The Iterative Signature Algorithm for the analysis of large scale gene expression data

We present a new approach for the analysis of genome-wide expression data. Our method is designed to overcome the limitations of traditional techniques, when applied to large-scale data. Rather than alloting each gene to a single cluster, we assign both genes and conditions to context-dependent and potentially overlapping transcription modules. We provide a rigorous definition of a transcription module as the object to be retrieved from the expression data. An efficient algorithm, that searches for the modules encoded in the data by iteratively refining sets of genes and conditions until they match this definition, is established. Each iteration involves a linear map, induced by the normalized expression matrix, followed by the application of a threshold function. We argue that our method is in fact a generalization of Singular Value Decomposition, which corresponds to the special case where no threshold is applied. We show analytically that for noisy expression data our approach leads to better classification due to the implementation of the threshold. This result is confirmed by numerical analyses based on in-silico expression data. We discuss briefly results obtained by applying our algorithm to expression data from the yeast S. cerevisiae.Comment: Latex, 36 pages, 8 figure

Effectiveness of physiotherapy exercise following hip arthroplasty for osteoarthritis: a systematic review of clinical trials

Background: Physiotherapy has long been a routine component of patient rehabilitation following hip joint replacement. The purpose of this systematic review was to evaluate the effectiveness of physiotherapy exercise after discharge from hospital on function, walking, range of motion, quality of life and muscle strength, for osteoarthritic patients following elective primary total hip arthroplasty. Methods: Design: Systematic review, using the Cochrane Collaboration Handbook for Systematic Reviews of Interventions and the Quorom Statement. Database searches: AMED, CINAHL, EMBASE, KingsFund, MEDLINE, Cochrane library (Cochrane reviews, Cochrane Central Register of Controlled Trials, DARE), PEDro, The Department of Health National Research Register. Handsearches: Physiotherapy, Physical Therapy, Journal of Bone and Joint Surgery (Britain) Conference Proceedings. No language restrictions were applied. Selection: Trials comparing physiotherapy exercise versus usual/standard care, or comparing two types of relevant exercise physiotherapy, following discharge from hospital after elective primary total hip replacement for osteoarthritis were reviewed. Outcomes: Functional activities of daily living, walking, quality of life, muscle strength and range of hip joint motion. Trial quality was extensively evaluated. Narrative synthesis plus meta-analytic summaries were performed to summarise the data. Results: 8 trials were identified. Trial quality was mixed. Generally poor trial quality, quantity and diversity prevented explanatory meta-analyses. The results were synthesised and meta-analytic summaries were used where possible to provide a formal summary of results. Results indicate that physiotherapy exercise after discharge following total hip replacement has the potential to benefit patients. Conclusion: Insufficient evidence exists to establish the effectiveness of physiotherapy exercise following primary hip replacement for osteoarthritis. Further well designed trials are required to determine the value of post discharge exercise following this increasingly common surgical procedure

Strengthening the Reporting of Observational Studies in Epidemiology (STROBE): Explanation and Elaboration

Much medical research is observational. The reporting of observational studies is often of insufficient quality. Poor reporting hampers the assessment of the strengths and weaknesses of a study and the generalisability of its results. Taking into account empirical evidence and theoretical considerations, a group of methodologists, researchers, and editors developed the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) recommendations to improve the quality of reporting of observational studies. The STROBE Statement consists of a checklist of 22 items, which relate to the title, abstract, introduction, methods, results and discussion sections of articles. Eighteen items are common to cohort studies, case-control studies and cross-sectional studies and four are specific to each of the three study designs. The STROBE Statement provides guidance to authors about how to improve the reporting of observational studies and facilitates critical appraisal and interpretation of studies by reviewers, journal editors and readers. This explanatory and elaboration document is intended to enhance the use, understanding, and dissemination of the STROBE Statement. The meaning and rationale for each checklist item are presented. For each item, one or several published examples and, where possible, references to relevant empirical studies and methodological literature are provided. Examples of useful flow diagrams are also included. The STROBE Statement, this document, and the associated Web site (http://www.strobe-statement.org/) should be helpful resources to improve reporting of observational research

Strengthening the Reporting of Observational Studies in Epidemiology (STROBE): Explanation and Elaboration.

Much medical research is observational. The reporting of observational studies is often of insufficient quality. Poor reporting hampers the assessment of the strengths and weaknesses of a study and the generalisability of its results. Taking into account empirical evidence and theoretical considerations, a group of methodologists, researchers, and editors developed the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) recommendations to improve the quality of reporting of observational studies. The STROBE Statement consists of a checklist of 22 items, which relate to the title, abstract, introduction, methods, results and discussion sections of articles. Eighteen items are common to cohort studies, case-control studies and cross-sectional studies and four are specific to each of the three study designs. The STROBE Statement provides guidance to authors about how to improve the reporting of observational studies and facilitates critical appraisal and interpretation of studies by reviewers, journal editors and readers. This explanatory and elaboration document is intended to enhance the use, understanding, and dissemination of the STROBE Statement. The meaning and rationale for each checklist item are presented. For each item, one or several published examples and, where possible, references to relevant empirical studies and methodological literature are provided. Examples of useful flow diagrams are also included. The STROBE Statement, this document, and the associated Web site (http://www. strobe-statement.org/) should be helpful resources to improve reporting of observational research. Present article is Russian-language translation of the original manuscript edited by Doctor of Medicine R.T. Saygitov.Present translation was first published in Digital Diagnostics. doi: 10.17816/DD70821. It is published with minor changes related to the literary editing of the translation itself

Повышение качества отчётов о наблюдательных исследованиях в эпидемиологии (STROBE): разъяснения и уточнения

Большинство медицинских исследований являются наблюдательными (observational). Сообщения о таких ис-следованиях часто невысокого качества, что затрудняет оценку сильных и слабых сторон работы, а также обоб-щаемости (generalizability) её результатов. Принимая во внимание эмпирические свидетельства и теоретические соображения, группа методологов, исследователей и научных редакторов разработала рекомендации «Повышение качества отчётов о наблюдательных исследованиях в эпидемиологии (STROBE): разъяснения и уточнения». Реко-мендации STROBE содержат 22 пункта, связанных с оформлением следующих разделов научных статей: название, аннотация, введение, методы, результаты и их обсуждение, при этом 18 пунктов являются общими для когортных исследований (cohort studies), исследований «случай–контроль» (case-control studies) и одномоментных исследова-ний (cross-sectional studies); 4 пункта специфичны для каждого из указанных дизайнов исследований (study designs). STROBE ― руководство для авторов, необходимое для повышения качества отчётов о наблюдательных исследова-ниях, облегчающее критическую оценку исследования и его интерпретацию рецензентами, редакторами журналов и читателями. Цель этой разъясняющей и уточняющей статьи ― способствовать более широкому применению, пониманию и распространению стандартов STROBE. В ней даётся разъяснение смысла и обоснование применения каждого пункта руководства (checklist). По каждому пункту приводятся один или несколько опубликованных при-меров правильного представления исследований и, при возможности, библиографические ссылки на подходящие эмпирические исследования и методологическую литературу. Представлены примеры потоковых диаграмм (flow diagrams) для описания последовательности исследования. Рекомендации STROBE, настоящая статья и соответ-ствующий веб-сайт (http://www.strobe-statement.org/) должны стать полезным источником для повышения качества отчётов о результатах наблюдательных исследований. This article is the reprint with Russian translation of the original that can be observed here: Vandenbroucke JP, von Elm E, Altman DG, Gotzsche PC, Mulrow CD, et al. Strengthening the Reporting of Observational Studies in Epidemiology (STROBE): Explanation and Elaboration. PLoS Med. 2007;4(10):e297. doi: 10.1371/journal.pmed.0040297

Mejorar la comunicación de estudios observacionales en epidemiología (STROBE): explicación y elaboración

Gran parte de la investigación biomédica es de tipo observacional. Los informes de los estudios observacionales a menudo poseen una calidad insuficiente, lo que dificulta la evaluación de sus fortalezas y debilidades para generalizar los resultados. Teniendo en cuenta la evidencia empírica y consideraciones teóricas, un grupo de expertos en metodología, investigadores y editores de revistas científicas, desarrollaron una lista de recomendaciones para aumentar la calidad de las publicaciones de los estudios observacionales: (STROBE). La Declaración STROBE consiste en una lista de verificación de 22 puntos que guardan relación con las diferentes secciones de un artículo: título, resumen, introducción, metodología, resultados y discusión. De ellos, 18 puntos son comunes a los tres diseños de estudio: cohorte, casos y controles, y transversales; los otros cuatro son específicos para cada una de estas tres modalidades. La Declaración STROBE proporciona a los autores información sobre cómo mejorar la calidad de los artículos sobre estudios observacionales y facilita a los revisores, editores de revistas y lectores su apreciación crítica y su interpretación. Este documento explicativo tiene el propósito de impulsar el uso, la comprensión y la difusión de la Declaración STROBE. Se presentan el significado y el análisis razonado para cada punto de la lista de verificación, proporcionando uno o varios ejemplos publicados en la literatura y, en lo posible, referencias de estudios empíricos relevantes y literatura metodológica. También se incluyen ejemplos de diagramas de flujo. La Declaración STROBE, el presente documento y la página Web asociada () son recursos útiles para mejorar la divulgación de la investigación observacional.Much medical research is observational. The reporting of observational studies is often of insufficient quality. Poor reporting hampers the assessment of the strengths and weaknesses of a study and the generalisability of its results. Taking into account empirical evidence and theoretical considerations, a group of methodologists, researchers, and editors developed the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) recommendations to improve the quality of reporting of observational studies. The STROBE Statement consists of a checklist of 22 items, which relate to the title, abstract, introduction, methods, results and discussion sections of articles. Eighteen items are common to cohort studies, case-control studies and cross-sectional studies and four are specific to each of the three study designs. The STROBE Statement provides guidance to authors about how to improve the reporting of observational studies and facilitates critical appraisal and interpretation of studies by reviewers, journal editors and readers. This explanatory and elaboration document is intended to enhance the use, understanding, and dissemination of the STROBE Statement. The meaning and rationale for each checklist item are presented. For each item, one or several published examples and, where possible, references to relevant empirical studies and methodological literature are provided. Examples of useful flow diagrams are also included. The STROBE Statement, this document, and the associated Web site () should be helpful resources to improve reporting of observational research

HER2 and ESR1 mRNA expression levels and response to neoadjuvant trastuzumab plus chemotherapy in patients with primary breast cancer

Introduction: Recent data suggest that benefit from trastuzumab and chemotherapy might be related to expression of HER2 and estrogen receptor (ESR1). Therefore, we investigated HER2 and ESR1 mRNA levels in core biopsies of HER2-positive breast carcinomas from patients treated within the neoadjuvant GeparQuattro trial. Methods: HER2 levels were centrally analyzed by immunohistochemistry (IHC), silver in-situ hybridization (SISH) and qRT-PCR in 217 pretherapeutic formalin-fixed, paraffin-embedded (FFPE) core biopsies. All tumors had been HER2-positive by local pathology and had been treated with neoadjuvant trastuzumab/ chemotherapy in GeparQuattro. Results: Only 73% of the tumors (158 of 217) were centrally HER2-positive (cHER2-positive) by IHC/SISH, with cHER2-positive tumors showing a significantly higher pCR rate (46.8% vs. 20.3%, p<0.0005). HER2 status by qRT-PCR showed a concordance of 88.5% with the central IHC/SISH status, with a low pCR rate in those tumors that were HER2-negative by mRNA analysis (21.1% vs. 49.6%, p<0.0005). The level of HER2 mRNA expression was linked to response rate in ESR1-positive tumors, but not in ESR1-negative tumors. HER2 mRNA expression was significantly associated with pCR in the HER2-positive/ESR1-positive tumors (p=0.004), but not in HER2-positive/ESR1-negative tumors. Conclusions: Only patients with cHER2-positive tumors - irrespective of the method used - have an increased pCR rate with trastuzumab plus chemotherapy. In patients with cHER2-negative tumors the pCR rate is comparable to the pCR rate in the non-trastuzumab treated HER-negative population. Response to trastuzumab is correlated to HER2 mRNA levels only in ESR1-positive tumors. This study adds further evidence to the different biology of both subsets within the HER2-positive group

Predictors of length of stay in psychiatry: analyses of electronic medical records

The article processing charge was funded by the German Research Foundation (DFG) and the Albert-Ludwigs-University Freiburg in the funding programme Open Access Publishing

Low adherence with antihypertensives in actual practice: the association with social participation – a multilevel analysis

BACKGROUND: Low adherence is a key factor in explaining impaired effectiveness and efficiency in the pharmacological treatment of hypertension. However, little is known about which factors determine low adherence in actual practice. The purpose of this study is to examine whether low social participation is associated with low adherence with antihypertensive medication, and if this association is modified by the municipality of residence. METHODS: 1288 users of antihypertensive medication were identified from The Health Survey in Scania 2000, Sweden. The outcome was low adherence with antihypertensives during the last two weeks. Multilevel logistic regression with participants at the first level and municipalities at the second level was used for analyses of the data. RESULTS: Low social participation was associated with low adherence with antihypertensives during the last two weeks (OR = 2.05, 95% CI: 1.05–3.99), independently of low educational level. However, after additional adjustment for poor self-rated health and poor psychological health, the association between low social participation and low adherence with antihypertensives during the last two weeks remained but was not conclusive (OR = 1.80, 95% CI: 0.90–3.61). Furthermore, the association between low social participation and low adherence with antihypertensives during the last two weeks varied among municipalities in Scania (i.e., cross-level interaction). CONCLUSION: Low social participation seems to be associated with low adherence with antihypertensives during the last two weeks, and this association may be modified by the municipality of residence. Future studies aimed at investigating health-related behaviours in general and low adherence with medication in particular might benefit if they consider area of residence