bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reliability issues in human brain temperature measurement
Authors: Childs Charmaine , Machin Graham 
Published: July 2009

Abstract
Introduction
The influence of brain temperature on clinical outcome after severe brain trauma is currently poorly understood. When brain temperature is measured directly, different values between the inside and outside of the head can occur. It is not yet clear if these differences are 'real' or due to measurement error.

Methods
The aim of this study was to assess the performance and measurement uncertainty of body and brain temperature sensors currently in use in neurocritical care. Two organic fixed-point, ultra stable temperature sources were used as the temperature references. Two different types of brain sensor (brain type 1 and brain type 2) and one body type sensor were tested under rigorous laboratory conditions and at the bedside. Measurement uncertainty was calculated using internationally recognised methods.

Results
Average differences between the 26°C reference temperature source and the clinical temperature sensors were +0.11°C (brain type 1), +0.24°C (brain type 2) and -0.15°C (body type), respectively. For the 36°C temperature reference source, average differences between the reference source and clinical thermometers were -0.02°C, +0.09°C and -0.03°C for brain type 1, brain type 2 and body type sensor, respectively. Repeat calibrations the following day confirmed that these results were within the calculated uncertainties. The results of the immersion tests revealed that the reading of the body type sensor was sensitive to position, with differences in temperature of -0.5°C to -1.4°C observed on withdrawing the thermometer from the base of the isothermal environment by 4 cm and 8 cm, respectively. Taking into account all the factors tested during the calibration experiments, the measurement uncertainty of the clinical sensors against the (nominal) 26°C and 36°C temperature reference sources for the brain type 1, brain type 2 and body type sensors were ± 0.18°C, ± 0.10°C and ± 0.12°C respectively.

Conclusions
The results show that brain temperature sensors are fundamentally accurate and the measurements are precise to within 0.1 to 0.2°C. Subtle dissociation between brain and body temperature in excess of 0.1 to 0.2°C is likely to be real. Body temperature sensors need to be secured in position to ensure that measurements are reliable.
Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana
Authors: Zhang Xiaoyu , Bernatavichute Yana V , Cokus Shawn , Pellegrini Matteo , Jacobsen Steven E 
Published: July 2009

Abstract
Background
Post-translational modifications of histones play important roles in maintaining normal transcription patterns by directly or indirectly affecting the structural properties of the chromatin. In plants, methylation of histone H3 lysine 4 (H3K4me) is associated with genes and required for normal plant development.

Results
We have characterized the genome-wide distribution patterns of mono-, di- and trimethylation of H3K4 (H3K4me1, H3K4me2 and H3K4me3, respectively) in Arabidopsis thaliana seedlings using chromatin immunoprecipitation and high-resolution whole-genome tiling microarrays (ChIP-chip). All three types of H3K4me are found to be almost exclusively genic, and two-thirds of Arabidopsis genes contain at least one type of H3K4me. H3K4me2 and H3K4me3 accumulate predominantly in promoters and 5' genic regions, whereas H3K4me1 is distributed within transcribed regions. In addition, H3K4me3-containing genes are highly expressed with low levels of tissue specificity, but H3K4me1 or H3K4me2 may not be directly involved in transcriptional activation. Furthermore, the preferential co-localization of H3K4me3 and H3K27me3 found in mammals does not appear to occur in plants at a genome-wide level, but H3K4me2 and H3K27me3 co-localize at a higher-than-expected frequency. Finally, we found that H3K4me2/3 and DNA methylation appear to be mutually exclusive, but surprisingly, H3K4me1 is highly correlated with CG DNA methylation in the transcribed regions of genes.

Conclusions
H3K4me plays widespread roles in regulating gene expression in plants. Although many aspects of the mechanisms and functions of H3K4me appear to be conserved among all three kingdoms, we observed significant differences in the relationship between H3K4me and transcription or other epigenetic pathways in plants and mammals.
Search for a 'Tree of Life' in the thicket of the phylogenetic forest
Authors: Puigbò Pere , Wolf Yuri I , Koonin Eugene V 
Published: July 2009

Abstract
Background
Comparative genomics has revealed extensive horizontal gene transfer among prokaryotes, a development that is often considered to undermine the 'tree of life' concept. However, the possibility remains that a statistical central trend still exists in the phylogenetic 'forest of life'.

Results
A comprehensive comparative analysis of a 'forest' of 6,901 phylogenetic trees for prokaryotic genes revealed a consistent phylogenetic signal, particularly among 102 nearly universal trees, despite high levels of topological inconsistency, probably due to horizontal gene transfer. Horizontal transfers seemed to be distributed randomly and did not obscure the central trend. The nearly universal trees were topologically similar to numerous other trees. Thus, the nearly universal trees might reflect a significant central tendency, although they cannot represent the forest completely. However, topological consistency was seen mostly at shallow tree depths and abruptly dropped at the level of the radiation of archaeal and bacterial phyla, suggesting that early phases of evolution could be non-tree-like (Biological Big Bang). Simulations of evolution under compressed cladogenesis or Biological Big Bang yielded a better fit to the observed dependence between tree inconsistency and phylogenetic depth for the compressed cladogenesis model.

Conclusions
Horizontal gene transfer is pervasive among prokaryotes: very few gene trees are fully consistent, making the original tree of life concept obsolete. A central trend that most probably represents vertical inheritance is discernible throughout the evolution of archaea and bacteria, although compressed cladogenesis complicates unambiguous resolution of the relationships between the major archaeal and bacterial clades.
An engineered CX3CR1 antagonist endowed with anti-inflammatory activity
Authors: Dorgham Karim , Ghadiri Ata , Hermand Patricia , Rodero Mathieu , Poupel Lucie , Iga Mutsumori , Hartley Oliver , Gorochov Guy , Combadière Christophe , Deterre Philippe 
Published: July 2009

Abstract
Identification of a chemokine analogue that antagonized CX3CL1-CX3CR1-dependent responses both in vitro and in vivo
Chemokines are mainly involved in the recruitment of leukocytes into tissues, a key feature of inflammation. Through its unique receptor CX3CR1, the chemokine CX3CL1 participates in diverse inflammatory processes including arterial atherosclerosis and cerebral or renal inflammation. Using a phage display strategy, we engineered a hCX3CL1 analog (named F1) with a modified N terminus. F1 bound specifically to cells expressing hCX3CR1 and had a Kd value close to that of native CX3CL1. F1 was not a signaling molecule and did not induce chemotaxis, calcium flux, or CX3CR1 internalization. However, it potently inhibited the CX3CL1-induced calcium flux and chemotaxis in CX3CR1-expressing primary cells of human and murine origin with an IC50 of 5–50 nM. It also efficiently inhibited the cell adhesion mediated by the CX3CL1-CX3CR1 axis. Finally, in a noninfectious murine model of peritonitis, F1 strongly inhibited macrophage accumulation. These data reveal a prototype molecule that is the first bona fide antagonist of hCX3CR1. This molecule could be used as a lead compound for the development of a novel class of anti-inflammatory substances that act by inhibiting CX3CR1.
Defence and coping in bipolar affective disorder: Stability and change of adaptational processes
Authors: Kramer Ueli 
Published: July 2009

Objectives. Defence mechanisms and coping have rarely been investigated from an integrative point of view. We are particularly interested in stability and change of these adaptational processes in clinical crisis situations of in‐patients presenting with bipolar affective disorder.Design. We conducted a controlled interview study including an in‐patient and a matched control group; longitudinal data are provided by follow‐up interviewing for all participants.Methods. A total of N=18 participants per group (patients presenting with bipolar affective disorder and non‐clinical controls) were recruited and interviewed twice. All interviews were transcribed and analysed according to observer–rater systems for coping (Coping Action Patterns) and defence mechanisms (Defence Mechanism Rating Scales). Symptom check list‐90‐R, as well as specific symptomatic measures, were used for symptomatic assessment and hierarchical linear modelling was used for statistical computation.Results. Overall, defensive functioning remains stable over a 3 month period, whereas overall, coping functioning increases over the same period in‐patients, as they are discharged from in‐patient treatment; no such effect was found in controls.Conclusions. Overall, stability in adaptational processes may be attributed to defensive functioning, whereas change over short periods of time are related to coping concepts in in‐patients presenting with bipolar affective disorder.
Monitoring Therapeutic Efficacy by Real-Time Detection of Mycobacterium tuberculosis mRNA in Sputum
Authors: Mdivani Nino , Li Haijing , Akhalaia Maka , Gegia Medea , Goginashvili Leila , Kernodle Douglas S , Khechinashvili George , Tang Yi-Wei 
Published: July 2009

Abstract
Background: Current laboratory methods for monitoring the response to therapy for tuberculosis (TB) rely on mycobacterial culture. Their clinical usefulness is therefore limited by the slow growth rate of Mycobacterium tuberculosis. Rapid methods to reliably quantify the response to anti-TB drugs are desirable.
Methods: We developed 2 real-time PCR assays that use hydrolysis probes to target DNA of the IS6110 insertion element and mRNA for antigen 85B. The nucleic acids are extracted directly from concentrated sputum samples decontaminated with sodium hydroxide and N-acetyl-l-cysteine. We prospectively compared these assays with results obtained by sputum mycobacterial culture for patients receiving anti-TB therapy.
Results: Sixty-five patients with newly diagnosed TB and receiving a standardized first-line anti-TB drug regimen were evaluated at week 2 and at months 1, 2, and 4 after therapy initiation. Both the DNA PCR assay (98.5% positive) and the mRNA reverse-transcription PCR (RT-PCR) assay (95.4% positive) were better than standard Ziehl–Neelsen staining techniques (83.1%) for detecting M. tuberculosis in culture-positive sputum samples. The overall agreement between culture and mRNA RT-PCR results for all 286 sputum samples was 87.1%, and compared with culture, the mRNA RT-PCR assay’s diagnostic sensitivity and specificity were 85.2% and 88.6%, respectively. For monitoring efficacy of therapy, mRNA RT-PCR results paralleled those of culture at the follow-up time points.
Conclusions: The continued presence of viable M. tuberculosis according to culture and results obtained by RT-PCR analysis of antigen 85B mRNA correlated clinically with resistance to anti-TB drugs, whereas the DNA PCR assay showed a high false-positive rate. This mRNA RT-PCR assay may allow rapid monitoring of the response to anti-TB therapy.
Experimental Characterization of Ice Hockey Pucks and Sticks
Authors: Bigford Rosanna L. , Smith Lloyd V. 
Published: July 2009

Abstract
In spite of the broad popularity of ice hockey, little has been done to characterize the performance of pucks or sticks used in play. Data representative of play conditions is particularly lacking. A high speed impact test was developed to measure the puck impact force and coefficient of restitution. Puck brand, temperature, and speed were all shown to have a measurable effect on the relative puck response. The high speed puck test was modified to measure the performance of hockey sticks. The performance of six wood and 11 composite sticks (including different shaft tapers for each group) were compared to evaluate the effect of modern materials on the game. Stick performance was expressed in terms of the maximum puck speed from an idealized slap shot model. In spite of the popularity of the relatively expensive composite sticks, on average the performance of the wood sticks was 10 % higher than the composite sticks. Shaft loading was found to increase the puck speed but did not significantly change the relative performance of the sticks. In contrast to balls in golf and baseball, puck hardness was shown to have a negligible effect on stick performance.
Defining the Flammability of Cylindrical Metal Rods Through Characterization of the Thermal Effects of the Ignition Promoter
Authors: Lynn David , Steinberg Ted , Sparks Kyle , Stoltzfus Joel M. 
Published: July 2009

Abstract
All relevant international standards for determining if a metallic rod is flammable in oxygen utilize some form of “promoted ignition” test. In this test, for a given pressure, an overwhelming ignition source is coupled to the end of the test sample and the designation flammable or nonflammable is based upon the amount burned, that is, a burn criteria. It is documented that (1) the initial temperature of the test sample affects the burning of the test sample both (a) in regards to the pressure at which the sample will support burning (threshold pressure) and (b) the rate at which the sample is melted (regression rate of the melting interface); and, (2) the igniter used affects the test sample by heating it adjacent to the igniter as ignition occurs. Together, these facts make it necessary to ensure, if a metallic material is to be considered flammable at the conditions tested, that the burn criteria will exclude any region of the test sample that may have undergone preheating during the ignition process. A two-dimensional theoretical model was developed to describe the transient heat transfer occurring and resultant temperatures produced within this system. Several metals (copper, aluminum, iron, and stainless steel) and ignition promoters (magnesium, aluminum, and Pyrofuze®) were evaluated for a range of oxygen pressures between 0.69 MPa (100 psia) and 34.5 MPa (5,000 psia). A MATLAB® program was utilized to solve the developed model that was validated against (1) a published solution for a similar system and (2) against experimental data obtained during actual tests at the National Aeronautics and Space Administration White Sands Test Facility. The validated model successfully predicts temperatures within the test samples with agreement between model and experiment increasing as test pressure increases and/or distance from the promoter increases. Oxygen pressure and test sample thermal diffusivity were shown to have the largest effect on the results. In all cases evaluated, there is no significant preheating (above about 38°C/100°F) occurring at distances greater than 30 mm (1.18 in.) during the time the ignition source is attached to the test sample. This validates a distance of 30 mm (1.18 in.) above the ignition promoter as a burn length upon which a definition of flammable can be based for inclusion in relevant international standards (that is, burning past this length will always be independent of the ignition event for the ignition promoters considered here).
Arsenic Binding to Iron(II) Minerals Produced by An Iron(III)-Reducing Aeromonas Strain Isolated from Paddy Soil
Authors: Wang Xin-Jun , Chen Xue-Ping , Kappler Andreas , Sun Guo-Xin , Zhu Yong-Guan 
Published: July 2009

Abstract
An iron-reducing bacterial strain was isolated from a paddy soil and identified as a member of the Aeromonas group by 16S rRNA gene sequence analysis. When the cells were growing with dissolved Fe(III) as the electron acceptor in the presence of As(V), Fe(II) minerals (siderite and vivianite) were formed and dissolved. As was removed efficiently from solution. When the cells were growing with the Fe(III) hydroxide mineral (ferrihydrite) as the electron acceptor in the presence of As(V), ferrihydrite was reduced and dissolved As(V) concentrations decreased sharply. The present study results demonstrated first that members of the Aeromonas group can reduce Fe(III) in paddy soils and second that iron reduction does not necessarily lead to arsenic mobilization. However, As immobilization can occur in environments that contain significant concentrations of counterions such as bicarbonate and phosphate.
Sublethal effects and predator-prey interactions: Implications for ecological risk assessment
Authors: Brooks Amy C. , Gaskell Paul N. , Maltby Lorraine L. 
Published: July 2009

Abstract
Ecological risk assessments tend to focus on contaminant effects on single species in isolation. However, additional effects from interactions between species (e.g., predator–prey interactions) may also occur in natural systems. The present study investigated the consequences of sublethal contaminant effects in prey on predator–prey interactions, particularly the interaction between prey behavioral changes and predation by predators with different hunting strategies. Ambush (Ischnura elegans Vander Linden [Insecta, Odonata]) and active (Notonecta glauca Linnaeus [Insecta, Heteroptera]) predator species were used in conjunction with three prey species (Asellus aquaticus Linnaeus [Crustacea, Isopoda], Cloëon dipterum Linnaeus [Insecta, Ephemeroptera], and Chironomus riparius Meigen [Insecta, Diptera]). Immobilized prey demonstrated the importance of prey behavior for determining predation rates for both single- and multiple-prey species. Chironomus riparius was less responsive following exposure to cadmium, becoming more vulnerable to attack by the active but not the ambush predator. Some evidence was also observed for reduced general activity in C. dipterum following cadmium exposure. Sublethal exposure of prey did not affect the prey choice of active predators, possibly because of prey behavioral changes being insufficient to influence their relative availabilities. However, cadmium exposure of prey did alter their susceptibility to ambush predators. There was a reduced proportion of C. dipterum and an increased proportion of A. aquaticus in the diet of ambush predators, possibly because of reduced activity in C. dipterum affecting their relative encounter rates with predators. Sublethal exposures can therefore result in reduced prey survival that would not be predicted by single-species toxicity tests.
A Detailed Comparison of Experimental and Numerical Data on Hydraulic Fracture Height Growth Through Stress Contrasts
Authors: Jeffrey Robert G. , Bunger Andrew 
Published: July 2009

Summary
This paper compares height, length, width, and pressure data from a laboratory experiment to predictions from a three-dimensional (3D) planar hydraulic fracture model for the case of a fracture propagating in a lower-stress payzone region bounded by two symmetric higher-stress barrier regions. A laboratory method that creates step-like stress changes on an interface between two transparent polymethylmethacrylate (PMMA) blocks is described. A fracture is propagated along this interface while measuring fracture geometry and full-field fracture width (opening) by analysis of the light intensity in images of the growing fracture. The fracture grew in overall height to 1.7 times the pay height and in half-length to 3 times the pay height. Results from a planar 3D numerical model closely matched the experimental data for overall fracture shape, length, height growth, and injection pressure. The data are presented so other numerical models can be compared with these detailed measurements.
Microseismic Monitoring Quality-Control (QC) Reports as an Interpretative Tool for Nonspecialists
Authors: Zimmer U. , Maxwell S. , Waltman C. , Warpinski N. 
Published: July 2009

Summary
In the oilfield industry, microseismic monitoring is widely applied to determine induced fracture network geometry and stress changes in reservoirs. The basic result is usually a map of the distribution of the microseismic events describing the area influenced by injection/production of reservoir fluids (e.g., hydraulic fracturing). As every microearthquake event (i.e., "dot" on the map) is processed individually, it has its own level of location accuracy. To prevent any misinterpretations based on events with low accuracy, quality-control (QC) reports can provide important information regarding location accuracy and other attributes that help in the overall interpretation of the maps, in addition to the standard event location. However, much of the information needed to assess the quality of the data is very specialized and technical, therefore, the figures presented in the QC reports often appear complicated and are not easy to read for the nonspecialist. By introducing easy-to-read figures that summarize the essential information, these reports have become more useful to the occasional user.
A Predictive Pore-Scale Model for Non-Darcy Flow in Porous Media
Authors: Balhoff Matthew T. , Wheeler Mary F. 
Published: July 2009

Summary
Non-Darcy flow is often observed near wells and in hydraulic fractures where relatively high velocities occur. In these regions, an empirical model, Forchheimer's equation, is used in place of Darcy's Law. It includes a quadratic correction to the linear model and has been adequately fit to many experimental data sets, while found to be insufficient in others. Furthermore, a number of numerical and theoretical approaches have shown limitations of the Forchheimer model in the laminar flow regime. It is important to understand the applicability of Forchheimer's equation and to be able to obtain good predictions of macroscopic properties so that nonlinear flow can be properly modeled in reservoir simulators.
In this work, non-Darcy flow of an incompressible fluid is modeled using a physically representative (Bryant et al. 1993) pore-scale network model. Quantitative and predictive results are obtained using both computer-generated porous media and real sandstones digitized through x-ray computed microtomography (XMT). A new friction factor correlation is developed for laminar flow in converging/diverging ducts using the numerical solution to the Navier-Stokes equations. The new equation is used to describe flow in pore throats of the network model. The permeability and non-Darcy coefficient, β, are determined for these isotropic and anisotropic media in which Forchheimer's equation is applicable. The numerical model is compared to existing experimental data and appears to be at least as successful as correlations for predicting the non-Darcy coefficient in isotropic media. Furthermore, limitations to Forchheimer's equation at both low and high velocities are determined and discussed.