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Physical activity and Native Americans: a review.

The physical activity behaviors of Native-American populations in the United States and Canada have received little attention in the health literature. The purpose of this review was to unite the literature regarding the physical activity behaviors of Native Americans. A majority of the literature was obtained using online databases. Reference lists were also reviewed to gain further access to the literature. Key-word searches included various combinations of Aboriginal, Native Indian, American Indian, Native American, First Nation, Métis, or Alaska Native with physical activity, exercise, and health behavior. Articles included were those published in English-language, peer-reviewed journals from 1990 until November 2005 that focused on participants aged 18 years and older. This review is organized according to ecologic models of health behavior, which take into account several correlates to explain human behavior, including demographic, personal health, environmental, and psychosocial. Correlates were included if they appeared at least three times in the literature. As a result of these inclusion criteria, the number of reviewed articles includes 28 quantitative, 4 qualitative, and 3 intervention studies. Results indicate that age, gender, and social support are important factors associated with physical activity. The remaining correlates show inconsistent or indeterminate results due in part to the paucity of research. It is suggested that an increase in the number of studies, especially those using longitudinal designs, is needed. Further, the application of psychosocial models to understand physical activity motivations as well as culturally appropriate and validated measurement tools are largely absent in the Native-American physical activity literature.

Adult↗

Hyperbaric oxygen therapy for traumatic brain injury: a systematic review of the evidence.

OBJECTIVE: To identify the benefits and harms of hyperbaric oxygen therapy (HBOT) to treat traumatic brain injury (TBI). DATA SOURCES: MEDLINE, EMBASE, the Cochrane Library, HealthSTAR, CINAHL, MANTIS, professional society databases, and reference lists. Databases were searched from inception through December 2003. STUDY SELECTION: We included English-language studies of patients with TBI given HBOT and evaluating functional health outcomes. DATA EXTRACTION: Data were abstracted by 1 reviewer and checked by a second. Study quality was rated as good, fair, or poor. DATA SYNTHESIS: Two fair-quality randomized controlled trials of patients with severe brain injury reported conflicting results. One found no difference in mortality (48% HBOT vs 55% control) or morbidity at 1 year. In young patients with brainstem contusion, significantly more regained consciousness at 1 month with HBOT (67%) than control (11%) (P<.03). The other found a significant decrease in mortality in the HBOT group at 1 year (17%) compared with controls (31%) (P=.037). This decrease in mortality was accompanied by an increase in proportion of patients with severe disability. Patients with intracranial pressure (ICP) greater than 20 mmHg or a Glasgow Coma Scale score of 4 to 6 had significantly lower mortality at 1 year than controls. Five observational studies did not provide better evidence of effectiveness or adverse events. Two indicated a potential for initially reducing elevated ICP in some patients. However, rebound elevations higher than pretreatment levels occurred in some patients. Adverse events, including seizures, pulmonary symptoms, and neurologic deterioration, were reported; however, no study systematically assessed adverse events, and none reported adverse events in control groups. CONCLUSIONS: The evidence for HBOT for TBI is insufficient to prove effectiveness or ineffectiveness, and more high-quality studies are needed. The evidence indicates that there is a small chance of a mortality benefit, which may depend on subgroup selection. The effect on functional status and the incidence and clinical significance of adverse effects are unclear.

Brain Injuries↗

Predictors and relationships of serum 25 hydroxyvitamin D concentration with bone turnover markers, bone mineral density, and vitamin D receptor genotype in Emirati women.

OBJECTIVES: To determine factors influencing serum 25 hydroxyvitamin D (25OHD) concentration and relationships between serum 25OHD concentration, bone turnover markers, bone mineral density (BMD), and vitamin D receptor (VDR) genotype in Emirati women. METHODS: Serum 25OHD, parathyroid hormone (PTH), osteocalcin (OC), vitamin D binding protein (VDBP), and urinary deoxypyrdinoline (UDPD) concentrations and VDR genotype were determined in Emirati women volunteers who were participating in a study aiming at establishing a reference database for BMD. RESULTS: Serum 25OHD concentration in the 259 women volunteers was 25.3 +/- 10.8 nmol/l (mean +/- SD), and all had vitamin D deficiency (25OHD <80 nmol/l). Mean serum 25OHD was highest in April (29.2 +/- 13.0 nmol/l), which marks the end of the short and cooler winter season, and lowest in August (18.2 +/- 5.9 nmol/l). No significant difference in 25OHD concentration was noted among Emirati women wearing different dress styles, but the mean serum 25OHD was significantly lower in comparison with non-Arab Caucasian women volunteers who dressed in a Western style (P < 0.001). Serum 25OHD correlated positively with age (r = 0.2), number of pregnancies (r = 0.16), dietary vitamin D intake (r = 0.15), serum calcium (r = 0.14), phosphorus (r = 0.14), VDBP (r = 0.15), and urinary calcium/creatinine (r = 0.2), and inversely with PTH (r = -0.22), OC (r = -0.13), and UDPD/creatinine (r = -0.15); P < 0.05 for all correlations. Multiple linear regression analysis showed that age, dietary vitamin D intake, multivitamin intake, and cooler season were independent positive predictors of serum 25OHD concentration (R(2) = 0.18). The frequencies of VDR genotypes were 36% GG, 44.1% AG, and 19.9% AA. Allele frequencies were 58% for G allele and 42% for A allele and were in Hardy-Weinberg equilibrium (x(2) = 1.44; P > 0.1). There was no statistically significant influence of VDR genotype on bone turnover or BMD. CONCLUSIONS: Vitamin D deficiency is highly prevalent in Emirati women and appears largely attributable to insufficient sunlight exposure. It is associated with increased bone turnover. VDR genotype does not appear to influence bone turnover markers or BMD in Emirati women.

Adult↗

Metax enables accurate cross-domain taxonomic profiling of metagenomes.

Taxonomic profiling is fundamental to microbiome research, yet achieving high species-level accuracy remains challenging for complex communities that span bacteria, viruses, eukaryotes, and archaea, and these limitations are exacerbated in low-biomass, host-dominated samples. We introduce Metax, a cross-domain taxonomic profiler that integrates coverage-based probabilistic modeling with an expectation-maximization framework to distinguish true microbial signals from artifacts. Across >600 samples from host-associated, environmental, wastewater, and low-biomass clinical settings, including benchmarks with limited reference representation, Metax improved profiling accuracy, achieving on average 55% higher F1 scores and 45% lower Bray-Curtis dissimilarity than other methods. Moreover, this broad evaluation demonstrated that Metax resolved bacterial and viral signatures of peri-implantitis in oral microbiomes and revealed signals suggestive of reagent-borne contaminants and reference misassemblies in plasma-cell-free DNA. By leveraging genome-wide coverage evidence, Metax enables robust cross-domain profiling across diverse sample types and sequencing depths, including settings where reference databases are highly incomplete.

abundance estimation↗

Grading of corneal transparency.

AIM: To examine the academic literature on the grading of corneal transparency and to assess the potential use of objective image analysis. METHOD: Reference databases of academic literature were searched and relevant manuscripts reviewed. Annunziato, Efron (Millennium Edition) and Vistakon-Synoptik corneal oedema grading scale images were analysed objectively for relative intensity, edges detected, variation in intensity and maximum intensity. In addition, corneal oedema was induced in one subject using a low oxygen transmissibility (Dk/t) hydrogel contact lens worn for 3h under a light eye patch. Recovery from oedema was monitored over time using ultrasound pachymetry, high and low contrast visual acuity measures, bulbar hyperaemia grading and transparency image analysis of the test and control eyes. RESULTS: Several methods for assessing corneal transparency are described in the academic literature, but none have gained widespread use in clinical practice. The change in objective image analysis with printed scale grade was best described by quadratic parametric or sigmoid 3-parameter functions. 'Pupil image scales' (Annunziato and Vistakon-Synoptik) were best correlated to average intensity; however, the corneal section scale (Efron) was strongly correlated to variations in intensity. As expected, patching an eye wearing a low Dk/t hydrogel contact lens caused a significant (F = 119.2, p < 0.001) 14.3% increase in corneal thickness, which gradually recovered under open eye conditions. Corneal section image analysis was the most affected parameter and intensity variation across the slit width, in isolation, was the strongest correlate, accounting for 85.8% of the variance with time following patching, and 88.7% of the variance with corneal thickness. CONCLUSION: Corneal oedema is best determined objectively by the intensity variation across the width of a corneal section. This can be easily measured using a slit-lamp camera connected to a computer. Oedema due to soft contact lens wear is not easily determined over the pupil area by sclerotic scatter illumination techniques.

Journal Article↗

Routine methods misidentify Serratia spp.: Limitations of MALDI-TOF MS revealed by whole-genome sequencing.

Accurate species-level identification within the genus Serratia remains challenging due to extensive phenotypic overlap and high genomic relatedness among closely related and recently described taxa. This study presents an evaluation of routine and genome-based identification approaches applied to clinical Serratia isolates, integrating phenotypic assays, MALDI-TOF MS (Bruker Daltonics), 16S rRNA gene sequencing, and Whole-Genome Sequencing (WGS). A total of 103 isolates collected from a teaching hospital were analyzed. WGS was performed on a subset of isolates. Conventional biochemical methods classified all isolates as Serratia marcescens, whereas MALDI-TOF MS identified 60.1% as S. marcescens, 11.6% as S. ureilytica, and 28.1% just at the genus level. Peak analysis from MALDI-TOF MS revealed specific peaks associated with S. marcescens and S. ureilytica, but limited discriminatory power. WGS of six isolates initially identified as S. ureilytica by MALDI-TOF MS revealed reclassification as Serratia sarumanii (n = 5) and Serratia montpellierensis (n = 1), supported by Average Nucleotide Identity (ANI), Average Amino Acid Identity (AAI), and Digital DNA-DNA Hybridization (dDDH) thresholds. In contrast, 16S rRNA analysis showed limited species-level resolution. Phylogenomic and SNP-based analyses confirmed these classifications with strong support. Overall, this study underscores the critical role of high-resolution genomic approaches for precise species identification and highlights the need for continuous expansion and curation of MALDI-TOF MS reference databases to support reliable clinical diagnostics and epidemiological surveillance of emerging Serratia species.

Spectrometry, Mass, Matrix-Assisted Laser Desorpti↗

Equity in genome sequencing for rare disease diagnosis: a cross-sectional analysis of data from the UK 100,000 Genomes Project.

BACKGROUND: Genome sequencing has improved rare disease diagnosis and is now part of routine clinical care in the National Health Service in England. Automated prioritisation pipelines narrow millions of variants per patient to a small subset for clinical review, a process that relies on allele frequency resources that do not fully represent human genetic diversity. We assessed ancestry-related differences in variant prioritisation and diagnostic outcomes in patients from the UK 100,000 Genomes Project. METHODS: We analysed 29,405 rare disease probands with genome sequencing and linked clinical outcomes data. We used multivariable regression to assess ancestry-related differences in the number of variants prioritised for clinical review, the proportion of prioritised variants that were recorded as diagnostic, and diagnostic yield. We also evaluated the use of ancestry-stratified allele frequency filters derived from an independent, diverse UK cohort (n = 33,724). FINDINGS: Compared with the European ancestry group, the East African group had nearly three times more variants prioritised for clinical review (IRR 2.77, 95% CI 2.33-3.29). Other non-European groups also had significantly higher counts. Diagnostic yield was similar across ancestry groups after adjustment (LRT p = 0.1650). Prioritised variants were less likely to be recorded as diagnostic in East African (OR 0.32, 95% CI 0.22-0.46), West African (0.47, 0.39-0.57), South Asian (0.65, 0.58-0.73), and Middle Eastern (0.68, 0.54-0.86) groups. Applying ancestry-stratified allele-frequency filters removed 3.1% of prioritised variants overall-24.3% in the East African group-without loss of diagnostic sensitivity, including 29.5% of recorded VUS in this group. INTERPRETATION: Differences in the likelihood of prioritised variants being recorded as diagnostic partly reflect limitations of current allele frequency resources, which use broad population groupings that mask within-group diversity. Increased representation of diverse ancestries in reference databases and better estimation of ancestry-appropriate allele frequencies will help reduce inefficiencies and improve equity in variant prioritisation for rare disease diagnosis. FUNDING: The UK Department of Health and Social Care and the EU's Horizon 2020 Research and Innovation Programme.

Humans↗

The use of nematodes in ecological soil classification and assessment concepts.

Although there has been extensive applied agricultural research (research on plant-parasitic species has a long tradition), insufficient taxonomical knowledge, especially of free-living nematodes, is a serious problem concerning the use of nematodes in soil classification and assessment. However, due to their essential and various roles in ecosystem functioning and their high diversity and abundance, interest in using these organisms for the assessment of soil quality is increasing. In particular in The Netherlands, but also in other countries (e.g., Germany, United Kingdom), progress in taxonomy is being achieved and evaluation strategies are being elaborated. While examples exist for the successful use of nematodes as part of a community approach comprising several organism groups, much work concerning the establishment of an adequate reference database remains to be done. This article is a general overview of the suitability and application of soil nematodes in soil assessments.

Animals↗

Population data for 16 Y-chromosome STRs in four populations from Pyrenees (Spain).

Population frequencies for the eight Y-STR loci included in the "minimal haplotype" from Y-STR Haplotype Reference Database (YHRD) plus other eight Y-STRs (DYS434, DYS435, DYS436, DYS437, DYS438, DYS439, GATA H4 and GATA A10) were obtained for a sample of 133 males from four main geographical areas in the Pyrenees (Spain): Vall D'Aran (Lérida), Cerdanya (Gerona), Alt Urgell (Lérida) and Jacetania (Huesca). Haplotype diversities were estimated in the four populations.

Chromosomes, Human, Y↗

Genetic variability of 16 Y-chromosome STRs in a sample from Equatorial Guinea (Central Africa).

Nine Y-STR loci from the "minimal haplotype" included in Y-STR Haplotype Reference Databases (YHRD) together with eight additional Y-STRs (DYS437, DYS438, DYS439, DYS460, DYS461, GATA C4, GATA H4 and GATA A10) were analyzed in a sample of 101 males from Equatorial Guinea living in Madrid. Haplotype and allelic frequencies were calculated and genetic diversities were estimated for each genetic system as well as for the whole haplotype. An unexpected high frequency (6%) of intermediate alleles (13.2 and 14.2) was found in DYS385. For DYS19, two alleles were found in one sample. Another sample failed to amplify with DYS393 primers using either PowerPlex Y System (Promega Corporation) or the Y-PLEXtrade mark 12 (Reliagene, New Orleans, LA) commercial kits. Comparison between Equatorial Guinea and another African population (Mozambique; South East Coast) revealed a significant pairwise Phi(st) value between them (Phi(st)=0.03309; P=0.00000).

Chromosomes, Human, Y↗

Human Y-specific STR haplotypes in the Western Croatian population sample.

Nine Y-chromosome STR loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385 and YCAII) were analysed in a sample of 101 unrelated males from Croatia. Allelic frequencies and gene diversities for each Y-STR locus and haplotype diversity were determined. Ninety-one different haplotypes were obtained from 101 unrelated males and 84 haplotypes were unique. Three most common haplotypes were shared by 3% of the sample, one of them was not found in the online Y-STR Haplotype Reference Database (http://www.ystr.org/).

Chromosomes, Human, Y↗

Forensic interpretation of Y-chromosomal DNA mixtures.

The mathematical concept previously introduced for the forensic interpretation of DNA mixtures using non-associated genetic markers has been adapted to the assessment of haplotypes. Such calculus is required, for example, when Y-chromosomal markers are used in forensics. In addition to outlining the general mathematical framework, we devise two approaches to its practical computational implementation, involving either the inclusion-exclusion principle of probability theory or a recursion in the number of unknown contributors invoked. The two approaches scale differently, depending upon the complexity of the case and the diversity of the markers used. The performance of Y-chromosomal microsatellites (Y-STRs) as a means of trace donor discrimination has been assessed by simulation, using the derived formulas. Based upon data from the Y-chromosomal Haplotype Reference Database (YHRD), the exclusion chance of a non-contributor is shown to vary between 95% in the case of two contributors, and 70% for five contributors. With only one additional contributor, half of all contributing suspects would yield a log-likelihood ratio in favour of donorship of 1.61 or higher, although the median drops to 0.66 with four additional contributors. It must be emphasised that these estimates of the discriminatory power of Y-STRs are likely to be conservative since the simulations involved only haplotypes known to occur in YHRD.

Chromosomes, Human, Y↗

Development of a heptaplex PCR system to analyse X-chromosome STR loci from five Italian population samples. A collaborative study.

Many X-chromosome short tandem repeats (X-STRs) have been validated for forensic use even if further studies are needed on allele frequencies and mutation rates to evaluate the extent of polymorphism in different populations and to establish reference databases useful for forensic applications and for anthropological studies. A single multiplex reaction of seven X-STRs, which includes the DXS6789, HUMARA, DXS10011, DXS7423, HPRTB, DXS6807, DXS101 loci, is presented and their allele frequency distribution in a large population sample including 556 subjects (268 females and 288 males) analysed by five forensic laboratories of Central and Northern Italy is shown. Our results demonstrate the feasibility of a single amplification/detection reaction involving seven markers of the X chromosome, which can be fruitfully used in complex kinship analysis.

Chromosomes, Human, X↗

Population data for Y-chromosome STR haplotypes from Piedmont (Italy).

Eight Y-chromosome STR loci (DYS19, DYS389-I, DYS389-II, DYS390, DYS391, DYS392, DYS393 and DYS385) were analysed in a sample of 236 unrelated males from four towns of Piedmont (Trino, Biella, Cavaglià, Postua). One hundred and fifty six different haplotypes were observed and 55 of them were not previously observed in the Y-STR Haplotype Reference Database (http://www.ystr.org/).

Chromosomes, Human, Y↗

Haplotypes for 13 Y-chromosomal STR loci in South Tunisian population (Sfax region).

Nine Y-STR loci from the "minimal haplotype" (DYS19, DYS385a/b, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393) included in Y-STR Haplotype Reference Databases (YHRD) with 4 additional Y-STRs (DYS436, DYS437, DYS438, DYS439) were analyzed by PCR using duplex and Y-PLEX 12 kit, followed by automatic genotyping in a sample of 105 Tunisian males originating from Sfax region (south Tunisia). Allelic frequencies and gene diversities for each Y-STR locus were determined. The high haplotype diversity (0.9932) and discrimination capacity (0.7714) show the usefulness of these loci for human identification in forensic studies and paternity tests in Tunisia. The most common haplotype was shared by 4.7% (5 individuals) of the sample was only found in samples from the Tunisian population reported in YHRD. One private allele for DYS392 (allele 17) was discovered and duplications were observed for five loci (DYS19, DYS389I, DYS393, DYS437 and DYS439).

Chromosomes, Human, Y↗

26-Locus Y-STR typing in a Bhutanese population sample.

26 Y chromosome short tandem repeat (STR) loci were amplified in a sample of 856 unrelated males from Bhutan, using two multiplex polymerase chain reaction (PCR) assays. The first multiplex is the Y-STR 20plex described by Butler et al. [J.M. Butler, R. Schoske, P.M. Vallone, M.C. Kline, A.J. Redd, M.F. Hammer, A novel multiplex for simultaneous amplification of 20 Y chromosome STR markers, Forensic Sci. Int. 129 (2002) 10-24], and the second is a novel (but overlapping) 14plex that targets six additional Y-STRs (DYS425, DYS434, DYS435, DYS436, DYS461, DYS462) and also amplifies the amelogenin locus. The 26-loci give a discriminating power of 0.9957, though even at this resolution one haplotype occurs 24 times. We identify novel alleles at five loci and microvariants at a further three, which were characterised by sequencing. Extended (11-locus) haplotypes for these samples have been submitted to the Y-STR Haplotype Reference Database (YHRD).

Amelogenin↗

Performance of the FearID earprint identification system.

The Forensic Ear Identification (FearID) research project was started in order to study the strength of evidence of earprints found on crime scenes. For this purpose, a sample of earprints from 1229 donors over three countries was collected. From each donor three left and three right earprints were gathered. On the one hand, operators denoted contours of the earprints to facilitate segmentation of the images, on the other anthropological specialists denoted anatomically specific locations. On the basis of this, methods for automated classification were developed and used for training of a system that classifies pairs of prints as 'matching' or 'non-matching'. Comparing lab quality prints, the system has an equal error rate of 4%. Starting from a reference database containing two prints per ear, hitlist behaviour is such that in 90% of all query searches the best hit is in the top 0.1% of the list. The results become less favourable (equal error rate of 9%) for print/mark comparisons.

Databases, Factual↗

Diversity of 26-locus Y-STR haplotypes in a Nepalese population sample: isolation and drift in the Himalayas.

Twenty-six Y-chromosomal short tandem repeat (STR) loci were amplified in a sample of 769 unrelated males from Nepal, using two multiplex polymerase chain reaction (PCR) assays. The 26 loci gave a discriminating power of 0.997, with 59% unique haplotypes, and the highest frequency haplotype occurring 12 times. We identified novel alleles at four loci, microvariants at a further two, and nine examples of amelogenin-Y deletions (1.2%). Comparison with a similarly sized Bhutanese sample typed with the same markers suggested histories of isolation and drift, with drift having a greater effect in Bhutan. Extended (11-locus) haplotypes for the Nepalese samples have been submitted to the Y-STR Haplotype Reference Database (YHRD).

Amelogenin↗