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PubMed2005

Finding support for educational projects in anatomy: tips, tools, and lessons learned.

This article is based on a presentation of the same name given on 20 April 2004 at a symposium entitled "Faculty Development: Funding Resources for Education Projects" at the annual meeting of the American Association of Anatomists in Washington, DC. It discusses various lessons learned by the authors from their own work on the development of an educational tool and the assessment of its use with funding from an educational research grant, as well as tips and tools gathered from other education researchers. The material is organized into two sections. The first provides information and suggestions useful in the development of an educational project in anatomy and the preparation of the grant application. The second consists of insights that may help ensure that the funded grant is successful.

Anatomy↗

PubMed2005

New tool for an old problem: can RNAi efficiently resolve the issue of genetic redundancy?

RNA interference (RNAi) has become a generally accepted tool for inhibiting gene expression in many laboratory organisms. Nagel et al.,(1) in a recent paper, give an example of how this tool can also be used to address the question of genetic redundancy. Their focus was on the redundancy in Drosophila melanogaster of the Enhancer of split gene complex [E(spl)-C] which comprises seven highly related genes. Their somewhat conflicting findings are probably the typical scenario for most RNAi experiments: some expected results and some surprises.

Animals↗

PubMed2006

Process parameter shifting: Part II. Biphasic cultivation-A tool for enhancing the volumetric productivity of batch processes using Epo-Fc expressing CHO cells.

Regulation of cell growth and protein expression potentially results in a sustainable enhancement of the volumetric productivity in a fermentation process. Following a biphasic cultivation strategy the process initially passes through a cell proliferation phase to generate a sufficiently high viable cell mass. In the subsequent production phase cells are maintained viable and productive without significant cell proliferation leading to increased viable cell days and product yields. In a previous work we have shown that the well directed alteration of the process environment based on process parameter shifting is a promising tool to regulate cell growth and protein expression. In continuation of this work we investigated process parameters which have been identified to affect cell proliferation in favor of an increased specific productivity and total product yield in a series of biphasic batch cultivation experiments. In most of these processes the integral of viable cells and the specific productivity were increased leading to a significant improvement of both final product concentration and volumetric productivity. In addition, combined parameter shifts (pH 6.90/30 degrees C and pH 6.90/33 degrees C) exerted a synergistic effect on product quality. The loss of product sialylation which occurred at reduced temperatures was prevented by simultaneously reducing the external pH. In conclusion, biphasic cultivation based on combined shifting of process parameters is a suitable tool for controlling cell proliferation and protein expression of mammalian cells in a batch bioreactor leading to enhanced volumetric productivities and therefore offers an enormous potential for bioprocess optimization.

Animals↗

PubMed2001

Teaching anatomy with surgeons' tools: use of the laparoscope in clinical anatomy.

The purpose of this study was to establish the feasibility of laparoscopy in embalmed cadavers to teach abdominal gross anatomy. One cadaver was selected based on body habitus and absence of previous abdominal operations. A standard trocar was used to enter the abdomen at the umbilicus. Two trocars were placed in the left upper quadrant. Pneumoperitoneum was achieved with continuous CO(2) pressure. Liver retraction was achieved percutaneously, exposing the porta hepatis and the gallbladder. The dissection was done with four first-year medical students using standard laparoscopic equipment. Following this, the demonstration was projected over multiple monitors so that all students could participate. Laparoscopic dissection in an embalmed cadaver is feasible and an excellent educational tool for both the medical student and the dissector. The dissector has the opportunity to manipulate laparoscopic tools in a human model closely paralleling operative experience, and the students have an opportunity to learn abdominal anatomy from a clinical perspective. Laparoscopic examination and dissection of fresh cadavers has been used for training surgeons on new procedures such as colon resection, antireflux procedures, and cholecystectomy. There is no report of this same technology used in embalmed cadavers to teach basic anatomy. This approach allows first-year medical students to learn the anatomy while exposing them to the technology currently used in surgical practice, and it affords surgical residents and students additional opportunities to practice laparoscopic skills.

Abdomen↗

PubMed2007

Anatomy reports on the internet: a web-based tool for student reports on cadaveric findings.

The difference between the idealization of anatomy atlases and the reality of human cadavers often frustrates gross anatomy students. To encourage students to celebrate rather than protest these differences, we describe a web site ARI (Anatomy Reports on the Internet) that allows students to document cadaveric findings online with photographs and text. We used several web languages for site construction, including mysql, php, html, and javascript. Faculty tools allow instructors to upload digital images of the structures, add relevant commentary, view and delete images, review submitted reports, and examine database statistics. Student tools allow dissection groups to choose and comment on images, enter and edit reports, and read reports submitted by other students. During the first two years of the site's use (2000-2001, 2002-2003), every dissection group at our institution submitted at least one report. Technical support requests were minimal.

Anatomy↗

PubMed2004

Tools for glycomics: mapping interactions of carbohydrates in biological systems.

The emerging field of glycomics has been challenged by difficulties associated with studying complex carbohydrates and glycoconjugates. Advances in the development of synthetic tools for glycobiology are poised to overcome some of these challenges and accelerate progress towards our understanding of the roles of carbohydrates in biology. Carbohydrate microarrays, fluorescent neoglycoconjugate probes, and aminoglycoside antibiotic microarrays are among the many new tools becoming available to glycobiologists.

Carbohydrate Metabolism↗

PubMed2007

Solving multicomponent chiral separation challenges using a new SFC tandem column screening tool.

A tool for improved tandem column chiral supercritical fluid chromatography (SFC) method development screening was prepared by modification of a commercial analytical SFC instrument with two different software-controllable, six position high-pressure column selection valves, each controlling a bank of five different columns and a pass through line. The resulting instrument, which has the ability to screen 10 different individual columns and 25 different tandem column arrangements, is a useful tool for facilitating the screening of tandem column SFC arrangements for separation of complex mixtures of stereoisomers or other multicomponent mixtures. Strategies for optimal use of the instrument are discussed, and several examples of the use of the instrument in developing tandem SFC methods for resolution of multicomponent mixtures are presented.

Chromatography, Supercritical Fluid↗

PubMed2002

Use of adenosine as a diagnostic tool for dual atrioventricular nodal pathways: response of control patients to incremental doses of adenosine.

BACKGROUND: Adenosine at low doses preferentially blocks fast over slow pathway conduction in patients with dual atrioventricular (AV) nodal physiology and typical AV nodal reentrant tachycardia (AVNRT). During atrial pacing, this effect is manifested as an abrupt increase in the AH interval with low doses of adenosine. This demonstration of dual AV nodal physiology may be useful as a diagnostic tool during electrophysiologic studies in patients with supraventricular tachycardia who are not easily inducible, as clear demonstration of dual AV nodal pathways may indicate that AVNRT is a likely diagnosis and that further attempts at arrhythmia induction should be tailored in that direction. However, to be a useful test, adenosine should not cause an abrupt increase in AH interval in patients without dual AV nodal physiology. HYPOTHESIS: This study was designed to investigate the prevalence of dual AV nodal pathways with administration of adenosine in patients with no history suggestive of AVNRT. METHODS: Thirty-seven patients who had no prior history of AVNRT and were undergoing electrophysiologic study for standard indications were enrolled. Baseline Wenckebach cycle length (WCL) and AV nodal effective refractory periods were measured at atrial pacing cycle lengths of 400 and 600 ms. The atrium was then paced at WCL + 50 ms, and WCL + 100 ms, while incrementally larger doses of intravenous adenosine were administered until AV nodal block occurred. RESULTS: The mean (+/- standard deviation) doses of adenosine required to cause AV nodal block while pacing at WCL + 50 ms and WCL + 100 ms were 7.1 +/- 3.9 and 7.4 +/- 4.5 mg, respectively. In 1 of 37 patients (2.7%, 95% confidence interval 0-8%), an abrupt prolongation of the AH interval was seen with the administration of adenosine during atrial pacing as well as during the atrial refractory period determination. In all other patients, no dual AV nodal physiology was demonstrated during the refractory period determination, and there were only gradual changes in the AH interval with atrial pacing during administration of adenosine. CONCLUSION: Among patients with no history suggestive of AV nodal reentrant tachycardia, only 2.7% have clinically silent dual AV nodal pathways using this method. Incremental adenosine infusion during electrophysiologic study can be used as a highly specific diagnostic tool for patients with dual AV nodal pathways.

Adenosine↗

PubMed2006

Causal mapping as a tool to mechanistically interpret phenomena in cell motility: application to cortical oscillations in spreading cells.

Biological processes that occur at the cellular level and consist of large numbers of interacting elements are highly nonlinear and generally involve multiple time and spatial scales. The quantitative description of these complex systems is of great importance but presents large challenges. We outline a new systems biology approach, causal mapping (CMAP), which is a coarse-grained biological network tool that permits description of causal interactions between the elements of the network and overall system dynamics. On one hand, the CMAP is an intermediate between experiments and physical modeling, describing major requisite elements, their interactions and paths of causality propagation. On the other hand, the CMAP is an independent tool to explore the hierarchical organization of cell and the role of uncertainties in the system. It appears to be a promising easy-to-use technique for cell biologists to systematically probe verbally formulated qualitative hypotheses. We apply the CMAP to study the phenomenon of contractility oscillations in spreading cells in which microtubules have been depolymerized. The precise mechanism by which these oscillations are governed by a complex mechano-chemical system is not known but the data observed in experiments can be described by a CMAP. The CMAP suggests that the source of the oscillations results from the opposing effects of Rho activation leading to a decreased level of myosin light chain phosphatase and a cyclic calcium influx caused by increased membrane tension and leading to a periodically enhanced activation of myosin light chain kinase.

Animals↗

PubMed2006

Validation of a tool for identifying women at high risk for hereditary breast cancer in population-based screening.

BACKGROUND: Recent scientific advances provide the opportunity to identify women in the general population at increased breast cancer risk and to offer effective early detection and disease prevention interventions. METHODS: A pedigree assessment tool (PAT) was designed to identify women in primary care settings who are at increased risk for hereditary breast cancer, including potential BRCA mutation carriers. The PAT is a simple point-scoring system based on family cancer history with points weighted to account for features associated with a higher probability that a BRCA mutation is present. The ability of the PAT and the Gail model to accurately identify potential BRCA mutation carriers in 3,906 women without a personal history of breast cancer presenting for a screening mammogram at a community hospital was tested. RESULTS: Eighty-six (2.2%) women had a family history indicative of a high probability (>10%) that a BRCA mutation was present within the family. The PAT performed better than the Gail model in correctly assigning women to the "high BRCA probability" cohort. The area under the receiver operating characteristic (ROC) curve for the PAT was 0.9625 compared with 0.389 and 0.5861 for the Gail model 5-year and lifetime risk estimates, respectively. At the optimal threshold score, the PAT performed with 100% sensitivity and 93% specificity. CONCLUSIONS: The PAT is a simple and accurate tool for identifying women at risk for the hereditary breast cancer syndromes that can be employed as part of a comprehensive breast cancer risk-screening strategy in the primary care setting.

Breast Neoplasms↗

PubMed1993

Germinal center analysis with the tools of mathematical morphology on graphs.

Only few studies devoted to quantitative analysis of tissue architecture have been performed. The analysis of neighborhood relationships between cells, using graphs and mathematical morphology (MM), constitutes one approach. We propose to analyse quantitatively the architecture of a tissue with the tools of MM on graphs. The use of graphs seems best suited to take into account the neighborhood relationships between cells, independently from their mutual distances: two cells are considered as neighbors if no interfering cell is placed in a given sense between them. Such neighboring cells are linked by an arc in a graph. On such a graph, all tools of MM may be applied. We investigate two of them in the present work: (1) the distance transforms permits to analyse the repartition of a cellular population A relative to population B, (2) the size distribution permits to analyse the tendancy of a cell population to form clusters. We have applied this method using Gabriel's graph, derived from the Voronoï diagram, to determine the "zone of influence" of a cell. We have analysed the neighborhood relationships between cells in germinal centers (GC) from lymph nodes. Twelve hyperplastic GCs from follicular hyperplasia (FH) and 5 neoplastic GCs from small cleaved cell follicular lymphoma (++SCCFL) have been studied; 2 microns hematoxylin-eosin plastic embedded sections have been analysed. Cell nuclei have been identified manually by the observer by giving a numerical and image color code. Gabriel's graphs have been constructed with all centrofollicular cells. Subgraphs with only lymphoid cells, large cells or small cleaved cells have also been studied. The application of MM transformations on the graphs using software package Morphograph has allowed a quantitative description of cell distribution in the tissue. The distances of centrofollicular lymphoid cells from the periphery of the GCs (mantle zone), from nonlymphoid cells as macrophages located within the GCs and between large lymphoid cells and small lymphoid cells have been determined in FH and SCCFL. Using iterative closings and openings, we have detected aggregates of small and large cells and characterized their size and distribution in the GCs. The application of this method on lymph node biopsy has allowed a quantitative description and comparison of GCs in different pathological conditions.

Biopsy↗

PubMed2006

Iterative restaining as a pivotal tool for n-color immunophenotyping by slide-based cytometry.

AIM: Slide-based cytometry (SBC) allows to "ask a cell a second time." We used this tool for detailed immunophenotyping of peripheral blood leukocytes (PBLs). METHODS: PBLs primarily stained for CD-markers and DNA were immobilized on a glass slide and analyzed by laser scanning cytometry. Then, iterative restaining was applied for a second and a third analysis. Based on the cells' fixed location, analyses were merged on a single-cell level. RESULTS: We analyzed six virtual immunostainings by "recycling" the PE-channel for four CD-markers. CONCLUSION: Iterative restaining might prove to be a pivotal tool for n-color immunophenotyping exclusive to SBC concepts.

Antibodies↗

PubMed2005

Peripheral blood MDS score: a new flow cytometric tool for the diagnosis of myelodysplastic syndromes.

BACKGROUND: Myelodysplastic syndromes (MDS) are a heterogeneous group of hematopoietic disorders diagnosed using morphologic and clinical findings supported by cytogenetics. Because abnormalities may be subtle, diagnosis using these approaches can be challenging. Flow cytometric (FCM) approaches have been described; however the value of bone marrow immunophenotyping in MDS remains unclear due to the variability in detected abnormalities. We sought to refine the FCM approach by using peripheral blood (PB) to create a clinically useful tool for the diagnosis of MDS. METHODS: PB from 15 patients with MDS was analyzed by multiparametric flow cytometry using an extensive panel of monoclonal antibodies. Patterns of neutrophil antigen expression were compared with those of normal controls (n = 16) to establish light scatter and/or immunophenotypic abnormalities that correlated with MDS. A scoring algorithm was developed and validated prospectively on a blinded patient set. RESULTS: PB neutrophils from patients with MDS had lower side scatter and higher expression of CD66 and CD11a than did controls. Some MDS PB neutrophils demonstrated abnormal CD116 and CD10 expression. Because none of these abnormalities proved consistently diagnostic, we sought to increase the power of the assay by devising a scoring system to allow the association of multiple abnormalities and account for phenotypic variations. The PB MDS score differentiated patients with MDS from controls (P < 0.0001) in the test set. In a prospective validation, the PB MDS score successfully identified patients with MDS (sensitivity 73%, specificity 90%). CONCLUSIONS: FCM analysis of side scatter and only four additional immunophenotypic parameters of PB neutrophils using the PB MDS score proved more sensitive than standard laboratory approaches and may provide an additional, more reliable diagnostic tool in the identification of MDS.

Aged↗

PubMed2003

Genetic and genomic tools for zebrafish research: the NIH zebrafish initiative.

The National Institutes of Health (NIH) has been a leading advocate of the zebrafish as a model organism for the study of vertebrate development, physiology, and disease. Genomic tools, developed with the support of NIH funding, have made zebrafish even more attractive as a genetic system and have stimulated research using this model. The NIH continues to provide support for new and existing community resources, such as the Zebrafish International Resource Center and the Zebrafish Information Network, research tool development and mutant screens, and a wide array of investigator-initiated studies that are using zebrafish to elucidate many aspects of vertebrate biology.

Animals↗

PubMed1998

Electrophoresis combined with novel mass spectrometry techniques: powerful tools for the analysis of proteins and proteomes.

Analytical and preparative electrophoresis separation techniques have been essential tools in protein biochemistry and the biological sciences in general. The combination of high resolution electrophoresis techniques with high performance analytical procedures has dramatically enhanced analytical protein biochemistry. In this report we describe the combination of electrophoretic separation techniques with electrospray ionization (ESI) tandem mass spectrometry (MS/MS). A series of different techniques, consisting of automated high performance liquid chromatography (HPLC)-MS/MS, capillary-HPLC-MS/MS, and solid phase extraction (SPE)-capillary zone electrophoresis (CZE)-MS/MS, are described in the context of the identification of high pmol to the low fmol amounts of proteins. Application of these powerful new tools for the analysis of proteins on a large proteome-wide scale is presented. Furthermore, the combination of orthogonal separation techniques, such as immobilized metal affinity chromatography (IMAC) with SPE-CZE-MS/MS, and IMAC followed by HPLC, and by SPE-CZE-MS/MS, are presented for the detailed investigation of post-translational modifications of specific proteins.

Amino Acid Sequence↗

PubMed2006

Multiplex_QA: an exploratory quality assessment tool for multiplexed electrophoretic assays.

Multiplex_QA is a data analysis tool for visualizing short- and long-term changes in the performance of multiplexed electrophoretic assays, particularly the commercial short tandem repeat (STR) kits used by the human forensic identity community. A number of quality metrics are calculated from the signal collected for the internal size standard included in nearly all multiplex assays. These quality metrics are related to the signal intensity, symmetry, retention, resolution, and noise of data collected by capillary electrophoresis systems. Interlocking graphical displays enable the identification of changes in the quality metrics with time, evaluation of relationships among the metrics, and detailed examination of electropherographic features of particularly interesting analyses. While primarily intended for exploring which metrics are most useful for documenting data quality, the current version of the tool is sufficiently robust for use by forensic scientists with an interest in data analysis and access to a fast desktop computer.

DNA↗

PubMed2002

High-efficiency gene transfer into adult fish: a new tool to study fin regeneration.

Zebrafish represents an excellent model to study the function of vertebrate genes (e.g., well-developed genetics, large number of mutants, and genomic sequencing in progress), inasmuch as we have tools to manipulate gene expression. Recent use of injected morpholinos in eggs provides a good method to " knockdown " gene expression in early development (Nasevicius and Ekker, 2000), and the "caged" RNA injected in eggs allows to overexpress a gene in a specific set of cells (Ando et al., 2001). However, a method to specifically modify gene expression in the juvenile or in the adult is still missing. Such a method would be a very powerful tool to understand gene function in differentiated tissues. We describe here an electroporation-based approach, which allows gene transfer in adult tissues. Its efficiency was assessed using a GFP (green fluorescent protein) dependent assay. We then used this method to disrupt the Fgf signalling pathway during the process of regeneration.

Animals↗

PubMed2007

Dementia care mapping as a research tool.

INTRODUCTION: Dementia Care Mapping (DCM) was originally developed as a clinical tool but has attracted interest as a potential observational measure of quality of life (QOL) and well-being of long-term care residents with dementia. DCM coding involves continuous observation over a 6-h period, with observers recording a Behavior Category Code (BCC, a recording of activity/interaction) and a Well/Ill Being (WIB) score at 5 min intervals. METHOD: Descriptive data from several different research teams on the distribution and psychometric properties of DCM data were compiled and summarized. RESULTS: Issues and problems identified include: complex scoring algorithms, inter-rater reliability of the BCCs, limited variability of WIB values, associations between resident characteristics and DCM assessments, rater time burden, and comparability of results across study settings. CONCLUSIONS: Despite the identified limitations, DCM has promise as a research measure, as it may come closer to rating QOL from the perspective of persons with dementia than other available measures. Its utility will depend on the manner in which it is applied and an appreciation of the measure's strength and limitations. Possible changes that might improve the reliability, validity, and practicality of DCM as a research tool include coding the predominant event (rather than the 'best' event), shortening the observation period, and adding '0' as a neutral WIB coding option.

Activities of Daily Living↗