bluuebunny/crossref_metadata_2025_split huggingface dataset:
Can the Quality of Care in Family Practice Be Measured Using Administrative Data?
Authors: Katz Alan , Soodeen Ruth‐Ann , Bogdanovic Bogdan , De Coster Carolyn , Chateau Dan 
Published: June 2006

Objective. To explore the feasibility of using administrative data to develop process indicators for measuring quality in primary care.Data Sources/Study Setting. The Population Health Research Data Repository (Repository) housed at the Manitoba Centre for Health Policy which includes physician claims, hospital discharge abstracts, pharmaceutical use (Drug Program Information Network (DPIN)), and the Manitoba Immunization Monitoring Program (MIMS) for all residents of Manitoba, Canada who used the health care system during the 2001/02 fiscal year. Family physicians were identified from the Physician Resource Database. Indicators were developed based on a literature review and focus group validation.Data Collection/Extraction Methods. Data files were extracted from administrative data available in the Repository. We extracted data based on the ICD‐9‐CM codes and ATC‐class drugs prescribed and then linked them to the Physician Resource Database. Physician practices were defined by allocating patients to their most responsible physician. Every family physician in Manitoba that met the inclusion criteria (having either 5 or 10 eligible patients depending on the indicator) was ‘scored’ on each indicator. Physicians were then grouped according to the proportion of the patients allocated to their practice who received the recommended care for the specific indicator.Principal Findings. Using administrative health data we were able to develop and measure eight indicators of quality of care covering both preventive care services and chronic disease management. The number of eligible physicians and patients varied for each indicator as did the percent of patients with recommended care, per physician. For example, the childhood immunization indicator included 544 physicians who, on average, provided immunization for 65 percent of their patients.Conclusions. Quality of care provided by family physicians can be measured using administrative data. Despite the limitations addressed in this paper, this work establishes a practical methodology to measure quality of care provided by family physicians that can be used for quality improvement initiatives.
Redacted Disclosure
Authors: VERRECCHIA ROBERT E. , WEBER JOSEPH 
Published: June 2006

ABSTRACTIn this paper we investigate a firm's decision to redact proprietary information from its material contract filings. Information redaction results when the Security and Exchange Commission (SEC) grants a firm's request to withhold information from investors in its material contract filings, presumably because the information is proprietary. We hypothesize that when firms redact information, measures of adverse selection deteriorate. That is, the redaction of proprietary information from material contracts should be associated with: a larger adverse selection component of the bid‐ask spread, reductions in market depth, and lower market turnover. In addition, we conjecture that the decision to redact depends on whether the firm plans on raising capital, the competitiveness of the firm's industry, and the performance of the firm. Overall the results of our analysis generally support our predictions. We find that when firms redact information, contemporaneous measures of the adverse selection component of the bid‐ask spread rise, and market depth and share turnover deteriorate; this suggests an increase in adverse selection. We also find firms are less likely to redact when they issue long‐term debt and are more likely to redact when they are in a competitive industry or experience losses.
Establishment of four pairs of canine mammary tumour cell lines derived from primary and metastatic origin and their E‐cadherin expression
Authors: Uyama R. , Nakagawa T. , Hong S.‐H. , Mochizuki M. , Nishimura R. , Sasaki N. 
Published: June 2006

AbstractFour new pairs of canine mammary carcinoma cell lines derived from both primary and metastatic lesions were established. The cells were cultured in RPMI‐1640 with 10% fetal bovine serum and they showed stable growth for more than 120 passages. Using these cell lines, the expression of E‐cadherin was measured by flow cytometry and the function of E‐cadherin was evaluated by cell aggregation assay and results from the primary and metastatic lesions were compared statistically. E‐cadherin was strongly expressed in all of the cell lines, without a notable difference between cells of primary and metastatic origin. In the cell aggregation assay, the function of E‐cadherin was significantly weaker in the cells of primary origin (p < 0.05), as compared with cells of metastatic origin. The present results suggest that a reduction in E‐cadherin function may be implicated in the invasive and metastatic potential of canine mammary tumour cells; however, further study will be needed to clarify E‐cadherin function in the context of the metastasis of canine mammary carcinoma.
Clinical usefulness of intradermal fluorescein and patent blue violet dyes for sentinel lymph node identification in dogs
Authors: Wells S. , Bennett A. , Walsh P. , Owens S. , Peauroi J. 
Published: June 2006

AbstractThe first lymph node receiving drainage from a specific anatomic region is referred to as the sentinel lymph node (SLN). This study sought to evaluate the intradermal use of two dyes, patent blue violet (PBV) and fluorescein (FL), for SLN mapping in the dog. Multiple intradermal injections were performed in five healthy dogs using two dyes, PBV in 0.9% NaCl and FL in solutions of 0.9% NaCl and 6% hetastarch. Skin flaps were raised and followed to the first area of discrete stain uptake. Areas of uptake were identified as lymph nodes grossly and by cytology. Identification of a SLN for each area of intradermal injection was accomplished for 98% of the injection sites. Intradermal injections of both PBV and FL dyes produce readily visible staining of lymphatic vessels and SLNs in healthy dogs and are sufficient to allow ready identification of these structures during postmortem dissection.
Protein-Protein Interactions amongHelicobacter pyloriCag Proteins
Authors: Busler Valerie J. , Torres Victor J. , McClain Mark S. , Tirado Oscar , Friedman David B. , Cover Timothy L. 
Published: June 2006

ABSTRACTManyHelicobacter pyloriisolates contain a 40-kb region of chromosomal DNA known as thecagpathogenicity island (PAI). The risk for development of gastric cancer or peptic ulcer disease is higher among humans infected withcagPAI-positiveH. pyloristrains than among those infected withcagPAI-negative strains. ThecagPAI encodes a type IV secretion system that translocates CagA into gastric epithelial cells. To identify Cag proteins that are expressed byH. pyloriduring growth in vitro, we compared the proteomes of a wild-typeH. pyloristrain and an isogeniccagPAI deletion mutant using two-dimensional difference gel electrophoresis (2D-DIGE) in multiple pH ranges. Seven Cag proteins were identified by this approach. We then used a yeast two-hybrid system to detect potential protein-protein interactions among 14 Cag proteins. One heterotypic interaction (CagY/7 with CagX/8) and two homotypic interactions (involvingH. pyloriVirB11/ATPase and Cag5) were similar to interactions previously reported to occur among homologous components of theAgrobacterium tumefacienstype IV secretion system. Other interactions involved Cag proteins that do not have known homologues in other bacterial species. Biochemical analysis confirmed selected interactions involving five of the proteins that were identified by 2D-DIGE. Protein-protein interactions among Cag proteins are likely to have an important role in the assembly of theH. pyloritype IV secretion apparatus.
The Crystal Structure of Beryllofluoride Spo0F in Complex with the Phosphotransferase Spo0B Represents a Phosphotransfer Pretransition State
Authors: Varughese Kottayil I. , Tsigelny Igor , Zhao Haiyan 
Published: June 2006

ABSTRACT

A number of regulatory circuits in biological systems function through the exchange of phosphoryl groups from one protein to another. Spo0F and Spo0B are components of a phosphorelay that control sporulation in the bacterium
Bacillus subtilis
through the exchange of a phosphoryl group. Using beryllofluoride as a mimic for phosphorylation, we trapped the interaction of the phosphorylated Spo0F with Spo0B in the crystal lattice. The transition state of phosphoryl transfer continues to be a highly debated issue, as to whether it is associative or dissociative in nature. The geometry of Spo0F binding to Spo0B favors an associative mechanism for phosphoryl transfer. In order to visualize the autophosphorylation of the histidine kinase, KinA, and the subsequent phosphoryl transfer to Spo0F, we generated in silico models representing these reaction steps.
YtsJ Has the Major Physiological Role of the Four Paralogous Malic Enzyme Isoforms in
Bacillus subtilis
Authors: Lerondel Guillaume , Doan Thierry , Zamboni Nicola , Sauer Uwe , Aymerich Stéphane 
Published: June 2006

ABSTRACT

The
Bacillus subtilis
genome contains several sets of paralogs. An extreme case is the four putative malic enzyme genes
maeA
,
malS
,
ytsJ
, and
mleA. maeA
was demonstrated to encode malic enzyme activity, to be inducible by malate, but also to be dispensable for growth on malate. We report systematic experiments to test whether these four genes ensure backup or cover different functions. Analysis of single- and multiple-mutant strains demonstrated that
ytsJ
has a major physiological role in malate utilization for which none of the other three genes could compensate. In contrast,
maeA
,
malS
, and
mleA
had distinct roles in malate utilization for which they could compensate one another. The four proteins exhibited malic enzyme activity; MalS, MleA, and MaeA exhibited 4- to 90-fold higher activities with NAD
+
than with NADP
+
. YtsJ activity, in contrast, was 70-fold higher with NADP
+
than with NAD
+
, with

K
m

values of 0.055 and 2.8 mM, respectively.
lacZ
fusions revealed strong transcription of
ytsJ
, twofold higher in malate than in glucose medium, but weak transcription of
malS
and
mleA
. In contrast,
mleA
was strongly transcribed in complex medium. Metabolic flux analysis confirmed the major role of YtsJ in malate-to-pyruvate interconversion. While overexpression of the NADP-dependent
Escherichia coli
malic enzyme MaeB did not suppress the growth defect of a
ytsJ
mutant on malate, overexpression of the transhydrogenase UdhA from
E. coli
partially suppressed it. These results suggest an additional physiological role of YtsJ beyond that of malate-to-pyruvate conversion.
Analysis of theAnaplasma marginaleMajor Surface Protein 1 Complex Protein Composition by Tandem Mass Spectrometry
Authors: Macmillan Henriette , Brayton Kelly A. , Palmer Guy H. , McGuire Travis C. , Munske Gerhard , Siems William F. , Brown Wendy C. 
Published: June 2006

ABSTRACTThe protective major surface protein 1 (MSP1) complex ofAnaplasma marginaleis a heteromer of MSP1a and MSP1b, encoded by a multigene family. Themsp1β sequences were highly conserved throughout infection. However, liquid chromatography-tandem mass spectrometry analysis identified only a single MSP1b protein, MSP1b1, within the MSP1 complex.
Involvement ofBacillus subtilisClpE in CtsR Degradation and Protein Quality Control
Authors: Miethke Marcus , Hecker Michael , Gerth Ulf 
Published: June 2006

ABSTRACTThe heat-inducible CtsR regulon ofBacillus subtiliscodes for three Clp proteins with chaperone or protease activity. While the importance of ClpC and ClpP has been elucidated for a wide range of cellular adaptation processes, this study deals with the physiological role ofB. subtilisClpE. Northern experiments and reporter gene analyses revealed that ClpE is essential both for efficient CtsR-dependent gene derepression and for rerepression during heat stress. ClpEP was found to destabilize the global regulator CtsR after heat shock in vivo with different kinetics than ClpCP, which is known to degrade CtsR in vitro and in vivo upon heat stress. Furthermore, ClpE was localized at heat-generated inclusion bodies by electron microscopy. The comparison of radiolabeled aggregated protein fractions of wild-type andclpEmutant cells during heat stress displayed a significant delay of protein disaggregation in the absence of ClpE. A kinetic Western blotting approach confirmed the long-term residence of ClpE in the insoluble cell fraction rather than in the cytoplasmic fraction. These observations indicate the involvement of ClpE in global protein disaggregation. As a characteristic structural element of ClpE, the N-terminal zinc finger domain was proven to be essential for basal in vitro ATPase activity.
Erwinia carotovoraSubspecies Produce Duplicate Variants of ExpR, LuxR Homologs That ActivatersmATranscription but Differ in Their Interactions withN-Acylhomoserine Lactone Signals
Authors: Cui Yaya , Chatterjee Asita , Hasegawa Hiroaki , Chatterjee Arun K. 
Published: June 2006

ABSTRACTTheN-acylhomoserine lactone (AHL) signaling system comprises a producing system that includes acylhomoserine synthase (AhlI, a LuxI homolog) and a receptor, generally a LuxR homolog. AHL controls exoprotein production inErwinia carotovoraand consequently the virulence for plants. In previous studies we showed that ExpR, a LuxR homolog, is an AHL receptor and that it activates transcription ofrsmA, the gene encoding an RNA binding protein which is a global negative regulator of exoproteins and secondary metabolites. An unusual finding was that the transcriptional activity of ExpR was neutralized by AHL. We subsequently determined that the genomes of most strains ofE. carotovorasubspecies tested possess two copies of theexpRgene:expR1, which was previously studied, andexpR2, which was the focus of this study. Comparative analysis of the two ExpR variants ofE. carotovorasubsp.carotovorashowed that while both variants activatedrsmAtranscription, there were significant differences in the patterns of their AHL interactions, thersmAsequences to which they bound, and their relative efficiencies of activation ofrsmAtranscription. An ExpR2−mutant produced high levels of exoproteins and reduced levels of RsmA in the absence of AHL. This contrasts with the almost complete inhibition of exoprotein production and the high levels of RsmA production in an AhlI−mutant that was ExpR1−. Our results suggest that ExpR2 activity is responsible for regulating exoprotein production primarily by modulating the levels of an RNA binding protein.
The Ribulose Monophosphate Pathway Substitutes for the Missing Pentose Phosphate Pathway in the Archaeon
Thermococcus kodakaraensis
Authors: Orita Izumi , Sato Takaaki , Yurimoto Hiroya , Kato Nobuo , Atomi Haruyuki , Imanaka Tadayuki , Sakai Yasuyoshi 
Published: June 2006

ABSTRACT

The ribulose monophosphate (RuMP) pathway, involving 3-hexulose-6-phosphate synthase (HPS) and 6-phospho-3-hexuloisomerase (PHI), is now recognized as a widespread prokaryotic pathway for formaldehyde fixation and detoxification. Interestingly, HPS and PHI homologs are also found in a variety of archaeal strains, and recent biochemical and genome analyses have raised the possibility that the reverse reaction of formaldehyde fixation, i.e., ribulose 5-phosphate (Ru5P) synthesis from fructose 6-phosphate, may function in the biosynthesis of Ru5P in some archaeal strains whose pentose phosphate pathways are imperfect. In this study, we have taken a genetic approach to address this possibility by using the hyperthermophilic archaeon
Thermococcus kodakaraensis
KOD1. This strain possesses a single open reading frame (TK0475) encoding an HPS- and PHI-fused protein. The recombinant HPS-PHI-fused enzyme exhibited the expected HPS and PHI activities in both directions (formaldehyde fixing and Ru5P synthesizing). The TK0475 deletion mutant Δ
hps-phi
-7A did not exhibit any growth in minimal medium, while growth of the mutant strain could be recovered by the addition of nucleosides to the medium. This auxotrophic phenotype together with the catalytic properties of the HPS-PHI-fused enzyme reveal that HPS and PHI are essential for the biosynthesis of Ru5P, the precursor of nucleotides, showing that the RuMP pathway is the only relevant pathway for Ru5P biosynthesis substituting for the classical pentose phosphate pathway missing in this archaeon.
Collapsing along monotone poset maps
Authors: Kozlov Dmitry N. 
Published: June 2006

We introduce the notion of nonevasive reduction and show that for any monotone poset map ϕ : P → P, the simplicial complex Δ(P) NE‐reduces to Δ(Q), for any Q⊇Fixϕ.As a corollary, we prove that for any order‐preserving map ϕ : P → P satisfying ϕ(x) ≥ x, for any
x ∈ P, the simplicial complex Δ(P) collapses to Δ(ϕ(P)). We also obtain a generalization of Crapo′s closure theorem.
Targeted disruption of cubilin reveals essential developmental roles in the structure and function of endoderm and in somite formation
Authors: Smith Brian T , Mussell Jason C , Fleming Paul A , Barth Jeremy L , Spyropoulos Demetri D , Cooley Marion A , Drake Christopher J , Argraves W Scott 
Published: June 2006

Abstract

Background
Cubilin is a peripheral membrane protein that interacts with the integral membrane proteins megalin and amnionless to mediate ligand endocytosis by absorptive epithelia such as the extraembryonic visceral endoderm (VE).

Results
Here we report the effects of the genetic deletion of cubilin on mouse embryonic development. Cubilin gene deletion is homozygous embryonic lethal with death occurring between 7.5–13.5 days post coitum (dpc). Cubilin-deficient embryos display developmental retardation and do not advance morphologically beyond the gross appearance of wild-type 8–8.5 dpc embryos. While mesodermal structures such as the allantois and the heart are formed in cubilin mutants, other mesoderm-derived tissues are anomalous or absent. Yolk sac blood islands are formed in cubilin mutants but are unusually large, and the yolk sac blood vessels fail to undergo remodeling. Furthermore, somite formation does not occur in cubilin mutants. Morphological abnormalities of endoderm occur in cubilin mutants and include a stratified epithelium in place of the normally simple columnar VE epithelium and a stratified cuboidal epithelium in place of the normally simple squamous epithelium of the definitive endoderm. Cubilin-deficient VE is also functionally defective, unable to mediate uptake of maternally derived high-density lipoprotein (HDL).

Conclusion
In summary, cubilin is required for embryonic development and is essential for the formation of somites, definitive endoderm and VE and for the absorptive function of VE including the process of maternal-embryo transport of HDL.
The CAP cancer protocols – a case study of caCORE based data standards implementation to integrate with the Cancer Biomedical Informatics Grid
Authors: Tobias Jonathan , Chilukuri Ram , Komatsoulis George A , Mohanty Sambit , Sioutos Nicholas , Warzel Denise B , Wright Lawrence W , Crowley Rebecca S 
Published: June 2006

Abstract

Background
The Cancer Biomedical Informatics Grid (caBIG™) is a network of individuals and institutions, creating a world wide web of cancer research. An important aspect of this informatics effort is the development of consistent practices for data standards development, using a multi-tier approach that facilitates semantic interoperability of systems. The semantic tiers include (1) information models, (2) common data elements, and (3) controlled terminologies and ontologies. The College of American Pathologists (CAP) cancer protocols and checklists are an important reporting standard in pathology, for which no complete electronic data standard is currently available.

Methods
In this manuscript, we provide a case study of Cancer Common Ontologic Representation Environment (caCORE) data standard implementation of the CAP cancer protocols and checklists model – an existing and complex paper based standard. We illustrate the basic principles, goals and methodology for developing caBIG™ models.

Results
Using this example, we describe the process required to develop the model, the technologies and data standards on which the process and models are based, and the results of the modeling effort. We address difficulties we encountered and modifications to caCORE that will address these problems. In addition, we describe four ongoing development projects that will use the emerging CAP data standards to achieve integration of tissue banking and laboratory information systems.

Conclusion
The CAP cancer checklists can be used as the basis for an electronic data standard in pathology using the caBIG™ semantic modeling methodology.
Follicle-stimulating hormone (FSH) activates extracellular signal-regulated kinase phosphorylation independently of beta-arrestin- and dynamin-mediated FSH receptor internalization
Authors: Piketty Vincent , Kara Elodie , Guillou Florian , Reiter Eric , Crepieux Pascale 
Published: June 2006

AbstractBackgroundThe follicle-stimulating hormone receptor (FSH-R) is a seven transmembrane spanning receptor (7TMR) which plays a crucial role in male and female reproduction. Upon FSH stimulation, the FSH-R activates the extracellular signal-regulated kinases (ERK). However, the mechanisms whereby the agonist-stimulated FSH-R activates ERK are poorly understood. In order to activate ERK, some 7 TMRs require beta-arrestin-and dynamin-dependent internalization to occur, whereas some others do not. In the present study, we examined the ability of the FSH-activated FSH-R to induce ERK phosphorylation, in conditions where its beta-arrestin- and dynamin-mediated internalization was impaired.MethodsHuman embryonic kidney (HEK) 293 cells were transiently transfected with the rat FSH-R. Internalization of the FSH-R was manipulated by co-expression of either a beta-arrestin (319–418) dominant negative peptide, either an inactive dynamin K44A mutant or of wild-type beta-arrestin 1 or 2. The outcomes on the FSH-R internalization were assayed by measuring 125I-FSH binding at the cell surface when compared to internalized 125I-FSH binding. The resulting ERK phosphorylation level was visualized by Western blot analysis.ResultsIn HEK 293 cells, FSH stimulated ERK phosphorylation in a dose-dependent manner. Co-transfection of the beta- arrestin (319–418) construct, or of the dynamin K44A mutant reduced FSH-R internalization in response to FSH, without affecting ERK phosphorylation. Likewise, overexpression of wild-type beta-arrestin 1 or 2 significantly increased the FSH-R internalization level in response to FSH, without altering FSH-induced ERK phosphorylation.ConclusionFrom these results, we conclude that the FSH-R does not require beta-arrestin- nor dynamin-mediated internalization to initiate ERK phosphorylation in response to FSH.