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PubMed2003

Classic papers in Urology.

OBJECTIVE: Most clinicians are aware of the importance of using "evidence based medicine" to support their clinical practice, but where does the evidence come from? The aim of this study was to examine the concordance between papers deemed "important" by urologists compared with those selected by the more objective criteria of the citation index. METHOD: To achieve this, two approaches were used; firstly "experts" in various fields of urology were asked to select what they felt were classic papers and secondly urology journals were searched to find the 100 most cited papers for 1982-1997 and 1935-1997. The results of both of these "league tables" were then combined. RESULTS: The most cited papers varied depending on the time period studied. When the experts' selections were combined with those obtained via citation index it was found that the experts had chosen papers with a high citation index from non-urological as well as urological journals. CONCLUSION: It is possible to collate the classic papers within urology and the most effective means of doing so is to combine objective selection with expert choice. This is an exercise that can be repeated within any specialty.

Bibliometrics↗

PubMed2000

Simplified screening for organic acidemia using GC/MS and dried urine filter paper: a study on neonatal mass screening.

A simplified method for organic acidemia screening using GC/MS, the urease/direct method, is now available. To establish a practical screening system for organic acidemias, we studied the usefulness of dried urine filter paper (filter paper urine) and the application of a personal computer-based system of automated metabolic profiling and interpretation (automated system) that we earlier developed. In a comparison of filter paper urine with liquid urine, creatinine levels ranging from 4.6 to 122.5 mg/dl, showed an excellent correlation (r=0.9554), when the volumes of blotted urine and distilled water soaked were the same. Recovery of all 17 compounds except for citrate was similar between liquid and filter paper urine. CV values of 22 compounds tested ranged from 5.5 to 22.4% in the liquid urine, and from 7.7 to 29.8% in the filter paper urine. The CV values in stable isotope dilution analysis were much smaller in all nine compounds tested. As to the stability of compounds, the percentage changes to values at day 0 were within about +/-25% on day 28. We compiled GC/MS data, including methylene unit values, quantifying and confirming ions of 163 different organic acids and others, to use the automated system. We analyzed specimens from 55 patients with 17 different metabolic disorders. In 54 of the 55 specimens, the correct diagnosis was successfully indicated. Neonatal mass screening for organic acidemias warrants ongoing attention using this simplified method and filter paper urine.

Acidosis↗

PubMed2001

Abstract to publication ratio for papers presented at scientific meetings: how does emergency medicine compare?

OBJECTIVES: The aims of the present study were to determine the publication rate of abstracts presented by Australasian emergency physicians at major emergency medicine meetings and to identify the site of publication of papers. METHOD: All free paper abstracts presented (oral and poster) by Australasian emergency physicians and trainees at five Australasian College for Emergency Medicine/Australasian Society for Emergency Medicine and International Conference on Emergency Medicine meetings between 1995 and 1998 were identified retrospectively from conference programmes. In order to determine whether or not the abstract had been published, the PubMed database (http://www4.ncbi.nlm.nih.gov/PubMed/) was searched using the presenter's name and key words from the abstract. In addition, a hand search of the non-abstracted journal Emergency Medicine was conducted. RESULTS: Of the 207 free paper abstracts identified, 73 (35%) had been published as full articles. Papers were published in a variety of journals; however, Emergency Medicine accounted for almost half the published papers. The mean time between presentation and publication was 12.6 months (median 11 months). CONCLUSION: The abstract to publication rate for papers presented by Australasian emergency physicians and trainees at Australasian College for Emergency Medicine/Australasian Society for Emergency Medicine and International Conference on Emergency Medicine meetings is 35%, which is lower than that reported by some other established specialities, but comparable to rates reported for US-based national and international emergency medicine meetings. Future research should look at barriers to the publication of findings and ways to assist the publication process.

Abstracting and Indexing↗

PubMed2004

BioRAT: extracting biological information from full-length papers.

MOTIVATION: Converting the vast quantity of free-format text found in journals into a concise, structured format makes the researcher's quest for information easier. Recently, several information extraction systems have been developed that attempt to simplify the retrieval and analysis of biological and medical data. Most of this work has used the abstract alone, owing to the convenience of access and the quality of data. Abstracts are generally available through central collections with easy direct access (e.g. PubMed). The full-text papers contain more information, but are distributed across many locations (e.g. publishers' web sites, journal web sites and local repositories), making access more difficult. In this paper, we present BioRAT, a new information extraction (IE) tool, specifically designed to perform biomedical IE, and which is able to locate and analyse both abstracts and full-length papers. BioRAT is a Biological Research Assistant for Text mining, and incorporates a document search ability with domain-specific IE. RESULTS: We show first, that BioRAT performs as well as existing systems, when applied to abstracts; and second, that significantly more information is available to BioRAT through the full-length papers than via the abstracts alone. Typically, less than half of the available information is extracted from the abstract, with the majority coming from the body of each paper. Overall, BioRAT recalled 20.31% of the target facts from the abstracts with 55.07% precision, and achieved 43.6% recall with 51.25% precision on full-length papers.

Abstracting and Indexing↗

PubMed1980

Electrophoretic transfer of DNA, RNA and protein onto diazobenzyloxymethyl (DBM) - paper.

A method has been developed for the electrophoretic transfer of DNA, RNA, protein and ribonucleoprotein particles from a variety of gels onto diazobenzyloxymethyl (DBM) - paper. Conditions for the electrophoretic transfer of these macromolecules have been optimized to allow for nearly quantitative transfer and covalent coupling. DNA and RNA electrophoretically transferred to DBM-paper retain their ability to hybridize with specific probes. The high efficiency of transfer and the high capacity of DBM-paper for nucleic acids makes possible the sensitive detection of specific nucleotide sequences. Similar efficiency is achieved in electrophoretic transfer and covalent coupling of proteins to DBM-paper. Macromolecules can also be electrophoretically transferred and bound to DBM-paper incapable of covalent bond formation. Their elution from the paper in high salt provides a new and useful preparative method for isolation of DNA, RNA and protein.

Coliphages↗

PubMed2005

Group-based Yule model for bipartite author-paper networks.

This paper presents a model for author-paper networks, which is based on the assumption that authors are organized into groups and that, for each research topic, the number of papers published by a group is based on a success-breeds-success model. Collaboration between groups is modeled as random invitations from a group to an outside member. To analyze the model, a number of different metrics that can be obtained in author-paper networks were extracted. A simulation example shows that this model can effectively mimic the behavior of a real-world author-paper network, extracted from a collection of 900 journal papers in the field of complex networks.

Journal Article↗

PubMed1990

Neonate blood IgE levels on filter paper as indicators of atopic disease.

Measurements of IgE levels in the blood of neonates were investigated using filter paper for blood collection in mass screening of congenital metabolic disorders. Time-resolved fluoroimmunometric assay system for the measurement of filter paper blood IgE levels was also studied. In an analysis of the present results, IgE values of at least 0.015U/ml, the measurement limit, were considered as high. High IgE levels in filter paper blood were seen in 28 (7.2%) of the 389 cases. When the relation with serum IgE levels at 18 months of age was investigated in 134 of 389 subjects, high serum IgE levels were also found in about 86.7% of the subjects with high IgE levels in filter paper blood. In addition, when the relation between family history of atopic disease and presence of atopic disease in the first 18 months of age was investigated in 203 of the 389 subjects, about 90% of the subjects with a family history of atopic disease and high IgE levels in filter paper blood developed atopic disease. Since filter paper blood is routinely collected in Japan, IgE levels in this blood should be widely checked for the prediction of onset of atopic disease in infants.

Female↗

PubMed2000

Measurement of in vivo rectal mucosal cytokine and eicosanoid production in ulcerative colitis using filter paper.

BACKGROUND: Excessive mucosal generation of cytokines and eicosanoids has been reported in vitro in ulcerative colitis (UC) using traumatising biopsy techniques, and in vivo using time consuming rectal dialysis. AIMS: To validate a simple filter paper technique to profile rectal mucosal production of cytokines and eicosanoids in vivo in patients with UC compared with controls. PATIENTS: Forty one patients with UC (21 with active disease) and 16 controls were studied. METHODS: In vitro, recovery of known concentrations of cytokine or mediator applied to filter papers was measured by ELISA following incubation in buffer. In vivo, patients and controls had filter papers apposed to the rectal mucosa briefly through a rigid sigmoidoscope. Filter papers were then incubated prior to assay by ELISA. RESULTS: In vitro validation studies showed that the filter paper technique could be used to measure mucosal release of interleukin-1beta (IL-1beta), tumour necrosis factor alpha (TNF-alpha), thromboxane B(2) (TXB(2)), and prostaglandin E(2) (PGE(2)), but not interferon gamma (IFN-gamma). Mucosal release of IL-1beta, TNF-alpha, TXB(2) and PGE(2) were significantly increased in active UC (p=0.001) and correlated directly with disease activity (p=0.02). CONCLUSIONS: The filter paper technique confirmed increased rectal mucosal release of cytokines and eicosanoids in UC, in proportion to disease activity. The simplicity, safety and speed of the technique make it a practicable option for use in the outpatient clinic to study the pathogenesis of inflammatory bowel disease, and potentially its response to treatment.

Adult↗

PubMed2006

Teaching the effects of gravity and intravascular and alveolar pressures on the distribution of pulmonary blood flow using a classic paper by West et al.

"Distribution of blood flow in isolated lung; relation to vascular and alveolar pressures" by J. B. West, C. T. Dollery, and A. Naimark (J Appl Physiol 19: 713-724, 1964) is a classic paper, although it has not yet been included in the Essays on the American Physiological Society Classic Papers Project (http://www.the-aps.org/publications/classics/). This is the paper that originally described the "zones of the lung." The final figure in the paper, which synthesizes the results and discussion, is now seen in most textbooks of physiology or respiratory physiology. The paper is also a model of clear, concise writing. The paper and its final figure can be used to teach or review a number of physiological concepts. These include the effects of gravity on pulmonary blood flow and pulmonary vascular resistance; recruitment and distention of pulmonary vessels; the importance of the transmural pressure on the diameter of collapsible distensible vessels; the Starling resistor; the interplay of the pulmonary artery, pulmonary vein, and alveolar pressures; and the vascular waterfall. In addition, the figure can be used to generate discovery learning and discussion of several physiological or pathophysiological effects on pulmonary vascular resistance and the distribution of pulmonary blood flow.

Gravitation↗

PubMed2006

Using a classic paper by Gottschalk and Mylle to teach the countercurrent model of urinary concentration.

Most undergraduates lack the scientific background to read and appreciate much of the primary literature in physiology. Even when the underlying concepts are elegantly simple, the inherent complexity of contemporary papers often makes the work inaccessible to them. However, with a little help, they can be guided to an understanding of the creative thought processes that underlie the research and to appreciate its significance. This is especially true of many classic papers in physiology that often rely on easily comprehensible techniques. Moreover, the American Physiological Society (APS) has invited prominent scientists to select important papers in their fields and to write essays that both put the work into historical context and explain why it is scientifically important. The APS Legacy Project makes these classic papers freely available online. One such paper by Gottschalk and Mylle presents data from a series of micropuncture studies that confirm all of the predictions of the countercurrent exchange model of concentrated urine production (2). The included handout of questions for discovery learning and teaching points suggest ways to use the paper as an instructional resource.

Animals↗

PubMed1999

Disparities in the geographical distribution of authorship between invited and peer reviewed papers.

Fifty issues of the British Medical Journal (BMJ), The Lancet, The British Journal of Psychiatry and Psychological Medicine were scrutinized. Papers were designated as invited or peer reviewed and the geographical location of the first author was recorded. For UK-based authors, the latitude and longitude of the host institution was noted and was allocated to one of the UK regions. Of invited papers 805 of 1227 (66%) were by UK-based authors compared with 1442 of 2896 peer reviewed papers (50%), odds ratio 1.92 (95% CI 1.67-2.21) with a similar pattern prevailing in each of the four journals. Within the UK, authorships of invited versus peer reviewed papers showed a preponderance of invited authors based in southeast England, odds ratio 1.30 (95% CI 1.09-1.56). For individual Journals, the Lancet and the British Journal of Psychiatry showed fewer regional disparities in authorship than the BMJ and Psychological Medicine. These disparities may lead to nationalism and parochiality in the content of invited papers. Journal editors may wish to review selection practices for authorship of invited papers.

Authorship↗

PubMed1983

pH testing paper for measurement of intragastric acidity: an assessment.

Regular evaluation of the pH of aspirated gastric juice is an important part of the routine prevention of the stress ulceration syndrome. This study has examined the use of commercially available pH paper for this purpose. Both clear buffer solutions and samples of gastric aspirate were used to assess the reliability of four products, Merck Universal pH Indicator strips (Art. 9535), Lyphan Universal pH Indicator paper, Whatman Wide Range pH paper and Macherey-Nagel Universal pH paper. The results show that the Merck strips and Lyphan paper are very reliable for measuring gastric aspirate pH and that intensive care nursing staff can make accurate observations when using these papers.

Gastric Acidity Determination↗

PubMed2003

Learning biology through research papers: a stimulus for question-asking by high-school students.

Question-asking is a basic skill, required for the development of scientific thinking. However, the way in which science lessons are conducted does not usually stimulate question-asking by students. To make students more familiar with the scientific inquiry process, we developed a curriculum in developmental biology based on research papers suitable for high-school students. Since a scientific paper poses a research question, demonstrates the events that led to the answer, and poses new questions, we attempted to examine the effect of studying through research papers on students' ability to pose questions. Students were asked before, during, and after instruction what they found interesting to know about embryonic development. In addition, we monitored students' questions, which were asked orally during the lessons. Questions were scored according to three categories: properties, comparisons, and causal relationships. We found that before learning through research papers, students tend to ask only questions of the properties category. In contrast, students tend to pose questions that reveal a higher level of thinking and uniqueness during or following instruction with research papers. This change was not observed during or following instruction with a textbook. We suggest that learning through research papers may be one way to provide a stimulus for question-asking by high-school students and results in higher thinking levels and uniqueness.

Curriculum↗

PubMed2000

[Development and evaluation of a local area network system to make drug information paper for inpatient--adaptation to characteristics of diseases, and expansibility to other hospitals and the Internet].

We developed and evaluated a local area network system to make drug information papers. Because pharmacists should explain drug information both orally and using papers to patients in response to their understanding and characteristics of their diseases. The merit of this system is as follows: pharmacists can use it without any education for its operation; most data can be inputted by selection from the lists and automatic reference; the data are adjustable for individuals; different contents are available for different wards; multiple users can access the same data file. Input data in this system are available for making explanation papers on the medical examination of outpatients, and making a plan for pharmaceutical care and guidance services. This system is also available in other hospitals, and on the internet. First, we surveyed the time required for preparing drug information papers. Making a hand written paper for typical patient takes 395 sec. for manuscript, 160 sec. with the system using text data only, and 178 sec. with the system using text and picture data. Next, we surveyed 27 patients' views on the addition of drug pictures to drug information papers, and with the result that 19 patients thought it very good. Last, we surveyed 13 ward pharmacists about their usage of this system. We found that 8 pharmacists used frequently this system, and 3 pharmacists used the same file in the same hours at the maximum.

Aged↗

PubMed2004

Reflectance study of compressed paper.

Reflectance of three paper grades was investigated using a pressure gauge, an imaging system, and a spectrophotometer. It was observed that under high pressure, dark-colored areas appear in paper when using the imaging system. The area of the dark pattern increases as the pressure is raised. Reflectance measurements as a function of wavelength confirmed that the dark patterns appear due to the contact of the paper and the probe window of the pressure gauge. Based on results by other researchers the amount and the nature of optical contact observed depends on structural properties of paper such as surface roughness, formation, and compressibility. Although there are differences in the spectral properties of different paper grades they all share the common feature that the reflectance is decreasing as a function of the applied pressure. An empiric result for the fine and the super-calendered (SC) paper samples measured is that they both have an exponential dependence of total reflectance as a function of applied pressure when the illumination wavelength is kept constant.

Journal Article↗

PubMed1976

Facilitating paper recycling: effects of prompts, raffles, and contests.

The effects of prompts and reinforcement to promote paper recycling were compared in six university dormitories. For a Prompt condition, residents were urged to recycle paper for ecological reasons via flyers distributed to each room. For a Raffle contingency, residents were given one raffle ticket for every pound of paper brought to a collection center. For a Contest contingency, two dorms were paired and the dorm whose residents delivered the most paper won $15 for its treasury. Contingency awareness was strengthened via a flyer placed under the door of each resident's room. Flyers alone had little effect in increasing paper-recycling behaviors, but the raffle (substantially) and the contest (somewhat) increased the amount of paper brought to a dorm's recycling center. Students whose rooms were closest to the collection center showed the greatest participation. Removal of the reinforcement contingencies resulted in a return to baseline levels.

Journal Article↗

PubMed1993

The authorship and fate of international health papers submitted to the American Journal of Public Health in 1989.

We reviewed the authorship characteristics, editorial processing, and final fate of 126 papers dealing with data from countries other than the United States and Canada and submitted to the American Journal of Public Health in 1989. The acceptance rate of these international health papers was 22%, similar to that of all papers (25%). Authors from developed countries had higher acceptance rates than authors from developing countries, but the highest acceptance rate (36%) was for international health papers with joint authorship from both developed and developing countries. Of 83 rejected papers, 72% were published in other journals. Of these, 45% were published in journals covered by Index Medicus, a figure similar to that for all papers rejected by the Journal.

Authorship↗

PubMed1996

Coauthors' contributions to major papers published in the AJR: frequency of undeserved coauthorship.

OBJECTIVE: Over half of the major papers published in the American Journal of Roentgenology (AJR) have five or more coauthors. This project was designed to evaluate the specific contributions of coauthors and the prevalence of undeserved authorship in major papers from institutions in the United States. MATERIALS AND METHODS: Questionnaires were mailed to the first author of 275 major papers from institutions in the United States that were published in the AJR in 1992 and 1993. Questions focused on coauthors' contributions to research design, data collection, data analysis, and manuscript preparation, and on undeserving authorship. RESULTS: One hundred ninety-six (72%) of the surveys were returned. Ninety-nine percent of first authors, 75% of second authors, fewer than half of third authors, and one third of fourth authors and beyond were said to have contributed to at least three of the following: research design, data collection, data analysis, and manuscript preparation (p < .02). A strong correlation was indicated between authorship position and contribution (r = -.69, p < .001), with a mean overall contribution of 63 +/- 17% (mean +/- SD) for the first author, 20 +/- 12% for the second author, 10 +/- 7% for the third author, 7 +/- 6% for the fourth author, and 5 +/- 5% for all other authors. Coauthors were listed in decreasing order of contribution in 70% of articles. However, the last author was the second major contributor in 10% of articles with three or more authors. The incidence of "undeserved" coauthors increased from 9% on papers with three authors to 30% on papers with more than six authors (mean, 17%; r = .97; p < .001). Undeserved authorship was attributed largely to individuals who contributed only cases (29%) or who created a sense of obligation or fear in the first author (40%). Manuscripts were more likely to include an undeserved coauthor when the first author was a nontenured staff member (45%) than when he or she was tenured faculty (28%) (p < .02). When decision about authorship were made at project conception, there were fewer coauthors (3.9 versus 5.4, p < .02) and a lower incidence of manuscripts with undeserving coauthors (23% versus 47%, p < .01). The final manuscript was read by all coauthors in 80% of manuscripts, and all coauthors were thought to understand the manuscript to the extent they could publicly defend it in 78% of manuscripts. The most commonly cited reason that otherwise honest individuals accept undeserved authorship was academic promotion. CONCLUSION: Undeserved authorship is a common and serious problem that is motivated primarily by academic promotion policies. The first two authors are said to account for the preponderance of work in almost all major papers.

Authorship↗