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The Open Microbiology Journal 2017The existence of infections caused by multidrug resistant (MDR) is a growing problem because of the difficulty to treat them. We examined the published literature and... (Review)
Review
The existence of infections caused by multidrug resistant (MDR) is a growing problem because of the difficulty to treat them. We examined the published literature and focused our analysis on the investigation of the synergism of colistin and rifampin against MDR isolates systematic review and meta-analysis. A systematic literature search was performed using the following 4 databases (PubMed, Scopus, EMBASE and ISI Web of Sciences). The related articles were evaluated during the period from December 2014 to January 2015. Information based on resistance and sensitivity to antibiotics, the minimum inhibitory concentration and the effects of two antibiotics on each other including synergism, antagonism, relative synergism and additive antagonism were extracted. A meta-analysis of 17 studies including 448 samples was brought into process and 2% (95% CI 0-4%) and 72% (95% CI 56-89%) resistance to colistin and rifampin were observed, respectively. 42% of all isolates showed MIC = 4 µg/ml (95% CI 14-69%) to rifampin and 30% MIC= 2 µg/ml to colistin (95% CI 3.8-78%). MIC and MIC for both rifampin and colistin were 2 µg/ml and 4 µg/ml, respectively. 63% of the strains demonstrated synergy (95% CI 37-90%), 7% were highlighted as relative synergism (95% CI 0.0- 13%), 3% showed an additive effect (95% CI -0.0-7%) and 14% were indifferent (95% CI 6-23%). The antagonistic effect was not observed in this combination. Synergy rates of time-kill assay in rifampin and colistin combinations were generally higher than those of check bored microdilution and E-test method. The results demonstrated that the combination therapy could be more useful when compared to monotherapy and that this strategy might reduce the resistance rate to rifampin in MDR isolates.
PubMed: 28553417
DOI: 10.2174/1874285801711010063 -
Neural Regeneration Research Dec 2024The search for reliable and easily accessible biomarkers in Parkinson's disease is receiving a growing emphasis, to detect neurodegeneration from the prodromal phase and...
The search for reliable and easily accessible biomarkers in Parkinson's disease is receiving a growing emphasis, to detect neurodegeneration from the prodromal phase and to enforce disease-modifying therapies. Despite the need for non-invasively accessible biomarkers, the majority of the studies have pointed to cerebrospinal fluid or peripheral biopsies biomarkers, which require invasive collection procedures. Saliva represents an easily accessible biofluid and an incredibly wide source of molecular biomarkers. In the present study, after presenting the morphological and biological bases for looking at saliva in the search of biomarkers for Parkinson's disease, we systematically reviewed the results achieved so far in the saliva of different cohorts of Parkinson's disease patients. A comprehensive literature search on PubMed and SCOPUS led to the discovery of 289 articles. After screening and exclusion, 34 relevant articles were derived for systematic review. Alpha-synuclein, the histopathological hallmark of Parkinson's disease, has been the most investigated Parkinson's disease biomarker in saliva, with oligomeric alpha-synuclein consistently found increased in Parkinson's disease patients in comparison to healthy controls, while conflicting results have been reported regarding the levels of total alpha-synuclein and phosphorylated alpha-synuclein, and few studies described an increased oligomeric alpha-synuclein/total alpha-synuclein ratio in Parkinson's disease. Beyond alpha-synuclein, other biomarkers targeting different molecular pathways have been explored in the saliva of Parkinson's disease patients: total tau, phosphorylated tau, amyloid-β1-42 (pathological protein aggregation biomarkers); DJ-1, heme-oxygenase-1, metabolites (altered energy homeostasis biomarkers); MAPLC-3beta (aberrant proteostasis biomarker); cortisol, tumor necrosis factor-alpha (inflammation biomarkers); DNA methylation, miRNA (DNA/RNA defects biomarkers); acetylcholinesterase activity (synaptic and neuronal network dysfunction biomarkers); Raman spectra, proteome, and caffeine. Despite a few studies investigating biomarkers targeting molecular pathways different from alpha-synuclein in Parkinson's disease, these results should be replicated and observed in studies on larger cohorts, considering the potential role of these biomarkers in determining the molecular variance among Parkinson's disease subtypes. Although the need for standardization in sample collection and processing, salivary-based biomarkers studies have reported encouraging results, calling for large-scale longitudinal studies and multicentric assessments, given the great molecular potentials and the non-invasive accessibility of saliva.
PubMed: 38595280
DOI: 10.4103/NRR.NRR-D-23-01677 -
BMJ Open Jul 2015To obtain a pooled risk estimate on the long-term impact of anaemia and related nutritional deficiencies in patients receiving Roux-en-Y gastric bypass (RYGB) surgery. (Meta-Analysis)
Meta-Analysis Review
OBJECTIVE
To obtain a pooled risk estimate on the long-term impact of anaemia and related nutritional deficiencies in patients receiving Roux-en-Y gastric bypass (RYGB) surgery.
DESIGN
Systematic review and meta-analysis.
DATA SOURCES
MEDLINE, EMBASE and Cochrane databases were searched to identify English reports published before 16 May 2014.
ELIGIBILITY CRITERIA
Articles with case numbers >100, follow-up period >12 months, and complete data from both before and after surgery were selected. Outcomes of interest were changes in baseline measurements of proportion of patients with anaemia, by haemoglobin, haematocrit, ferritin, iron, vitamin B12 and folate levels.
DATA COLLECTION AND ANALYSIS
Two reviewers independently reviewed data and selected six prospective and nine retrospective studies with a total of 5909 patients. A random effect model with inverse variance weighting was used to calculate summary estimates of outcomes at 6, 12, 24 and 36 months postoperatively.
RESULTS
Proportion of patients with anaemia was 12.2% at baseline, which, respectively, increased to 20.9% and 25.9% at 12 and 24 months follow-up, consistent with decreases in haemoglobin and haematocrit levels. Although the serum iron level did not change substantially after surgery, the frequency of patients with ferritin deficiency increased from 7.9% at baseline to 13.4% and 23.0% at 12 and 24 months, respectively, postoperation. Vitamin B12 deficiency increased from 2.3% at baseline to 6.5% at 12 months after surgery in those subjects receiving RYGB. There was no obvious increase in folate deficiency.
CONCLUSIONS
RYGB surgery is associated with an increased risk of anaemia and deficiencies of iron and vitamin B12, but not folate. Ferritin is more sensitive when serum iron level is within normal range.
Topics: Anemia; Ferritins; Gastric Bypass; Humans; Iron; Obesity, Morbid; Postoperative Period; Vitamin B 12 Deficiency
PubMed: 26185175
DOI: 10.1136/bmjopen-2014-006964 -
International Journal of Molecular... Jun 2022Alport syndrome (AS) is the second most common cause of inherited chronic kidney disease. This disorder is caused by genetic variants on , and genes. These genes... (Review)
Review
Alport syndrome (AS) is the second most common cause of inherited chronic kidney disease. This disorder is caused by genetic variants on , and genes. These genes encode the proteins that constitute collagen type IV of the glomerular basement membrane (GBM). The heterodimer COL4A3A4A5 constitutes the majority of the GBM, and it is essential for the normal function of the glomerular filtration barrier (GFB). Alterations in any of collagen type IV constituents cause disruption of the GMB structure, allowing leakage of red blood cells and albumin into the urine, and compromise the architecture of the GFB, inducing inflammation and fibrosis, thus resulting in kidney damage and loss of renal function. The advances in DNA sequencing technologies, such as next-generation sequencing, allow an accurate diagnose of AS. Due to the important risk of the development of progressive kidney disease in AS patients, which can be delayed or possibly prevented by timely initiation of therapy, an early diagnosis of this condition is mandatory. Conventional biomarkers such as albuminuria and serum creatinine increase relatively late in AS. A panel of biomarkers that might detect early renal damage, monitor therapy, and reflect the prognosis would have special interest in clinical practice. The aim of this systematic review is to summarize the biomarkers of renal damage in AS as described in the literature. We found that urinary Podocin and Vascular Endothelial Growth Factor A are important markers of podocyte injury. Urinary Epidermal Growth Factor has been related to tubular damage, interstitial fibrosis and rapid progression of the disease. Inflammatory markers such as Transforming Growth Factor Beta 1, High Motility Group Box 1 and Urinary Monocyte Chemoattractant Protein- 1 are also increased in AS and indicate a higher risk of kidney disease progression. Studies suggest that miRNA-21 is elevated when renal damage occurs. Novel techniques, such as proteomics and microRNAs, are promising.
Topics: Biomarkers; Collagen Type IV; Fibrosis; Humans; Kidney; Nephritis, Hereditary; Vascular Endothelial Growth Factor A
PubMed: 35806283
DOI: 10.3390/ijms23137276 -
Clinical Infectious Diseases : An... Jan 2022The emergence and spread of Plasmodium falciparum parasites that lack HRP2/3 proteins and the resulting decreased utility of HRP2-based malaria rapid diagnostic tests...
BACKGROUND
The emergence and spread of Plasmodium falciparum parasites that lack HRP2/3 proteins and the resulting decreased utility of HRP2-based malaria rapid diagnostic tests (RDTs) prompted the World Health Organization and other global health stakeholders to prioritize the discovery of novel diagnostic biomarkers for malaria.
METHODS
To address this pressing need, we adopted a dual, systematic approach by conducting a systematic review of the literature for publications on diagnostic biomarkers for uncomplicated malaria and a systematic in silico analysis of P. falciparum proteomics data for Plasmodium proteins with favorable diagnostic features.
RESULTS
Our complementary analyses led us to 2 novel malaria diagnostic biomarkers compatible for use in an RDT format: glyceraldehyde 3-phosphate dehydrogenase and dihydrofolate reductase-thymidylate synthase.
CONCLUSIONS
Overall, our results pave the way for the development of next-generation malaria RDTs based on new antigens by identifying 2 lead candidates with favorable diagnostic features and partially de-risked product development prospects.
Topics: Antigens, Protozoan; Biomarkers; Diagnostic Tests, Routine; Humans; Malaria; Malaria, Falciparum; Plasmodium falciparum; Protozoan Proteins; Sensitivity and Specificity
PubMed: 34718455
DOI: 10.1093/cid/ciab251 -
Cancers Mar 2023While many components of the ECM have been isolated and characterized, its modifications in the specific setting of GBMs have only been recently explored in the... (Review)
Review
BACKGROUND AND AIM
While many components of the ECM have been isolated and characterized, its modifications in the specific setting of GBMs have only been recently explored in the literature. The aim of this paper is to provide a systematic review on the topic and to assess the ECM's role in shaping tumoral development.
METHODS
An online literature search was launched on PubMed/Medline and Scopus using the research string "((Extracellular matrix OR ECM OR matrix receptor OR matrix proteome) AND (glioblastoma OR GBM) AND (tumor invasion OR tumor infiltration))", and a systematic review was conducted in accordance with the PRISMA-P guidelines.
RESULTS
The search of the literature yielded a total of 693 results. The duplicate records were then removed (n = 13), and the records were excluded via a title and abstract screening; 137 studies were found to be relevant to our research question and were assessed for eligibility. Upon a full-text review, 59 articles were finally included and were summarized as follows based on their focus: (1) proteoglycans; (2) fibrillary proteins, which were further subdivided into the three subcategories of collagen, fibronectin, and laminins; (3) glycoproteins; (4) degradative enzymes; (5) physical forces; (6) and glioma cell and microglia migratory and infiltrative patterns.
CONCLUSIONS
Our systematic review demonstrates that the ECM should not be regarded anymore as a passive scaffold statically contributing to mechanical support in normal and pathological brain tissue but as an active player in tumor-related activity.
PubMed: 36980765
DOI: 10.3390/cancers15061879 -
The Cochrane Database of Systematic... Apr 2016About 10% of reproductive-aged women suffer from endometriosis, which is a costly, chronic disease that causes pelvic pain and subfertility. Laparoscopy is the gold... (Meta-Analysis)
Meta-Analysis Review
BACKGROUND
About 10% of reproductive-aged women suffer from endometriosis, which is a costly, chronic disease that causes pelvic pain and subfertility. Laparoscopy is the gold standard diagnostic test for endometriosis, but it is expensive and carries surgical risks. Currently, there are no non-invasive tests available in clinical practice that accurately diagnose endometriosis. This is the first diagnostic test accuracy review of endometrial biomarkers for endometriosis that utilises Cochrane methodologies, providing an update on the rapidly expanding literature in this field.
OBJECTIVES
To determine the diagnostic accuracy of the endometrial biomarkers for pelvic endometriosis, using a surgical diagnosis as the reference standard. We evaluated the tests as replacement tests for diagnostic surgery and as triage tests to inform decisions to undertake surgery for endometriosis.
SEARCH METHODS
We did not restrict the searches to particular study designs, language or publication dates. To identify trials, we searched the following databases: CENTRAL (2015, July), MEDLINE (inception to May 2015), EMBASE (inception to May 2015), CINAHL (inception to April 2015), PsycINFO (inception to April 2015), Web of Science (inception to April 2015), LILACS (inception to April 2015), OAIster (inception to April 2015), TRIP (inception to April 2015) and ClinicalTrials.gov (inception to April 2015). We searched DARE and PubMed databases up to April 2015 to identify reviews and guidelines as sources of references to potentially relevant studies. We also performed searches for papers recently published and not yet indexed in the major databases. The search strategies incorporated words in the title, abstract, text words across the record and the medical subject headings (MeSH).
SELECTION CRITERIA
We considered published peer-reviewed, randomised controlled or cross-sectional studies of any size that included prospectively collected samples from any population of reproductive-aged women suspected of having one or more of the following target conditions: ovarian, peritoneal or deep infiltrating endometriosis (DIE).
DATA COLLECTION AND ANALYSIS
Two authors independently extracted data from each study and performed a quality assessment. For each endometrial diagnostic test, we classified the data as positive or negative for the surgical detection of endometriosis and calculated the estimates of sensitivity and specificity. We considered two or more tests evaluated in the same cohort as separate data sets. We used the bivariate model to obtain pooled estimates of sensitivity and specificity whenever sufficient data were available. The predetermined criteria for a clinically useful test to replace diagnostic surgery was one with a sensitivity of 94% and a specificity of 79%. The criteria for triage tests were set at sensitivity at or above 95% and specificity at or above 50%, which in case of negative results rules out the diagnosis (SnOUT test) or sensitivity at or above 50% with specificity at or above 95%, which in case of positive result rules in the diagnosis (SpIN test).
MAIN RESULTS
We included 54 studies involving 2729 participants, most of which were of poor methodological quality. The studies evaluated endometrial biomarkers either in specific phases of the menstrual cycle or outside of it, and the studies tested the biomarkers either in menstrual fluid, in whole endometrial tissue or in separate endometrial components. Twenty-seven studies evaluated the diagnostic performance of 22 endometrial biomarkers for endometriosis. These were angiogenesis and growth factors (PROK-1), cell-adhesion molecules (integrins α3β1, α4β1, β1 and α6), DNA-repair molecules (hTERT), endometrial and mitochondrial proteome, hormonal markers (CYP19, 17βHSD2, ER-α, ER-β), inflammatory markers (IL-1R2), myogenic markers (caldesmon, CALD-1), neural markers (PGP 9.5, VIP, CGRP, SP, NPY, NF) and tumour markers (CA-125). Most of these biomarkers were assessed in single studies, whilst only data for PGP 9.5 and CYP19 were available for meta-analysis. These two biomarkers demonstrated significant diversity for the diagnostic estimates between the studies; however, the data were too limited to reliably determine the sources of heterogeneity. The mean sensitivities and specificities of PGP 9.5 (7 studies, 361 women) were 0.96 (95% confidence interval (CI) 0.91 to 1.00) and 0.86 (95% CI 0.70 to 1.00), after excluding one outlier study, and for CYP19 (8 studies, 444 women), they were were 0.77 (95% CI 0.70 to 0.85) and 0.74 (95% CI 0.65 to 84), respectively. We could not statistically evaluate other biomarkers in a meaningful way. An additional 31 studies evaluated 77 biomarkers that showed no evidence of differences in expression levels between the groups of women with and without endometriosis.
AUTHORS' CONCLUSIONS
We could not statistically evaluate most of the biomarkers assessed in this review in a meaningful way. In view of the low quality of most of the included studies, the findings of this review should be interpreted with caution. Although PGP 9.5 met the criteria for a replacement test, it demonstrated considerable inter study heterogeneity in diagnostic estimates, the source of which could not be determined. Several endometrial biomarkers, such as endometrial proteome, 17βHSD2, IL-1R2, caldesmon and other neural markers (VIP, CGRP, SP, NPY and combination of VIP, PGP 9.5 and SP) showed promising evidence of diagnostic accuracy, but there was insufficient or poor quality evidence for any clinical recommendations. Laparoscopy remains the gold standard for the diagnosis of endometriosis, and using any non-invasive tests should only be undertaken in a research setting. We have also identified a number of biomarkers that demonstrated no diagnostic value for endometriosis. We recommend that researchers direct future studies towards biomarkers with high diagnostic potential in good quality diagnostic studies.
Topics: Biomarkers; Endometriosis; Endometrium; Female; Humans; Menstrual Cycle; Menstruation
PubMed: 27094925
DOI: 10.1002/14651858.CD012165 -
BioMed Research International 2022Artificial intelligence (AI) techniques are used in precision medicine to explore novel genotypes and phenotypes data. The main aims of precision medicine include early... (Review)
Review
PURPOSE
Artificial intelligence (AI) techniques are used in precision medicine to explore novel genotypes and phenotypes data. The main aims of precision medicine include early diagnosis, screening, and personalized treatment regime for a patient based on genetic-oriented features and characteristics. The main objective of this study was to review AI techniques and their effectiveness in neoplasm precision medicine.
MATERIALS AND METHODS
A comprehensive search was performed in Medline (through PubMed), Scopus, ISI Web of Science, IEEE Xplore, Embase, and Cochrane databases from inception to December 29, 2021, in order to identify the studies that used AI methods for cancer precision medicine and evaluate outcomes of the models.
RESULTS
Sixty-three studies were included in this systematic review. The main AI approaches in 17 papers (26.9%) were linear and nonlinear categories (random forest or decision trees), and in 21 citations, rule-based systems and deep learning models were used. Notably, 62% of the articles were done in the United States and China. R package was the most frequent software, and breast and lung cancer were the most selected neoplasms in the papers. Out of 63 papers, in 34 articles, genomic data like gene expression, somatic mutation data, phenotype data, and proteomics with drug-response which is functional data was used as input in AI methods; in 16 papers' (25.3%) drug response, functional data was utilized in personalization of treatment. The maximum values of the assessment indicators such as accuracy, sensitivity, specificity, precision, recall, and area under the curve (AUC) in included studies were 0.99, 1.00, 0.96, 0.98, 0.99, and 0.9929, respectively.
CONCLUSION
The findings showed that in many cases, the use of artificial intelligence methods had effective application in personalized medicine.
Topics: Artificial Intelligence; Bibliometrics; Delivery of Health Care; Humans; Neoplasms; Precision Medicine
PubMed: 35434134
DOI: 10.1155/2022/7842566 -
Gastroenterology and Hepatology From... 2022This systematic review and meta-analysis evaluated the subtyped sp. isolated from humans in Iran. (Review)
Review
AIM
This systematic review and meta-analysis evaluated the subtyped sp. isolated from humans in Iran.
BACKGROUND
sp. is an anaerobic intestinal protozoan that infects humans as well as domestic and wild animals, i.e. mammals, amphibians, reptiles, and arthropods.
METHODS
A comprehensive search for papers published before April 2022 was undertaken utilizing English and Persian databases. The following MeSH keywords were used in the electronic search: ( sp.) AND (molecular OR subtype) AND (prevalence OR epidemiology) AND Iran. The quality of the included studies was evaluated. Thereafter, a random-effects meta-analysis was conducted to estimate the pooled prevalence and odds ratios regarding the included studies.
RESULTS
A total of 32 studies comprised of five case-control studies and 27 cross-sectional studies met the eligibility criteria. The overall pooled prevalence of subtyped sp. in Iran was estimated to be 10% (95% confidence interval: 6 to 15%). Eight subtypes of sp. (ST1- ST7 and ST9) were identified in our study, of which ST3 was the most common subtype (0.04); 0.02-0.07). The difference in subtypes between two case and control groups in reported studies was not significant, but the odds ratio of infection by ST3 (0.98; 95% CI, 0.30 to 3.20) was higher in cases.
CONCLUSION
The current systematic review showed that with the exception of ST8 and ST12, all human sp. subtypes reported in the world are found in different parts of Iran.
PubMed: 36762220
DOI: 10.22037/ghfbb.v15i4.2475 -
Metabolism: Clinical and Experimental Jan 2022The global COVID-19 pandemic has led to extensive development in many fields, including the diagnosis of COVID-19 infection by mass spectrometry. The aim of this... (Meta-Analysis)
Meta-Analysis
BACKGROUND
The global COVID-19 pandemic has led to extensive development in many fields, including the diagnosis of COVID-19 infection by mass spectrometry. The aim of this systematic review and meta-analysis was to assess the accuracy of mass spectrometry diagnostic tests developed so far, across a wide range of biological matrices, and additionally to assess risks of bias and applicability in studies published to date.
METHOD
23 retrospective observational cohort studies were included in the systematic review using the PRISMA-DTA framework, with a total of 2858 COVID-19 positive participants and 2544 controls. Risks of bias and applicability were assessed via a QUADAS-2 questionnaire. A meta-analysis was also performed focusing on sensitivity, specificity, diagnostic accuracy and Youden's Index, in addition to assessing heterogeneity.
FINDINGS
Sensitivity averaged 0.87 in the studies reviewed herein (interquartile range 0.81-0.96) and specificity 0.88 (interquartile range 0.82-0.98), with an area under the receiver operating characteristic summary curve of 0.93. By subgroup, the best diagnostic results were achieved by viral proteomic analyses of nasopharyngeal swabs and metabolomic analyses of plasma and serum. The performance of other sampling matrices (breath, sebum, saliva) was less good, indicating that these protocols are currently insufficiently mature for clinical application.
CONCLUSIONS
This systematic review and meta-analysis demonstrates the potential for mass spectrometry and 'omics in achieving accurate test results for COVID-19 diagnosis, but also highlights the need for further work to optimize and harmonize practice across laboratories before these methods can be translated to clinical applications.
Topics: COVID-19; COVID-19 Testing; Humans; Mass Spectrometry; Sensitivity and Specificity
PubMed: 34715115
DOI: 10.1016/j.metabol.2021.154922