A step-by-step guide to systematically identify all relevant animal studies

Before starting a new animal experiment, thorough analysis of previously performed experiments is essential from a scientific as well as from an ethical point of view. The method that is most suitable to carry out such a thorough analysis of the literature is a systematic review (SR). An essential first step in an SR is to search and find all potentially relevant studies. It is important to include all available evidence in an SR to minimize bias and reduce hampered interpretation of experimental outcomes. Despite the recent development of search filters to find animal studies in PubMed and EMBASE, searching for all available animal studies remains a challenge. Available guidelines from the clinical field cannot be copied directly to the situation within animal research, and although there are plenty of books and courses on searching the literature, there is no compact guide available to search and find relevant animal studies. Therefore, in order to facilitate a structured, thorough and transparent search for animal studies (in both preclinical and fundamental science), an easy-to-use, step-by-step guide was prepared and optimized using feedback from scientists in the field of animal experimentation. The step-by-step guide will assist scientists in performing a comprehensive literature search and, consequently, improve the scientific quality of the resulting review and prevent unnecessary animal use in the future.     

Search filters for finding prognostic and diagnostic prediction studies in Medline to enhance systematic reviews

Background

The interest in prognostic reviews is increasing, but to properly review existing evidence an accurate search filer for finding prediction research is needed. The aim of this paper was to validate and update two previously introduced search filters for finding prediction research in Medline: the Ingui filter and the Haynes Broad filter.

Methodology/Principal Findings

Based on a hand search of 6 general journals in 2008 we constructed two sets of papers. Set 1 consisted of prediction research papers (n = 71), and set 2 consisted of the remaining papers (n = 1133). Both search filters were validated in two ways, using diagnostic accuracy measures as performance measures. First, we compared studies in set 1 (reference) with studies retrieved by the search strategies as applied in Medline. Second, we compared studies from 4 published systematic reviews (reference) with studies retrieved by the search filter as applied in Medline. Next – using word frequency methods – we constructed an additional search string for finding prediction research. Both search filters were good in identifying clinical prediction models: sensitivity ranged from 0.94 to 1.0 using our hand search as reference, and 0.78 to 0.89 using the systematic reviews as reference. This latter performance measure even increased to around 0.95 (range 0.90 to 0.97) when either search filter was combined with the additional string that we developed. Retrieval rate of explorative prediction research was poor, both using our hand search or our systematic review as reference, and even combined with our additional search string: sensitivity ranged from 0.44 to 0.85.

Conclusions/Significance

Explorative prediction research is difficult to find in Medline, using any of the currently available search filters. Yet, application of either the Ingui filter or the Haynes broad filter results in a very low number missed clinical prediction model studies.     

Dissemination Bias in Systematic Reviews of Animal Research: A Systematic Review

Background

Systematic reviews of preclinical studies, in vivo animal experiments in particular, can influence clinical research and thus even clinical care. Dissemination bias, selective dissemination of positive or significant results, is one of the major threats to validity in systematic reviews also in the realm of animal studies. We conducted a systematic review to determine the number of published systematic reviews of animal studies until present, to investigate their methodological features especially with respect to assessment of dissemination bias, and to investigate the citation of preclinical systematic reviews on clinical research.

Methods

Eligible studies for this systematic review constitute systematic reviews that summarize in vivo animal experiments whose results could be interpreted as applicable to clinical care. We systematically searched Ovid Medline, Embase, ToxNet, and ScienceDirect from 1^st January 2009 to 9^th January 2013 for eligible systematic reviews without language restrictions. Furthermore we included articles from two previous systematic reviews by Peters et al. and Korevaar et al.

Results

The literature search and screening process resulted in 512 included full text articles. We found an increasing number of published preclinical systematic reviews over time. The methodological quality of preclinical systematic reviews was low. The majority of preclinical systematic reviews did not assess methodological quality of the included studies (71%), nor did they assess heterogeneity (81%) or dissemination bias (87%). Statistics quantifying the importance of clinical research citing systematic reviews of animal studies showed that clinical studies referred to the preclinical research mainly to justify their study or a future study (76%).

Discussion

Preclinical systematic reviews may have an influence on clinical research but their methodological quality frequently remains low. Therefore, systematic reviews of animal research should be critically appraised before translating them to a clinical context.     

Irreproducibility in searches of scientific literature: A comparative analysis

1. Repeatability is the cornerstone of science, and it is particularly important for systematic reviews. However, little is known on how researchers’ choice of database, and search platform influence the repeatability of systematic reviews. Here, we aim to unveil how the computer environment and the location where the search was initiated from influence hit results.
2. We present a comparative analysis of time‐synchronized searches at different institutional locations in the world and evaluate the consistency of hits obtained within each of the search terms using different search platforms.
3. We revealed a large variation among search platforms and showed that PubMed and Scopus returned consistent results to identical search strings from different locations. Google Scholar and Web of Science''s Core Collection varied substantially both in the number of returned hits and in the list of individual articles depending on the search location and computing environment. Inconsistency in Web of Science results has most likely emerged from the different licensing packages at different institutions.
4. To maintain scientific integrity and consistency, especially in systematic reviews, action is needed from both the scientific community and scientific search platforms to increase search consistency. Researchers are encouraged to report the search location and the databases used for systematic reviews, and database providers should make search algorithms transparent and revise access rules to titles behind paywalls. Additional options for increasing the repeatability and transparency of systematic reviews are storing both search metadata and hit results in open repositories and using Application Programming Interfaces (APIs) to retrieve standardized, machine‐readable search metadata.

     

Mapping Systematic Reviews on Atopic Eczema—An Essential Resource for Dermatology Professionals and Researchers

Background

Many research studies have been published on atopic eczema and these are often summarised in systematic reviews (SRs). Identifying SRs can be time-consuming for health professionals, and researchers. In order to facilitate the identification of important research, we have compiled an on-line resource that includes all relevant eczema reviews published since 2000.

Methods

SRs were searched for in MEDLINE (Ovid), EMBASE (Ovid), PubMed, the Cochrane Database of Systematic Reviews, DARE and NHS Evidence. Selected SRs were assessed against the pre-defined eligibility criteria and relevant articles were grouped by treatment category for the included interventions. All identified systematic reviews are included in the Global Resource of EczemA Trials (GREAT) database (www.greatdatabase.org.uk) and key clinical messages are summarised here.

Results

A total of 128 SRs reviews were identified, including three clinical guidelines. Of these, 46 (36%) were found in the Cochrane Library. No single database contained all of the SRs found. The number of SRs published per year has increased substantially over the last thirteen years, and reviews were published in a variety of clinical journals. Of the 128 SRs, 1 (1%) was on mechanism, 37 (29%) were on epidemiology, 40 (31%) were on eczema prevention, 29 (23%) were on topical treatments, 31 (24%) were on systemic treatments, and 24 (19%) were on other treatments. All SRs included searches of MEDLINE in their search methods. One hundred six SRs (83%) searched more than one electronic database. There were no language restrictions reported in the search methods of 52 of the SRs (41%).

Conclusions

This mapping of atopic eczema reviews is a valuable resource. It will help healthcare practitioners, guideline writers, information specialists, and researchers to quickly identify relevant up-to-date evidence in the field for improving patient care.     

Health-Risk Behaviour in Deprived Neighbourhoods Compared with Non-Deprived Neighbourhoods: A Systematic Literature Review of Quantitative Observational Studies

Background

There has been increasing interest in neighbourhoods’ influence on individuals’ health-risk behaviours, such as smoking, alcohol consumption, physical activity and diet. The aim of this review was to systematically review recent studies on health-risk behaviour among adults who live in deprived neighbourhoods compared with those who live in non-deprived neighbourhoods and to summarise what kind of operationalisations of neighbourhood deprivation that were used in the studies.

Methods

PRISMA guidelines for systematic reviews were followed. Systematic searches were performed in PubMed, Embase, Web of Science and Sociological Abstracts using relevant search terms, Boolean operators, and truncation, and reference lists were scanned. Quantitative observational studies that examined health-risk behaviour in deprived neighbourhoods compared with non-deprived neighbourhoods were eligible for inclusion.

Results

The inclusion criteria were met by 22 studies. The available literature showed a positive association between smoking and physical inactivity and living in deprived neighbourhoods compared with non-deprived neighbourhoods. In regard to low fruit and vegetable consumption and alcohol consumption, the results were ambiguous, and no clear differences were found. Numerous different operationalisations of neighbourhood deprivation were used in the studies.

Conclusion

Substantial evidence indicates that future health interventions in deprived neighbourhoods should focus on smoking and physical inactivity. We suggest that alcohol interventions should be population based rather than based on the specific needs of deprived neighbourhoods. More research is needed on fruit and vegetable consumption. In future studies, the lack of a uniform operationalisation of neighbourhood deprivation must be addressed.     

Maximizing the value of systematic reviews in ecology when data or resources are limited

Systematic reviews provide a rigorous, repeatable and quantitative method for assessing and synthesizing all available empirical evidence to evaluate a specific research, management, or policy question. They are particularly well suited for evaluating the effectiveness of environmental management actions, and thus for underpinning evidence‐based adaptive natural resource management. However, their current utility may be limited in countries like Australia, where both the amount of research relative to land area and of well‐monitored, active land management for environmental purposes are relatively low. Based on our experience conducting two of the first ecological systematic reviews in Australia, we have developed a number of recommendations for conducting systematic reviews in situations where resources and/or primary research data are limited. We discuss potential modification or augmentation of most aspects of the systematic review process including selection of a review team, question formulation, search strategy, data analysis, and the communication of results, as well as the inherent tradeoffs between systematic thoroughness and available resources that are involved in these changes. We hope that our recommendations will encourage more ecologists to undertake systematic reviews even if primary research and resources to conduct the review appear to be limited, as even a modified systematic review can provide more defensible evidence‐based guidelines for management of natural resources.     

Prognostic serum biomarkers in cancer patients with COVID-19: A systematic review

PurposeCancer patients with COVID-19 likely express biomarker changes in circulation. However, the biomarkers used in SARS-CoV-2 infected cancer patients for COVID-19 severity and prognosis are largely unclear. Therefore, this systematic review aims to determine what biomarkers were measured in cancer patients with COVID-19 and their prognostic utility.MethodsA systematic literature review in PubMed, Embase, and Scopus was performed on June 16th, 2021. The search keywords coronavirus, neoplasm, biomarkers, and disease progression were used to filter out 17 eligible studies, which were then carefully evaluated.ResultsA total of 4,168 patients, 16 types of cancer, and 60 biomarkers were included. Seven up-regulated markers, including CRP, d-dimer, ferritin, IL-2R, IL-6, LDH, and PCT, were identified in eligible studies. Albumin and hemoglobin were significantly down-regulated in cancer patients with COVID-19. Moreover, we observed that the SARS-CoV-2 infected cancer patients with lower CRP, ferritin, and LDH levels successfully survived from COVID-19 treatments.ConclusionSeveral important clinical biomarkers, such as CRP, ferritin, and LDH, may serve as the prognostic markers to predict the outcomes following COVID-19 treatment and monitor the deterioration of COVID-19 in cancer patients.     

Using Multiple Types of Studies in Systematic Reviews of Health Care Interventions – A Systematic Review

Background

A systematic review may evaluate different aspects of a health care intervention. To accommodate the evaluation of various research questions, the inclusion of more than one study design may be necessary. One aim of this study is to find and describe articles on methodological issues concerning the incorporation of multiple types of study designs in systematic reviews on health care interventions. Another aim is to evaluate methods studies that have assessed whether reported effects differ by study types.

Methods and Findings

We searched PubMed, the Cochrane Database of Systematic Reviews, and the Cochrane Methodology Register on 31 March 2012 and identified 42 articles that reported on the integration of single or multiple study designs in systematic reviews. We summarized the contents of the articles qualitatively and assessed theoretical and empirical evidence. We found that many examples of reviews incorporating multiple types of studies exist and that every study design can serve a specific purpose. The clinical questions of a systematic review determine the types of design that are necessary or sufficient to provide the best possible answers. In a second independent search, we identified 49 studies, 31 systematic reviews and 18 trials that compared the effect sizes between randomized and nonrandomized controlled trials, which were statistically different in 35%, and not different in 53%. Twelve percent of studies reported both, different and non-different effect sizes.

Conclusions

Different study designs addressing the same question yielded varying results, with differences in about half of all examples. The risk of presenting uncertain results without knowing for sure the direction and magnitude of the effect holds true for both nonrandomized and randomized controlled trials. The integration of multiple study designs in systematic reviews is required if patients should be informed on the many facets of patient relevant issues of health care interventions.     

The circadian rhythm of heart rate variability

Purpose: In recent years, the measurement of heart rate variability (HRV) has gained ground even outside research settings in everyday clinical and outpatient practice and in health promotion. Methods: Using the search terms “heart rate variability”, “hrv” and “circadian”, a systematic review was carried out in the PubMed database to find original work that analysed the course of HRV parameters over a 24-h period. Results: A total of 26 original studies were found. Almost all the studies detected a circadian rhythm for the HRV parameters analysed. HRV increased during the night in particular and a nighttime peak during the second half of the night was identified. Conclusions: HRV follows a circadian rhythm. But until today, there isn′t any possibility to make quantitative statements about changes over the course of the day for planning short-term measurements. More qualitative studies must be carried in order to close this knowledge gaps.     

The Health Effects of Passive Smoking: An Overview of Systematic Reviews Based on Observational Epidemiological Evidence

Purpose

We aim to systematically summarize the available epidemiological evidence to identify the impact of environmental tobacco smoke on health.

Methods

A systematic literature search of PubMed, Embase, Web of Science, and Scopus for meta-analyses was conducted through January 2015. We included systematic reviews that investigated the association between passive smoking and certain diseases. Quantitative outcomes of association between passive smoking and the risk of certain diseases were summarized.

Results

Sixteen meta-analyses covering 130 cohort studies, 159 case-control studies, and 161 cross-sectional studies and involving 25 diseases or health problems were reviewed. Passive smoking appears not to be significantly associated with eight diseases or health problems, but significantly elevates the risk for eleven specific diseases or health problems, including invasive meningococcal disease in children (OR 2.18; 95% CI 1.63–2.92), cervical cancer (OR 1.73; 95% CI 1.35–2.21), Neisseria meningitidis carriage (OR 1.68; 95% CI 1.19–2.36), Streptococcus pneumoniae carriage (OR 1.66; 95% CI 1.33–2.07), lower respiratory infections in infancy (OR 1.42; 95% CI 1.33–1.51), food allergy (OR 1.43; 95% CI 1.12–1.83), and so on.

Conclusions

Our overview of systematic reviews of observational epidemiological evidence suggests that passive smoking is significantly associated with an increasing risk of many diseases or health problems, especially diseases in children and cancers.     

Glucocorticoid-Induced Hyperglycemia Including Dexamethasone-Associated Hyperglycemia in COVID-19 Infection: A Systematic Review

ObjectiveOptimal glucocorticoid-induced hyperglycemia (GCIH) management is unclear. The COVID-19 pandemic has made this issue more prominent because dexamethasone became the standard of care in patients needing respiratory support. This systematic review aimed to describe the management of GCIH and summarize available management strategies for dexamethasone-associated hyperglycemia in patients with COVID-19.MethodsA systematic review was conducted using the PubMed/MEDLINE, Cochrane Library, Embase, and Web of Science databases with results from 2011 through January 2022. Keywords included synonyms for “steroid-induced diabetes” or “steroid-induced hyperglycemia.” Randomized controlled trials (RCTs) were included for review of GCIH management. All studies focusing on dexamethasone-associated hyperglycemia in COVID-19 were included regardless of study quality.ResultsInitial search for non-COVID GCIH identified 1230 references. After screening and review, 33 articles were included in the non-COVID section of this systematic review. Initial search for COVID-19–related management of dexamethasone-associated hyperglycemia in COVID-19 identified 63 references, whereas 7 of these were included in the COVID-19 section. RCTs of management strategies were scarce, did not use standard definitions for hyperglycemia, evaluated a variety of treatment strategies with varying primary end points, and were generally not found to be effective except for Neutral Protamine Hagedorn insulin added to basal-bolus regimens.ConclusionFew RCTs are available evaluating GCIH management. Further studies are needed to support the formulation of clinical guidelines for GCIH especially given the widespread use of dexamethasone during the COVID-19 pandemic.     

Peptide sequence tag-based blind identification of post-translational modifications with point process model

An important but difficult problem in proteomics is the identification of post-translational modifications (PTMs) in a protein. In general, the process of PTM identification by aligning experimental spectra with theoretical spectra from peptides in a peptide database is very time consuming and may lead to high false positive rate. In this paper, we introduce a new approach that is both efficient and effective for blind PTM identification. Our work consists of the following phases. First, we develop a novel tree decomposition based algorithm that can efficiently generate peptide sequence tags (PSTs) from an extended spectrum graph. Sequence tags are selected from all maximum weighted antisymmetric paths in the graph and their reliabilities are evaluated with a score function. An efficient deterministic finite automaton (DFA) based model is then developed to search a peptide database for candidate peptides by using the generated sequence tags. Finally, a point process model-an efficient blind search approach for PTM identification, is applied to report the correct peptide and PTMs if there are any. Our tests on 2657 experimental tandem mass spectra and 2620 experimental spectra with one artificially added PTM show that, in addition to high efficiency, our ab-initio sequence tag selection algorithm achieves better or comparable accuracy to other approaches. Database search results show that the sequence tags of lengths 3 and 4 filter out more than 98.3% and 99.8% peptides respectively when applied to a yeast peptide database. With the dramatically reduced search space, the point process model achieves significant improvement in accuracy as well. AVAILABILITY: The software is available upon request.     

The Role of Google Scholar in Evidence Reviews and Its Applicability to Grey Literature Searching

Google Scholar (GS), a commonly used web-based academic search engine, catalogues between 2 and 100 million records of both academic and grey literature (articles not formally published by commercial academic publishers). Google Scholar collates results from across the internet and is free to use. As a result it has received considerable attention as a method for searching for literature, particularly in searches for grey literature, as required by systematic reviews. The reliance on GS as a standalone resource has been greatly debated, however, and its efficacy in grey literature searching has not yet been investigated. Using systematic review case studies from environmental science, we investigated the utility of GS in systematic reviews and in searches for grey literature. Our findings show that GS results contain moderate amounts of grey literature, with the majority found on average at page 80. We also found that, when searched for specifically, the majority of literature identified using Web of Science was also found using GS. However, our findings showed moderate/poor overlap in results when similar search strings were used in Web of Science and GS (10–67%), and that GS missed some important literature in five of six case studies. Furthermore, a general GS search failed to find any grey literature from a case study that involved manual searching of organisations’ websites. If used in systematic reviews for grey literature, we recommend that searches of article titles focus on the first 200 to 300 results. We conclude that whilst Google Scholar can find much grey literature and specific, known studies, it should not be used alone for systematic review searches. Rather, it forms a powerful addition to other traditional search methods. In addition, we advocate the use of tools to transparently document and catalogue GS search results to maintain high levels of transparency and the ability to be updated, critical to systematic reviews.     

Pharmacological effects of Cimicifuga racemosa

Cimicifuga racemosa is widely employed to relieve menopause symptoms for its hormonal-like action. However, recent experimental studies have not found an estrogenic action by this plant. The purpose of this systematic review is to analyse all experimental studies (in vivo and in vitro) performed on C. racemosa to elucidate its mechanism of action. Animal and in vitro experiments on C. racemosa were identified through a computerised literature searches performed on Medline (PubMed), Embase, Amed, CISCOM and Cochrane Library databases. In addition, bibliographies of the articles thus located were scanned for further relevant publications and manufactures of commercial C. racemosa preparations were asked to contribute published and unpublished material. No language restrictions were imposed. A total of 15 animal and 15 in vitro studies on C. racemosa have been found. Their results suggest that C. racemosa possesses a central activity instead of a hormonal effect. Further biological and chemical investigations are required to define its mechanism of action and to identify the compounds responsible of its actions.     

Prognostic molecular markers in pediatric liver disease – Are there any?

Pediatric liver disease (PLD) is a major cause of severe morbidity and prolonged hospitalizations in children. Stratifying patients in terms of prognosis remains challenging. The limited knowledge about molecular mechanisms causing and accompanying PLD remains the main obstacle in a search for reliable prognostic biomarkers. A systematic search of MEDLINE via PubMed and Embase via OVID was conducted on studies published between August 2007 and August 2017. Molecular markers with a prognostic potential in terms of survival, need for liver transplantation or disease progression/regression were selected. In general, identified studies were single center smaller case-control studies or case series with a low level of evidence and a high risk of bias. Only 23 studies comprising 898 patients could be included, mostly focusing on biliary atresia, non-alcoholic fatty liver disease, viral hepatitis, and LT; and markers related to morphogenesis and fibrosis. Furthermore, molecular markers in metabolic pathways and inflammation shown to be relevant, however requiring further validation. Hence, further biological and clinical studies are needed to gain greater molecular insight into PLD.     

Impact of PubMed search filters on the retrieval of evidence by physicians

Background:

Physicians face challenges when searching PubMed for research evidence, and they may miss relevant articles while retrieving too many nonrelevant articles. We investigated whether the use of search filters in PubMed improves searching by physicians.

Methods:

We asked a random sample of Canadian nephrologists to answer unique clinical questions derived from 100 systematic reviews of renal therapy. Physicians provided the search terms that they would type into PubMed to locate articles to answer these questions. We entered the physician-provided search terms into PubMed and applied two types of search filters alone or in combination: a methods-based filter designed to identify high-quality studies about treatment (clinical queries “therapy”) and a topic-based filter designed to identify studies with renal content. We evaluated the comprehensiveness (proportion of relevant articles found) and efficiency (ratio of relevant to nonrelevant articles) of the filtered and nonfiltered searches. Primary studies included in the systematic reviews served as the reference standard for relevant articles.

Results:

The average physician-provided search terms retrieved 46% of the relevant articles, while 6% of the retrieved articles were nonrelevant (the ratio of relevant to nonrelevant articles was 1:16). The use of both filters together produced a marked improvement in efficiency, resulting in a ratio of relevant to nonrelevant articles of 1:5 (16 percentage point improvement; 99% confidence interval 9% to 22%; p < 0.003) with no substantive change in comprehensiveness (44% of relevant articles found; p = 0.55).

Interpretation:

The use of PubMed search filters improves the efficiency of physician searches. Improved search performance may enhance the transfer of research into practice and improve patient care.Retrieving health literature is a cornerstone of evidence-based practice. With the rapid increase in available evidence, physicians can no longer rely on one or two key journals to stay current. Increasingly, physicians search bibliographic databases, such as PubMed, for research evidence, which is dispersed across hundreds of journals. Each year, physicians perform over 200 million searches in PubMed.^1,2 Physicians face challenges while searching PubMed and often miss relevant articles while retrieving too many nonrelevant articles.^3–6 Clinical decision-making based on evidence from a search may be impaired if relevant articles are missed. Retrieving many nonrelevant articles impedes the efficiency of searching. Improved search strategies are therefore necessary to retrieve a manageable amount of information. The use of PubMed search filters may help solve this problem. Filters are objectively derived, pretested strategies optimized to help users efficiently retrieve articles for a specific purpose.^7,8PubMed provides two types of clinical search filters: methods-based and topic-based. Methods-based filters (known as clinical queries) were designed to retrieve articles on therapy, diagnosis, prognosis and etiology.^9–13 For example, the clinical queries “therapy” filter is optimized to retrieve publications of randomized controlled trials. Methods-based filters can be used for any clinical discipline and are available for general use in PubMed (www.ncbi.nlm.nih.gov/pubmed/clinical). Topic-based filters, in contrast, are designed to retrieve articles within a specific discipline or topic. For example, the recently developed nephrology filters were optimized to retrieve articles with renal content.¹Physicians can use methods- and topic-based filters alone or in combination. For example, Figure 1A shows a search without search filters for studies about the effectiveness of hepatitis B vaccination in patients with chronic kidney disease. Alternatively, this search could be performed with search filters (Figure 1B). Using filters removes the task of generating and including method-specific or topic-specific terms in a search strategy because the filters act as optimized substitutes. For example, applying the nephrology filter eliminates the need to enter renal terms and synonyms in a search query (e.g., chronic kidney disease, end-stage renal disease, chronic renal failure). The nephrology filter, instead, maximizes the retrieval of all renal content (see the nephrology filter strategy in Figure 1B).Open in a separate windowFigure 1:PubMed searches without (A) and with (B) filters. This figure was created from the PubMed clinical queries Web interface; this page currently does not feature a “clinical category” section. When we performed searches with the nephrology filter (B), we removed the term “chronic kidney disease” because the filter acts as an optimized substitute for clinical content terms.In theory, filters should make searching more efficient; however, empiric evidence of this among physicians is lacking. We conducted this study to determine whether the use of methods-based filters and topic-based filters (alone and in combination) improve the efficiency of physician searches in PubMed. The area of renal medicine is an excellent test model because the literature in this field is dispersed across 400 multidisciplinary journals, and many nephrologists search PubMed for information to guide patient care.^14,15     

Automated reprocessing pipeline for searching heterogeneous mass spectrometric data of the HUPO Brain Proteome Project pilot phase

The newly available techniques for sensitive proteome analysis and the resulting amount of data require a new bioinformatics focus on automatic methods for spectrum reprocessing and peptide/protein validation. Manual validation of results in such studies is not feasible and objective enough for quality relevant interpretation. The necessity for tools enabling an automatic quality control is, therefore, important to produce reliable and comparable data in such big consortia as the Human Proteome Organization Brain Proteome Project. Standards and well-defined processing pipelines are important for these consortia. We show a way for choosing the right database model, through collecting data, processing these with a decoy database and end up with a quality controlled protein list merged from several search engines, including a known false-positive rate.     

Prevalence of Depression among Chinese University Students: A Meta-Analysis

BackgroundDepression is a major mental health issue worldwide, and university students with heavy burdens of study are at a high risk for depression. While a number of studies have been conducted regarding depression among university students in China, there is a lack of information regarding the national prevalence of depression among Chinese university students. Therefore, we performed a meta-analysis to statistically pool the prevalence of depression among Chinese university students.MethodsA systematic search of scientific databases was conducted, including Chinese Web of Knowledge, Embase, PubMed, Wanfang (a Chinese database) and Weipu (a Chinese database) to find relevant publications published between 1995 and December 2015. This was supplemented by a secondary review of the reference lists of all retrieved papers to find additional relevant citations. Studies published in either English or Chinese that provided prevalence estimates of depression in Chinese university students were considered. Prevalence estimates of each eligible study were extracted and pooled in our meta-analysis using a random-effects model.ResultsA total of 39 studies conducted between 1997 and 2015 including 32,694 university students were analyzed. Our results indicate that the overall prevalence of depression among Chinese university students is 23.8% (95% CI: 19.9%–28.5%). Substantial heterogeneity in prevalence estimates was noted. Subgroup analysis revealed that the prevalence of depression among medical students is higher than among other students.ConclusionsOverall, the prevalence of depression among Chinese university students is exceedingly high. This suggests that it is imperative that more attention be given to the development of appropriate mental healthcare strategies for university students in China.