bluuebunny/crossref_metadata_2025_split huggingface dataset:
Confronting a biome crisis: global disparities of habitat loss and protection
Authors: Hoekstra Jonathan M. , Boucher Timothy M. , Ricketts Taylor H. , Roberts Carter 
Published: December 2004

AbstractHuman impacts on the natural environment have reached such proportions that in addition to an ‘extinction crisis’, we now also face a broader ‘biome crisis’. Here we identify the world's terrestrial biomes and, at a finer spatial scale, ecoregions in which biodiversity and ecological function are at greatest risk because of extensive habitat conversion and limited habitat protection. Habitat conversion exceeds habitat protection by a ratio of 8 : 1 in temperate grasslands and Mediterranean biomes, and 10 : 1 in more than 140 ecoregions. These regions include some of the most biologically distinctive, species rich ecosystems on Earth, as well as the last home of many threatened and endangered species. Confronting the biome crisis requires a concerted and comprehensive response aimed at protecting not only species, but the variety of landscapes, ecological interactions, and evolutionary pressures that sustain biodiversity, generate ecosystem services, and evolve new species in the future.
Generalized Linear Mixed Models for Ordered Responses in Complex Multilevel Structures: Effects Beneath the School or College in Education
Authors: Fielding Antony , Yang Min 
Published: December 2004

SummaryThe complexities of educational processes and structure and the need for disentangling effects beneath the level of the school or college are discussed. Ordinal response multilevel crossed random-effects models for educational grades are introduced. Weighted random effects for teacher contributions are then added. Estimation methodology is reviewed. Specially written macros for quasi-likelihood with second-order terms are described. The application discusses General Certificate of Education at advanced level grades cross-classified by student and teaching group within a number of institutions. The methods handle teacher effects where several teachers contribute to provision and where each teacher deals with several groups. Some methodological lessons are drawn for sparse data and the use of extra-multinomial variation. Developments of the analysis yield conclusions about the sources of variation in educational progress, and particularly the effect of teachers.
Releasing Multiply Imputed, Synthetic Public use Microdata: An Illustration and Empirical Study
Authors: Reiter Jerome P. 
Published: December 2004

SummaryThe paper presents an illustration and empirical study of releasing multiply imputed, fully synthetic public use microdata. Simulations based on data from the US Current Population Survey are used to evaluate the potential validity of inferences based on fully synthetic data for a variety of descriptive and analytic estimands, to assess the degree of protection of confidentiality that is afforded by fully synthetic data and to illustrate the specification of synthetic data imputation models. Benefits and limitations of releasing fully synthetic data sets are discussed.
Multiple‐Choice Tests and Student Understanding: What Is the Connection?
Authors: Simkin Mark G. , Kuechler William L. 
Published: December 2004

ABSTRACTInstructors can use both “multiple‐choice” (MC) and “constructed response” (CR) questions (such as short answer, essay, or problem‐solving questions) to evaluate student understanding of course materials and principles. This article begins by discussing the advantages and concerns of using these alternate test formats and reviews the studies conducted to test the hypothesis (or perhaps better described as the hope) that MC tests, by themselves, perform an adequate job of evaluating student understanding of course materials. Despite research from educational psychology demonstrating the potential for MC tests to measure the same levels of student mastery as CR tests, recent studies in specific educational domains find imperfect relationships between these two performance measures. We suggest that a significant confound in prior experiments has been the treatment of MC questions as homogeneous entities when in fact MC questions may test widely varying levels of student understanding. The primary contribution of the article is a modified research model for CR/MC research based on knowledge‐level analyses of MC test banks and CR question sets from basic computer language programming. The analyses are based on an operationalization of Bloom's Taxonomy of Learning Goals for the domain, which is used to develop a skills‐focused taxonomy of MC questions. However, we propose that their analyses readily generalize to similar teaching domains of interest to decision sciences educators such as modeling and simulation programming.
Within‐Class Variability in Student–Teacher Evaluations: Examples and Problems
Authors: Clayson Dennis E. 
Published: December 2004

ABSTRACTAlthough student evaluation of instruction has been shown to produce reliable results over class averages, considerable within‐class variability exists that has not been investigated. This study looked at examples of student evaluations in which students diametrically differed in their evaluation of the same instructor. Patterns were noted. A survey was conducted to determine the self‐reported incident of students changing evaluations based on noninstructional factors. About 60% of students admitted that they had changed evaluations for reasons related to the instructor's personality, while 30% admitted to changing evaluations based on grades and rigor. Possible reasons and effects of such changes are discussed.
An experimental model to demonstrate the carcinogenic action of oral chronic traumatic ulcer
Authors: Pérez Miguel Angel , Raimondi Ana Rosa , Itoiz María Elina 
Published: December 2004

Background:  Oral chronic traumatic ulcer (CTU) is caused by constant irritation by dental edges or restorations and could behave as a pre‐malignant lesion in a field initiated by carcinogens such as tobacco or alcohol.Methods:  We developed an experimental model in the hamster cheek pouch, combining the chemical carcinogen 7,12‐dimethyl‐benzanthracene (DMBA) with CTU.Results:  The successive or simultaneous action of both agents induced a significantly larger number of endophytic carcinomas than larger doses of DMBA alone. CTU alone failed to induce tumor development. Ploidy analysis revealed significantly higher malignancy indices in endophytic than in exophytic carcinomas. 5‐Bromo‐2‐deoxyuridine labeling evidenced greater proliferation around the ulcers in chemically cancerized epithelium than around ulcers in healthy epithelium.Conclusions:  The results show that CTU acts as a tumor promoter in this model. This finding is clinically relevant in that CTU may increase the risk of malignant transformation in patients with subclinical tumor initiation.
MMP‐3 and ‐8 expression is found in the condylar surface of temporomandibular joints with internal derangement
Authors: Tiilikainen P. , Pirttiniemi P. , Kainulainen T. , Pernu H. , Raustia A. 
Published: December 2004

Background:  Internal derangement is one of the most common disorder of the temporomandibular joint (TMJ). The aim of this study was to investigate the associations of matrix metalloproteinase (MMP)‐3 and ‐8 expression in articular condylar surface with different stages of TMJ internal derangement according to Wilkes (Minn Med, 1978; 61: 645–52) and osteoarthrosis (OA) according to Dijkgraaf et al. (J Oral Maxillofac Surg, 1995; 53: 1182–92).Methods:  The study was based on 54 condylar specimens obtained during TMJ surgery. Immunohistochemistry using antibodies specific to MMP‐3 and ‐8, represented in cartilage destruction, was carried out.Results:  In all tissue specimens, MMP‐3 expression was intense in the surface layer but showed less intensive staining in the deeper layers. Some MMP‐8 expression was also seen. The severity of TMJ internal derangement, however, did not seem to have a statistically significant correlation (P < 0.05) with the expression of these enzymes.Conclusion:  The study confirms that distinct expression of MMP‐3 and ‐8 is found in the condylar surface of TMJs with internal derangement.
Clinical and immunological effects of azithromycin in Behçet's disease
Authors: Mumcu G. , Ergun T. , Elbir Y. , Eksioglu‐Demiralp E. , Yavuz S. , Atalay T. , Direskeneli H. 
Published: December 2004

Background:  The aim of this study was to evaluate the effects of azithromycin on mucocutaneous manifestations, oral health and immune response in Behçet's disease (BD).Methods:  Eight BD patients with active mucocutaneous symptoms were treated with azithromycin for 4 weeks. Oral health, clinical manifestations and in vitro interleukin (IL)‐12, interferon (IFN)‐γ, IL‐10 and monocyte chemotactic protein (MCP)‐1 responses were evaluated before and after treatment.Results:  The number of folliculitic lesions, healing time of oral ulcers and scores of plaque indexes (PLIs) were lower after azithromycin treatment (P < 0.05). Scores of PLIs correlated positively with the healing time of oral ulcers (P = 0.02). Although a trend towards increased stimulated IL‐10 responses with azithromycin was observed, no statistically significant difference was found. Stimulated and unstimulated MCP‐1, IFN‐γ and IL‐12 responses were similar before and after treatment (P > 0.05).Conclusion:  Azithromycin was observed to be effective in decreasing folliculitic lesions and fastening the healing time of oral ulcers in BD.
Autolysis of
Lactococcus lactis
Is Increased upon
d
-Alanine Depletion of Peptidoglycan and Lipoteichoic Acids
Authors: Steen Anton , Palumbo Emmanuelle , Deghorain Marie , Cocconcelli Pier Sandro , Delcour Jean , Kuipers Oscar P. , Kok Jan , Buist Girbe , Hols Pascal 
Published: December 2004

ABSTRACT

Mutations in the genes encoding enzymes responsible for the incorporation of
d
-Ala into the cell wall of
Lactococcus lactis
affect autolysis. An
L. lactis
alanine racemase (
alr
) mutant is strictly dependent on an external supply of
d
-Ala to be able to synthesize peptidoglycan and to incorporate
d
-Ala in the lipoteichoic acids (LTA). The mutant lyses rapidly when
d
-Ala is removed at mid-exponential growth. AcmA, the major lactococcal autolysin, is partially involved in the increased lysis since an
alr acmA
double mutant still lyses, albeit to a lesser extent. To investigate the role of
d
-Ala on LTA in the increased cell lysis, a
dltD
mutant of
L. lactis
was investigated, since this mutant is only affected in the
d
-alanylation of LTA and not the synthesis of peptidoglycan. Mutation of
dltD
results in increased lysis, showing that
d
-alanylation of LTA also influences autolysis. Since a
dltD acmA
double mutant does not lyse, the lysis of the
dltD
mutant is totally AcmA dependent. Zymographic analysis shows that no degradation of AcmA takes place in the
dltD
mutant, whereas AcmA is degraded by the extracellular protease HtrA in the wild-type strain. In
L. lactis
, LTA has been shown to be involved in controlled (directed) binding of AcmA. LTA lacking
d
-Ala has been reported in other bacterial species to have an improved capacity for autolysin binding. Mutation of
dltD
in
L. lactis
, however, does not affect peptidoglycan binding of AcmA; neither the amount of AcmA binding to the cells nor the binding to specific loci is altered. In conclusion,
d
-Ala depletion of the cell wall causes lysis by two distinct mechanisms. First, it results in an altered peptidoglycan that is more susceptible to lysis by AcmA and also by other factors, e.g., one or more of the other (putative) cell wall hydrolases expressed by
L. lactis
. Second, reduced amounts of
d
-Ala on LTA result in decreased degradation of AcmA by HtrA, which results in increased lytic activity.
Regulation of thePseudomonassp. Strain ADP Cyanuric Acid Degradation Operon
Authors: García-González Vicente , Govantes Fernando , Porrúa Odil , Santero Eduardo 
Published: December 2004

ABSTRACTPseudomonassp. strain ADP is the model strain for studying bacterial degradation of thes-triazine herbicide atrazine. In this work, we focused on the expression of theatzDEFoperon, involved in mineralization of the central intermediate of the pathway, cyanuric acid. Expression analysis ofatzD-lacZfusions inPseudomonassp. strain ADP andPseudomonas putidashowed thatatzDEFis subjected to dual regulation in response to nitrogen limitation and cyanuric acid. The gene adjacent toatzD,orf99(renamed hereatzR), encoding a LysR-like regulator, was found to be required for both responses. Expression ofatzR-lacZwas induced by nitrogen limitation and repressed by AtzR. Nitrogen regulation ofatzD-lacZandatzR-lacZexpression was dependent on the alternative σ factor σNand NtrC, suggesting that the cyanuric acid degradation operon may be subject to general nitrogen control. However, whileatzRis transcribed from a σN-dependent promoter,atzDEFtranscription appears to be driven from a σ70-type promoter. Expression ofatzRfrom a heterologous promoter revealed that although NtrC regulation ofatzD-lacZrequires the AtzR protein, it is not the indirect result of NtrC-activated AtzR synthesis. We propose that expression of the cyanuric acid degradation operonatzDEFis controlled by means of a complex regulatory circuit in which AtzR is the main activator. AtzR activity is in turn modulated by the presence of cyanuric acid and by a nitrogen limitation signal transduced by the Ntr system.
Molecular Diversity of a Putative Virulence Factor: Purification and Characterization of Isoforms of an Extracellular Serine Glutamyl Endopeptidase of
Enterococcus faecalis
with Different Enzymatic Activities
Authors: Kawalec Magdalena , Potempa Jan , Moon Jonathan L. , Travis James , Murray Barbara E. 
Published: December 2004

ABSTRACT

A previously identified gene
sprE
of
Enterococcus faecalis
strain OG1 was shown to encode an extracellular serine protease that appears to belong to the glutamyl endopeptidase I staphylococcal group. A single form of SprE with a molecular mass of 25 kDa and a pH optimum between 7.0 and 7.5 was isolated from culture supernatant of wild-type
E. faecalis
strain OG1RF (TX4002); this form was apparently generated by cleavage of the Ser
−1
-Leu
1
and Arg
230
-Leu
231
peptide bonds of the secreted zymogen. In contrast, the culture supernatant of the gelatinase-null mutant, TX5264, with a nonpolar deletion of
gelE
which encodes the
E. faecalis
gelatinase, was found to contain several forms of SprE proteolytically processed on both the N and C termini; in addition to a full-length zymogen and a truncated zymogen, three mature forms of the SprE proteinase, Leu
1
-Ala
237
, Ser
−1
-Glu
227
, and Leu
1
-Glu
227
, were identified. As with the V8 proteinase of
Staphylococcus aureus
, the closest homologue of SprE, all of the active forms cleaved specifically Glu-Xaa peptide bonds but with substantially different efficiencies, while none was able to hydrolyze peptide bonds with Asp in the P1 position. The most active of all these enzyme forms against several substrates, including human fibrinogen and β-chain insulin, was the Ser
−1
-Glu
227
(
−1
S-SprE) isolated from TX5264;
−1
S-SprE, in contrast to other forms of SprE, was unstable at 37°C, apparently due to autodegradation. In conclusion, our results demonstrate that
sprE
encodes a highly specific serine-type glutamyl endopeptidase, the maturation of which is dependent on the presence of gelatinase. In the absence of gelatinase activity, the aberrant processing of pro-SprE results in the appearance of a “superactive” form of the enzyme,
−1
S-SprE.
The
katA
Catalase Gene Is Regulated by OxyR in both Free-Living and Symbiotic
Sinorhizobium meliloti
Authors: Jamet Alexandre , Kiss Ernö , Batut Jacques , Puppo Alain , Hérouart Didier 
Published: December 2004

ABSTRACT

The characterization of an
oxyR
insertion mutant provides evidences that
katA
, which encodes the unique H
2
O
2
-inducible HPII catalase, is regulated by OxyR not only in free-living
Sinorhizobium meliloti
but also in symbiotic
S. meliloti
. Moreover,
oxyR
is expressed independently of exogenous H
2
O
2
and downregulates its own expression in
S. meliloti
.
Simulated Diffusion of Phosphorylated CheY through the Cytoplasm of
Escherichia coli
Authors: Lipkow Karen , Andrews Steven S. , Bray Dennis 
Published: December 2004

ABSTRACT

We describe the use of a computational model to study the effects of cellular architecture and macromolecular crowding on signal transduction in
Escherichia coli
chemotaxis. A newly developed program,
Smoldyn
, allows the movement and interaction of a large number of individual molecules in a structured environment to be simulated (S. S. Andrews and D. Bray, Phys. Biol., in press). With
Smoldyn
, we constructed a three-dimensional model of an
E. coli
cell and examined the diffusion of CheYp from the cluster of receptors to the flagellar motors under control conditions and in response to attractant and repellent stimuli. Our simulations agree well with experimental observations of cell swimming responses and are consistent with the diffusive behavior expected in wild-type and mutant cells. The high resolution available to us in the new program allows us to calculate the loci of individual CheYp molecules in a cell and the distribution of their lifetimes under different cellular conditions. We find that the time delay between stimulus and response differs for flagellar motors located at different positions in the cell. We explore different possible locations for the phosphatase CheZ and show conditions under which a gradient of CheYp exists in the cell. The introduction of inert blocks into the cytoplasm, representing impenetrable structures such as the nucleoid and large protein complexes, produces a fall in the apparent diffusion coefficient of CheYp and enhances the differences between motors. These and other results are left as predictions for future experiments.
Identification of a Region in the Herpes Simplex Virus Scaffolding Protein Required for Interaction with the Portal
Authors: Singer Gregory P. , Newcomb William W. , Thomsen Darrel R. , Homa Fred L. , Brown Jay C. 
Published: December 2004

ABSTRACT

The herpes simplex virus type 1 capsid is a protective shell that acts as a container for the genetic material of the virus. After assembly of the capsid, the viral DNA is translocated into the capsid interior through a channel formed by the portal. The portal is composed of a dodecamer of U
L
6 molecules which form a ring-like structure found at a single vertex within the icosahedron. Formation of portal-containing capsids minimally requires the four structural proteins (VP5, VP19C, VP23, and U
L
6) and a scaffolding protein (U
L
26.5). Recently, an interaction between U
L
26.5 and the portal has been identified, suggesting the scaffold functions by delivering the portal to the growing capsid shell. The aim of this study was to identify regions within U
L
26.5 required for its interaction with the portal. A specific region was identified by mutational analysis. Deletion of scaffold amino acids (aa) 143 to 151 was found to be sufficient to inhibit formation of the scaffold-portal complex as assayed in vitro. The aa 143 to 151 contain the sequence YYPGE, which is highly conserved among alphaherpesviruses. Although it did not bind to the portal, the Δ143-151 mutant was found to retain the ability to support assembly of morphologically normal capsids in vitro. Such capsids, however, did not contain the portal. The results suggest assembly of portal-containing capsids requires formation of a scaffold-portal complex in which intermolecular contact is dependent on scaffold aa 143 to 151.
Unrestricted Hepatocyte Transduction with Adeno-Associated Virus Serotype 8 Vectors in Mice
Authors: Nakai Hiroyuki , Fuess Sally , Storm Theresa A. , Muramatsu Shin-ichi , Nara Yuko , Kay Mark A. 
Published: December 2004

ABSTRACT

Recombinant adeno-associated virus (rAAV) vectors can mediate long-term stable transduction in various target tissues. However, with rAAV serotype 2 (rAAV2) vectors, liver transduction is confined to only a small portion of hepatocytes even after administration of extremely high vector doses. In order to investigate whether rAAV vectors of other serotypes exhibit similar restricted liver transduction, we performed a dose-response study by injecting mice with β-galactosidase-expressing rAAV1 and rAAV8 vectors via the portal vein. The rAAV1 vector showed a blunted dose-response similar to that of rAAV2 at high doses, while the rAAV8 vector dose-response remained unchanged at any dose and ultimately could transduce all the hepatocytes at a dose of 7.2 × 10
12
vector genomes/mouse without toxicity. This indicates that all hepatocytes have the ability to process incoming single-stranded vector genomes into duplex DNA. A single tail vein injection of the rAAV8 vector was as efficient as portal vein injection at any dose. In addition, intravascular administration of the rAAV8 vector at a high dose transduced all the skeletal muscles throughout the body, including the diaphragm, the entire cardiac muscle, and substantial numbers of cells in the pancreas, smooth muscles, and brain. Thus, rAAV8 is a robust vector for gene transfer to the liver and provides a promising research tool for delivering genes to various target organs. In addition, the rAAV8 vector may offer a potential therapeutic agent for various diseases affecting nonhepatic tissues, but great caution is required for vector spillover and tight control of tissue-specific gene expression.
Crystal Structure of Complete Rhinovirus RNA Polymerase Suggests Front Loading of Protein Primer
Authors: Appleby Todd C. , Luecke Hartmut , Shim Jae Hoon , Wu Jim Z. , Cheney I. Wayne , Zhong Weidong , Vogeley Lutz , Hong Zhi , Yao Nanhua 
Published: December 2004

ABSTRACT

Picornaviruses utilize virally encoded RNA polymerase and a uridylylated protein primer to ensure replication of the entire viral genome. The molecular details of this mechanism are not well understood due to the lack of structural information. We report the crystal structure of human rhinovirus 16 3D RNA-dependent RNA polymerase (HRV16 3D
pol
) at a 2.4-Å resolution, representing the first complete polymerase structure from the
Picornaviridae
family. HRV16 3D
pol
shares the canonical features of other known polymerase structures and contains an N-terminal region that tethers the
fingers
and
thumb
subdomains, forming a completely encircled active site cavity which is accessible through a small tunnel on the backside of the molecule. The small
thumb
subdomain contributes to the formation of a large cleft on the front face of the polymerase which also leads to the active site. The cleft appears large enough to accommodate a template:primer duplex during RNA elongation or a protein primer during the uridylylation stage of replication initiation. Based on the structural features of HRV16 3D
po1
and the catalytic mechanism known for all polymerases, a front-loading model for uridylylation is proposed.