TiMMing: developing an innovative suite of bioinformatic tools to harmonize and track the origin of copy number alterations in the evolutive history of multiple myeloma

Multiple Myeloma (MM) is a hematologic cancer with heterogeneous and complex genomic landscape, where Copy Number Alterations (CNAs) play a key role in the disease's pathogenesis and prognosis. It is of biological and clinical interest to study the temporal occurrence of early alterations, as they play a disease "driver" function by deregulating key tumor pathways. This study presents an innovative bioinformatic tools suite created for harmonizing and tracing the origin of CNAs throughout the evolutionary history of MM. To this aim, large cohorts of newly-diagnosed MM (NDMM, N=1582) and Smoldering-MM (SMM, N=282) were aggregated. The tools developed in this study enable the harmonization of CNAs as obtained from different genomic platforms in such a way that a high statistical power can be obtained. By doing so, the high numerosity of those cohorts was harnessed for the identification of novel genes characterized as "driver" (NFKB2, NOTCH2, MAX, EVI5 and MYC-ME2-enhancer), and the generation of an innovative timing model, implemented with a statistical method to introduce confidence intervals in the CNAs-calls. By applying this model on both NDMM and SMM cohorts, it was possible to identify specific CNAs (1q(CKS1B)amp, 13q(RB1)del, 11q(CCND1)amp and 14q(MAX)del) and categorize them as "early"/ "driver" events. A high level of precision was guaranteed by the narrow confidence intervals in the timing estimates. These CNAs were proposed as critical MM alterations, which play a foundational role in the evolutionary history of both SMM and NDMM. Finally, a multivariate survival model was able to identify the independent genomic alterations with the greatest effect on patients’ survival, including RB1-del, CKS1B-amp, MYC-amp, NOTCH2-amp and TRAF3-del/mut. In conclusion, the alterations that were identified as both "early-drivers” and correlated with patients’ survival were proposed as biomarkers that, if included in wider survival models, could provide a better disease stratification and an improved prognosis definition.

Long-Term Prospective, Randomized, Controlled Study Using Repetitive Education at Six-Month Intervals and Monitoring for Adherence in Heart Failure Outpatients The REMADHE Trial

Background-The effectiveness of heart failure disease management proarams in patients under cardiologists` care over long-term follow-up is not established. Methods and Results-We investigated the effects of a disease management program with repetitive education and telephone monitoring on primary (combined death or unplanned first hospitalization and quality-of-life changes) and secondary end points (hospitalization, death, and adherence). The REMADHE [Repetitive Education and Monitoring for ADherence for Heart Failure] trial is a long-term randomized, prospective, parallel trial designed to compare intervention with control. One hundred seventeen patients were randomized to usual care, and 233 to additional intervention. The mean follow-up was 2.47 +/- 1.75 years, with 54% adherence to the program. In the intervention group, the primary end point composite of death or unplanned hospitalization was reduced (hazard ratio, 0.64; confidence interval, 0.43 to 0.88; P=0.008), driven by reduction in hospitalization. The quality-of-life questionnaire score improved only in the intervention group (P<0.003). Mortality was similar in both groups. Number of hospitalizations (1.3 +/- 1.7 versus 0.8 +/- 1.3, P<0.0001), total hospital days during the follow-up (19.9 +/- 51 versus 11.1 +/- 24 days, P<0.0001), and the need for emergency visits (4.5 +/- 10.6 versus 1.6 +/- 2.4, P<0.0001) were lower in the intervention group. Beneficial effects were homogeneous for sex, race, diabetes and no diabetes, age, functional class, and etiology. Conclusions-For a longer follow-up period than in previous studies, this heart failure disease management program model of patients under the supervision of a cardiologist is associated with a reduction in unplanned hospitalization, a reduction of total hospital days, and a reduced need for emergency care, as well as improved quality of life, despite modest program adherence over time. (Circ Heart Fail. 2008;1:115-124.)

The Total Deviation Index estimated by Tolerance Intervals to evaluate the concordance of measurement devices

Background In an agreement assay, it is of interest to evaluate the degree of agreement between the different methods (devices, instruments or observers) used to measure the same characteristic. We propose in this study a technical simplification for inference about the total deviation index (TDI) estimate to assess agreement between two devices of normally-distributed measurements and describe its utility to evaluate inter- and intra-rater agreement if more than one reading per subject is available for each device. Methods We propose to estimate the TDI by constructing a probability interval of the difference in paired measurements between devices, and thereafter, we derive a tolerance interval (TI) procedure as a natural way to make inferences about probability limit estimates. We also describe how the proposed method can be used to compute bounds of the coverage probability. Results The approach is illustrated in a real case example where the agreement between two instruments, a handle mercury sphygmomanometer device and an OMRON 711 automatic device, is assessed in a sample of 384 subjects where measures of systolic blood pressure were taken twice by each device. A simulation study procedure is implemented to evaluate and compare the accuracy of the approach to two already established methods, showing that the TI approximation produces accurate empirical confidence levels which are reasonably close to the nominal confidence level. Conclusions The method proposed is straightforward since the TDI estimate is derived directly from a probability interval of a normally-distributed variable in its original scale, without further transformations. Thereafter, a natural way of making inferences about this estimate is to derive the appropriate TI. Constructions of TI based on normal populations are implemented in most standard statistical packages, thus making it simpler for any practitioner to implement our proposal to assess agreement.

Confidence Regions for Calibrated Parameters in Computable General Equilibrium Models

We consider the problem of accessing the uncertainty of calibrated parameters in computable general equilibrium (CGE) models through the construction of confidence sets (or intervals) for these parameters. We study two different setups under which this can be done.

Average dip directions from intervals of dipmeter log in drill hole CRP-2A

Bedding dips in the CRP-2A drillhole were determined in two ways (1) analysis of a dipmeter log, and (2) identification of bed boundaries on digital images of the outer core surface. The two methods document the downhole increase in structural dip, to a maximum of 15° in the lowest 150 m of the hole. Dipmeter data, which are azimuthally oriented, indicate a 75° azimuth for structural tilting, in agreement with seismic reflection profiles. Core and log dips indicate that structural dip increases by 5-7° between 325 and 480 mbsf. Both, however, also exhibit high dip inhomogeneity because of depositional (e.g., cross bedding) and post-depositional (e.g., softsediment deformation) processes. This variability adds ambiguity to the search for angular unconformities within the CRP-2A drillhole. Dip directions of different lithologies are generally similar, as are dip directions for the four kinds of systems tracts. Downdip azimuths of sands and muds are slightly different from those of diamicts, possibly reflecting the divergence between ENE offshore dip and ESE glacial advance.

The effect of pre-clinical fieldwork subject on the confidence and professional skills of undergraduate occupational therapy students

Objectives: This study investigated the effect of a pre-clinical fieldwork subject on the confidence and professional skills of undergraduate occupational therapy students during their first full-time clinical fieldwork placement. Methods: Participants were 31 third year students enrolled in the pre-clinical fieldwork subject (experimental group), and 25 students not enrolled in the subject (control group). Both quantitative and qualitative methodologies were employed to address the research question. Student anxiety levels were measured using the State-Trait Anxiety Inventory (STAI) and compared at three different intervals - prior to commencing the university semester, prior to commencing full-time practical placement, and following this full-time placement. Individual interviews were conducted with six students (three from the experimental group, three from the control group) to explore their perceptions regarding confidence levels and skill proficiencies during full-time placement. At each data analysis interval, responses for both groups were compared using independent samples t-tests. Responses were compared over time using analysis of variance (ANOVA). The qualitative data were subjected to thematic and content analysis. Results and Conclusions: In general, student anxiety levels did not differ between the experimental and control groups over time. However, qualitative results suggest that students who were enrolled in the pre-clinical subject have greater confidence and competence with occupational therapy skills, and have heightened awareness of the expectations on full-time placement.

Conditional Confidence Interval for the Scale Parameter of a Weibull Distribution

2000 Mathematics Subject Classification: 62F25, 62F03.

Effect of delay of first interview and repetition of interview on accuracy and confidence of recall of a flashbulb -type memory

Hearing of the news of the death of Diana, Princess of Wales, in a traffic accident, is taken as an analogue for being a percipient but uninvolved witness to a crime, or a witness to another person's sudden confession to some illegal act. This event (known in the literature as a “reception event”) has previously been hypothesized to cause one to form a special type of memory commonly known as a “flashbulb memory” (FB) (Brown and Kulik, 1977). FB's are hypothesized to be especially resilient against forgetting, highly detailed including peripheral details, clear, and inspiring great confidence in the individual for their accuracy. FB's are dependent for their formation upon surprise, emotional valence, and impact, or consequentiality to the witness of the initiating event. FB's are thought to be enhanced by frequent rehearsal. FB's are very important in the context of criminal investigation and litigation in that investigators and jurors usually place great store in witnesses, regardless of their actual accuracy, who claim to have a clear and complete recollection of an event, and who express this confidently. Therefore, the lives, or at least the freedom, of criminal defendants, and the fortunes of civil litigants hang on the testimony of witnesses professing to have FB's. ^ In this study, which includes a large and diverse sample (N = 305), participants were surveyed within 2–4 days after hearing of the fatal accident, and again at intervals of 2 and 4 weeks, 6, 12, and 18 months. Contrary to the FB hypothesis, I found that participants' FB's degraded over time beginning at least as early as two weeks post event. At about 12 months the memory trace stabilized, resisting further degradation. Repeated interviewing did not have any negative affect upon accuracy, contrary to concerns in the literature. Analysis by correlation and regression indicated no effect or predictive power for participant age, emotionality, confidence, or student status, as related to accuracy of recall; nor was participant confidence in accuracy predicted by emotional impact as hypothesized. Results also indicate that, contrary to the notions of investigators and jurors, witnesses become more inaccurate over time regardless of their confidence in their memories, even for highly emotional events. ^

Factors Associated With The Onset Of Hypertension In Women Of 50 Years Of Age Or More In A City In Southeastern Brazil.

To evaluate factors associated with hypertension in Brazilian women of 50 years of age or more. A cross-sectional population based study using self-reports. A total of 622 women were included. The association between sociodemographic, clinical and behavioral factors and the woman's age at the onset of hypertension was evaluated. Data were analyzed according to cumulative continuation rates without hypertension, using the life-table method and considering annual intervals. Next, a Cox multiple regression analysis model was adjusted to analyze the occurrence rates of hypertension according to various predictor variables. Significance level was pre-established at 5% (95% confidence level) and the sampling plan (primary sampling unit) was taken into consideration. Median age at onset of hypertension was 64.3 years. Cumulative continuation rate without hypertension at 90 years was 20%. Higher body mass index (BMI) at 20-30 years of age was associated with a higher cumulative occurrence rate of hypertension over time (coefficient=0.078; p<0.001). Being white was associated with a lower cumulative occurrence rate of hypertension over time (coefficient= -0.439; p=0.003), while smoking >15 cigarettes/day was associated with a higher rate over time (coefficient=0.485; p=0.004). The results of the present study highlight the importance of weight control in young adulthood and of avoiding smoking in preventing hypertension in women aged ≥50 years.

Temporal variation of the phytoplankton community at short sampling intervals in the Mundaú reservoir, Northeastern Brazil

The aim of this study was to determine how abiotic factors drive the phytoplankton community in a water supply reservoir within short sampling intervals. Samples were collected at the subsurface (0.1 m) and bottom of limnetic (8 m) and littoral (2 m) zones in both the dry and rainy seasons. The following abiotic variables were analyzed: water temperature, dissolved oxygen, electrical conductivity, total dissolved solids, turbidity, pH, total nitrogen, nitrite, nitrate, total phosphorus, total dissolved phosphorus and orthophosphate. Phytoplankton biomass was determined from biovolume values. The role abiotic variables play in the dynamics of phytoplankton species was determined by means of Canonical Correspondence Analysis. Algae biomass ranged from 1.17×10(4) to 9.21×10(4) µg.L-1; cyanobacteria had biomass values ranging from 1.07×10(4) to 8.21×10(4) µg.L-1. High availability of phosphorous, nitrogen limitation, alkaline pH and thermal stability all favored cyanobacteria blooms, particularly during the dry season. Temperature, pH, total phosphorous and turbidity were key factors in characterizing the phytoplankton community between sampling times and stations. Of the species studied, Cylindrospermopsis raciborskii populations were dominant in the phytoplankton in both the dry and rainy seasons. We conclude that the phytoplankton was strongly influenced by abiotic variables, particularly in relation to seasonal distribution patterns.

Herbage accumulation, growth and structural characteristics of Mombasa grass (Panicum maximum Jacq.) harvested at different cutting intervals

The objective of the present study was to evaluate herbage accumulation, morphological composition, growth rate and structural characteristics in Mombasa grass swards subject to different cutting intervals (3, 5 and 7 wk) during the rainy and dry seasons of the year. Treatments were assigned to experimental units (17.5 m(2)) according to a complete randomised block design, with four replicates. Herbage accumulation was greater in the rainy than in the dry season (83 and 17%, respectively). Herbage accumulation (24,300 kg DM ha(-1)), average growth rate (140 kg DM ha(-1) d(-1)) and sward height (111 cm) were highest in the 7 wk cutting interval, but leaf proportion (56%), leaf:stem (1.6) and leaf:non leaf (1.3) ratios decreased. Herbage accumulation, morphological composition and sward structure of Mombasa grass sward may be manipulated through defoliation frequency. The highest leaf proportion was recorded in the 3-wk cutting interval. Longer cutting intervals affected negatively sward structure, with potential negative effects on utilization efficiency, animal intake and performance.

Additive genetic relationship of longevity with fertility and production traits in Nellore cattle based on bivariate models

Survival or longevity is an economically important trait in beef cattle. The main inconvenience for its inclusion in selection criteria is delayed recording of phenotypic data and the high computational demand for including survival in proportional hazard models. Thus, identification of a longevity-correlated trait that could be recorded early in life would be very useful for selection purposes. We estimated the genetic relationship of survival with productive and reproductive traits in Nellore cattle, including weaning weight (WW), post-weaning growth (PWG), muscularity (MUSC), scrotal circumference at 18 months (SC18), and heifer pregnancy (HP). Survival was measured in discrete time intervals and modeled through a sequential threshold model. Five independent bivariate Bayesian analyses were performed, accounting for cow survival and the five productive and reproductive traits. Posterior mean estimates for heritability (standard deviation in parentheses) were 0.55 (0.01) for WW, 0.25 (0.01) for PWG, 0.23 (0.01) for MUSC, and 0.48 (0.01) for SC18. The posterior mean estimates (95% confidence interval in parentheses) for the genetic correlation with survival were 0.16 (0.13-0.19), 0.30 (0.25-0.34), 0.31 (0.25-0.36), 0.07 (0.02-0.12), and 0.82 (0.78-0.86) for WW, PWG, MUSC, SC18, and HP, respectively. Based on the high genetic correlation and heritability (0.54) posterior mean estimates for HP, the expected progeny difference for HP can be used to select bulls for longevity, as well as for post-weaning gain and muscle score.

AFFINE INTERVAL EXCHANGE TRANSFORMATIONS WITH FLIPS AND WANDERING INTERVALS

There exist uniquely ergodic affine interval exchange transformations of [0,1] with flips which have wandering intervals and are such that the support of the invariant measure is a Cantor set.