bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regulation of Excision Genes of theBacteroidesConjugative Transposon CTnDOT
Authors: Moon Kyung , Shoemaker Nadja B. , Gardner Jeffrey F. , Salyers Abigail A. 
Published: August 2005

ABSTRACTThe first step in the transfer of theBacteroidesconjugative transposon CTnDOT is excision of the integrated element from the chromosome to form a circular transfer intermediate. Excision occurs only after the bacteria are exposed to tetracycline. Previously, four excision genes were identified. One was the integrase geneintDOT, which appeared to be expressed constitutively. Three other genes essential for excision (orf2c,orf2d, andexc) were found located in a cluster 13 kbp downstream ofintDOT. By usinguidAfusions and real-time reverse transcriptase PCR, we demonstrate here that the excision genesorf2c,orf2d, andexcare part of an operon that also contains open reading frameorf3, previously shown not to be essential for excision. We also show that operon expression is regulated at the transcriptional level in response to tetracycline. The transcript start site for the operon has been localized. Three CTnDOT regulatory genes are thought to be involved in tetracycline regulation of excision,rteA,rteB, andrteC. By placingrteCunder the control of a heterologous promoter, we found that RteC alone was sufficient for induction of theorf2coperon. If, however, therteCgene was under the control of its own promoter, it was not able to induceorf2coperon expression unlessrteAandrteBwere present. Thus, RteA and RteB participate in excision by stimulating transcription ofrteC. Using electrophoretic mobility shift analysis, we found that a purified His6-tagged form of RteC bound DNA upstream of the −33 region of the promoter. Changing the sequence in the region between bp −50 and −70 reduced the expression of theorf2coperon in vivo. Taken together, our results support the hypothesis that RteC acts as a DNA-binding protein that binds upstream of theorf2cpromoter and is responsible for tetracycline-regulated transcriptional regulation of theorf2coperon.
Using Continuous System Level Assessment to Build School Capacity
Authors: Smith Christopher L. , Freeman Rachel L. 
Published: August 2005

The purpose of this article is to introduce a conceptual model for internal assessment and professional development planning. The continuous systems-level assessment (CSLA) is a model that can provide school and other professionals with a method for making data-based decisions, and is intended to foster local expertise by utilizing assessment information to design effective professional development strategies. The CSLA model includes three phases: needs assessment and problem identification; designing interventions and building staff capacity; and implementing and evaluating interventions. The authors outline the values associated with the CSLA model, the major phases involved in the process, and provide an example of how the process is currently being implemented in an urban school in Kansas. School-based programs are complex, dynamic, and usually involve long-term commitments from a variety of partners. In addition, program implementation often occurs within the context of organic, changing organizations and therefore, requires a flexible model of evaluation. Several bottom-up program evaluation models have been developed that can be used to guide an assessment of the commitments, values, and capacities of schools and other organizations (Fawcett et al., 1996; Fetterman, 1996; Greenwood, Whyte, & Harkavy, 1993; Knoff, 1996; Levin, 1996; Millett, 1996; Scriven, 1967; Stake, 1967, 197 6). The approach described here is similar to these bottom-up program evaluation models, and is being used to assess ongoing improvement efforts and identify professional development needs for schools.
Durable hematologic complete response and suppression of HTLV-1 viral load following alemtuzumab in zidovudine/IFN-α–refractory adult T-cell leukemia
Authors: Mone Andrew , Puhalla Shannon , Whitman Susan , Baiocchi Robert A. , Cruz Julio , Vukosavljevic Tamara , Banks Amy , Eisenbeis Charles F. , Byrd John C. , Caligiuri Michael A. , Porcu Pierluigi 
Published: August 2005

AbstractAdult T-cell leukemia (ATL) is a highly chemoresistant and usually fatal T-cell malignancy due to the human T-cell lymphotropic virus-1 (HTLV-1). After chemotherapy failure, antiretrovirals and interferon-α (IFN-α) produce brief responses followed by progression and death. More effective agents and new approaches to detect and treat minimal residual disease are needed. ATL cells express CD52, the target of the antibody alemtuzumab, which is active in a preclinical model of ATL and is cytotoxic for p53-deficient cells. A patient with refractory chronic ATL in transformation achieved longer than a 1-year complete hematologic response following 12 weeks of outpatient subcutaneous alemtuzumab. Persistent suppression of HTLV-1 viral load, even at recovery of T cells, after alemtuzumab and efficient in vitro complement-mediated cytotoxicity of primary ATL cells with mutated TP53 were observed. The unprecedented response and the profound suppression of HTLV-1 viral load observed in this patient suggest that further clinical investigation of alemtuzumab in ATL is warranted.
Ku80 autoantigen as a cellular coreceptor for human parvovirus B19 infection
Authors: Munakata Yasuhiko , Saito-Ito Takako , Kumura-Ishii Keiko , Huang Jie , Kodera Takao , Ishii Tomonori , Hirabayashi Yasuhiko , Koyanagi Yoshio , Sasaki Takeshi 
Published: August 2005

AbstractHuman parvovirus B19 (B19) infects human erythroid cells expressing P antigen. However, some cell lines that were positive for P antigen failed to bind B19, whereas some cell lines had an ability to bind B19 despite undetectable expression of P antigen. We here demonstrate that B19 specifically binds with Ku80 autoantigen on the cell surface. Furthermore, transfection of HeLa cells with the gene of Ku80 enabled the binding of B19 and allowed its entry into cells. Moreover, reduction of cell-surface expression of Ku80 in KU812Ep6 cells, which was a high-sensitive cell line for B19 infection, by short interfering RNA for Ku80 resulted in the marked inhibition of B19 binding in KU812Ep6 cells. Although Ku80 originally has been described as a nuclear protein, human bone marrow erythroid cells with glycophorin A or CD36, B cells with CD20, or T cells with CD3 were all positive for cell-surface expression of Ku80. B19 infection of KU812Ep6 cells and bone marrow cells was inhibited in the presence of anti-Ku80 antibody. Our data suggest that Ku80 functions as a novel coreceptor for B19 infection, and this finding may provide an explanation for the pathologic immunity associated with B19 infection.
Multiple roles of Rap1 in hematopoietic cells: complementary versus antagonistic functions
Authors: Stork Philip J. S. , Dillon Tara J. 
Published: August 2005

AbstractSmall G proteins serve as critical control points in signal transduction, integrating a wide range of stimuli to dictate discrete cellular outcomes. The outcomes of small G-protein signaling can both potentiate and antagonize one another. Studies in hematopoietic cells have uncovered multiple functions for the small G protein, Rap1 (Ras-proximate-1). Because Rap1 can regulate cell proliferation, differentiation, and adhesion through distinct mechanisms, it serves as a paradigm for the need for tight cellular control of small G-protein function. Rap1 has received recent attention for its role in enhancing integrin-dependent signals. This action of Rap1 augments a variety of processes that characterize hematopoietic-cell function, including aggregation, migration, extravasation, and homing to target tissues. Rap1 may also regulate cellular differentiation and proliferation via pathways that are distinct from those mediating adhesion, and involve regulation of the mitogen-activated protein (MAP) kinase or ERK (extracellular signal-regulated kinase) cascade. These actions of Rap1 occur in selected cell types to enhance or diminish ERK signaling, depending on the expression pattern of the MAP kinase kinase kinases of the Raf family: Raf-1 and B-Raf. This review will examine the functions of Rap1 in hematopoietic cells, and focus on 3 cellular scenarios where the multiple actions of Rap1 function have been proposed. Recent studies implicating Rap1 in the maturation of megakaryocytes, the pathogenesis of chronic myelogenous leukemia (CML), and activation of peripheral T cells will receive particular attention.
Immunoglobulin light chain repertoire in chronic lymphocytic leukemia
Authors: Stamatopoulos Kostas , Belessi Chrysoula , Hadzidimitriou Anastasia , Smilevska Tatjana , Kalagiakou Evangelia , Hatzi Katerina , Stavroyianni Niki , Athanasiadou Anastasia , Tsompanakou Aliki , Papadaki Theodora , Kokkini Garyfallia , Paterakis George , Saloum Riad , Laoutaris Nikolaos , Anagnostopoulos Achilles , Fassas Athanasios 
Published: August 2005

AbstractImmunoglobulin kappa (IGK) and immunoglobulin lambda (IGL) light chain repertoire was analyzed in 276 chronic lymphocytic leukemia (CLL) cases and compared with the relevant repertoires from normal, autoreactive, and neoplastic cells. Twenty-one functional IGKV genes were used in IGKV-J rearrangements of 179 kappa-CLL cases; the most frequent genes were IGKV3-20(A27), IGKV1-39/1D-39(O2/O12), IGKV1-5(L12), IGKV4-1(B3), and IGKV2-30(A17); 90 (50.3%) of 179 IGK sequences were mutated (similarity &lt; 98%). Twenty functional IGLV genes were used in IGLV-J rearrangements of 97 lambda-CLL cases; the most frequent genes were IGLV3-21(VL2-14), IGLV2-8(VL1-2), and IGLV2-14(VL1-4); 44 of 97 IGL sequences (45.4%) were mutated. Subsets with “CLL-biased” homologous complementarity-determining region 3 (CDR3) were identified: (1) IGKV2-30-IGKJ2, 7 sequences with homologous kappa CDR3 (KCDR3), 5 of 7 associated with homologous IGHV4-34 heavy chains; (2) IGKV1-39/1D-39-IGKJ1/4, 4 unmutated sequences with homologous KCDR3, 2 of 4 associated with homologous IGHV4-39 heavy chains; (3) IGKV1-5-IGKJ1/3, 4 sequences with homologous KCDR3, 2 of 4 associated with unmutated nonhomologous IGHV4-39 heavy chains; (4) IGLV1-44-IGLJ2/3, 2 sequences with homologous lambda CDR3 (LCDR3), associated with homologous IGHV4-b heavy chains; and (5) IGLV3-21-IGLJ2/3, 9 sequences with homologous LCDR3, 3 of 9 associated with homologous IGHV3-21 heavy chains. The existence of subsets that comprise given IGKV-J/IGLV-J domains associated with IGHV-D-J domains that display homologous CDR3 provides further evidence for the role of antigen in CLL pathogenesis.
Sample phenotype clusters in high-density oligonucleotide microarray data sets are revealed using Isomap, a nonlinear algorithm
Authors: Dawson Kevin , Rodriguez Raymond L , Malyj Wasyl 
Published: August 2005

Abstract
Background
Life processes are determined by the organism's genetic profile and multiple environmental variables. However the interaction between these factors is inherently non-linear [1]. Microarray data is one representation of the nonlinear interactions among genes and genes and environmental factors. Still most microarray studies use linear methods for the interpretation of nonlinear data. In this study, we apply Isomap, a nonlinear method of dimensionality reduction, to analyze three independent large Affymetrix high-density oligonucleotide microarray data sets.

Results
Isomap discovered low-dimensional structures embedded in the Affymetrix microarray data sets. These structures correspond to and help to interpret biological phenomena present in the data. This analysis provides examples of temporal, spatial, and functional processes revealed by the Isomap algorithm. In a spinal cord injury data set, Isomap discovers the three main modalities of the experiment – location and severity of the injury and the time elapsed after the injury. In a multiple tissue data set, Isomap discovers a low-dimensional structure that corresponds to anatomical locations of the source tissues. This model is capable of describing low- and high-resolution differences in the same model, such as kidney-vs.-brain and differences between the nuclei of the amygdala, respectively. In a high-throughput drug screening data set, Isomap discovers the monocytic and granulocytic differentiation of myeloid cells and maps several chemical compounds on the two-dimensional model.

Conclusion
Visualization of Isomap models provides useful tools for exploratory analysis of microarray data sets. In most instances, Isomap models explain more of the variance present in the microarray data than PCA or MDS. Finally, Isomap is a promising new algorithm for class discovery and class prediction in high-density oligonucleotide data sets.
Comparison of spatial scan statistic and spatial filtering in estimating low birth weight clusters
Authors: Ozdenerol Esra , Williams Bryan L , Kang Su Young , Magsumbol Melina S 
Published: August 2005

AbstractBackgroundThe purpose of this study is to examine the spatial and population (e.g., socio-economic) characteristics of low birthweight using two different cluster estimation techniques. We compared the results of Kulldorff's Spatial Scan Statistic with the results of Rushton's Spatial filtering technique across increasing sizes of spatial filters (circle). We were able to demonstrate that varying approaches exist to explore spatial variation in patterns of low birth weight.ResultsSpatial filtering results did not show any particular area that was not statistically significant based on SaTScan. The high rates, which remain as the filter size increases to 0.4, 0.5 to 0.6 miles, respectively, indicate that these differences are less likely due to chance. The maternal characteristics of births within clusters differed considerably between the two methods. Progressively larger Spatial filters removed local spatial variability, which eventually produced an approximate uniform pattern of low birth weight.ConclusionSaTScan and Spatial filtering cluster estimation methods produced noticeably different results from the same individual level birth data. SaTScan clusters are likely to differ from Spatial filtering clusters in terms of population characteristics and geographic area within clusters. Using the two methods in conjunction could provide more detail about the population and spatial features contained with each type of cluster.
A pilot study comparing the cognitive demand of walking for transfemoral amputees using the Intelligent Prosthesis with that using conventionally damped knees
Authors: Heller B W , Datta D , Howitt J 
Published: August 2005

Objective: To compare the cognitive demand of walking when using a conventional prosthesis with that using a microprocessor-controlled prosthesis. Design: Ten unilateral transfemoral amputees wearing conventional pneumatic swing phase control (conventional prosthesis) prostheses walked on a treadmill which enforced a pattern of constantly varying speeds. The subjects simultaneously performed a simple or a complex distracting task. Following a period of accustomization, the subjects performed the same test wearing a prosthesis with microprocessor control of swing phase damping (the Intelligent Prosthesis). Outcome measures: The three-dimensional trajectory (sway) of a retroreflective marker attached to the forehead was measured by a video-based motion analysis system, and used as a measure of gait quality. The ratio of the sway for the complex task over the simple task (the ‘automation index’) was used as a measure of the degree of automation of gait. Results: No significant differences were found in the automation index between the two devices. However, the total sway for the conventional prosthesis was significantly higher. Sway during the complex distracting task was significantly higher than during the simple task. Conclusions: The microprocessor-controlled prosthesis was not found to be less cognitively demanding than a conventional prosthesis.
Clinical standards for inpatient specialist rehabilitation services in the UK
Authors: Turner-Stokes Lynne , Williams Heather , Abraham Rachel , Duckett Stephane 
Published: August 2005

Objective: To develop a set of clinical standards for specialist inpatient rehabilitation services in the UK and to undertake a preliminary survey of consultants who provide those services. Design: The proposed set of standards was developed by group consensus followed by an iterative consultation process. A postal survey was conducted on behalf of the British Society for Rehabilitation Medicine (BSRM) amongst its consultant members in the UK (n = 163), who were asked to assess their services in relation to these standards, and to comment on the standards themselves, their usefulness and applicability. Results: The response rate was 61%, of which 81 respondents ran an inpatient rehabilitation service. Overall, the standards appeared to be acceptable to most, and mainly struck the right level, being attained by the majority of services. Specific suggestions were incorporated into the revised standards. Further work is required to establish agreed outcomes that are systematically measured and recorded: only half the respondents (50%) routinely recorded a standardized outcome measure, and only a quarter (26%) routinely reviewed patients to record long-term outcome. Conclusions: Clinical standards have been developed for specialist inpatient rehabilitation services in the UK. The BSRM proposes to adopt these standards for a test period of 2–3 years in the first instance. It is likely that they will require further refinement with time, and modification is required to adapt them to different subspecialities and settings.
Balance function and fall-related efficacy in patients with newly operated hip fracture
Authors: Ingemarsson A Hellzén , Frändin K , Hellström K , Rundgren Å 
Published: August 2005

Objective: To investigate the relation between fall-related efficacy in daily-life activities and functional as well as instrumental tests of balance in patients with hip fracture. Design: Analysis of different aspects of balance using the Falls Efficacy Scale, Swedish version FES(S), questions on fear of falling, Functional Reach (FR) and tests on a balance platform (Chattanooga). Subjects: Fifty-five elderly inpatients (mean age 82.3) with newly operated hip fracture who were assessed during the last week in hospital before discharge. Results: The results showed a significant relationship between the subjective ability measured with the FES(S) and the objectively measured balance in the Functional Reach test and also between fall-related efficacy measured with FES(S) and fear of falling. Very few significant correlations were found between the results from balance tests on the force platform and those obtained with FES(S) and FR. Conclusions: Both the Falls Efficacy Scale, Swedish version, and the Functional Reach have been shown to be useful in analysing balance function in elderly patients newly operated on for hip fracture. The Falls Efficacy Scale also indicates which of the daily activities the patient perceives as troublesome and thus require further training.
The effectiveness of community-based rehabilitation for stroke patients who remain at home: a pilot randomized trial
Authors: Wolfe Charles DA , Tilling Kate , Rudd Anthony G 
Published: August 2005

Objective: To assess the effectiveness of community-based rehabilitation for stroke patients who were not admitted to hospital in South London. Design: Randomized controlled trial. Setting: Patients' homes in South London. Subjects: Stroke patients not admitted to hospital after a stroke. Intervention: Rehabilitation at home by rehabilitation team for up to three months or usual care. Main outcome measures: The primary outcome measure was the Barthel score. Secondary measures included the Motricity Index, Rivermead ADL, Hospital Anxiety and Depression score and Nottingham Health Profile. Results: Forty-three patients who remained at home were randomized to rehabilitation team (23) or ‘usual’ care (20). The mean number of physiotherapy sessions was three (range 1–14) for the rehabilitation team group and two for the usual care group. Patients (with a deficit) in the rehabilitation arm of the trial were more likely to receive occupational, physical and speech therapy than those in the control arm (p = 0.03, 0.01 and 0.008, respectively). For those patients actually receiving therapy, there was no evidence that the amount received differed between the groups. However, the number of patients in each of these comparisons was very small. The outcome for patients in the rehabilitation team arm of the trial was nonsignificantly higher (0.05 < p < 0.2) than for those in the control arm for the areas of Nottingham Health Profile, anxiety, depression, caregiver strain and the proportion of patients living at home. Based on the data observed here, a trial with approximately 150 patients in each arm would be needed to have adequate power to detect a 33% difference between intervention and control groups in these outcomes. Conclusion: Community therapy support for patients not admitted to hospital is feasible but to determine whether it is cost- or clinically effective would require trials of adequate size.
Reliability of a measure of post-stroke shoulder pain in patients with and without aphasia and/or unilateral spatial neglect
Authors: Pomeroy Valerie M , Frames Christine , Faragher Eric B , Hesketh Anne , Hill Elizabeth , Watson Paul , Main Chris J 
Published: August 2005

Objective: To determine the inter/intra-rater reliability of expert physiotherapists (PTs) measuring post-stroke shoulder pain with 100 mm vertical visual analogue scales (VAS; intensity, frequency and affective response) and a categorical site-of-pain scale. Design: Three PTs independently rated subjects (normal clinical procedure but with a standardized starting position) on three days, at the same time of day, during one week in a randomized order determined by a nested latin square. Reliability for VAS scores was determined with the intraclass correlation coefficient (ICC) and for site-of-pain with the kappa statistic (. Acceptable reliability was set at 0.75. The limits of agreement were also calculated. Setting: Community. Subjects: Thirty-three patients, mean time post stroke 42 months (range 7–360). Results: Mean inter-rater reliability was 0.79 for intensity, 0.75 for frequency and 0.62 for affective response (ICC). The limits of agreement were wide and rater bias was significant for 6/27 ratings. Mean intra-rater reliability was 0.70 for intensity, 0.77 for frequency and 0.69 for affective response (ICC). For site-of-pain inter-rater reliability ranged from 0.156 (to 0.385 (and intrarater reliability ranged from 0.300 (to 0.559 (. Conclusions: Although inter-rater reliability was acceptable for intensity and frequency there was a consistently large systematic bias between pairs of raters. Agreement might be improved if a standardized assessment procedure was used and/or if training in pain behaviour interpretation was provided.