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Goldberg D, Slagle AL. A global assessment of deep-sea basalt sites for carbon sequestration. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.egypro.2009.02.165] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Goldberg D. Hanns Martin Goldberg. West J Med 2009. [DOI: 10.1136/bmj.b141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Plakun EM, Sudak DM, Goldberg D. The Y model: an integrated, evidence-based approach to teaching psychotherapy competencies. J Psychiatr Pract 2009; 15:5-11. [PMID: 19182560 DOI: 10.1097/01.pra.0000344914.54082.eb] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE The authors' goal was to develop an integrated model for teaching psychotherapy competencies across schools of therapy. METHOD The authors surveyed the comparative psychotherapy process literature to identify core features of psychotherapy shared across schools and differentiate those features from the defining features of psychodynamic therapy and cognitive-behavioral therapy. RESULTS The resulting Y Model for teaching psychotherapy competencies locates core processes of therapy that are shared across schools on the stem of the Y, differentiates psychodynamic therapy and cognitive-behavioral therapy on the branches of the Y, and locates supportive therapy largely on the stem of the Y. CONCLUSIONS The Y Model offers an efficient, integrated, evidence-based system for teaching psychotherapy competencies across schools in a conceptually clear way that is free of competition and bias between schools.
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Goldberg D, Weisberg I, Diuguid D, Gaglio P, Alobeid B, Fink S, Radhakrishnan J. Worth a second look. Am J Med 2009; 122:24-6. [PMID: 19114166 DOI: 10.1016/j.amjmed.2008.09.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2008] [Revised: 09/19/2008] [Accepted: 09/19/2008] [Indexed: 10/21/2022]
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Goldberg D, Bern M, North SJ, Haslam SM, Dell A. Glycan family analysis for deducing N-glycan topology from single MS. ACTA ACUST UNITED AC 2008; 25:365-71. [PMID: 19073587 DOI: 10.1093/bioinformatics/btn636] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
MOTIVATION In the past few years, mass spectrometry (MS) has emerged as the premier tool for identification and quantification of biological molecules such as peptides and glycans. There are two basic strategies: single-MS, which uses a single round of mass analysis, and MS/MS (or higher order MS(n)), which adds one or more additional rounds of mass analysis, interspersed with fragmentation steps. Single-MS offers higher throughput, broader mass coverage and more direct quantitation, but generally much weaker identification. Single-MS, however, does work fairly well for the case of N-glycan identification, which are more constrained than other biological polymers. We previously demonstrated single-MS identification of N-glycans to the level of 'cartoons' (monosaccharide composition and topology) by a system that incorporates an expert's detailed knowledge of the biological sample. In this article, we explore the possibility of ab initio single-MS N-glycan identification, with the goal of extending single-MS, or primarily-single-MS, identification to non-expert users, novel conditions and unstudied tissues. RESULTS We propose and test three cartoon-assignment algorithms that make inferences informed by biological knowledge about glycan synthesis. To test the algorithms, we used 71 single-MS spectra from a variety of tissues and organisms, containing more than 2800 manually annotated peaks. The most successful of the algorithms computes the most richly connected subgraph within a 'cartoon graph'. This algorithm uniquely assigns the correct cartoon to more than half of the peaks in 41 out of the 71 spectra.
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Bern M, Goldberg D. Improved ranking functions for protein and modification-site identifications. J Comput Biol 2008; 15:705-19. [PMID: 18651800 DOI: 10.1089/cmb.2007.0119] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
There are a number of computational tools for assigning identifications to peptide tandem mass spectra, but only a few tools, most notably ProteinProphet, for the crucial next step of integrating peptide identifications into higher-level identifications, such as proteins or modification sites. Here we describe a new program called ComByne for scoring and ranking higher-level identifications. Unlike other identification integration tools, ComByne corrects for protein lengths; it also makes use of more information, such as retention times and spectrum-to-spectrum corroborations. We compare ComByne to existing algorithms on several complex biological samples, including a sample of mouse blood plasma spiked with known concentrations of human proteins. On our samples, the combination of ComByne with our database search tool ByOnic is more sensitive than the combinations of Mascot with ProteinProphet and SEQUEST with DTASelect, with over 40% more proteins identified at 1% false discovery rate. A Web interface to our software is at http://bio.parc.xerox.com.
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Goldberg D. Towards DSM-V: the relationship between generalized anxiety disorder and major depressive episode. Psychol Med 2008; 38:1671-1675. [PMID: 18985867 DOI: 10.1017/s003329170800295x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Katz A, Goldberg D, Smith J, Trick WE. Tobacco, alcohol, and drug use among hospital patients: concurrent use and willingness to change. J Hosp Med 2008; 3:369-75. [PMID: 18951399 DOI: 10.1002/jhm.358] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
BACKGROUND Data are limited on concurrent smoking and substance use among hospital patients. To better inform hospital-based intervention strategies, we evaluated the prevalence and concurrent use of these behaviors. This study evaluated the association between tobacco, alcohol, and other drug use, compared willingness to quit smoking among patients with and without substance use, and evaluated the relationship between willingness to quit smoking and readiness to change substance use. METHODS This study was a cross-sectional survey of non-Intensive Care Unit hospital patients at 2 public hospitals (a 464-bed tertiary-care hospital and a 100-bed community hospital) by bedside interview. Severity of use and willingness to change behavior was determined. We evaluated the association between smoking and substance use by multivariable methods. RESULTS Of 7,391 patients with known smoking status, 2,684 (36%) were current smokers. Among them, 1,376 hospitalized smokers (51%) had concurrent substance use. Among the 1,972 patients with at-risk alcohol or drug use, the prevalence of smoking was 70% compared to 24% for non-substance users (P < .01). Compared to other patients who smoked, substance-dependent patients were more likely (Prevalence Rate Ratio = 1.4, 95% Confidence Interval = 1.1-1.9) to be moderate to heavy smokers. Regardless of substance use pattern, most patients (60%) expressed a desire to immediately quit smoking. CONCLUSION Hospital patients who describe at-risk substance use are likely to smoke and express willingness to quit smoking. Given the prevalence of concurrent smoking and substance use and patients' desire to change both behaviors, there is a need for coordination of substance use and smoking cessation interventions.
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Yirrell DL, Shaw L, Campbell E, Burns SM, Cameron SO, Goldberg D. HIV subtypes in Scotland, 2000-2006. Epidemiol Infect 2008; 136:1069-75. [PMID: 17922931 PMCID: PMC2870891 DOI: 10.1017/s0950268807009545] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2007] [Indexed: 11/06/2022] Open
Abstract
The purpose of this study was to document the dynamics of HIV-1 subtypes in Scotland over a 6-year period. Viral RNA from all-new diagnoses was amplified by nested PCR and sequenced in the gag and/or env regions. Subtype was assigned by phylogenetic analysis, and aligned with demographic data including likely route and geographical origin of infection. We present data on 80% of all new diagnoses in Scotland between April 2000 and April 2006. Within the background of an expanding epidemic, subtype B predominates in men who have sex with men and intravenous drug users but there is a small but consistent number of UK-acquired infections in these risk groups caused by non-B subtypes. In heterosexuals, non-B subtypes acquired abroad, especially Africa, are still the largest group but again UK-acquired numbers are rising. The social and clinical significance of the spread of non-B subtypes in different ethnic and risk groups remains to be established.
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Kornfeld S, Reitman ML, Varki A, Goldberg D, Gabel CA. Steps in the phosphorylation of the high mannose oligosaccharides of lysosomal enzymes. CIBA FOUNDATION SYMPOSIUM 2008:138-56. [PMID: 6295719 DOI: 10.1002/9780470720745.ch8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The phosphomannosyl recognition marker of acid hydrolases, which mediates their translocation to lysosomes, has been shown to be synthesized in two steps. First, N-acetylglucosamine 1-phosphate is transferred to an acceptor mannose by UDP-N-acetylglucosamine:lysosomal enzyme N-acetylglucosamine-1-phosphotransferase, resulting in a phosphate group in diester linkage between the outer N-acetylglucosamine and the inner mannose. Next, an a-N-acetylglucosaminyl phosphodiesterase removes the N-acetylglucosamine, leaving the phosphate in monoester linkage with the underlying mannose residue. This exposed phosphomannosyl residue serves as the essential component of a recognition marker which leads to binding to high-affinity receptors and subsequent translocation to lysosomes. We propose that the first enzyme in this scheme, N-acetylglucosaminylphosphotransferase, catalyses the initial, determining step by which newly synthesized acid hydrolases are distinguished from other newly synthesized glycoproteins and thus are eventually targeted to lysosomes. The absence of this enzyme activity, as in inclusion-cell (I-cell) disease and pseudo-Hurler polydystrophy, precludes the receptor-mediated targeting of newly synthesized acid hydrolases to lysosomes. As a consequence, the enzymes are secreted into the extracellular milieu.
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Goldberg D, Brown G, Hutchinson S, Dillon J, Taylor A, Howie G, Ahmed S, Roy K, King M. Hepatitis C action plan for Scotland: phase II (May 2008-March 2011). ACTA ACUST UNITED AC 2008; 13. [PMID: 18761968 DOI: 10.2807/ese.13.21.18876-en] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Yom Din S, Hurvitz A, Goldberg D, Jackson K, Levavi-Sivan B, Degani G. Cloning of Russian sturgeon (Acipenser gueldenstaedtii) growth hormone and insulin-like growth factor I and their expression in male and female fish during the first period of growth. J Endocrinol Invest 2008; 31:201-10. [PMID: 18401201 DOI: 10.1007/bf03345591] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
In this study, the GH and IGF-I of the Russian sturgeon (rs), Acipenser gueldenstaedtii, were cloned and sequenced, and their mRNA gene expression determined. In addition, to improve our understanding of the GH function, the expression of this hormone was assessed in young males and females. Moreover, IGF-I expression was quantified in young males and compared to that in older ones. The nucleotide sequence of the rsGH cDNA was 980 bp long and had an open reading frame of 642 bp, beginning with the first ATG codon at position 39 and ending with the stop codon at position 683. A putative polyadenylation signal, AATAAA, was recognized 42 bp upstream of the poly (A) tail. The position of the signal- peptide cleavage site was predicted to be at position 111, yielding a signal peptide of 24 amino-acids (aa) and a mature peptide of 190 aa. When the rsGH aa sequence was compared with other species, the highest degree of identity was found to be with mammalians (66-70% identity), followed by anguilliformes and amphibia (61%) and other fish (39-47%). The level of rsGH mRNA was discovered to be similar in pituitaries of females and males of 5 age groups (1, 2, 3, 4, and 5- yr-old). In females and males, the levels did not change dramatically during the first 5 yr of growth. The partial nucleotide sequence of the rsIGF-I was 445 bp long and had an open reading frame of 396 bp, beginning with the ATG codon at position 50. The position of the signal-peptide cleavage site was predicted to be at position 187, yielding a signal peptide of 44 aa. The highest level of IGF-I mRNA expression was recorded in the kidney of adult sturgeons. The IGF-I mRNA expression levels in the intestine, pituitary gland, and liver were not significantly different. Low levels of expression were found in the brain, heart, and muscle. In most tissues, there was no significant difference between mRNA levels of one and 5-yr-old fish. In conclusion, based on the GH-sequence analysis, A. gueldenstaedtii is genetically distant from other teleosts. The expression of the GH mRNA was similar in males and females, and its level remained constant during the first 5 yr of growth. While the IGF-I mRNA expression differed amongst various tissues, the level in each tissue was similar in 1 and 5-yr-old fish.
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Das-Munshi J, Goldberg D, Bebbington PE, Bhugra DK, Brugha TS, Dewey ME, Jenkins R, Stewart R, Prince M. Public health significance of mixed anxiety and depression: beyond current classification. Br J Psychiatry 2008; 192:171-7. [PMID: 18310574 DOI: 10.1192/bjp.bp.107.036707] [Citation(s) in RCA: 139] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
BACKGROUND The public health significance of mixed anxiety-depressive disorder (MADD) and the distinctiveness of its phenomenology have yet to be established. AIMS To determine the public health significance of MADD, and to compare its phenomenology with ICD-10 anxiety, depressive, and comorbid anxiety and depressive disorders. METHOD Weighted analysis of data from the Great Britain National Psychiatric Morbidity survey was conducted with a representative household sample of 8580 persons aged 16-74 years. RESULTS The 1-month prevalence of MADD was 8.8%. A fifth of all days off work in Britain occurred in this group. The symptom profile of MADD was similar to 'pure' ICD-10 anxiety and depression, but with a lower overall symptom count. The disorder was associated with significant impairment of health-related quality of life. Differences in health-related quality of life measures between diagnostic groups were accounted for by overall symptom severity, which remained strongly associated with health-related quality of life measures after adjusting for diagnostic group. The finding that half of the anxiety, depression and MADD cases and a third of the comorbid depression and anxiety cases grouped into a single latent class challenges the notion of these conditions as having distinct phenomenologies. Mixed presentations may be the norm in the population. CONCLUSIONS The data support the pathological significance of MADD in its negative impact upon population health. Dimensional approaches to classification may provide a more parsimonious description of anxiety and depressive disorders compared with categorical approaches.
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Abstract
BACKGROUND This paper examines what has been achieved in the specialist mental health services by the vastly increased health expenditures that the National Health Service (NHS) has enjoyed in the past 5 years. AIMS To describe the way money has been spent in specialist mental health services and examine why problems remain after such admirable changes to already available resources. METHOD Changes in staff employed by mental health services, where the extra staff are deployed, and patterns of expenditure within the whole service and within community mental health teams are examined. RESULTS Some of the new expenditure has been well spent, and has produced improvements in the service. However, one must also take account of the costs of the greatly increased numbers of managers, who impose two sorts of costs: that of their own salaries, and the opportunity costs of front-line staff having to attend meetings and write reports rather than seeing patients. Throughout the rest of the NHS, money has been wasted on needless reorganisations, on consultant and general practitioner contracts, and on information technology that has so far failed to deliver tangible advantages. CONCLUSIONS The emphasis on central control undermines local initiatives and wastes resources. Some central control is inevitable, but policies need to be developed in collaboration with clinicians. At local level, expenditure by primary care trusts and mental health trusts also needs to be scrutinised by committees that should include representatives of front-line mental health staff.
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Palmateer N, Anderson N, Wadd S, Hutchinson S, Taylor A, Goldberg D. Exploring associations between perceived HCV status and injecting risk behaviors among recent initiates to injecting drug use in Glasgow. Subst Use Misuse 2008; 43:375-88. [PMID: 18365938 DOI: 10.1080/10826080701202908] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The aim of this study was to explore the influence of testing for hepatitis C virus (HCV) and perceived HCV status on injecting risk behavior. A cross-sectional, community-wide survey was undertaken at multiple sites throughout Greater Glasgow during 2001-2002. Four hundred ninety-seven injecting drug users (IDUs) consented to participate and were interviewed using a structured questionnaire to ascertain HCV test history and injecting risk behavior. The average age of participants was 27 years and the majority of the sample were male (70.4%). Participants had been injecting for an average duration of 2.5 years. Logistic regression analysis revealed no significant associations between having been tested and injecting risk behavior. After adjustment for potential confounding variables, HCV-negatives were significantly less likely to borrow needles/syringes and spoons or filters as compared with unawares and were significantly less likely to borrow spoons or filters as compared with HCV-positives. Due to the cross-sectional design of the study, it is uncertain whether this reduction in risk behavior could be attributed to perception of HCV status. Further research is recommended to consolidate the evidence for this relationship.
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Furman N, Goldberg D, Lusin N. Enrollments in Languages other than English in United States Institutions of Higher Education, Fall 2006. ACTA ACUST UNITED AC 2008. [DOI: 10.1632/adfl.39.2.66] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Jenkins R, Lancashire S, McDaid D, Samyshkin Y, Green S, Watkins J, Potasheva A, Nikiforov A, Bobylova Z, Gafurov V, Goldberg D, Huxley P, Lucas J, Purchase N, Atun R. Mental health reform in the Russian Federation: an integrated approach to achieve social inclusion and recovery. Bull World Health Organ 2007; 85:858-66. [PMID: 18038076 PMCID: PMC2636246 DOI: 10.2471/blt.06.039156] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2006] [Revised: 04/29/2007] [Accepted: 05/02/2007] [Indexed: 10/18/2022] Open
Abstract
OBJECTIVE To facilitate mental health reform in one Russian oblast (region) using systematic approaches to policy design and implementation. METHODS The authors undertook a three-year action-research programme across three pilot sites, comprising a multifaceted set of interventions combining situation appraisal to inform planning, sustained policy dialogue at federal and regional levels to catalyse change, introduction of multidisciplinary and intersectoral-working at all levels, skills-based training for professionals, and support for nongovernmental organizations (NGOs) to develop new care models. FINDINGS Training programmes developed in this process have been adopted into routine curricula with measurable changes in staff skills. Approaches to care improved through multidisciplinary and multisectoral service delivery, with an increase in NGO activities, user involvement in care planning and delivery in all pilot sites. Hospital admissions at start and end of the study fell in two pilot sites, while the rate of readmissions in all three pilot sites by 2006 was below that for the region as a whole. Lessons learned have informed the development of regional and federal mental health policies. CONCLUSION A multifaceted and comprehensive programme can be effective in overcoming organizational barriers to the introduction of evidence-based multisectoral interventions in one Russian region. This can help facilitate significant and sustainable changes in policy and reduce institutionalization.
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Sharp L, Hutchinson SJ, Goldberg D, Taylor A, Carr S. Gauging acceptance of a hepatitis C test by family planning clinic attendees in Glasgow, UK. ACTA ACUST UNITED AC 2007; 33:263-6. [PMID: 17925111 DOI: 10.1783/147118907782101805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND In the UK, pregnant women are not offered and recommended a hepatitis C virus (HCV) test because no effective intervention to prevent vertical transmission of HCV exists following conception. Mother-to-child transmission of HCV could, however, be reduced if infected women planning to have children underwent a course of therapy prior to conception. OBJECTIVE To determine what proportion of female family planning clinic (FPC) attendees would hypothetically accept an HCV test if they were offered it and to identify the factors associated with such a decision. METHODS Opportunistic sampling was used to recruit 1000 women attending FPCs in Glasgow during 2002/2003. Participants were asked to self-complete a brief questionnaire about HCV and testing. RESULTS Of 964 participants, 62% reported that they would accept an HCV test if it was offered in the family planning setting and 24% indicated that they were undecided. Only 4% of women reported that they would be offended if offered an HCV test. The highest rates of hypothetical acceptance of an HCV test were reported among those who had ever injected drugs (88%) and those who felt that they were at risk of being infected with HCV (84%). Women who were single [adjusted odds ratio (OR) 1.4, 95% CI 1.1-1.8] and who were of non-white ethnic origin (adjusted OR 2.5, 95% CI 1.0-6.2) were also significantly more inclined to hypothetically accept an HCV test. CONCLUSION Selective HCV testing to those women at high risk of HCV infection should be encouraged in the family planning setting.
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Walters P, Tylee A, Fisher J, Goldberg D. Teaching junior doctors to manage patients who somatise: is it possible in an afternoon? MEDICAL EDUCATION 2007; 41:995-1001. [PMID: 17908117 DOI: 10.1111/j.1365-2923.2007.02833.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
CONTEXT Many patients in primary care somatise psychological distress. Training general practitioners (GPs) to manage somatisation has been shown to lead to improvements in their management of these patients. However, the training has been intensive and conducted by psychiatrists, making it impractical for widespread use. The aim of this research was to determine the effectiveness of a teaching package in improving the ability of GP registrars to manage patients who somatise, when taught by GP vocational course tutors within the constraints of a general practice vocational training scheme. METHODS This was a before-and-after training evaluation of GP registrars' skills. A total of 22 GP registrars and 6 GP course organisers were recruited from 3 GP vocational training schemes. The GP trainees had 2 videotaped consultations with trained actors role-playing patients with somatised depression, before and 1 month after training. RESULTS There was a significant overall improvement in the ability of GP registrars to manage patients who somatise (mean scores on a 4-point Likert scale: pre-training 1.4 [standard deviation, SD, 0.6]; post-training 2.2 [SD 0.9]; P = 0.002). General practice registrars improved their ability to use a negotiating style of consultation (skill present in 8/22 pre-training, 16/22 post-training; P = 0.02) and also demonstrated more empathy during the 'consultation' after training (mean scores on a 5-point Likert scale: pre-training 2.3 [SD 1.0]; post-training 3.0 [SD 0.8]; P = 0.03). CONCLUSIONS Using a structured training package, it is possible for GP vocational course tutors to successfully teach GP registrars to manage patients who somatise psychological distress. Given limited resources for teaching in terms of cost and time, this training package could have important implications for training medical staff.
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Goldberg D, Bern M, Parry S, Sutton-Smith M, Panico M, Morris HR, Dell A. Automated N-glycopeptide identification using a combination of single- and tandem-MS. J Proteome Res 2007; 6:3995-4005. [PMID: 17727280 DOI: 10.1021/pr070239f] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe Peptoonist, a program that can automatically identify the glycans (sugars) present at each N-glycosylation site of a protein. The input to Peptoonist is a series of mass spectra, both MS and MS/MS, obtained from a liquid chromatography (LC) run of proteolytically digested purified glycoproteins. The program uses MS/MS to identify glycosylated peptides and single-MS to identify the N-glycans present on each of these peptides, at least to the level of monosaccharide composition. We validate the program on an LC run of mouse zona pellucida proteins that had been intensively hand annotated by a human expert. Our program doubled the number of glycopeptide identifications, and also found several possible errors in the hand annotation. In addition, it automatically made most of the same glycan isomer identifications as the expert annotator.
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Bern M, Goldberg D, McDonald WH, Yates JR. Automatic quality assessment of peptide tandem mass spectra. Bioinformatics 2007; 20 Suppl 1:i49-54. [PMID: 15262780 DOI: 10.1093/bioinformatics/bth947] [Citation(s) in RCA: 168] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION A powerful proteomics methodology couples high-performance liquid chromatography (HPLC) with tandem mass spectrometry and database-search software, such as SEQUEST. Such a set-up, however, produces a large number of spectra, many of which are of too poor quality to be useful. Hence a filter that eliminates poor spectra before the database search can significantly improve throughput and robustness. Moreover, spectra judged to be of high quality, but that cannot be identified by database search, are prime candidates for still more computationally intensive methods, such as de novo sequencing or wider database searches including post-translational modifications. RESULTS We report on two different approaches to assessing spectral quality prior to identification: binary classification, which predicts whether or not SEQUEST will be able to make an identification, and statistical regression, which predicts a more universal quality metric involving the number of b- and y-ion peaks. The best of our binary classifiers can eliminate over 75% of the unidentifiable spectra while losing only 10% of the identifiable spectra. Statistical regression can pick out spectra of modified peptides that can be identified by a de novo program but not by SEQUEST. In a section of independent interest, we discuss intensity normalization of mass spectra.
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Jordanova V, Stewart R, Goldberg D, Bebbington PE, Brugha T, Singleton N, Lindesay JEB, Jenkins R, Prince M, Meltzer H. Age variation in life events and their relationship with common mental disorders in a national survey population. Soc Psychiatry Psychiatr Epidemiol 2007; 42:611-6. [PMID: 17520161 DOI: 10.1007/s00127-007-0209-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/20/2007] [Indexed: 10/23/2022]
Abstract
BACKGROUND Life events (LEs) are recognised to be important risk factors for common mental disorders (CMD). Their prominence may vary across age groups but this issue has received little systematic investigation. METHOD Data were analysed from the 2000 UK National Survey of Psychiatric Morbidity comprising 8,580 participants aged 16-74 years. A history of recent life events pertaining to health threats, bereavement, interpersonal problems and redundancy was established for the preceding six months. Participants were also asked about earlier lifetime stressors including sexual abuse and expulsion from school. CMD, depression and generalised anxiety disorder were ascertained through the revised Clinical Interview Schedule. RESULTS The strongest associations between LEs and CMD were for recent threats to health, recent interpersonal problems and lifetime stressors. Recent LEs were more strongly associated with depression than anxiety whereas the associations for lifetime stressors were similar in strength. The strength of association between recent LEs and CMD increased steadily up to the 45-54 years age group and then declined. In the 65-74 year age range, CMD was not significantly associated with any recent LE but instead was associated with the following lifetime stressors: bullying, sexual abuse, running away from home, and institutional care in childhood. CONCLUSIONS Recent life events were most strongly associated with CMD in mid-rather than early or late adult life. In later life, stronger associations were found with lifetime stressors than recent events.
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Moffitt TE, Harrington H, Caspi A, Kim-Cohen J, Goldberg D, Gregory AM, Poulton R. Depression and Generalized Anxiety Disorder. ACTA ACUST UNITED AC 2007; 64:651-60. [PMID: 17548747 DOI: 10.1001/archpsyc.64.6.651] [Citation(s) in RCA: 407] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
CONTEXT The close association between generalized anxiety disorder (GAD) and major depressive disorder (MDD) prompts questions about how to characterize this association in future diagnostic systems. Most information about GAD-MDD comorbidity comes from patient samples and retrospective surveys. OBJECTIVE To revisit the sequential and cumulative comorbidity between GAD and MDD using data from a prospective longitudinal cohort. DESIGN Prospective longitudinal cohort study. SETTING New Zealand. PARTICIPANTS The representative 1972-1973 Dunedin birth cohort of 1037 members was followed up to age 32 years with 96% retention. MAIN OUTCOME MEASURES Research diagnoses of anxiety and depression were made at ages 11, 13, 15, 18, 21, 26, and 32 years. Mental health services were reported on a life history calendar. RESULTS Sequentially, anxiety began before or concurrently in 37% of depression cases, but depression began before or concurrently in 32% of anxiety cases. Cumulatively, 72% of lifetime anxiety cases had a history of depression, but 48% of lifetime depression cases had anxiety. During adulthood, 12% of the cohort had comorbid GAD + MDD, of whom 66% had recurrent MDD, 47% had recurrent GAD, 64% reported using mental health services, 47% took psychiatric medication, 8% were hospitalized, and 11% attempted suicide. In this comorbid group, depression onset occurred first in one third of the participants, anxiety onset occurred first in one third, and depression and anxiety onset began concurrently in one third. CONCLUSIONS Challenging the prevailing notion that generalized anxiety usually precedes depression and eventually develops into depression, these findings show that the reverse pattern occurs almost as often. The GAD-MDD relation is strong, suggesting that the disorders could be classified in 1 category of distress disorders. Their developmental relation seems more symmetrical than heretofore presumed, suggesting that MDD is not necessarily primary over GAD in diagnostic hierarchy. This prospective study suggests that the lifetime prevalence of GAD and MDD may be underestimated by retrospective surveys and that comorbid GAD + MDD constitutes a greater mental health burden than previously thought.
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Goldberg D, Kryszak D, Fasano A, Green PHR. Screening for celiac disease in family members: is follow-up testing necessary? Dig Dis Sci 2007; 52:1082-6. [PMID: 17380406 DOI: 10.1007/s10620-006-9518-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2006] [Accepted: 07/07/2006] [Indexed: 12/24/2022]
Abstract
Celiac disease is a genetically determined intolerance to gluten that results in villous atrophy in the small intestine. Because celiac disease occurs in families, relatives of affected individuals are tested for the disease. However, there are no evidence-based guidelines for when, or how often, to test relatives. Our goal was to determine if one-time screening of relatives is sufficient. Of 171 family members with an initially negative endomysial antibody who were tested on more than one occasion, 6 (3.5%) were positive on repeat testing. The average time to seroconversion was 1.7+/-1.2 years (range, 6 months-3 years 2 months). Only one of the seroconverters had diarrhea; the remainder were asymptomatic. None of the patients had a change in symptoms between testing. We conclude that one-time testing for celiac disease among families with affected members is insufficient. Repeat testing should occur irrespective of the presence of symptoms.
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Goldberg D. International Society for Enzymology (ISE), Newsletter, December 2006. Clin Chim Acta 2007. [DOI: 10.1016/j.cca.2006.12.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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