bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pathway studio—the analysis and navigation of molecular networks
Authors: Nikitin Alexander , Egorov Sergei , Daraselia Nikolai , Mazo Ilya 
Published: November 2003

Abstract
Summary: PathwayAssist is a software application developed for navigation and analysis of biological pathways, gene regulation networks and protein interaction maps. It comes with the built-in natural language processing module MedScan and the comprehensive database describing more than 100 000 events of regulation, interaction and modification between proteins, cell processes and small molecules.
Availability: PathwayAssist is available for commercial licensing from Ariadne Genomics, Inc. The light version with limited functionality will be available for free for academic users at www.ariadnegenomics.com/downloads/
GARBAN: genomic analysis and rapid biological annotation of cDNA microarray and proteomic data
Authors: Martínez-Cruz Luis A. , Rubio Angel , Martínez-Chantar María L. , Labarga Alberto , Barrio Isabel , Podhorski Adam , Segura Victor , Sevilla Campo José L. , Avila Matías A. , Mato Jose M. 
Published: November 2003

Abstract
Summary: Genomic Analysis and Rapid Biological ANnotation (GARBAN) is a new tool that provides an integrated framework to analyze simultaneously and compare multiple data sets derived from microarray or proteomic experiments. It carries out automated classifications of genes or proteins according to the criteria of the Gene Ontology Consortium at a level of depth defined by the user. Additionally, it performs clustering analysis of all sets based on functional categories or on differential expression levels. GARBAN also provides graphical representations of the biological pathways in which all the genes/proteins participate.
Availability: http://garban.tecnun.es
The History of Sexual Anatomy and Self‐Referential Philosophy of Science
Authors: Soble Alan G. 
Published: November 2003

Abstract:This essay is a case study of the self‐destruction that occurs in the work of a social‐constructionist historian of science who embraces a radical philosophy of science. It focuses on Thomas Laqueur's Making Sex: Body and Gender from the Greeks to Freud in arguing that a history of science committed to the social construction of science and to the central theses of Kuhnian, Duhemian, and Quinean philosophy of science is incoherent through self‐reference. Laqueur's text is examined in detail in order to make the main point; a similar phenomenon in the work of the feminist historian of science Evelyn Fox Keller is then briefly discussed.
Analytic and Continental Philosophy: Explaining the Differences
Authors: Levy Neil 
Published: November 2003

Abstract:A number of writers have tackled the task of characterizing the differences between analytic and Continental philosophy. I suggest that these attempts have indeed captured the most important divergences between the two styles but have left the explanation of the differences mysterious. I argue that analytic philosophy is usefully seen as philosophy conducted within a paradigm, in Kuhn's sense of the word, whereas Continental philosophy assumes much less in the way of shared presuppositions, problems, methods and approaches. This important opposition accounts for all those features that have rightly been held to constitute the difference between the two traditions. I finish with some reflections on the relative superiority of each tradition and by highlighting the characteristic deficiencies of each.
Shades of Orientalism: Paradoxes and Problems in Indian Historiography
Authors: Heehs Peter 
Published: November 2003

AbstractIn Orientalism, Edward Said attempts to show that all European discourse about the Orient is the same, and all European scholars of the Orient complicit in the aims of European imperialism. There may be “manifest” differences in discourse, but the underlying “latent” orientalism is “more or less constant.” This does not do justice to the marked differences in approach, attitude, presentation, and conclusions found in the works of various orientalists. I distinguish six different styles of colonial and postcolonial discourse about India (heuristic categories, not essential types), and note the existence of numerous precolonial discourses. I then examine the multiple ways exponents of these styles interact with one another by focusing on the early‐twentieth‐century nationalist orientalist, Sri Aurobindo. Aurobindo's thought took form in a colonial framework and has been used in various ways by postcolonial writers. An anti‐British nationalist, he was by no means complicit in British imperialism. Neither can it be said, as some Saidians do, that the nationalist style of orientalism was just an imitative indigenous reversal of European discourse, using terms like “Hinduism” that had been invented by Europeans. Five problems that Aurobindo dealt with are still of interest to historians: the significance of the Vedas, the date of the vedic texts, the Aryan invasion theory, the Aryan‐Dravidian distinction, and the idea that spirituality is the essence of India. His views on these topics have been criticized by Leftist and Saidian orientalists, and appropriated by reactionary “Hindutva” writers. Such critics concentrate on that portion of Aurobindo's work which stands in opposition to or supports their own views. A more balanced approach to the nationalist orientalism of Aurobindo and others would take account of their religious and political assumptions, but view their project as an attempt to create an alternative language of discourse. Although in need of criticism in the light of modern scholarship, their work offers a way to recognize cultural particularity while keeping the channels of intercultural dialogue open.
Local Area Management and Planning (LAMP) in India
Authors: Datta S. 
Published: November 2003

To assist decentralised planning, the Department of Science and Technology, Government of India has taken the initiative to develop a computer‐based spatial information system for planning and management of the natural resources at the district and sub‐district level. At present ten district level database centres called Natural Resources Data Management System (NRDMS) have been functioning in different geo‐environments in India.The present paper discusses the experience of the Centre for Applied Systems Analysis in Development (CASAD). CASAD is involved in managing the NRDMS database centre at Bankura district and was associated with the development of DSS models in Kheda district. Finally, a few case studies on the use of Decision Support Systems (DSS) for decentralised decision making at the district level are discussed.
Introduction to Jesse Burkhead Symposium
Authors: Jump Bernard 
Published: November 2003

Government budgeting is one of the major processes by which the use of public resources is planned and controlled. To the extent that this is done well, governmental programs are brought increasingly to the service of its citizens, enhancing their material and cultural status.The study of government budgeting is a study in applied economics—in the allocation of scarce resources. This study must look at operations and begin with organization and procedure, the routines which have been established for decision–making in government. It should extend to an examination of the influences, governmental and nongovernmental, that come to bear on the decision‐making process.Ours is both an organized society and a society of organizations. The significance of organization is nowhere more evident than in the public sector. Here organizational arrangements bring together the learning of all social scientists. The patterns for decision‐making do not provide separate compartments for economic knowledge, for political knowledge, for social knowledge. These are merged in the organizational arrangements which have been established for the conduct of governmental affairs.1
Identification and Characterization of Phytoplasmal Genes, Employing a Novel Method of Isolating Phytoplasmal Genomic DNA
Authors: Melamed Sharon , Tanne Edna , Ben-Haim Raz , Edelbaum Orit , Yogev David , Sela Ilan 
Published: November 2003

ABSTRACT

Phytoplasmas are unculturable, insect-transmissible plant pathogens belonging to the class
Mollicutes
. To be transmitted, the phytoplasmas replicate in the insect body and are delivered to the insect's salivary glands, from where they are injected into the recipient plant. Because phytoplasmas cannot be cultured, any attempt to recover phytoplasmal DNA from infected plants or insects has resulted in preparations with a large background of host DNA. Thus, studies of the phytoplasmal genome have been greatly hampered, and aside from the rRNA genes, only a few genes have hitherto been isolated and characterized. We developed a unique method to obtain host-free phytoplasmal genomic DNA from the insect vector's saliva, and we demonstrated the feasibility of this method by isolating and characterizing 78 new putative phytoplasmal open reading frames and their deduced proteins. Based on the newly accumulated information on phytoplasmal genes, preliminary characteristics of the phytoplasmal genome are discussed.
Cosmid-Based System for Transient Expression and Absolute Off-to-On Transcriptional Control ofEscherichia coliGenes
Authors: Cronan John E. 
Published: November 2003

ABSTRACTCosmids are plasmids that contain the phage λ sequences (cos) required for packaging of the phage DNA into the virion. Induction of a λ prophage in anEscherichia colistrain carrying a cosmid results in lysates containing phage particles that are filled with cosmid DNA. However, the lysates also contain a large excess of infectious phage particles which complicate use of the packaged cosmids. I report that cosmids packaged by induction of a strain carrying a prophage with an alteredcosregion results in lysates containing very high levels (>1010/ml) of particles that contain cosmid DNA together with very few infectious phage particles. These lysates can be used to transduce cosmid DNA into all of the cells of a growing culture with minimal physiological disturbance. When the cosmid carries a conditionally active origin of replication, transductional introduction of the cosmid under nonreplicative conditions provides a system of transient expression. Transient expression has been used to make arecAstrain temporarily recombination proficient and to temporarily introduce a site-specific recombinase. Transductional introduction of a cosmid also allows absolute off-to-on transcriptional control of nonessential genes. Two examples are given showing that when a strain carrying a null mutation in the gene of interest is transduced with a packaged cosmid carrying a functional copy of that gene, the expression of the gene rapidly goes from absolutely off to high-level expression. Additional possible uses of in vivo-packaged cosmids are proposed.
Assembly of TolC, a Structurally Unique and Multifunctional Outer Membrane Protein of
Escherichia coli
K-12
Authors: Werner John , Augustus Anne Marie , Misra Rajeev 
Published: November 2003

ABSTRACT

TolC is a multifunctional outer membrane protein of
Escherichia coli
that folds into a novel α-β-barrel conformation absent in the other model outer membrane proteins used in assembly studies. The data presented in this work show that the unique folded structure of TolC reflects a unique assembly pathway. During its assembly, the newly translocated nascent TolC monomers are released in the periplasm. Maturation of these nascent monomers, and possibly their oligomerization, in the periplasm precedes their insertion in the outer membrane. The completion of the assembly process is signaled by the development of a characteristic proteinase K-resistant fragment generated by cleavage at a single, periplasmically exposed, protease-sensitive site of the membrane-anchored trimer. None of the assembly steps of TolC is affected by known folding factors, such as SurA, Skp, and lipopolysaccharide, which have profound effects on the assembly of other model trimeric outer membrane proteins. Two assembly-defective TolC mutants were isolated and characterized. One of the mutants (TolC
I106N
) was defective in the folding of nascent monomers, while the other (TolC
S350F
) was impaired in steps involving trimerization and membrane insertion of folded monomers.
MtaR, a Regulator of Methionine Transport, Is Critical for Survival of Group B Streptococcus In Vivo
Authors: Shelver Daniel , Rajagopal Lakshmi , Harris Theresa O. , Rubens Craig E. 
Published: November 2003

ABSTRACT

The group B streptococcus (GBS) is an important human pathogen that infects newborns as well as adults. GBS also provides a model system for studying adaptation to different host environments due to its ability to survive in a variety of sites within the host. In this study, we have characterized a transcription factor, MtaR, that is essential for the ability of GBS to survive in vivo. An isogenic strain bearing a kanamycin insertion in
mtaR
was attenuated for survival in a neonatal-rat model of sepsis. The
mtaR
mutant grew poorly in human plasma, suggesting that its utilization of plasma-derived nutrients was inefficient. When an excess of exogenous methionine (200 μg/ml) was provided to the
mtaR
mutant, its growth rate in plasma was restored to that of the wild-type strain. The
mtaR
mutant grew poorly in chemically defined medium (CDM) prepared with methionine at a concentration similar to that of plasma (4 μg/ml) but was able to grow normally in CDM prepared with a high concentration of methionine (400 μg/ml). Both the wild-type strain and the
mtaR
mutant were incapable of growth in CDM lacking methionine, indicating that GBS cannot synthesize methionine de novo. When the abilities of the strains to incorporate radiolabeled methionine were compared, the
mtaR
mutant incorporated fivefold less methionine than the wild-type strain during a 10-min period. Collectively, the results from this study suggest that the ability to regulate expression of a methionine transport system is critical for GBS survival in vivo.
MgrA, an Orthologue of Mga, Acts as a Transcriptional Repressor of the Genes within therlrAPathogenicity Islet inStreptococcus pneumoniae
Authors: Hemsley Carolyn , Joyce Elizabeth , Hava David L. , Kawale Amita , Camilli Andrew 
Published: November 2003

ABSTRACTStreptococcus pneumoniaenormally resides in the human nasopharynx in a nondisease state. In response to unknown triggers this organism can descend to the lower respiratory tract and/or invade the bloodstream. Regulation and activation of virulence genes play essential roles in this process of disease development. Characterization ofS. pneumoniaeregulatory networks has been a recent area of interest, but despite inroads little is known about regulation of virulence genes in this pathogen. A putative transcriptional regulator inS. pneumoniae,mgrA, which exhibits homology to the virulence gene activatormgaof group A streptococcus, was previously identified as a regulator that is required for development of pneumonia in a murine model. In this study we confirmed thatmgrAplays a role in both nasopharyngeal carriage and pneumonia. Transcriptional profiling by microarray technology was used to show thatmgrAacts as a repressor of the previously characterizedrlrApathogenicity islet. This is manifested phenotypically by a decrease in adherence to epithelial cells in tissue culture since therlrApathogenicity islet contains genes mediating adherence.
Flavobacterium johnsoniae
GldH Is a Lipoprotein That Is Required for Gliding Motility and Chitin Utilization
Authors: McBride Mark J. , Braun Timothy F. , Brust Jessica L. 
Published: November 2003

ABSTRACT

Cells of
Flavobacterium johnsoniae
move rapidly over surfaces by gliding motility. The mechanism of this form of motility is not known. Six genes (
gldA
,
gldB
,
gldD
,
gldF
,
gldG
, and
ftsX
) that are required for gliding have been described. Tn
4351
mutagenesis was used to identify another gene,
gldH
, which is required for cell movement. GldH mutants formed nonspreading colonies, and individual cells lacked the cell movements and ability to propel latex spheres along their surfaces that are characteristic of wild-type cells.
gldH
mutants also failed to digest chitin and were resistant to bacteriophages that infect wild-type cells. Introduction of pMM293, which carries wild-type
gldH
, restored to the
gldH
mutants colony spreading, cell motility, the ability to move latex spheres, phage sensitivity, and the ability to digest chitin.
gldH
encodes a predicted 141-amino-acid protein that localized to the membrane fraction. Labeling studies with [
3
H]palmitate demonstrated that GldH is a lipoprotein. GldB and GldD, which were previously described, also appear to be lipoproteins. GldH does not exhibit significant amino acid similarity to proteins of known function in the databases. Putative homologs of
gldH
of unknown function are found in motile (
Cytophaga hutchinsonii
) and apparently nonmotile (
Bacteroides thetaiotaomicron
,
Bacteroides fragilis
,
Tannerella forsythensis
,
Porphyromonas gingivalis
, and
Prevotella intermedia
) members of the
Cytophaga
-
Flavobacterium
-
Bacteroides
group.
Flagellin Glycosylation Island in
Pseudomonas syringae
pv. glycinea and Its Role in Host Specificity
Authors: Takeuchi Kasumi , Taguchi Fumiko , Inagaki Yoshishige , Toyoda Kazuhiro , Shiraishi Tomonori , Ichinose Yuki 
Published: November 2003

ABSTRACT

The deduced amino acid sequences of the flagellins of
Pseudomonas syringae
pv. tabaci and
P. syringae
pv. glycinea are identical; however, their abilities to induce a hypersensitive reaction are clearly different. The reason for the difference seems to depend on the posttranslational modification of the flagellins. To investigate the role of this posttranslational modification in the interactions between plants and bacterial pathogens, we isolated genes that are potentially involved in the posttranslational modification of flagellin in
P. syringae
pv. glycinea (glycosylation island); then defective mutants with mutations in these genes were generated. There are three open reading frames in the glycosylation island, designated
orf1
,
orf2
, and
orf3
.
orf1
and
orf2
encode putative glycosyltransferases, and mutants with defects in these open reading frames, Δ
orf1
and Δ
orf2
, secreted nonglycosylated and slightly glycosylated flagellins, respectively. Inoculation tests performed with these mutants and original nonhost tobacco leaves revealed that Δ
orf1
and Δ
orf2
could grow on tobacco leaves and caused symptom-like changes. In contrast, these mutants failed to cause symptoms on original host soybean leaves. These data indicate that putative glycosyltransferases encoded in the flagellin glycosylation island are strongly involved in recognition by plants and could be the specific determinants of compatibility between phytopathogenic bacteria and plant species.
In Vivo Effect of Mutations at the PRPP Binding Site of the
Bacillus subtilis
Purine Repressor
Authors: Rappu Pekka , Pullinen Terhi , Mäntsälä Pekka 
Published: November 2003

ABSTRACT

The
Bacillus subtilis
PurR mediates adenine repression and guanosine induction of
purA
. PRPP inhibits binding of PurR to DNA in vitro. Mutations in the PRPP binding motif of PurR caused strong repression regardless of purine exclusions or additions, establishing the role of PRPP as regulator of PurR.
Structure of Haloacetate-Catabolic IncP-1β Plasmid pUO1 and Genetic Mobility of Its Residing Haloacetate-Catabolic Transposon
Authors: Sota Masahiro , Kawasaki Haruhiko , Tsuda Masataka 
Published: November 2003

ABSTRACT

The self-transmissible plasmid pUO1 from
Delftia acidovorans
strain B carries two haloacetate-catabolic transposons, Tn
Had1
and Tn
Had2
, and the
mer
genes for resistance to mercury. The complete 67,066-bp sequence of pUO1 revealed that the
mer
genes were also carried by two Tn
402
/Tn
5053
-like transposons, Tn
4671
and Tn
4672
, and that the pUO1 backbone regions shared 99% identity to those of the archetype IncP-1β plasmid R751. Comparison of pUO1 with three other IncP-1β plasmids illustrated the importance of transposon insertion in the diversity and evolution of this group of plasmids. Mutational analysis of the four outermost residues in the inverted repeats (IRs) of Tn
Had2
, a Tn
21
-related transposon, revealed a crucial role of the second residue of its IRs in transposition.
"THE QUEEN WHO SERVES THE SLAVES": FROM POLITICS TO METAPOETICS IN THE POETRY OF QĀSIM HADDĀD
Authors: Huri Yair 
Published: November 2003

AbstractThe following article deals with the poetry of the Bahraini poet Qāsim Haddād, one of the most prominent modernist Arab poets of our time. One of Haddād's main characteristics in his habit of recurrently changing his poetic style and poetic themes over the years, and this article seeks to highlight the significant transformations Haddād's poetry underwent during his career. The article argues that one of the most important transformations is the shift Haddād made from leftist committed poetry in the 1970s toward a highly modernist poetics in the 1980s and 90s. Influenced by Adonis, the key figure among Arab modernist poets, Haddād tends to reflect upon meta-poetic themes in his later poetic works—themes such as the exploration of the creative process, the poem as a creator of a new world, the innate gap between language and the poet's personal and poetic experience, etc. Haddād tackles these themes by using an innovative poetic style and a low-key tone, and succeeds in drawing the reader's attention to the complexity and the poignancy of his poetry.
Predictors of efficacy in depression prevention programmes
Authors: Jané-Llopis Eva , Hosman Clemens , Jenkins Rachel , Anderson Peter 
Published: November 2003

BackgroundWorldwide, 340 million people are affected by depression, with high comorbid, social and economic costs.AimsTo identify potential predictors of effect in prevention programmes.MethodA meta-analysis was made of 69 programmes to reduce depression or depressive symptoms.ResultsThe weighted mean effect size of 0.22 was effective for different age groups and different levels of risk, and in reducing risk factors and depressive or psychiatric symptoms. Programmes with larger effect sizes were multi-component, included competence techniques, had more than eight sessions, had sessions 60–90 min long, had a high quality of research design and were delivered by a health care provider in targeted programmes. Older people benefited from social support, whereas behavioural methods were detrimental.ConclusionsAn 11% improvement in depressive symptoms can be achieved through prevention programmes. Single trial evaluations should ensure high quality of the research design and detailed reporting of results and potential predictors.