Modeling multilevel sleep transitional data via Poisson log-linear multilevel models

This paper proposes Poisson log-linear multilevel models to investigate population variability in sleep state transition rates. We specifically propose a Bayesian Poisson regression model that is more flexible, scalable to larger studies, and easily fit than other attempts in the literature. We further use hierarchical random effects to account for pairings of individuals and repeated measures within those individuals, as comparing diseased to non-diseased subjects while minimizing bias is of epidemiologic importance. We estimate essentially non-parametric piecewise constant hazards and smooth them, and allow for time varying covariates and segment of the night comparisons. The Bayesian Poisson regression is justified through a re-derivation of a classical algebraic likelihood equivalence of Poisson regression with a log(time) offset and survival regression assuming piecewise constant hazards. This relationship allows us to synthesize two methods currently used to analyze sleep transition phenomena: stratified multi-state proportional hazards models and log-linear models with GEE for transition counts. An example data set from the Sleep Heart Health Study is analyzed.

Comparative study of biphasic calcium phosphates with different HA/TCP ratios in mandibular bone defects. A long-term histomorphometric study in minipigs

Three biphasic calcium phosphate (BCP) bone substitute materials with hydroxyapatite (HA)/tricalcium phosphate (TCP) ratios of 20/80, 60/40, and 80/20 were compared to coagulum, particulated autogenous bone, and deproteinized bovine bone mineral (DBBM) in membrane-protected bone defects. The defects were prepared in the mandibles of 24 minipigs that were divided into four groups of six with healing times of 4, 13, 26, and 52 weeks, respectively. The histologic and histomorphometric evaluation focused on differences in amount and pattern of bone formation, filler degradation, and the interface between bone and filler. Collapse of the expanded polytetrafluoroethylene barrier membrane into the coagulum defects underlined the necessity of a filler material to maintain the augmented volume. Quantitatively, BCP 20/80 showed bone formation and degradation of the filler material similar to autografts, whereas BCP 60/40 and BCP 80/20 rather equaled DBBM. Among the three BCP's, the amount of bone formation and degradation of filler material seemed to be inversely proportional to the HA/TCP ratio. The fraction of filler surface covered with bone was highest for autografts at all time points and was higher for DBBM than BCP 80/20 and 60/40 at the early healing phase. TRAP-positive multinucleated cells were identified on BCP and DBBM surfaces without showing typical signs of resorption lacunae.

Isometric rate of force development, maximum voluntary contraction, and balance in women with and without joint hypermobility

OBJECTIVE: To determine differences between hypermobile subjects and controls in terms of maximum strength, rate of force development, and balance. METHODS: We recruited 13 subjects with hypermobility and 18 controls. Rate of force development and maximal voluntary contraction (MVC) during single leg knee extension of the right knee were measured isometrically for each subject. Balance was tested twice on a force plate with 15-second single-leg stands on the right leg. Rate of force development (N/second) and MVC (N) were extracted from the force-time curve as maximal rate of force development (= limit Deltaforce/Deltatime) and the absolute maximal value, respectively. RESULTS: The hypermobile subjects showed a significantly higher value for rate of force development (15.2% higher; P = 0.038, P = 0.453, epsilon = 0.693) and rate of force development related to body weight (16.4% higher; P = 0.018, P = 0.601, epsilon = 0.834) than the controls. The groups did not differ significantly in MVC (P = 0.767, P = 0.136, epsilon = 0.065), and MVC related to body weight varied randomly between the groups (P = 0.921, P = 0.050, epsilon = 0.000). In balance testing, the mediolateral sway of the hypermobile subjects showed significantly higher values (11.6% higher; P = 0.034, P = 0.050, epsilon = 0.000) than that of controls, but there was no significant difference (4.9% difference; P = 0.953, P = 0.050, epsilon = 0.000) in anteroposterior sway between the 2 groups. CONCLUSION: Hypermobile women without acute symptoms or limitations in activities of daily life have a higher rate of force development in the knee extensors and a higher mediolateral sway than controls with normal joint mobility.

Application of well log tomography to the Dundee and Rogers City Limestones, Michigan Basin, USA

The Michigan Basin is located in the upper Midwest region of the United States and is centered geographically over the Lower Peninsula of Michigan. It is filled primarily with Paleozoic carbonates and clastics, overlying Precambrian basement rocks and covered by Pleistocene glacial drift. In Michigan, more than 46,000 wells have been drilled in the basin, many producing significant quantities of oil and gas since the 1920s in addition to providing a wealth of data for subsurface visualization. Well log tomography, formerly log-curve amplitude slicing, is a visualization method recently developed at Michigan Technological University to correlate subsurface data by utilizing the high vertical resolution of well log curves. The well log tomography method was first successfully applied to the Middle Devonian Traverse Group within the Michigan Basin using gamma ray log curves. The purpose of this study is to prepare a digital data set for the Middle Devonian Dundee and Rogers City Limestones, apply the well log tomography method to this data and from this application, interpret paleogeographic trends in the natural radioactivity. Both the Dundee and Rogers City intervals directly underlie the Traverse Group and combined are the most prolific reservoir within the Michigan Basin. Differences between this study and the Traverse Group include increased well control and “slicing” of a more uniform lithology. Gamma ray log curves for the Dundee and Rogers City Limestones were obtained from 295 vertical wells distributed over the Lower Peninsula of Michigan, converted to Log ASCII Standard files, and input into the well log tomography program. The “slicing” contour results indicate that during the formation of the Dundee and Rogers City intervals, carbonates and evaporites with low natural radioactive signatures on gamma ray logs were deposited. This contrasts the higher gamma ray amplitudes from siliciclastic deltas that cyclically entered the basin during Traverse Group deposition. Additionally, a subtle north-south, low natural radioactive trend in the center of the basin may correlate with previously published Dundee facies tracts. Prominent trends associated with the distribution of limestone and dolomite are not observed because the regional range of gamma ray values for both carbonates are equivalent in the Michigan Basin and additional log curves are needed to separate these lithologies.

Sonic log prediction in carbonates

This work is conducted to study the complications associated with the sonic log prediction in carbonate logs and to investigate the possible solutions to accurately predict the sonic logs in Traverse Limestone. Well logs from fifty different wells were analyzed to define the mineralogy of the Traverse Limestone by using conventional 4-mineral and 3-mineral identification approaches. We modified the conventional 3-mineral identification approach (that completely neglects the gamma ray response) to correct the shale effects on the basis of gamma ray log before employing the 3-mineral identification. This modification helped to get the meaningful insight of the data when a plot was made between DGA (dry grain density) and UMA (Photoelectric Volumetric Cross-section) with the characteristic ternary diagram of the quartz, calcite and dolomite. The results were then compared with the 4-mineral identification approach. Contour maps of the average mineral fractions present in the Traverse Limestone were prepared to see the basin wide mineralogy of Traverse Limestone. In the second part, sonic response of Traverse Limestone was predicted in fifty randomly distributed wells. We used the modified time average equation that accounts for the shale effects on the basis of gamma ray log, and used it to predict the sonic behavior from density porosity and average porosity. To account for the secondary porosity of dolomite, we subtracted the dolomitic fraction of clean porosity from the total porosity. The pseudo-sonic logs were then compared with the measured sonic logs on the root mean square (RMS) basis. Addition of dolomite correction in modified time average equation improved the results of sonic prediction from neutron porosity and average porosity. The results demonstrated that sonic logs could be predicted in carbonate rocks with a root mean square error of about 4μsec/ft. We also attempted the use of individual mineral components for sonic log prediction but the ambiguities in mineral fractions and in the sonic properties of the minerals limited the accuracy of the results.

Different response to eccentric and concentric training in older men and women

Sarcopenia is the age-related loss of muscle mass and strength and has been associated with an increased risk of falling and the development of metabolic diseases. Various training protocols, nutritional and hormonal interventions have been proposed to prevent sarcopenia. This study explores the potential of continuous eccentric exercise to retard age-related loss of muscle mass and function. Elderly men and women (80.6 +/- 3.5 years) were randomized to one of three training interventions demanding a training effort of two sessions weekly for 12 weeks: cognitive training (CT; n = 16), conventional resistance training (RET; n = 23) and eccentric ergometer training (EET; n = 23). Subjects were tested for functional parameters and body composition. Biopsies were collected from M. vastus lateralis before and after the intervention for the assessment of fiber size and composition. Maximal isometric leg extension strength (MEL: +8.4 +/- 1.7%) and eccentric muscle coordination (COORD: -43 +/- 4%) were significantly improved with EET but not with RET (MEL: +2.3 +/- 2.0%; COORD: -13 +/- 3%) and CT (MEL: -2.3 +/- 2.5%; COORD: -12 +/- 5%), respectively. We observed a loss of body fat (-5.0 +/- 1.1%) and thigh fat (-6.9 +/- 1.5%) in EET subjects only. Relative thigh lean mass increased with EET (+2.5 +/- 0.6%) and RET (+2.0 +/- 0.3%) and correlated negatively with type IIX/type II muscle fiber ratios. It was concluded that both RET and EET are beneficial for the elderly with regard to muscle functional and structural improvements but differ in their spectrum of effects. A training frequency of only two sessions per week seems to be the lower limit for a training stimulus to reveal measurable benefits.

Optimized Demineralization Technique for the Measurement of Stable Isotope Ratios of Nonexchangeable H in Soil Organic Matter

To make use of the isotope ratio of nonexchangeable hydrogen (δ2Hn (nonexchangeable)) of bulk soil organic matter (SOM), the mineral matrix (containing structural water of clay minerals) must be separated from SOM and samples need to be analyzed after H isotope equilibration. We present a novel technique for demineralization of soil samples with HF and dilute HCl and recovery of the SOM fraction solubilized in the HF demineralization solution via solid-phase extraction. Compared with existing techniques, organic C (Corg) and organic N (Norg) recovery of demineralized SOM concentrates was significantly increased (Corg recovery using existing techniques vs new demineralization method: 58% vs 78%; Norg recovery: 60% vs 78%). Chemicals used for the demineralization treatment did not affect δ2Hn values as revealed by spiking with deuterated water. The new demineralization method minimized organic matter losses and thus artificial H isotope fractionation, opening up the opportunity to use δ2Hn analyses of SOM as a new tool in paleoclimatology or geospatial forensics.

ROSINA/DFMS capabilities to measure isotopic ratios in water at comet 67P/Churyumov–Gerasimenko

The likelihood that comets may have delivered part of the water to Earth has been reinforced by the recent observation of the earth-like D/H ratio in Jupiter-family comet 103P/Hartley 2 by Hartogh et al. (2011). Prior to this observation, results from several Oort cloud comets indicated a factor of 2 enrichment of deuterium relative to the abundance at Earth. The European Space Agency’s Rosetta spacecraft will encounter comet 67P/Churyumov-Gerasimenko, another Jupiter-family comet of likely Kuiper belt origin, in 2014 and accompany it from almost aphelion to and past perihelion. Onboard Rosetta is the Rosetta Orbiter Spectrometer for Ion and Neutral Analysis (ROSINA) which consists of two mass spectrometers and a pressure sensor [Balsiger et al. 2007]. With its unprecedented mass resolution, for a space-borne instrument, the Double Focusing Mass Spectrometer (DFMS), one of the major subsystems of ROSINA, will be able to obtain unambiguously the ratios of the isotopes in water from in situ measurements in the coma around the comet. We will discuss the performance of this sensor on the basis of measurements of the terrestrial hydrogen and oxygen isotopic ratios performed with the flight spare instrument in the lab. We also show that the instrument on Rosetta is capable of measuring the D/H even in the very low density water background released by the spacecraft. This capability demonstrates that ROSINA should obtain very sensitive measurements of these ratios in the cometary environment. These measurements will allow detection of fractionation as function of the distance from the nucleus as well as fractionation due to mechanisms that are correlated with heliocentric distance.

Magma differentiation fractionates Mo isotope ratios: Evidence from the Kos Plateau Tuff (Aegean Arc)

We investigated high temperature Mo isotope fractionation in a hydrous supra-subduction volcano-plutonic system (Kos, Aegean Arc, Greece) in order to address the debate on the δ98/95Mo variability of the continental crust. In this igneous system, where differentiation is interpreted to be dominated by fractional crystallization, bulk rock data from olivine basalt to dacite show δ98/95Mo ratios increasing from +0.3 to +0.6‰ along with Mo concentrations increasing from 0.8 to 4.1 μg g−1. Data for hornblende and biotite mineral separates reveal the extraction of light Mo into crystallizing silicates, with minimum partition coefficients between hornblende- silicate melt and biotite-silicate melt of 0.6 and 0.4 δ98/95Mo, respectively. Our data document significant Mo isotope fractionation at magmatic temperatures, hence, the igneous contribution to continental runoff is variable, besides probable source-related variability. Based on these results and published data an average continental δ98/95Mo of +0.3 to +0.4‰ can be derived. This signature corresponds more closely to the average of published data of dissolved Mo loads of large rivers than previous estimates and is consistent with an upper limit of δ98/95Mo = 0.4‰ of the Earth's upper crust as derived from the analysis of molybdenites.

A day in the life of PubMed: analysis of a typical day's query log.

OBJECTIVE: To characterize PubMed usage over a typical day and compare it to previous studies of user behavior on Web search engines. DESIGN: We performed a lexical and semantic analysis of 2,689,166 queries issued on PubMed over 24 consecutive hours on a typical day. MEASUREMENTS: We measured the number of queries, number of distinct users, queries per user, terms per query, common terms, Boolean operator use, common phrases, result set size, MeSH categories, used semantic measurements to group queries into sessions, and studied the addition and removal of terms from consecutive queries to gauge search strategies. RESULTS: The size of the result sets from a sample of queries showed a bimodal distribution, with peaks at approximately 3 and 100 results, suggesting that a large group of queries was tightly focused and another was broad. Like Web search engine sessions, most PubMed sessions consisted of a single query. However, PubMed queries contained more terms. CONCLUSION: PubMed's usage profile should be considered when educating users, building user interfaces, and developing future biomedical information retrieval systems.

Diffusive equilibration of N2, O2 and CO2 mixing ratios in a 1.5-million-years-old ice core

In the framework of the International Partnerships in Ice Core Sciences, one of the most important targets is to retrieve an Antarctic ice core that extends over the last 1.5 million years (i.e. an ice core that enters the climate era when glacial–interglacial cycles followed the obliquity cycles of the earth). In such an ice core the annual layers of the oldest ice would be thinned by a factor of about 100 and the climatic information of a 10 000 yr interval would be contained in less than 1 m of ice. The gas record in such an Antarctic ice core can potentially reveal the role of greenhouse gas forcing on these 40 000 yr cycles. However, besides the extreme thinning of the annual layers, also the long residence time of the trapped air in the ice and the relatively high ice temperatures near the bedrock favour diffusive exchanges. To investigate the changes in the O2 / N2 ratio, as well as the trapped CO2 concentrations, we modelled the diffusive exchange of the trapped gases O2, N2 and CO2 along the vertical axis. However, the boundary conditions of a potential drilling site are not yet well constrained and the uncertainties in the permeation coefficients of the air constituents in the ice are large. In our simulations, we have set the drill site ice thickness at 2700 m and the bedrock ice temperature at 5–10 K below the ice pressure melting point. Using these conditions and including all further uncertainties associated with the drill site and the permeation coefficients, the results suggest that in the oldest ice the precessional variations in the O2 / N2 ratio will be damped by 50–100%, whereas CO2 concentration changes associated with glacial–interglacial variations will likely be conserved (simulated damping 5%). If the precessional O2 / N2 signal will have disappeared completely in this future ice core, orbital tuning of the ice-core age scale will be limited.