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Combining short interval MRI in Alzheimer's disease: Implications for therapeutic trials.

Cerebral atrophy calculated from serial MRI is a marker of Alzheimer's disease (AD) progression, and a potential outcome measure for therapeutic trials. Reducing within-subject variability in cerebral atrophy rates by acquiring more than two serial scans could allow for shorter clinical trials requiring smaller patient numbers. Forty-six patients with AD and 23 controls each had up to 10 serial MR brain scans over two years. Whole brain atrophy was calculated for each subject from every scan-pair. 708 volumetric MRI scans were acquired: 2199 measures of atrophy were made for patients, and 1182 for controls. A linear mixed model was used to characterise between and within-individual variability. These results were used to investigate the power of combining multiple serial scans in treatment trials of varying lengths. In AD, the mean whole brain atrophy rate was 2.23%/year (95% CI: 1.90-2.56%/year). The linear mixed model was shown to fit the data well and led to a formula (0.99(2) + (0.82/t)2) for the variance of atrophy rates calculated from two scans "t" years apart. Utilising five optimally timed scans with repeat scans at each visit reduced the component of atrophy rate variance attributable to within-subject variability by approximately 56%, equating to a approximately 40% sample size reduction (228 vs 387 patients per arm to detect 20% reduction in atrophy rate) in a six-month placebo-controlled trial. This benefit in terms of sample size is relatively reduced in longer trials, although adding extra scanning visits may have benefits when patient drop-outs are accounted for. We conclude that sample sizes required in short interval therapeutic trials using cerebral atrophy as an outcome measure may be reduced if multiple serial MRI is performed.

Aged↗

Prostate cancer evaluated with ferumoxtran-10-enhanced T2*-weighted MR Imaging at 1.5 and 3.0 T: early experience.

PURPOSE: To prospectively evaluate the feasibility of ferumoxtran-10-enhanced magnetic resonance (MR) imaging at high magnetic field strength (3.0 T) and to compare image quality between 1.5- and 3.0-T MR imaging in terms of lymph node detection in patients with prostate cancer. MATERIALS AND METHODS: This study was institutional review board approved, and all patients gave written informed consent. Forty-eight consecutive patients aged 51-79 years (mean, 65.5 years) with prostate cancer were enrolled. T2*-weighted 1.5- and 3.0-T MR images of the pelvis were acquired in a sagittal plane parallel to the psoas muscle 24 hours after ferumoxtran-10 administration. A pelvic and body phased-array coil was used and yielded an in-plane resolution of 0.56 x 0.56 x 3.00 mm at 1.5 T and 0.50 x 0.50 x 2.50 mm at 3.0 T. All images were evaluated by three readers for total image quality, lymph node border delineation, muscle-fat contrast, and vessel-fat contrast. Statistical significance was calculated by using the Mann-Whitney U test. Subsequently, the general linear mixed model was used to estimate the contributions of three factors-patient, reader, and technique-to the variability of the imaging results. RESULTS: Significantly (P < .05) better muscle-fat contrast, vessel-fat contrast, lymph node border delineation, and total image quality were observed at 3.0-T MR imaging. The general linear mixed model revealed that the variability of all results could be attributed to the use of 3.0-T imaging. CONCLUSION: Ferumoxtran-10-enhanced MR imaging can be performed at high magnetic field strengths and result in improved image quality, which may lead to improved detection of small positive lymph nodes.

Aged↗

Association of hospital resource use with comorbidity status and patient age among hip fracture patients in Japan.

OBJECTIVES: This study examined the association of resource use with comorbidity status and patient age among hip fracture patients who underwent surgical treatment. DESIGN: We used a database from the Voluntary Hospitals of Japan Quality Indicator Project that involved 10 privately owned leading teaching hospitals in Japan. SETTING: Four of these hospitals in Japan. PARTICIPANTS: We selected 778 operable hip fracture patients aged 65 or older who were admitted to these hospitals between January 1996 and August 2000 (mean age: 80.3 +/- 7.3 years). MEASUREMENTS: A linear mixed model was performed to identify factors associated with the resource use, such as total length of stay (LOS), LOS before surgery, LOS after surgery, total hospital charges, charges for diagnostic examinations, charges for surgery, and length of theater time, among operable hip fracture patients. RESULTS: The mean LOS was 45.9 days, and the mean total hospital charges were US dollars 14,495.0. Results from linear mixed models revealed that higher age was significantly associated with shorter length of theater time (P < 0.01), and that the presence of comorbidity among hip fracture patients was significantly associated with longer total LOS (P < 0.01), longer LOS after surgery (P < 0.001), higher charges for diagnostic examinations (P < 0.001), and shorter length of theater time (P < 0.01). CONCLUSION: These results suggest that the presence of comorbidity among operable hip fracture patients requires greater resource use during their hospital stay, but higher age is not significantly associated with greater resource use at all.

Aged↗

Distinguishing animal subsets in toxicokinetic studies: comparison of non-linear mixed effects modelling with non-compartmental methods.

The purpose of this study was to compare the ability of non-compartmental analysis and compartmental mixed effects modelling (MEM) to determine the existence and magnitude of exposure differences (i.e. exposure ratio estimates) between subsets of animals during destructive toxicokinetic studies. Data from five toxicokinetic studies of an experimental compound were analysed using a linear trapezoidal calculation of the area under the curve (non-compartmental analysis) or modelled using MEM. With the non-compartmental method the Bailer-Satterthwaite approximation was used to construct confidence intervals around the exposure estimates of each subset of animals and these were used to determine if exposure differed between the subsets. The MEM analyses were performed on the full datasets and on datasets with arbitrary reductions in the number of animal replicates. With MEM, additional model parameters were used to differentiate between subsets of animals, and were incorporated only if they were justified statistically. Estimates of the existence and magnitude of exposure differences between animal subsets were similar with the two techniques. The MEM analyses were influenced only marginally by substantial reductions in the number of animals studied and were less compromised by extremely limited or unbalanced data. These analyses show that MEM and non-compartmental methods are similarly effective at detecting exposure differences between animal subsets in toxicokinetic studies. Estimates provided by both methods were influenced by the degree of variance in the data. These results support the proposition that it may be possible to reduce the number of animals employed in toxicokinetic studies if MEM is used.

Animals↗

Has the in situ right internal thoracic artery been overlooked? An angiographic study of the radial artery, internal thoracic arteries and saphenous vein graft patencies in symptomatic patients.

OBJECTIVE: The right internal thoracic artery is being used infrequently despite favorable observational angiographic data. Conversely, the radial artery utilization has increased with only limited data available. The purpose of this paper is to re-evaluate the roles of the right internal thoracic artery and the radial artery grafts. METHODS: We reviewed all ischemia-directed coronary angiographic procedures from January 1996 to December 2003. A total of 219 patients had primary coronary artery bypass grafting with an internal thoracic artery and a radial artery as two of the bypass grafts. Six hundred and seventy-nine (679) graft angiograms (45 saphenous vein, 363 radial artery, 54 right internal thoracic artery and 217 left internal thoracic artery) were studied. The mean period from operation to re-angiogram was 1104+/-761 days. Angiographic outcomes were divided into groups as: (1) patent (<50% stenosis) or (2) failed (>or=50% stenosis, string sign or occluded). A generalized linear mixed model was used to analyze predictors of graft patency. Turnbull's estimates of cumulative patency were used to compare graft failure rates over time. RESULTS: A total of 632/679 (93%) grafts were patent and 47/679 (7%) grafts had failed. Empirical saphenous vein graft patency was 40/45 (89%), radial artery patency 329/363 (91%), right internal thoracic artery patency 51/54 (94%) and left internal thoracic artery patency 212/217 (98%). Pairwise comparisons of patency from the generalized linear mixed model were: LITA>RITA, OR=1.5 (P=0.5); LITA>RA, OR=5.7 (P<0.001); LITA>SV, OR=6.5 (P<0.001); RITA>RA, OR=3.9 (P=0.01); RITA>SV, OR=4.4 (P=0.01); RA>SV, OR=1.1 (P=0.7). Five-year patency estimates from the Turnbull's model were the left internal thoracic artery (95.9%), right internal thoracic artery (91.2%), the radial artery (90.6%) and the saphenous vein (81.8%). CONCLUSIONS: Consideration should be given to the routine use of both internal thoracic arteries for coronary artery bypass grafting. When additional grafts are required, there is no evidence to suggest that either the radial artery or saphenous vein is superior.

Aged↗

Analysis of oligonucleotide array experiments with repeated measures using mixed models.

BACKGROUND: Two or more factor mixed factorial experiments are becoming increasingly common in microarray data analysis. In this case study, the two factors are presence (Patients with Alzheimer's disease) or absence (Control) of the disease, and brain regions including olfactory bulb (OB) or cerebellum (CER). In the design considered in this manuscript, OB and CER are repeated measurements from the same subject and, hence, are correlated. It is critical to identify sources of variability in the analysis of oligonucleotide array experiments with repeated measures and correlations among data points have to be considered. In addition, multiple testing problems are more complicated in experiments with multi-level treatments or treatment combinations. RESULTS: In this study we adopted a linear mixed model to analyze oligonucleotide array experiments with repeated measures. We first construct a generalized F test to select differentially expressed genes. The Benjamini and Hochberg (BH) procedure of controlling false discovery rate (FDR) at 5% was applied to the P values of the generalized F test. For those genes with significant generalized F test, we then categorize them based on whether the interaction terms were significant or not at the alpha-level (alphanew = 0.0033) determined by the FDR procedure. Since simple effects may be examined for the genes with significant interaction effect, we adopt the protected Fisher's least significant difference test (LSD) procedure at the level of alphanew to control the family-wise error rate (FWER) for each gene examined. CONCLUSIONS: A linear mixed model is appropriate for analysis of oligonucleotide array experiments with repeated measures. We constructed a generalized F test to select differentially expressed genes, and then applied a specific sequence of tests to identify factorial effects. This sequence of tests applied was designed to control for gene based FWER.

Algorithms↗

New technology, old standards: disparate activated clotting time measurements by the Hemochron Jr compared with the standard Hemochron.

BACKGROUND: Accurate control of the anticoagulation level is important for safe initiation of cardiopulmonary bypass. Using the Hemochron Jr., we consistently noted a higher than customary heparin dose required to achieve an activated clotting time (ACT) that, according to the literature and our quality standards, should be more than 480 seconds. This study was designed to determine whether there existed a significant difference in ACT values measured by the newer Hemochron Jr. and the older Hemochron 801 assay system. METHODS: A total of 30 patients underwent cardiovascular surgical procedures requiring heparinization (300 U/kg). Multiple samples for measurement of the ACT were obtained from all patients before heparinization, after heparinization, during cardiopulmonary bypass, and after protamine administration. Arterial samples were collected, and ACT was determined simultaneously on the same sample using both Hemochron Jr. and Hemochron 801. Activated clotting time data were analyzed with a linear mixed model using an unstructured variance-covariance matrix. RESULTS: Descriptive statistics on all heparinized patients revealed that the Hemochron Jr. yielded ACT results that on average were 121.28 seconds lower than the determination by the standard Hemochron 801 on the same sample of blood. This difference was -139.04 in on-pump cases and -90.51 in off-pump cases, primarily a function of the fact that higher heparin doses and therefore longer ACTs were used in patients having operations using the heart-lung machine. From the linear mixed model, the estimated average paired difference between the Hemochron Jr. and Hemochron 801 was found to be -86.03, yielding a highly significant test statistic (t(28) = -6.18; p < 0.0001). CONCLUSIONS: Lower ACT values determined by Hemochron Jr. are consistent with higher, clinically acceptable ACT values as measured by the Hemochron 801. These findings would suggest that safe levels of anticoagulation are determined in part by the specific assay used.

Blood Coagulation Tests↗

Dam-related effects on heart girth at birth, morbidity and growth rate from birth to 90 days of age in Swedish dairy calves.

We investigated the effects of dam-related factors (such as calving performance, milk leakage, diseases, milk production, and somatic-cell count (SCC)) on heart girth at birth and the incidence risk of diarrhoea and respiratory disease during the first 90 days in Swedish dairy calves. The effects of these dam-related factors and environmental and management-related (but not dietary) factors on the calves' growth rate during the first 90 days of life also were analysed. The study used nearly 3,000 heifer calves born in 1998 on 122 farms in the south-west of Sweden. Individual health records were kept by the farmers and visiting project veterinarians. The calf's heart girth was measured at birth and weaning. We used generalised linear mixed models for the size of the calf at birth and growth rate. Variables associated with the heart girth at birth were breed, calving performance, mastitis in the dam in the last 49 days before calving, milk production and parity. Variables associated with the growth rate were breed, calving performance, disease in the calf during its first 90 days of life, heart girth at birth, and housing of calves. The effect of the dam on the relative risk of diarrhoea and/or respiratory disease in the calf was evaluated by a generalised linear mixed model with a logit link. Morbidity in the dam during late pregnancy, retained placenta and SCC were associated with the relative risk of respiratory disease in the calf. None of the explanatory variables (other then breed) was associated with the relative risk of diarrhoea.

Animals↗

The efficacy of modified psychodynamic psychotherapy for patients with schizophrenia-spectrum disorders in Germany: a prospective, single-centre, assessor-blinded, parallel-group, randomised controlled trial.

BACKGROUND: People with schizophrenia-spectrum disorders have difficulties in interpersonal functioning that remain insufficiently addressed by standard care. Despite long-standing clinical use, psychodynamic psychotherapy has little empirical support compared with other psychosocial treatments for people with schizophrenia-spectrum disorders. We evaluated the efficacy of Modified Psychodynamic Psychotherapy for Schizophrenia (MPP-S), a manualised treatment tailored to the interpersonal vulnerability characteristic of this population, plus treatment as usual (TAU), compared with TAU alone. METHODS: This prospective, single-centre, assessor-blinded, parallel-group, randomised controlled trial was conducted at the Psychiatric University Hospital of the Charit&#xe9; at St Hedwig Hospital in Berlin, Germany. Participants were outpatients aged 18-64 years who were diagnosed with schizophrenia or schizoaffective disorder and exclusion criteria included organic brain disorder, somatic illness affecting cerebral function, and current or past alcohol or illicit drug misuse requiring addiction-specific treatment. Participants were randomly assigned 1:1 in blocks of ten to MPP-S (minimum 30 sessions) plus TAU or TAU alone. Outcome assessors were masked, but participants and therapists were not. The primary outcome was psychosocial functioning, measured using the Mini International Classification of Functioning, Disability and Health Rating for Limitations of Activities and Participation in Psychological Disorders (Mini-ICF-APP) and evaluated at baseline and prespecified post-treatment (24 months) and follow-up (36 months) assessments. Analyses followed the intention-to-treat principle. Linear mixed models were used to analyse incomplete longitudinal data under a missing-at-random assumption. People with lived experience were not formally involved in the design, conduct, or reporting of this study. This trial was preregistered at ClinicalTrials.gov (NCT02576613) and is complete. FINDINGS: From Oct 12, 2015, to Dec 7, 2021, 130 participants (57 [44%] female and 73 [56%] male) were randomly assigned to either MPP-S plus TAU (n=65) or TAU alone (n=64). One participant withdrew consent to data analysis. Regarding the primary outcome of psychosocial functioning, linear mixed models showed significant group-by-time interactions favouring the intervention: estimated marginal means indicated adjusted between-group differences in Mini-ICF-APP scores of -3&#xb7;45 (95% CI -5&#xb7;51 to -1&#xb7;40; p=0&#xb7;0011) at 24 months and -4&#xb7;07 (-6&#xb7;19 to -1&#xb7;94; p=0&#xb7;0002) at 36 months. The frequency of adverse events was similar between groups. There were three serious adverse events: two participants died by suicide (one in the MPP-S plus TAU group who did not start psychotherapy and one in the TAU alone group) and one participant in the MPP-S plus TAU group was admitted to a forensic hospital. INTERPRETATION: MPP-S added to TAU could improve psychosocial functioning compared with TAU alone. Our findings suggest efficacy and possible long-term benefits of psychodynamic psychotherapy for schizophrenia-spectrum disorders and indicate its potential role alongside other psychotherapeutic and psychosocial treatments. FUNDING: Berlin Institute of Health, Deutsche Gesellschaft f&#xfc;r Psychoanalyse, Psychotherapie, Psychosomatik und Tiefenpsychologie, International Psychoanalytic University Berlin, and K&#xf6;hler-Stiftung.

Humans↗

Analysis of case-crossover designs using longitudinal approaches: a simulation study.

BACKGROUND: Application of case-crossover designs provides an alternative to time-series analysis for analyzing the health-related effects of air pollution. Although some case-crossover studies can control for trend and seasonality by design, to date they have been analyzed as matched case-control studies. Such analyses may exhibit biases and a lower statistical efficiency than traditional time series analyzed with Poisson. METHODS: In this article, case-crossover studies are treated as cohort studies in which each subject is observed for a short period of time before and/or after the event, thus making possible analyzing with Andersen-Gill and generalized linear mixed models. We conducted a simulation study to compare the behavior of these models applied to case-crossover designs with time series analyzed with Poisson and with case-crossover analyzed by conditional logistic regression. To this end, we created a random variable that follows a Poisson distribution of low (2/day) and high mean events (22/day). This variable is a function of an unobserved confounding variable (that introduces trend and seasonality) and data on small particulate matter (PM10) from Barcelona. In addition, scenarios were created to assess the effect on exposure exerted by autocorrelation and the magnitude of the pollutant coefficient. RESULTS: The full semisymmetric design analyzed with generalized linear mixed models yields good coverage and a high statistical power for air-pollution effect magnitudes close to the real values but shows bias for high effect magnitudes. This bias seems to be attributable to autocorrelation in the exposure variable. CONCLUSIONS: Longitudinal approaches applied to case-crossover designs may prove useful for analyzing the acute effects of environmental exposures.

Air Pollutants↗

Association between environmental stress and epidermal papillomatosis of roach Rutilus rutilus.

We studied the association between environmental stress and epidermal papillomatosis of roach Rutilus rutilus L. in Finnish waters using a 'matched pairs' design. Populations impacted by industrial and/or sewage effluents were compared to reference populations from pristine sites. We examined both the prevalence (proportion of diseased fish) and intensity (number of scales covered by tumors) of the disease. Results of Generalized Linear Mixed Models (GLMM) indicated that the risk of papillomatosis was 7.5 times higher in males than females, and increased 1.3 times for every 10 mm increment in fish length. We controlled for the possible effects of fish size, sex and temporal variation through sampling procedures and statistical analyses. Mean prevalence of epidermal papillomatosis was 16.6 and 5.8% in impact and reference populations, respectively (10 population pairs; nfish = 1714). Results of GLMM suggested that the risk of being diseased was 2.7 times higher in the impact than reference populations. Thus, the prevalence of epidermal papillomatosis in roach can be used as an indicator of environmental stress. Results of Linear Mixed Models indicated no difference in the intensity of the disease between impact and reference populations (5 population pairs; nfish = 73; mean+/-SE 10.7+/-1.8 and 11.7+/- 2.9 scales, respectively), although prevalence was higher in impact populations in those 5 population pairs. The possible relationship between environmental stress and intensity of epidermal papillomatosis in natural roach populations remains to be demonstrated.

Animals↗

The sleep, subjective fatigue, and sustained attention of commercial airline pilots during an international pattern.

International commercial airline pilots may experience heightened fatigue due to irregular sleep schedules, long duty days, night flying, and multiple time zone changes. Importantly, current commercial airline flight and duty time regulations are based on work/rest factors and not sleep/wake factors. Consequently, the primary aim of the current study was to investigate pilots' amount of sleep, subjective fatigue, and sustained attention before and after international flights. A secondary aim was to determine whether prior sleep and/or duty history predicted pilots' subjective fatigue and sustained attention during the international flights. Nineteen pilots (ten captains, nine first officers; mean age: 47.42+/-7.52 years) participated. Pilots wore wrist activity monitors and completed sleep and duty diaries during a return pattern from Australia to Europe via Asia. The pattern included four flights: Australia-Asia, Asia-Europe, Europe-Asia, and Asia-Australia. Before and after each flight, pilots completed a 5 min PalmPilot-based psychomotor vigilance task (PVT) and self-rated their level of fatigue using the Samn-Perelli Fatigue Checklist. Separate repeated-measures ANOVAs were used to determine the impact of stage of flight and flight sector on the pilots' sleep in the prior 24 h, self-rated fatigue, and PVT mean response speed. Linear mixed model regression analyses were conducted to examine the impact of sleep in the prior 24 h, prior wake, duty length, and flight sector on pilots' self-rated fatigue and sustained attention before and after the international flights. A significant main effect of stage of flight was found for sleep in the prior 24 h, self-rated fatigue, and mean response speed (all p < 0.05). In addition, a significant main effect of flight sector on self-rated fatigue was found (p < .01). The interaction between flight sector and stage of flight was significant for sleep in the prior 24 h and self-rated fatigue (both p < .05). Linear mixed model analyses indicated that sleep in the prior 24 h was a significant predictor of self-rated fatigue and mean response speed after the international flight sectors. Flight sector was also a significant predictor of self-rated fatigue. These findings highlight the importance of sleep and fatigue countermeasures during international patterns. Furthermore, in order to minimize the risk of fatigue, the sleep obtained by pilots should be taken into account in the development of flight and duty time regulations.

Adult↗

Expansion of Oropouche virus in non-endemic Brazilian regions: analysis of genomic characterisation and ecological drivers.

BACKGROUND: Oropouche virus (OROV) is an arbovirus endemic in the Amazon region that closely resembles other arboviruses in terms of human disease, leading to potential misdiagnoses. The virus ecology has mostly restricted its occurrence to the Amazon biome; however, after a large 2023-24 OROV epidemic in the Brazilian Amazon region, outbreaks are being reported across Brazil and in other countries in Latin America. Here, we investigate the OROV spread outside Amazonia. METHODS: In this genomic and epidemiological study, OROV cases from January, 2023, to July, 2024, provided by the General Coordination of Public Health Laboratories of Brazil on Aug 1, 2024, were compared by geographical location (Amazon vs non-Amazon) and municipal population size, and a linear mixed model was employed to assess the relationship between agricultural area size and cases. OROV-positive samples from central laboratories of five non-Amazonian Brazilian states were sequenced using an amplicon-based approach. Bayesian phylogeographical analysis was performed with near full-length viral genomes, incorporating individual travel histories when relevant. The estimated dates of viral introductions in each sampled location were then contextualised with public epidemiological data. FINDINGS: Epidemic data show that outside the Amazon region, OROV cases frequency was 3&#xb7;9-times higher in small municipalities than in large municipalities. The planted areas of some agricultural products, such as banana plantations, were positively correlated (r=0&#xb7;39, p<0&#xb7;0001) with OROV cases. The linear mixed model revealed that, besides banana, cassava also has larger (p<0&#xb7;05) planted areas in municipalities with OROV cases when compared with those with no cases. The phylogenetic analysis of 32 new OROV genomes reconstructed multiple exportation events of the newly identified reassortant lineage from the Amazon to other Brazilian regions between January and March, 2024. At least three of the previously described OROV phylogenetic clades circulating in the Amazon were the source of viral introductions. Molecular clock analysis estimated that viral introductions happened from 50 days to 100 days before detecting the outbreaks in each state. INTERPRETATION: Our results confirm that the novel OROV reassortant lineage spread from the Amazon to other regions in early 2024, successfully establishing local transmission. The fact that outbreaks were observed in small municipalities, instead of large urban centres, suggests that local ecological conditions that are ideal for OROV vector occurrence, such as the banana plantation environment, might be important factors driving its spread in Brazil. FUNDING: DECIT, CNPq, FAPEAM, and Inova-Fiocruz. TRANSLATION: For the Portuguese translation of the abstract see Supplementary Materials section.

Brazil↗

Association and linkage for age at onset of a common oligogenic disease using genetic variance component models.

The aims of our analysis were: (1) to investigate association of single nucleotide polymorphisms (SNPs) and other covariates with age at onset in the simulated Genetic Analysis Workshop (GAW) 12 general population data, and (2) to use the polygenic random effects estimated during model fitting (sigma squared A random effects) as input to a Haseman-Elston linkage analysis. The association analyses used genetic variance component models in a generalized linear mixed models framework and were fitted using Gibbs sampling. This method successfully detected the only three sequenced genes that were also major genes. The single-point linkage analysis used all markers provided. Regions of linkage were found close to all four of the sites of major genes that explained a non-trivial component of the variance of age at onset. In all four cases the linkage peak fell within 5 cM of the true location. In three cases the peak significance was p < 0.01.

Adolescent↗

Pharmacodynamic and pharmacokinetic effects in gingival crevicular fluid from re-dosing during brushing.

The IntelliClean System from Sonicare and Crest combines a rechargeable sonic power toothbrush and a novel liquid toothpaste into one integrated system, providing the opportunity to re-dose with toothpaste during the brushing cycle. The purpose of this study was to investigate cleaning effects from in-mouth re-dosing with toothpaste during the brushing cycle vs conventional bolus dosing. This was a randomized, examiner-blind, six-period, crossover clinical study. Eighteen adult subjects used an experimental integrated system employing either a re-dosing regimen (2 doses at the start of brushing with 1 additional in-mouth dose during the last 30 seconds of brushing [2+1]) or a conventional regimen (2 doses at the start of brushing only [2+0]). Gingival crevicular fluid (GCF) was sampled at the final brushing quadrant from a preselected site in the gingival sulcus using filter strips at baseline and at 4, 15, and 120 minutes postbrushing. Mean change from baseline in the concentrations of total facultative anaerobes (TFAs) and gram-negative anaerobes (GNAs) in the GCF at 120 minutes posttreatment were modeled separately using general linear mixed models. Area under the curve of surfactant (sodium dodecyl sulfate [SDS]) in GCF over 2 hours postbrushing was calculated and modeled using an analysis of variance model. All hypotheses were tested 2-sided at the 5% significance level. Relative to the conventional regimen, the re-dosing (2+1) regimen produced a significantly greater reduction in log10 (TFA colony-forming units [CFU]/microL GCF) after brushing, 0.99+/-0.12 vs 0.65+/-0.12 (mean change +/- standard error), and a significantly greater reduction in log10 (GNA CFU/microL GCF) after brushing, 0.75 +/-0.14 vs 0.45 +/- 0.14. The re-dosing regimen led to significantly more SDS in GCF relative to the conventional regimen over the 2-hour time period. Re-dosing of liquid toothpaste during the brushing cycle with the IntelliClean System leads to a significantly increased cleaning effect, as defined by a reduced bacterial count in GCF, and significantly higher levels of surfactant in the GCF up to 2 hours after the brushing event.

Adult↗

Improved detection of microbiome-disease associations via population structure-aware generalized linear mixed effects models (microSLAM).

Microbiome association studies typically link host disease or other traits to summary statistics measured in metagenomics data, such as diversity or taxonomic composition. But identifying disease-associated species based on their relative abundance does not provide insight into why these microbes act as disease markers, and it overlooks cases where disease risk is related to specific strains with unique biological functions. To bridge this knowledge gap, we developed microSLAM, a mixed-effects model and an R package that performs association tests that connect host traits to the presence/absence of genes within each microbiome species, while accounting for strain genetic relatedness across hosts. Traits can be quantitative or binary (such as case/control). MicroSLAM is fit in three steps for each species. The first step estimates population structure across hosts. Step two calculates the association between population structure and the trait, enabling detection of species for which a subset of related strains confer risk. To identify specific genes whose presence/absence across diverse strains is associated with the trait, step three models the trait as a function of gene occurrence plus random effects estimated from step two. Applying microSLAM to 710 gut metagenomes from inflammatory bowel disease (IBD) samples, we discovered 56 species whose population structure correlates with IBD, meaning that different lineages are found in cases versus controls. After controlling for population structure, 20 species had genes significantly associated with IBD. Twenty-one of these genes were more common in IBD patients, while 32 genes were enriched in healthy controls, including a seven-gene operon in Faecalibacterium prausnitzii that is involved in utilization of fructoselysine from the gut environment. The vast majority of species detected by microSLAM were not significantly associated with IBD using standard relative abundance tests. These findings highlight the importance of accounting for within-species genetic variation in microbiome studies.

Humans↗

Joint modelling of bivariate longitudinal data with informative dropout and left-censoring, with application to the evolution of CD4+ cell count and HIV RNA viral load in response to treatment of HIV infection.

Several methodological issues occur in the context of the longitudinal study of HIV markers evolution. Three of them are of particular importance: (i) correlation between CD4+ T lymphocytes (CD4+) and plasma HIV RNA; (ii) left-censoring of HIV RNA due to a lower quantification limit; (iii) and potential informative dropout. We propose a likelihood inference for a parametric joint model including a bivariate linear mixed model for the two markers and a lognormal survival model for the time to drop out. We apply the model to data from patients starting antiretroviral treatment in the CASCADE collaboration where all of the three issues needed to be addressed.

Anti-HIV Agents↗

Bayesian ranking of sites for engineering safety improvements: decision parameter, treatability concept, statistical criterion, and spatial dependence.

In recent years, there has been a renewed interest in applying statistical ranking criteria to identify sites on a road network, which potentially present high traffic crash risks or are over-represented in certain type of crashes, for further engineering evaluation and safety improvement. This requires that good estimates of ranks of crash risks be obtained at individual intersections or road segments, or some analysis zones. The nature of this site ranking problem in roadway safety is related to two well-established statistical problems known as the small area (or domain) estimation problem and the disease mapping problem. The former arises in the context of providing estimates using sample survey data for a small geographical area or a small socio-demographic group in a large area, while the latter stems from estimating rare disease incidences for typically small geographical areas. The statistical problem is such that direct estimates of certain parameters associated with a site (or a group of sites) with adequate precision cannot be produced, due to a small available sample size, the rareness of the event of interest, and/or a small exposed population or sub-population in question. Model based approaches have offered several advantages to these estimation problems, including increased precision by "borrowing strengths" across the various sites based on available auxiliary variables, including their relative locations in space. Within the model based approach, generalized linear mixed models (GLMM) have played key roles in addressing these problems for many years. The objective of the study, on which this paper is based, was to explore some of the issues raised in recent roadway safety studies regarding ranking methodologies in light of the recent statistical development in space-time GLMM. First, general ranking approaches are reviewed, which include naïve or raw crash-risk ranking, scan based ranking, and model based ranking. Through simulations, the limitation of using the naïve approach in ranking is illustrated. Second, following the model based approach, the choice of decision parameters and consideration of treatability are discussed. Third, several statistical ranking criteria that have been used in biomedical, health, and other scientific studies are presented from a Bayesian perspective. Their applications in roadway safety are then demonstrated using two data sets: one for individual urban intersections and one for rural two-lane roads at the county level. As part of the demonstration, it is shown how multivariate spatial GLMM can be used to model traffic crashes of several injury severity types simultaneously and how the model can be used within a Bayesian framework to rank sites by crash cost per vehicle-mile traveled (instead of by crash frequency rate). Finally, the significant impact of spatial effects on the overall model goodness-of-fit and site ranking performances are discussed for the two data sets examined. The paper is concluded with a discussion on possible directions in which the study can be extended.

Accidents, Traffic↗