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feat(xml-jats): parse XML JATS documents (#967)
* chore(xml-jats): separate authors and affiliations In XML PubMed (JATS) backend, convert authors and affiliations as they are typically rendered on PDFs. Signed-off-by: Cesar Berrospi Ramis <75900930+ceberam@users.noreply.github.com> * fix(xml-jats): replace new line character by a space Instead of removing new line character from text, replace it by a space character. Signed-off-by: Cesar Berrospi Ramis <75900930+ceberam@users.noreply.github.com> * feat(xml-jats): improve existing parser and extend features Partially support lists, respect reading order, parse more sections, support equations, better text formatting. Signed-off-by: Cesar Berrospi Ramis <75900930+ceberam@users.noreply.github.com> * chore(xml-jats): rename PubMed objects to JATS Signed-off-by: Cesar Berrospi Ramis <75900930+ceberam@users.noreply.github.com> --------- Signed-off-by: Cesar Berrospi Ramis <75900930+ceberam@users.noreply.github.com>
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tests/data/jats/bmj_sample.xml
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<?xml version="1.0" encoding="UTF-8"?>
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<!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Publishing DTD v1.1 20151215//EN" "JATS-journalpublishing1.dtd">
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<article article-type="research-article" dtd-version="1.1" xml:lang="en"
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xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" >
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<front>
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<journal-meta>
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<journal-id journal-id-type="pmc">bmj</journal-id>
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<journal-id journal-id-type="pubmed">BMJ</journal-id>
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<journal-id journal-id-type="publisher">BMJ</journal-id>
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<issn>0959-8138</issn>
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<publisher>
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<publisher-name>BMJ</publisher-name>
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</publisher>
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</journal-meta>
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<article-meta>
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<article-id pub-id-type="other">jBMJ.v324.i7342.pg880</article-id>
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<article-id pub-id-type="pmid">11950738</article-id>
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<article-categories>
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<subj-group>
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<subject>Primary care</subject>
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<subj-group>
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<subject>190</subject>
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<subject>10</subject>
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<subject>218</subject>
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<subject>219</subject>
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<subject>355</subject>
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<subject>357</subject>
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</subj-group>
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</subj-group>
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</article-categories>
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<title-group>
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<article-title>Evolving general practice consultation in Britain: issues of length and
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context</article-title>
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</title-group>
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<contrib-group>
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<contrib contrib-type="author">
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<name>
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<surname>Freeman</surname>
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<given-names>George K</given-names>
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</name>
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<role>professor of general practice</role>
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<xref ref-type="aff" rid="aff-a"/>
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</contrib>
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<contrib contrib-type="author">
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<name>
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<surname>Horder</surname>
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<given-names>John P</given-names>
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</name>
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<role>past president</role>
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<xref ref-type="aff" rid="aff-b"/>
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</contrib>
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<contrib contrib-type="author">
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<name>
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<surname>Howie</surname>
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<given-names>John G R</given-names>
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</name>
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<role>emeritus professor of general practice</role>
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<xref ref-type="aff" rid="aff-c"/>
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</contrib>
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<contrib contrib-type="author">
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<name>
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<surname>Hungin</surname>
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<given-names>A Pali</given-names>
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</name>
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<role>professor of general practice</role>
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<xref ref-type="aff" rid="aff-d"/>
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</contrib>
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<contrib contrib-type="author">
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<name>
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<surname>Hill</surname>
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<given-names>Alison P</given-names>
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</name>
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<role>general practitioner</role>
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<xref ref-type="aff" rid="aff-e"/>
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</contrib>
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<contrib contrib-type="author">
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<name>
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<surname>Shah</surname>
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<given-names>Nayan C</given-names>
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</name>
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<role>general practitioner</role>
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<xref ref-type="aff" rid="aff-b"/>
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</contrib>
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<contrib contrib-type="author">
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<name>
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<surname>Wilson</surname>
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<given-names>Andrew</given-names>
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</name>
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<role>senior lecturer</role>
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<xref ref-type="aff" rid="aff-f"/>
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</contrib>
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</contrib-group>
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<aff id="aff-a">Centre for Primary Care and Social Medicine, Imperial College of Science,
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Technology and Medicine, London W6 8RP</aff>
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<aff id="aff-b">Royal College of General Practitioners, London SW7 1PU</aff>
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<aff id="aff-c">Department of General Practice, University of Edinburgh, Edinburgh EH8 9DX</aff>
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<aff id="aff-d">Centre for Health Studies, University of Durham, Durham DH1 3HN</aff>
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<aff id="aff-e">Kilburn Park Medical Centre, London NW6</aff>
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<aff id="aff-f">Department of General Practice and Primary Health Care, University of Leicester,
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Leicester LE5 4PW</aff>
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<author-notes>
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<fn fn-type="con">
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<p>Contributors: GKF wrote the paper and revised it after repeated and detailed comments from
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all of the other authors and feedback from the first referee and from the <italic>BMJ</italic>
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editorial panel. All other authors gave detailed and repeated comments and cristicisms. GKF is
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the guarantor of the paper.</p>
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</fn>
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<fn>
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<p>Correspondence to: G Freeman <email>g.freeman@ic.ac.uk</email> </p>
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</fn>
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</author-notes>
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<pub-date date-type="pub" publication-format="print" iso-8601-date="2002-04-13">
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<day>13</day>
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<month>4</month>
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<year>2002</year>
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</pub-date>
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<volume>324</volume>
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<issue>7342</issue>
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<fpage>880</fpage>
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<lpage>882</lpage>
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<history>
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<date date-type="accepted" iso-8601-date="2002-02-07" publication-format="print">
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<day>7</day>
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<month>2</month>
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<year>2002</year>
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</date>
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</history>
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<permissions>
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<copyright-statement>Copyright © 2002, BMJ</copyright-statement>
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<copyright-year>2002, </copyright-year>
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</permissions>
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</article-meta>
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</front>
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<body>
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<p>In 1999 Shah<xref ref-type="bibr" rid="B1">1</xref> and others said that the Royal College of
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General Practitioners should advocate longer consultations in general practice as a matter of
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policy. The college set up a working group chaired by A P Hungin, and a systematic review of
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literature on consultation length in general practice was commissioned. The working group agreed
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that the available evidence would be hard to interpret without discussion of the changing context
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within which consultations now take place. For many years general practitioners and those who
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have surveyed patients' opinions in the United Kingdom have complained about short consultation
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time, despite a steady increase in actual mean length. Recently Mechanic pointed out that this is
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also true in the United States.<xref ref-type="bibr" rid="B2">2</xref> Is there any justification
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for a further increase in mean time allocated per consultation in general practice?</p>
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<p>We report on the outcome of extensive debate among a group of general practitioners with an
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interest in the process of care, with reference to the interim findings of the commissioned
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systematic review and our personal databases. The review identified 14 relevant papers. <boxed-text>
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<sec>
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<title>Summary points</title>
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<p> <list list-type="bullet">
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<list-item>
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<p>Longer consultations are associated with a range of better patient outcomes</p>
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</list-item>
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<list-item>
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<p>Modern consultations in general practice deal with patients with more serious and chronic
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conditions</p>
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</list-item>
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<list-item>
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<p>Increasing patient participation means more complex interaction, which demands extra
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time</p>
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</list-item>
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<list-item>
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<p>Difficulties with access and with loss of continuity add to perceived stress and poor
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performance and lead to further pressure on time</p>
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</list-item>
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<list-item>
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<p>Longer consultations should be a professional priority, combined with increased use of
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technology and more flexible practice management to maximise interpersonal continuity</p>
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</list-item>
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<list-item>
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<p>Research on implementation is needed</p>
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</list-item>
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</list> </p>
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</sec>
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</boxed-text> </p>
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<sec sec-type="subjects">
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<title>Longer consultations: benefits for patients</title>
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<p>The systematic review consistently showed that doctors with longer consultation times
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prescribe less and offer more advice on lifestyle and other health promoting activities. Longer
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consultations have been significantly associated with better recognition and handling of
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psychosocial problems<xref ref-type="bibr" rid="B3">3</xref> and with better patient
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enablement.<xref ref-type="bibr" rid="B4">4</xref> Also clinical care for some chronic illnesses
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is better in practices with longer booked intervals between one appointment and the next.<xref
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ref-type="bibr" rid="B5">5</xref> It is not clear whether time is itself the main influence or
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whether some doctors insist on more time.</p>
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<p>A national survey in 1998 reported that most (87%) patients were satisfied with the
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length of their most recent consultation.<xref ref-type="bibr" rid="B6">6</xref> Satisfaction
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with any service will be high if expectations are met or exceeded. But expectations are modified
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by previous experience.<xref ref-type="bibr" rid="B7">7</xref> The result is that primary care
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patients are likely to be satisfied with what they are used to unless the context modifies the
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effects of their own experience.</p>
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</sec>
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<sec>
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<title>Context of modern consultations</title>
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<p>Shorter consultations were more appropriate when the population was younger, when even a brief
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absence from employment due to sickness required a doctor's note, and when many simple remedies
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were available only on prescription. Recently at least five important influences have increased
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the content and hence the potential length of the consultation.</p>
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</sec>
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<sec>
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<title>Participatory consultation style</title>
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<p>The most effective consultations are those in which doctors most directly acknowledge and
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perhaps respond to patients' problems and concerns. In addition, for patients to be committed to
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taking advantage of medical advice they must agree with both the goals and methods proposed. A
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landmark publication in the United Kingdom was <italic>Meetings Between Experts</italic>, which
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argued that while doctors are the experts about medical problems in general patients are the
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experts on how they themselves experience these problems.<xref ref-type="bibr" rid="B8">8</xref>
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New emphasis on teaching consulting skills in general practice advocated specific attention to
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the patient's agenda, beliefs, understanding, and agreement. Currently the General Medical
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Council, aware that communication difficulties underlie many complaints about doctors, has
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further emphasised the importance of involving patients in consultations in its revised guidance
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to medical schools.<xref ref-type="bibr" rid="B9">9</xref> More patient involvement should give
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a better outcome, but this participatory style usually lengthens consultations.</p>
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</sec>
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<sec>
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<title>Extended professional agenda</title>
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<p>The traditional consultation in general practice was brief.<xref ref-type="bibr" rid="B2"
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>2</xref> The patient presented symptoms and the doctor prescribed treatment. In 1957 Balint
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gave new insights into the meaning of symptoms.<xref ref-type="bibr" rid="B10">10</xref> By 1979
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an enhanced model of consultation was presented, in which the doctors dealt with ongoing as well
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as presenting problems and added health promotion and education about future appropriate use of
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services.<xref ref-type="bibr" rid="B11">11</xref> Now, with an ageing population and more
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community care of chronic illness, there are more issues to be considered at each consultation.
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Ideas of what constitutes good general practice are more complex.<xref ref-type="bibr" rid="B12"
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>12</xref> Good practice now includes both extended care of chronic medical problems—for
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example, coronary heart disease<xref ref-type="bibr" rid="B13">13</xref>—and a public
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health role. At first this model was restricted to those who lead change (“early
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adopters”) and enthusiasts<xref ref-type="bibr" rid="B14">14</xref> but now it is
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embedded in professional and managerial expectations of good practice.</p>
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<p>Adequate time is essential. It may be difficult for an elderly patient with several active
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problems to undress, be examined, and get adequate professional consideration in under 15
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minutes. Here the doctor is faced with the choice of curtailing the consultation or of reducing
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the time available for the next patient. Having to cope with these situations often contributes
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to professional dissatisfaction.<xref ref-type="bibr" rid="B15">15</xref> This combination of
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more care, more options, and more genuine discussion of those options with informed patient
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choice inevitably leads to pressure on time.</p>
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</sec>
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<sec>
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<title>Access problems</title>
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<p>In a service free at the point of access, rising demand will tend to increase rationing by
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delay. But attempts to improve access by offering more consultations at short notice squeeze
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consultation times.</p>
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<p>While appointment systems can and should reduce queuing time for consultations, they have long
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tended to be used as a brake on total demand.<xref ref-type="bibr" rid="B16">16</xref> This may
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seriously erode patients' confidence in being able to see their doctor or nurse when they need
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to. Patients are offered appointments further ahead but may keep these even if their symptoms
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have remitted “just in case.” Availability of consultations is thus blocked.
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Receptionists are then inappropriately blamed for the inadequate access to doctors.</p>
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<p>In response to perception of delay, the government has set targets in the NHS plan of
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“guaranteed access to a primary care professional within 24 hours and to a primary care
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doctor within 48 hours.” Implementation is currently being negotiated.</p>
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<p>Virtually all patients think that they would not consult unless it was absolutely necessary.
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They do not think they are wasting NHS time and do not like being made to feel so. But
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underlying general practitioners' willingness to make patients wait several days is their
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perception that few of the problems are urgent. Patients and general practitioners evidently do
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not agree about the urgency of so called minor problems. To some extent general practice in the
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United Kingdom may have scored an “own goal” by setting up perceived access
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barriers (appointment systems and out of hours cooperatives) in the attempt to increase
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professional standards and control demand in a service that is free at the point of access.</p>
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<p>A further government initiative has been to bypass general practice with new
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services—notably, walk-in centres (primary care clinics in which no appointment is
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needed) and NHS Direct (a professional telephone helpline giving advice on simple remedies and
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access to services). Introduced widely and rapidly, these services each potentially provide
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significant features of primary care—namely, quick access to skilled health advice and
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first line treatment.</p>
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</sec>
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<sec>
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<title>Loss of interpersonal continuity</title>
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<p>If a patient has to consult several different professionals, particularly over a short period
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of time, there is inevitable duplication of stories, risk of naive diagnoses, potential for
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conflicting advice, and perhaps loss of trust. Trust is essential if patients are to accept the
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“wait and see” management policy which is, or should be, an important part of the
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management of self limiting conditions, which are often on the boundary between illness and
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non-illness.<xref ref-type="bibr" rid="B17">17</xref> Such duplication again increases pressure
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for more extra (unscheduled) consultations resulting in late running and professional
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frustration.<xref ref-type="bibr" rid="B18">18</xref> </p>
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<p>Mechanic described how loss of longitudinal (and perhaps personal and relational<xref
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ref-type="bibr" rid="B19">19</xref>) continuity influences the perception and use of time
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through an inability to build on previous consultations.<xref ref-type="bibr" rid="B2">2</xref>
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Knowing the doctor well, particularly in smaller practices, is associated with enhanced patient
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enablement in shorter time.<xref ref-type="bibr" rid="B4">4</xref> Though Mechanic pointed out
|
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that three quarters of UK patients have been registered with their general practitioner five
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years or more, this may be misleading. Practices are growing, with larger teams and more
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registered patients. Being registered with a doctor in a larger practice is usually no guarantee
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that the patient will be able to see the same doctor or the doctor of his or her choice, who may
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be different. Thus the system does not encourage adequate personal continuity. This adds to
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pressure on time and reduces both patient and professional satisfaction.</p>
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</sec>
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<sec>
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<title>Health service reforms</title>
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<p>Finally, for the past 15 years the NHS has experienced unprecedented change with a succession
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of major administrative reforms. Recent reforms have focused on an NHS led by primary care,
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including the aim of shifting care from the secondary specialist sector to primary care. One
|
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consequence is increased demand for primary care of patients with more serious and less stable
|
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problems. With the limited piloting of reforms we do not know whether such major redirection can
|
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be achieved without greatly altering the delicate balance between expectations (of both patients
|
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and staff) and what is delivered.</p>
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</sec>
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<sec>
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<title>The future</title>
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<p>We think that the way ahead must embrace both longer mean consultation times and more
|
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flexibility. More time is needed for high quality consultations with patients with major and
|
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complex problems of all kinds. But patients also need access to simpler services and advice.
|
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This should be more appropriate (and cost less) when it is given by professionals who know the
|
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patient and his or her medical history and social circumstances. For doctors, the higher quality
|
||||
associated with longer consultations may lead to greater professional satisfaction and, if these
|
||||
longer consultations are combined with more realistic scheduling, to reduced levels of
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stress.<xref ref-type="bibr" rid="B20">20</xref> They will also find it easier to develop
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||||
further the care of chronic disease.</p>
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<p>The challenge posed to general practice by walk-in centres and NHS Direct is considerable, and
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the diversion of funding from primary care is large. The risk of waste and duplication increases
|
||||
as more layers of complexity are added to a primary care service that started out as something
|
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familiar, simple, and local and which is still envied in other developed countries.<xref
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ref-type="bibr" rid="B21">21</xref> Access needs to be simple, and the advantages of personal
|
||||
knowledge and trust in minimising duplication and overmedicalisation need to be exploited.</p>
|
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<p>We must ensure better communication and access so that patients can more easily deal with
|
||||
minor issues and queries with someone they know and trust and avoid the formality and
|
||||
inconvenience of a full face to face consultation. Too often this has to be with a different
|
||||
professional, unfamiliar with the nuances of the case. There should be far more managerial
|
||||
emphasis on helping patients to interact with their chosen practitioner<xref ref-type="bibr"
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||||
rid="B22">22</xref>; such a programme has been described.<xref ref-type="bibr" rid="B23"
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>23</xref> Modern information systems make it much easier to record which doctor(s) a patient
|
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prefers to see and to monitor how often this is achieved. The telephone is hardly modern but is
|
||||
underused. Email avoids the problems inherent in arranging simultaneous availability necessary
|
||||
for telephone consultations but at the cost of reducing the communication of emotions. There is
|
||||
a place for both.<xref ref-type="bibr" rid="B2">2</xref> Access without prior appointment is a
|
||||
valued feature of primary care, and we need to know more about the right balance between planned
|
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and ad hoc consulting.</p>
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</sec>
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<sec>
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||||
<title>Next steps</title>
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||||
<p>General practitioners do not behave in a uniform way. They can be categorised as slow, medium,
|
||||
and fast and react in different ways to changes in consulting speed.<xref ref-type="bibr"
|
||||
rid="B18">18</xref> They are likely to have differing views about a widespread move to lengthen
|
||||
consultation time. We do not need further confirmation that longer consultations are desirable
|
||||
and necessary, but research could show us the best way to learn how to introduce them with
|
||||
minimal disruption to the way in which patients and practices like primary care to be
|
||||
provided.<xref ref-type="bibr" rid="B24">24</xref> We also need to learn how to make the most of
|
||||
available time in complex consultations.</p>
|
||||
<p>Devising appropriate incentives and helping practices move beyond just reacting to demand in
|
||||
the traditional way by working harder and faster is perhaps our greatest challenge in the United
|
||||
Kingdom. The new primary are trusts need to work together with the growing primary care research
|
||||
networks to carry out the necessary development work. In particular, research is needed on how a
|
||||
primary care team can best provide the right balance of quick access and interpersonal knowledge
|
||||
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<ack>
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<p>We thank the other members of the working group: Susan Childs, Paul Freeling, Iona Heath,
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<lpage>1617</lpage>
|
||||
<pub-id pub-id-type="pmid">10856043</pub-id>
|
||||
</element-citation>
|
||||
</ref>
|
||||
<ref id="B22">
|
||||
<label>22</label>
|
||||
<element-citation publication-type="journal" publication-format="print">
|
||||
<person-group person-group-type="author"> <name>
|
||||
<surname>Freeman</surname>
|
||||
<given-names>G</given-names>
|
||||
</name> <name>
|
||||
<surname>Hjortdahl</surname>
|
||||
<given-names>P</given-names>
|
||||
</name> </person-group>
|
||||
<article-title>What future for continuity of care in general practice?</article-title>
|
||||
<source>BMJ</source>
|
||||
<year iso-8601-date="1997">1997</year>
|
||||
<volume>314</volume>
|
||||
<fpage>1870</fpage>
|
||||
<lpage>1873</lpage>
|
||||
<pub-id pub-id-type="pmid">9224130</pub-id>
|
||||
</element-citation>
|
||||
</ref>
|
||||
<ref id="B23">
|
||||
<label>23</label>
|
||||
<element-citation publication-type="journal" publication-format="print">
|
||||
<person-group person-group-type="author"> <name>
|
||||
<surname>Kibbe</surname>
|
||||
<given-names>DC</given-names>
|
||||
</name> <name>
|
||||
<surname>Bentz</surname>
|
||||
<given-names>E</given-names>
|
||||
</name> <name>
|
||||
<surname>McLaughlin</surname>
|
||||
<given-names>CP</given-names>
|
||||
</name> </person-group>
|
||||
<article-title>Continuous quality improvement for continuity of care</article-title>
|
||||
<source>J Fam Pract</source>
|
||||
<year iso-8601-date="1993">1993</year>
|
||||
<volume>36</volume>
|
||||
<fpage>304</fpage>
|
||||
<lpage>308</lpage>
|
||||
<pub-id pub-id-type="pmid">8454977</pub-id>
|
||||
</element-citation>
|
||||
</ref>
|
||||
<ref id="B24">
|
||||
<label>24</label>
|
||||
<element-citation publication-type="journal" publication-format="print">
|
||||
<person-group person-group-type="author"> <name>
|
||||
<surname>Williams</surname>
|
||||
<given-names>M</given-names>
|
||||
</name> <name>
|
||||
<surname>Neal</surname>
|
||||
<given-names>RD</given-names>
|
||||
</name> </person-group>
|
||||
<article-title>Time for a change? The process of lengthening booking intervals in general
|
||||
practice</article-title>
|
||||
<source>Br J Gen Pract</source>
|
||||
<year iso-8601-date="1998">1998</year>
|
||||
<volume>48</volume>
|
||||
<fpage>1783</fpage>
|
||||
<lpage>1786</lpage>
|
||||
<pub-id pub-id-type="pmid">10198490</pub-id>
|
||||
</element-citation>
|
||||
</ref>
|
||||
</ref-list>
|
||||
<fn-group>
|
||||
<fn id="fn1">
|
||||
<p>Funding: Meetings of the working group in 1999-2000 were funded by the
|
||||
<funding-source>Scientific Foundation Board of the RCGP</funding-source>.</p>
|
||||
</fn>
|
||||
<fn id="fn2">
|
||||
<p>Competing interests: None declared.</p>
|
||||
</fn>
|
||||
</fn-group>
|
||||
</back>
|
||||
</article>
|
||||
8
tests/data/jats/elife-56337.nxml
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8
tests/data/jats/elife-56337.nxml
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8
tests/data/jats/elife-56337.txt
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8
tests/data/jats/elife-56337.txt
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8
tests/data/jats/elife-56337.xml
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8
tests/data/jats/elife-56337.xml
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3089
tests/data/jats/pnas_sample.xml
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3089
tests/data/jats/pnas_sample.xml
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Load Diff
96
tests/data/jats/pntd.0008301.nxml
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96
tests/data/jats/pntd.0008301.nxml
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File diff suppressed because one or more lines are too long
96
tests/data/jats/pntd.0008301.txt
Normal file
96
tests/data/jats/pntd.0008301.txt
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96
tests/data/jats/pntd.0008301.xml
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96
tests/data/jats/pntd.0008301.xml
Normal file
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60
tests/data/jats/pone.0234687.nxml
Normal file
60
tests/data/jats/pone.0234687.nxml
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60
tests/data/jats/pone.0234687.txt
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60
tests/data/jats/pone.0234687.txt
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60
tests/data/jats/pone.0234687.xml
Normal file
60
tests/data/jats/pone.0234687.xml
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File diff suppressed because one or more lines are too long
Reference in New Issue
Block a user