy of three other models: the Local/Global (L-G) graph, the Stochastic Petri Net (SPN) graph and a neural network (NN) model. The application focus is the description of activity of actors in a video (or multi-sensor) scene, from the snapshot state description through higher levels of organization into events. The concept of importance is the distinction and interaction between structural knowledge, or knowledge about physical state, and functional knowledge, knowledge about change and events. The L-G graph provides a powerful description of the structural image features presented in an event, and the SPN model offers a description of the functional behavior. The NN (or other adaptive) model provides the capability of leaning behavioral patterns for classification of posture and activity, and forecasting possible events in a free environment.
Magnetically Induced Large Mesoporous Single‐Domain Monoliths Using a Mineral Liquid Crystal as a Template
Authors: Camerel F. , Gabriel J.‐C.P. , Batail P. 
Published: April 2003

AbstractIn this paper, we report on how the properties of the suspensions of a lyotropic nematic mineral liquid crystal (MLC) based on V2O5 ribbons are exploited to synthesize single‐domain mesostructured inorganic–inorganic composites, aligned at the centimeter length scale by application of a relatively small magnetic field (0.85 T). In addition, the removal of the mineral template from the inorganic matrix leaves aligned empty channels, fingerprints of the V2O5 ribbons. Large colorless and birefringent mesoporous material is obtained where the orientational order of the channel director has retain the magnetic‐field alignment of its mineral template up to the centimeter length scale within the porous macroscopic silica matrix. A representative material exhibits slit‐like pores with cross‐sectional dimensions of 2 × 20 nm over 600 nm, and has a specific surface area of 207 m2 g–1.
Social and familial context of prenatal genetic testing decisions: Are there racial/ethnic differences?
Authors: Learman Lee A. , Kuppermann Miriam , Gates Elena , Nease Robert F. , Gildengorin Virginia , Washington A. Eugene 
Published: April 2003

AbstractThe purpose of this cross‐sectional study of 999 socioeconomically and racially/ethnically diverse pregnant women was to explore prenatal genetic testing attitudes and beliefs and the role of external influences. Surveys in English, Spanish, and Chinese included questions regarding the value of testing, pregnancy, and motherhood; the acceptability of Down syndrome in the subject's community; and the role of social and cultural influences in prenatal testing decisions. We analyzed racial/ethnic differences in all attitudinal and external influence variables, controlling for age, relationship status, and socioeconomic status. We found statistically significant racial/ethnic group differences in familiarity with an individual with Down syndrome and in 10 of 12 attitude, belief, and external influence variables, even after controlling for other sociodemographic characteristics. We also observed substantial variation within racial/ethnic groups for each of these measures. Despite the statistically significant group differences observed, R2 values for all multivariate models were modest and response distributions overlapped substantially. Social and familial contexts for prenatal testing decisions differ among racial/ethnic groups even after accounting for age, marital status, and other socioeconomic factors. However, substantial variation within groups and overlap between groups suggest that racial/ethnic differences play a small role in the social and familial context of prenatal genetic testing decisions. © 2002 Wiley‐Liss, Inc.
Effect of family history on disclosure patterns of cystic fibrosis carrier status
Authors: Ormond Kelly E. , Mills Patti L. , Lester Lucille A. , Ross Lainie F. 
Published: April 2003

AbstractAs general population screening becomes more common, an increasing number of cystic fibrosis (CF) carriers will be identified who do not have a family history of CF. Whether these carriers inform their relatives of their carrier status and whether their relatives are motivated to pursue carrier screening is unknown. We surveyed CF carriers with and without a family history of CF to understand whether and how information dissemination patterns differ, why information is or is not shared, and to what extent relatives are known to undergo testing. CF carriers were identified from a general population carrier screening clinic (group B = 18) or were parents of affected children followed at a CF clinic (group A = 30). CF carriers with a family history told essentially 100% of their living parents, siblings, and half‐siblings, while those without a family history told 84% of living parents and 56% of siblings (P < 0.05). Despite the high rate of information dissemination in both groups, few siblings were known to have undergone carrier screening (14/74). Significantly fewer second‐ and third‐degree relatives were informed about carrier status or were known to have undergone carrier screening. Group A was more likely to inform second‐ and third‐degree relatives about carrier status. Our study documents that the frequency and reasons for disclosing CF carrier status differ between individuals with and without a family history of CF despite the fact that the reproductive risks for their relatives are the same. © 2003 Wiley‐Liss, Inc.
Jüngste Entwicklungen bei der gekreuzten Olefinmetathese
Authors: Connon Stephen J. , Blechert Siegfried 
Published: April 2003

AbstractUnter den vielen übergangsmetallvermittelten C‐C‐verknüpfenden Reaktionen ist die Olefinmetathese in den letzten Jahren durch die große Bandbreite an möglichen Umsetzungen mit käuflichen und leicht handhabbaren Katalysatoren hervorgetreten und gilt heutzutage als eine der mächtigsten Synthesemethoden in der Organischen Chemie. Die intermolekulare Variante dieser Reaktion, die Kreuzmetathese, führte trotz ihres hohen synthetischen Nutzens bis vor kurzem eher ein Schattendasein. Durch die Entwicklung neuer, besserer Katalysatoren konnte die Selektivität, die Toleranz gegen funktionelle Gruppen und die Effizienz der Katalyse jedoch auf ein Niveau gesteigert werden, das noch bis vor wenigen Jahren als unvorstellbar galt. Dank dieser Fortschritte und dem verbesserten Verständnis des Reaktionsmechanismus und der Katalysator‐Substrat‐Wechselwirkungen werden Kreuzmetathesen heute in zunehmendem Maße in mehrstufigen Reaktionssequenzen und Naturstoffsynthesen verwendet. Die kürzlich vorgestellte Einbeziehung von Alkinen und sterisch gehinderten bicyclischen Olefinen als Substrate für bimolekulare Kupplungen, die Entwicklung von enantioselektiven und in Wasser ausführbaren Kreuzmetathesen und die erfolgreiche Kombination der Olefinmetathese und der Festphasensynthese in der Organischen Chemie haben die Anwendungsbreite der Kreuzmetathese noch zusätzlich vergrößert.
Recent Developments in Olefin Cross‐Metathesis
Authors: Connon Stephen J. , Blechert Siegfried 
Published: April 2003

AbstractAmong the many types of transition‐metal‐catalyzed CC bond‐forming reactions, olefin metathesis has come to the fore in recent years owing to the wide range of transformations that are possible with commercially available and easily handled catalysts. Consequently, olefin metathesis is now widely considered as one of the most powerful synthetic tools in organic chemistry. Until recently the intermolecular variant of this reaction, cross‐metathesis, had been neglected despite its potential. With the evolution of new catalysts, the selectivity, efficiency, and functional‐group compatibility of this reaction have improved to a level that was unimaginable just a few years ago. These advances, together with a better understanding of the mechanism and catalyst–substrate interactions, have brought us to a stage where more and more researchers are employing cross‐metathesis reactions in multistep procedures and in the synthesis of natural products. The recent inclusion of alkynes and hindered bicyclic olefins as viable substrates for bimolecular metathesis coupling, the discovery of enantioselective cross‐metathesis and cross‐metathesis in water, and the successful marriage of metathesis and solid‐phase organic synthesis has further widened the scope of this versatile reaction.
The loss of genetic diversity in Dabry's sturgeon (Acipenser dabryanus, Dumeril) as revealed by DNA fingerprinting
Authors: Wan Qiu‐Hong , Fang Sheng‐Guo , Li Ya‐Nan 
Published: April 2003

Abstract
Dabry's sturgeon, a large, long‐lived migratory fish is endemic to the Yangtze River. Over‐fishing and habitat destruction have caused large‐scale declines in natural stocks in the last two decades.
Examining patterns of genetic diversity has become an integral component of many management plans for endangered species. DNA fingerprinting was applied to detect genetic diversity in Dabry's sturgeon collected in 1958–1959, 1980–1981 and 1998–1999.
Studies on direct genetic parameters (genetic variability, hypervariable loci and heterozygosity) and indirect parameters (band‐sharing coefficient and allelic frequency) showed that the continuous decline in wild populations has caused the loss of genetic diversity in present‐day sturgeon.
The present‐day populations have the lowest genetic variability; thus, effective management is needed to preserve genetic diversity.
A conservation strategy is urgently required, comprising artificial rearing facilities coupled with breeding management plans.
Copyright © 2003 John Wiley & Sons, Ltd.
Ontologies: Formalising biological knowledge for bioinformatics
Authors: Bard Jonathan 
Published: April 2003

AbstractAn ontology is a domain of knowledge structured through formal rules so that it can be interpreted and used by computers. Ontologies are becoming increasingly important in bioinformatics because they can be linked to the information in databases and their knowledge then used to query the databases. Typical examples in current use are the Gene Ontology, which incorporates much of our knowledge about gene products, and ontologies of developmental anatomy, which, for example, facilitate tissue‐based queries to gene expression databases both textually and spatially. This article considers the production, formulation and types of bio‐ontologies together with the reasons why they are so useful. © BioEssays 25:501–506, 2003. © 2003 Wiley Periodicals, Inc.
Teratogenic alleles and neurodevelopmental disorders
Authors: Johnson William G. 
Published: April 2003

AbstractThe genetic interaction between mother and fetus during pregnancy is discussed, focusing on teratogenic alleles that act in the mother to alter fetal development and contribute to a neurodevelopmental disorder. For these alleles, the mother is the genetic patient. Teratogenic alleles interact with modifying and specificity alleles that act in the fetus and with environmental factors. Based on examples of the model, two candidate mechanisms emerge as contributors to neurodevelopmental disorders, folate‐homocysteine pathways and immune/inflammatory mechanisms. Both, acting in mothers, affect fetal development and contain many polymorphic genes. These two systems interact with each other. Common functional polymorphisms of mild effect in these two systems of interacting genes are good candidates for teratogenic alleles. The presence of teratogenic alleles complicates gene identification for neurodevelopmental disorders. However, using the special methods required to identify teratogenic alleles is important because this could lead to new approaches to prevention and improved therapy of these disorders. BioEssays 25:464–477, 2003. © 2003 Wiley Periodicals, Inc.
Pathfinding and growth termination of primary trigeminal sensory afferents in the embryonic rat hindbrain
Authors: Miyahara Mikiko , Shirasaki Ryuichi , Tashiro Yasura , Muguruma Keiko , Heizmann Claus W. , Murakami Fujio 
Published: April 2003

AbstractAxons of the trigeminal ganglion convey sensory information from mechanoreceptors, thermoreceptors, and nociceptors in the face and nasal mucosa, then terminate on several groups of neurons including the principal sensory nucleus and the nuclei of the spinal trigeminal tract. To understand guidance mechanisms during the development of trigeminal sensory axons (TA) in the embryonic brain, we first investigated the growth pattern of TA in relation to organization in the hindbrain using flat whole‐mount preparation from rat. We found that the primary TA from the trigeminal ganglion entered the brainstem and grew longitudinally within the hindbrain. Whereas descending axons ran just medial to the primary vestibular axons to innervate the spinal nucleus, ascending axons stayed near the entry point. In flat whole‐mount culture, the TA extended both ascending and descending branches as they do in vivo. Rostral hindbrain was found to be a less permissive substrate for the TA compared to caudal hindbrain. In addition, the nonpermissive property of the ventral hindbrain substrate restricted the invasion of TA along the entire length of the hindbrain. Thus, cooperation of absolute and relative permissiveness of the substrate plays important roles in the guidance of TA to their targets. J. Comp. Neurol. 460:503–513, 2003. © 2003 Wiley‐Liss, Inc.
CD2 mediates activation of the IFN‐γ intronic STAT binding region in mucosal T cells
Authors: Gonsky Rivkah , Deem Richard L. , Young Howard A. , Targan Stephan R. 
Published: April 2003

AbstractThe pathways leading to activation of mucosal lamina propria (LP) T cells differ from those of peripheral T cells. LP T cells exhibit enhanced IFN‐γ secretion when activated through the CD2 pathway. This study demonstrates CD2 signaling is followed by activation of STAT proteins in both peripheral blood mononuclear cells (PBMC) and lamina propria mononuclear cells (LPMC), although, distinct differences exist in regulation of IFN‐γ promoter gene expression. Both PBMC and LPMC exhibit enhanced secretion and transactivation of the –2.7 kb IFN‐γ promoter region following CD2 signaling, but the IFN‐γ STAT‐binding region (within the first intron) serves as an orientation‐independent enhancer of promoter activity only in LPMC. Mutation of the STAT site impairs enhancer activity. In LPMC, but not PBMC, CD2 mediates binding of STAT1 and STAT4 to the IFN‐γ intronic element. Unstimulated LMPC exhibit low levels of phosphotyrosine‐STAT4 and STAT1 and phosphoserine‐STAT1, which increase substantially following CD2 activation. In PBMC, CD2‐mediated phosphorylation is primarily restricted to enhanced levels of phosphotyrosine‐STAT1. Thus, these results indicate that both common as well as unique molecular mechanisms are involved in CD2 signaling and activation of the STAT pathway in LP T cells which are critical for regulation of IFN‐γ expression in the gut.
TNF‐α impairs peripheral tolerance towards β‐cells, and local costimulation by B7.1 enhances the effector function of diabetogenic T cells
Authors: Skak Kresten , Guerder Sylvie , Picarella Dominic E. , Brenden Nina , Flavell Richard A. , Michelsen Birgitte K. 
Published: April 2003

AbstractMaintenance of peripheral tolerance and inactivation of autoreactive T cells is based on a delicate balance between pro‐inflammatory and protective cytokines that is poorly understood. We havehere addressed how the local expression of the inflammatory cytokine TNF‐α can impair peripheral tolerance and lead to autoreactivity. After transplantation of pancreata that are immunogenic due to β‐cell expression of B7.1 and TNF‐α, into thymectomized and euthymic syngeneic mice, we found that only euthymic mice rejected the grafts. This result suggests that under normal circumstances autoreactive T cells are functionally inactivated, and initiation of an autoreactive response requires de‐novo generation of T cells. By contrast, thymectomized mice expressing TNF‐α on the endogenous islets rejected the grafts, showing that expression of TNF‐α prevents functional silencing of the autoreactive T cells. Thus, this study provides a mechanism by which TNF‐α and possibly chronic inflammatory responses may promote autoimmune diseases. Furthermore, we have investigated whether B7.1 can enhance T cell responses of already activated T cells leading to islet rejection. By transplantation of wild‐type and B7.1‐expressing islets into overtly diabetic mice we found that only the wild‐type islets could restore normoglycemia, suggesting that costimulation by B7.1 is required in the expansion or effector phase of the response.
Decreasing the threshold for thymocyte activation biases CD4+ T cells toward a regulatory (CD4+CD25+) lineage
Authors: Stephens Geoffrey L. , Ignatowicz Leszek 
Published: April 2003

AbstractThymus‐derived CD4+CD25+ regulatory T (Tr) cells play a critical role in suppressing aberrant responses to self in vivo. The factors that influence a CD4+ T cell's decision to commit to an immunoregulatory Tr cell lineage are currently unknown. In the present study, we found that in mice, abundantly expressing a few or one peptide(s) bound to MHC class II molecules, a large portion of conventional CD4+ T cells could be biased towards the commitment to a Tr lineage by reducing the threshold required for thymocyte activation. This occurred in the presence of either an antisense glucocorticoid receptor transgene or a pharmacological inhibitor of glucocorticoid synthesis. These results demonstrate a novel in vivo pathway for the generation of Tr cells, and raise the possibility that therapeutic enhancement of the Tr cell repertoire through pharmacological manipulation of TCR signaling thresholds may provide a feasible means of ameliorating autoimmunity.
Exchange Interactions and Covalency in Dinuclear Complexes of Iron(III) and Gallium(III) Containing the Redox‐Noninnocent Ligand 1,2‐Bis(3,5‐di‐tert‐butyl‐2‐hydroxyphenyl)oxamide
Authors: Beckmann Udo , Bill Eckhard , Weyhermüller Thomas , Wieghardt Karl 
Published: April 2003

AbstractThe dinucleating ligand 1,2‐bis(3,5‐di‐tert‐butyl‐2‐hydroxyphenyl)oxamide [H4(bbpo)] has been synthesized. From its reaction with GaCl3 or FeCl3 in CH3OH/NaOH the salts [N(nBu)4]2[MIII2(bbpo)Cl4] [M = Ga (1), Fe (2)] have been isolated as crystalline solids upon addition of [N(nBu)4]Cl. Complexes 1 and 2 have been characterized by single‐crystal X‐ray crystallography. Cyclic voltammetry established that both species undergo two successive, reversible one‐electron oxidations in CH2Cl2 {0.10 M [N(nBu)4]PF6} which are shown to be ligand‐centered: one and then two N,O‐coordinated o‐iminobenzosemiquinonate π‐radicals form which couple antiferromagnetically with the high‐spin ferric ions in 2. Thus, the monoanion of 2 has an St = 1/2 ground state. The complexes have been characterized by Mössbauer, UV/Vis, and EPR spectroscopy. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003)
Mechanisms of the Axial Ligand Substitution Reactions of Dinuclear, Head‐to‐Head α‐Pyrrolidonato‐ and Pivalamidato‐Bridged cis‐Diammineplatinum(III) Complexes with Halide Ions
Authors: Shimazaki Kazuhiro , Sekiya Hideo , Inoue Haruhiko , Saeki Nami , Ishihara Koji , Matsumoto Kazuko 
Published: April 2003

AbstractThe acid dissociation constant of the axial aqua ligand in the Head‐to‐Head (HH) dinuclear pivalamidato‐bridged cis‐diammineplatinum(III) complex ([(H2O)Pt(NH3)2(μ‐C5H10NO)2Pt(NH3)2(H2O)]4+) and the formation constants of the successive substitution reactions on the axial sites of the HH α‐pyrrolidonato‐bridged cis‐diammineplatinum(III) dinuclear complex and the HH pivalamidato‐bridged cis‐diammineplatinum(III) dinuclear complex with halide ions X− (X− = Cl− and Br−) to give monohalo and dihalo complexes were determined spectrophotometrically at 25 °C and I = 2.0 M. A kinetic study was also performed for the monohalo and dihalo complex formations. The effect of the bridging ligand upon the axial site reactivity was compared and discussed. The ligand substitution behavior of the monohalo complex was affected by the axial ligand on the opposite Pt site and also by the bridging ligand. For both the α‐pyrrolidonato‐ and the pivalamidato‐bridged complexes, the formation of dichloro complexes proceeds only through the simple substitution path (k2 path), whereas the formation of dibromo complexes proceeds through the two parallel reaction paths: the k2 and k3 paths for the former and the k2 and k2# paths for the latter. The difference of the reaction paths is reasonably explained by the different trans effect of the halide ion on the opposite axial site for the former complex, but for the latter complex, the reaction paths are not easy to explain. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003)