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Progress in Orthodontics Oct 2013No meta-analyses or systematic reviews have been conducted to evaluate numerous potential biasing factors contributing to the controversial results on congenitally... (Meta-Analysis)
Meta-Analysis Review
No meta-analyses or systematic reviews have been conducted to evaluate numerous potential biasing factors contributing to the controversial results on congenitally missing teeth (CMT). We aimed to perform a rather comprehensive meta-analysis and systematic review on this subject. A thorough search was performed during September 2012 until April 2013 to find the available literature regarding CMT prevalence. Besides qualitatively discussing the literature, the meta-sample homogeneity, publication bias, and the effects of sample type, sample size, minimum and maximum ages of included subjects, gender imbalances, and scientific credit of the publishing journals on the reported CMT prevalence were statistically analyzed using Q-test, Egger regression, Spearman coefficient, Kruskal-Wallis, Welch t test (α=0.05), and Mann-Whitney U test (α=0.016, α=0.007). A total of 111 reports were collected. Metadata were heterogeneous (P=0.000). There was not a significant publication bias (Egger Regression P=0.073). Prevalence rates differed in different types of populations (Kruskal-Wallis P=0.001). Studies on orthodontic patients might report slightly (about 1%) higher prevalence (P=0.009, corrected α=0.016). Non-orthodontic dental patients showed a significant 2% decline [P=0.007 (Mann-Whitney U)]. Enrolling more males in researches might significantly reduce the observed prevalence (Spearman ρ=-0.407, P=0.001). Studies with higher minimums of subjects' age showed always slightly less CMT prevalence. This reached about -1.6% around the ages 10 to 13 and was significant for ages 10 to 12 (Welch t test P<0.05). There seems to be no limit over the maximum age (Welch t test P>0.2). Studies' sample sizes were correlated negatively with CMT prevalence (ρ=-0.250, P=0.009). It was not verified whether higher CMT rates have better chances of being published (ρ=0.132, P=0.177). CMT definition should be unified. Samples should be sex-balanced. Enrolling both orthodontic and dental patients in similar proportions might be preferable over sampling from each of those groups. Sampling from children over 12 years seems advantageous. Two or more observers should examine larger samples to reduce the false negative error tied with such samples.
Topics: Age Factors; Anodontia; Bias; False Negative Reactions; Female; Humans; Male; Observer Variation; Prevalence; Publication Bias; Research Design; Sample Size; Sex Factors
PubMed: 24325806
DOI: 10.1186/2196-1042-14-33 -
Frontiers in Oncology 2022Machine learning and semantic analysis are computer-based methods to evaluate complex relationships and predict future perspectives. We used these technologies to define...
Machine learning and semantic analysis are computer-based methods to evaluate complex relationships and predict future perspectives. We used these technologies to define recent, current and future topics in pancreatic cancer research. Publications indexed under the Medical Subject Headings (MeSH) term 'Pancreatic Neoplasms' from January 1996 to October 2021 were downloaded from PubMed. Using the statistical computing language R and the interpreted, high-level, general-purpose programming language Python, we extracted publication dates, geographic information, and abstracts from each publication's metadata for bibliometric analyses. The generative statistical algorithm "latent Dirichlet allocation" (LDA) was applied to identify specific research topics and trends. The unsupervised "Louvain algorithm" was used to establish a network to identify relationships between single topics. A total of 60,296 publications were identified and analyzed. The publications were derived from 133 countries, mostly from the Northern Hemisphere. For the term "pancreatic cancer research", 12,058 MeSH terms appeared 1,395,060 times. Among them, we identified the four main topics "Clinical Manifestation and Diagnosis", "Review and Management", "Treatment Studies", and "Basic Research". The number of publications has increased rapidly during the past 25 years. Based on the number of publications, the algorithm predicted that "Immunotherapy", Prognostic research", "Protein expression", "Case reports", "Gemcitabine and mechanism", "Clinical study of gemcitabine", "Operation and postoperation", "Chemotherapy and resection", and "Review and management" as current research topics. To our knowledge, this is the first study on this subject of pancreatic cancer research, which has become possible due to the improvement of algorithms and hardware.
PubMed: 35419289
DOI: 10.3389/fonc.2022.832385 -
BMC Geriatrics Nov 2023Delirium is a prevalent neuropsychiatric medical phenomenon that causes serious emergency outcomes, including mortality and morbidity. It also increases the suffering...
Exploration of key drug target proteins highlighting their related regulatory molecules, functional pathways and drug candidates associated with delirium: evidence from meta-data analyses.
BACKGROUND
Delirium is a prevalent neuropsychiatric medical phenomenon that causes serious emergency outcomes, including mortality and morbidity. It also increases the suffering and the economic burden for families and carers. Unfortunately, the pathophysiology of delirium is still unknown, which is a major obstacle to therapeutic development. The modern network-based system biology and multi-omics analysis approach has been widely used to recover the key drug target biomolecules and signaling pathways associated with disease pathophysiology. This study aimed to identify the major drug target hub-proteins associated with delirium, their regulatory molecules with functional pathways, and repurposable drug candidates for delirium treatment.
METHODS
We used a comprehensive proteomic seed dataset derived from a systematic literature review and the Comparative Toxicogenomics Database (CTD). An integrated multi-omics network-based bioinformatics approach was utilized in this study. The STRING database was used to construct the protein-protein interaction (PPI) network. The gene set enrichment and signaling pathways analysis, the regulatory transcription factors and microRNAs were conducted using delirium-associated genes. Finally, hub-proteins associated repurposable drugs were retrieved from CMap database.
RESULTS
We have distinguished 11 drug targeted hub-proteins (MAPK1, MAPK3, TP53, JUN, STAT3, SRC, RELA, AKT1, MAPK14, HSP90AA1 and DLG4), 5 transcription factors (FOXC1, GATA2, YY1, TFAP2A and SREBF1) and 6 microRNA (miR-375, miR-17-5, miR-17-5p, miR-106a-5p, miR-125b-5p, and miR-125a-5p) associated with delirium. The functional enrichment and pathway analysis revealed the cytokines, inflammation, postoperative pain, oxidative stress-associated pathways, developmental biology, shigellosis and cellular senescence which are closely connected with delirium development and the hallmarks of aging. The hub-proteins associated computationally identified repurposable drugs were retrieved from database. The predicted drug molecules including aspirin, irbesartan, ephedrine-(racemic), nedocromil, and guanidine were characterized as anti-inflammatory, stimulating the central nervous system, neuroprotective medication based on the existing literatures. The drug molecules may play an important role for therapeutic development against delirium if they are investigated more extensively through clinical trials and various wet lab experiments.
CONCLUSION
This study could possibly help future research on investigating the delirium-associated therapeutic target biomarker hub-proteins and repurposed drug compounds. These results will also aid understanding of the molecular mechanisms that underlie the pathophysiology of delirium onset and molecular function.
Topics: Humans; Gene Regulatory Networks; Proteomics; MicroRNAs; Transcription Factors; Delirium
PubMed: 37993790
DOI: 10.1186/s12877-023-04457-1 -
Plants (Basel, Switzerland) Apr 2021The early life-history stages of plants, such as germination and seedling establishment, depend on favorable environmental conditions. Changes in the environment at high... (Review)
Review
The early life-history stages of plants, such as germination and seedling establishment, depend on favorable environmental conditions. Changes in the environment at high altitude and high latitude regions, as a consequence of climate change, will significantly affect these life stages and may have profound effects on species recruitment and survival. Here, we synthesize the current knowledge of climate change effects on treeline, tundra, and alpine plants' early life-history stages. We systematically searched the available literature on this subject up until February 2020 and recovered 835 potential articles that matched our search terms. From these, we found 39 studies that matched our selection criteria. We characterized the studies within our review and performed a qualitative and quantitative analysis of the extracted meta-data regarding the climatic effects likely to change in these regions, including projected warming, early snowmelt, changes in precipitation, nutrient availability and their effects on seed maturation, seed dormancy, germination, seedling emergence and seedling establishment. Although the studies showed high variability in their methods and studied species, the qualitative and quantitative analysis of the extracted data allowed us to detect existing patterns and knowledge gaps. For example, warming temperatures seemed to favor all studied life stages except seedling establishment, a decrease in precipitation had a strong negative effect on seed stages and, surprisingly, early snowmelt had a neutral effect on seed dormancy and germination but a positive effect on seedling establishment. For some of the studied life stages, data within the literature were too limited to identify a precise effect. There is still a need for investigations that increase our understanding of the climate change impacts on high altitude and high latitude plants' reproductive processes, as this is crucial for plant conservation and evidence-based management of these environments. Finally, we make recommendations for further research based on the identified knowledge gaps.
PubMed: 33919792
DOI: 10.3390/plants10040768 -
Systematic Reviews Aug 2016Meta-research studies investigating methods, systems, and processes designed to improve the efficiency of systematic review workflows can contribute to building an... (Review)
Review
BACKGROUND
Meta-research studies investigating methods, systems, and processes designed to improve the efficiency of systematic review workflows can contribute to building an evidence base that can help to increase value and reduce waste in research. This study demonstrates the use of an economic evaluation framework to compare the costs and effects of four variant approaches to identifying eligible studies for consideration in systematic reviews.
METHODS
A cost-effectiveness analysis was conducted using a basic decision-analytic model, to compare the relative efficiency of 'safety first', 'double screening', 'single screening' and 'single screening with text mining' approaches in the title-abstract screening stage of a 'case study' systematic review about undergraduate medical education in UK general practice settings. Incremental cost-effectiveness ratios (ICERs) were calculated as the 'incremental cost per citation 'saved' from inappropriate exclusion' from the review. Resource use and effect parameters were estimated based on retrospective analysis of 'review process' meta-data curated alongside the 'case study' review, in conjunction with retrospective simulation studies to model the integrated use of text mining. Unit cost parameters were estimated based on the 'case study' review's project budget. A base case analysis was conducted, with deterministic sensitivity analyses to investigate the impact of variations in values of key parameters.
RESULTS
Use of 'single screening with text mining' would have resulted in title-abstract screening workload reductions (base case analysis) of >60 % compared with other approaches. Across modelled scenarios, the 'safety first' approach was, consistently, equally effective and less costly than conventional 'double screening'. Compared with 'single screening with text mining', estimated ICERs for the two non-dominated approaches (base case analyses) ranged from £1975 ('single screening' without a 'provisionally included' code) to £4427 ('safety first' with a 'provisionally included' code) per citation 'saved'. Patterns of results were consistent between base case and sensitivity analyses.
CONCLUSIONS
Alternatives to the conventional 'double screening' approach, integrating text mining, warrant further consideration as potentially more efficient approaches to identifying eligible studies for systematic reviews. Comparable economic evaluations conducted using other systematic review datasets are needed to determine the generalisability of these findings and to build an evidence base to inform guidance for review authors.
Topics: Cost-Benefit Analysis; Data Mining; Humans; Patient Safety; Research Design
PubMed: 27535658
DOI: 10.1186/s13643-016-0315-4 -
International Journal of Qualitative... 2015The aim is to identify facilitators and barriers for physical activity (PA) experienced by morbidly obese adults in the Western world. Inactivity and a sedentary... (Review)
Review
The aim is to identify facilitators and barriers for physical activity (PA) experienced by morbidly obese adults in the Western world. Inactivity and a sedentary lifestyle have become a major challenge for health and well-being, particularly among persons with morbid obesity. Lifestyle changes may lead to long-term changes in activity level, if facilitators and barriers are approached in a holistic way by professionals. To develop lifestyle interventions, the perspective and experiences of this group of patients are essential for success. The methodology of the systematic review followed the seven-step procedure of the Joanna Briggs Institute and was published in a protocol. Six databases were searched using keywords and index terms. Manual searches were performed in reference lists and in cited citations up until March 2015. The selected studies underwent quality appraisal in the Joanna Briggs-Qualitative Assessment and Review Instrument. Data from primary studies were extracted and were subjected to a hermeneutic text interpretation and a data-driven coding in a five-step procedure focusing on meaning and constant targeted comparison through which they were categorized and subjected into a meta-synthesis. Eight papers were included for the systematic review, representing the experiences of PA among 212 participants. One main theme developed from the meta-data analysis: "Identity" with the three subthemes: "considering weight," "being able to," and "belonging with others." The theme and subthemes were merged into a meta-synthesis: "Homecoming: a change in identity." The experiences of either suffering or well-being during PA affected the identity of adults with morbid obesity either by challenging or motivating them. A change in identity may be needed to feel a sense of "homecoming" when active.
Topics: Attitude; Exercise; Health Behavior; Humans; Life Style; Motivation; Obesity, Morbid; Self Efficacy; Stress, Psychological
PubMed: 26400462
DOI: 10.3402/qhw.v10.28577 -
Facts, Views & Vision in ObGyn Dec 2016In case of preterm birth in twins, it is not well established if the second twin benefits from a delayed-interval delivery. (Review)
Review
BACKGROUND
In case of preterm birth in twins, it is not well established if the second twin benefits from a delayed-interval delivery.
OBJECTIVE
The main objective of this systematic review is to evaluate survival benefit of the second twin from delayed interval delivery compared to the first twin. Secondly, we will evaluate the survival benefit of the procedure when performed equal to or after 24 weeks gestational age of the first born.
METHODS
Delayed interval delivery was defined as every attempt to perform a delayed interval delivery with at minimum placement of a high ligature of the umbilical cord and a delay of delivery of at least 24 hours. Based on the PRISMA method, a systematic review was performed. Controlled and observational studies reporting at least 3 cases of delayed interval delivery in dichorionic diamniotic twin pregnancy describing the outcome of the first and the second twin were included. Case reports and papers on triplet or higher order pregnancies were excluded. Primary data included gestational age and outcome of the first and second born. Metadata concern management strategies (tocolysis, antibiotics, cerclage), neonatal data (sex, birth weight and morbidity) and maternal complications. The methodological quality of included studies was assessed using the "IHE quality appraisal checklist for assessing the quality of case series". Meta-analysis was performed by computing relative risk (RR) with its 95% confidence interval (CI) using the random-effects model. Statistical heterogeneity was tested using the and Chi statistics. Since there is no control group for the secondary outcomes, these are presented by narrative synthesis.
RESULTS
Mortality data were extracted from 13 articles, reporting a total of 128 cases of delayed interval delivery. In the analysis, the second born had a significantly lower mortality risk compared to the first born (relative risk = 0.44, 95% confidence interval = 0.34 - 0.57, P<0.0001, I= 0%, P=0.70). For the analysis of mortality of the second born foetus versus the first born when the first delivery was at ≥24 weeks of gestational age, 12 articles were included. In the analysis 4 reports were excluded since there were no events (no mortality) in both groups (first and second born) making analysis impossible. For the 36 cases included, the second born had a significantly lower mortality risk compared to the first born if delivery of the first born occurred at ≥ 24 weeks gestational age (relative risk=0.37, 95% confidence interval= 0.17 - 0.82, P=0.014, I=0%, P=0.82).
CONCLUSIONS AND IMPLICATIONS
In carefully selected twin pregnancies the survival of the second born twin may improve with delayed interval delivery, also if the first was born at or after 24 weeks. Management protocols in the studies included vary, making it difficult to propose a uniform strategy for delayed interval delivery. Families must be informed about the possibility that a nonviable infant would survive to a periviable gestational age with a risk of severe sequels after birth as well as the possibility of maternal complications.
PubMed: 28210482
DOI: No ID Found -
Systematic Reviews Oct 2016Overviews of methods are potentially useful means to increase clarity and enhance collective understanding of specific methods topics that may be characterized by... (Review)
Review
BACKGROUND
Overviews of methods are potentially useful means to increase clarity and enhance collective understanding of specific methods topics that may be characterized by ambiguity, inconsistency, or a lack of comprehensiveness. This type of review represents a distinct literature synthesis method, although to date, its methodology remains relatively undeveloped despite several aspects that demand unique review procedures. The purpose of this paper is to initiate discussion about what a rigorous systematic approach to reviews of methods, referred to here as systematic methods overviews, might look like by providing tentative suggestions for approaching specific challenges likely to be encountered. The guidance offered here was derived from experience conducting a systematic methods overview on the topic of sampling in qualitative research.
RESULTS
The guidance is organized into several principles that highlight specific objectives for this type of review given the common challenges that must be overcome to achieve them. Optional strategies for achieving each principle are also proposed, along with discussion of how they were successfully implemented in the overview on sampling. We describe seven paired principles and strategies that address the following aspects: delimiting the initial set of publications to consider, searching beyond standard bibliographic databases, searching without the availability of relevant metadata, selecting publications on purposeful conceptual grounds, defining concepts and other information to abstract iteratively, accounting for inconsistent terminology used to describe specific methods topics, and generating rigorous verifiable analytic interpretations. Since a broad aim in systematic methods overviews is to describe and interpret the relevant literature in qualitative terms, we suggest that iterative decision making at various stages of the review process, and a rigorous qualitative approach to analysis are necessary features of this review type.
CONCLUSIONS
We believe that the principles and strategies provided here will be useful to anyone choosing to undertake a systematic methods overview. This paper represents an initial effort to promote high quality critical evaluations of the literature regarding problematic methods topics, which have the potential to promote clearer, shared understandings, and accelerate advances in research methods. Further work is warranted to develop more definitive guidance.
Topics: Databases, Bibliographic; Decision Making; Evidence-Based Medicine; Humans; Publications; Qualitative Research; Research Design
PubMed: 27729071
DOI: 10.1186/s13643-016-0343-0 -
Scandinavian Journal of Surgery : SJS :... 2022Patients presenting with synchronous colorectal liver metastases are increasingly being considered for a curative treatment, and the liver-first approach is gaining... (Meta-Analysis)
Meta-Analysis
BACKGROUND
Patients presenting with synchronous colorectal liver metastases are increasingly being considered for a curative treatment, and the liver-first approach is gaining popularity in this context. However, little is known about the completion rates of the liver-first approach and its effects on survival.
METHODS
A systematic review and meta-analysis of liver-first strategy for colorectal liver metastasis. The primary outcome was an assessment of the completion rates of the liver-first approach. Secondary outcomes included overall survival, causes of non-completion, and clinicopathologic data.
RESULTS
Seventeen articles were amenable for inclusion and the total study population was 1041. The median completion rate for the total population was 80% (range 20-100). The median overall survival for the completion and non-completion groups was 45 (range 12-69) months and 13 (range 10.5-25) months, respectively. Metadata showed a significant survival benefit for the completion group, with a univariate hazard ratio of 12.0 (95% confidence interval, range 5.7-24.4). The major cause of non-completion (76%) was liver disease progression before resection of the primary tumor. Pearson tests showed significant negative correlation between median number of lesions and median size of the largest metastasis and completion rate.
CONCLUSIONS
The liver-first approach offers a complete resection to most patients enrolled, with an overall survival benefit when completion can be assured. One-fifth fails to return to intended oncologic therapy and the major cause is interim metastatic progression, most often in the liver. Risk of non-completion is related to a higher number of lesions and large metastases. The majority of studies stem from primary rectal cancers, which may influence on the return to intended oncologic therapy as well. 170459.
Topics: Abdomen; Colorectal Neoplasms; Hepatectomy; Humans; Liver Neoplasms; Retrospective Studies; Treatment Outcome
PubMed: 34605325
DOI: 10.1177/14574969211030131 -
BMJ Open Jun 2022Identify and describe the available evidence on the effects food systems interventions on food security and nutrition outcomes in low-income and middle-income countries.
OBJECTIVE
Identify and describe the available evidence on the effects food systems interventions on food security and nutrition outcomes in low-income and middle-income countries.
METHODS
An adapted version of the high-level panel of experts food systems framework defined the interventions and outcomes included studies. Included study designs were experimental and quasi-experimental quantitative impact evaluations and systematic reviews. Following standards for evidence gap maps developed by 3ie, a systematic search of 17 academic databases and 31 sector-specific repositories in May 2020 identified articles for inclusion. Trained consultants screened titles/abstracts, then full texts of identified articles. Studies meeting eligibility criteria had meta-data systematically extracted and were descriptively analysed. Systematic reviews were critically appraised.
RESULTS
The map includes 1838 impact evaluations and 178 systematic reviews. The most common interventions, with over 100 impact evaluations and 20 systematic reviews each, were: provision of supplements, fortification, nutrition classes, direct provision of foods and peer support/counselling. Few studies addressed national-level interventions or women's empowerment. The most common final outcomes were: anthropometry, micronutrient status, and diet quality and adequacy. Intermediate outcomes were less studied.Most evaluations were conducted in sub-Saharan Africa (33%) or South Asia (20%). Many studies occurred in lower-middle-income countries (43%); few (7%) were in fragile countries. Among studies in a specific age group, infants were most frequently included (19%); 14% of these also considered mothers.Few evaluations considered qualitative or cost analysis; 75% used randomisation as the main identification strategy.
DISCUSSION
The uneven distribution of research means that some interventions have established impacts while other interventions, often affecting large populations, are underevaluated. Areas for future research include the evaluation of national level policies, evaluation of efforts to support women's empowerment within the food system, and the synthesis of dietary quality. Quasi-experimental approaches should be adopted to evaluate difficult to randomise interventions.
Topics: Developing Countries; Dietary Supplements; Female; Humans; Income; Infant; Micronutrients; Poverty
PubMed: 35732381
DOI: 10.1136/bmjopen-2021-055062