From caging to rouse dynamics in polymer melts with intramolecular barriers: a critical test of the mode coupling theory

By means of computer simulations and solution of the equations of the mode coupling theory (MCT),we investigate the role of the intramolecular barriers on several dynamic aspects of nonentangled polymers. The investigated dynamic range extends from the caging regime characteristic of glass-formers to the relaxation of the chain Rouse modes. We review our recent work on this question,provide new results, and critically discuss the limitations of the theory. Solutions of the MCT for the structural relaxation reproduce qualitative trends of simulations for weak and moderate barriers. However, a progressive discrepancy is revealed as the limit of stiff chains is approached. This dis-agreement does not seem related with dynamic heterogeneities, which indeed are not enhanced by increasing barrier strength. It is not connected either with the breakdown of the convolution approximation for three-point static correlations, which retains its validity for stiff chains. These findings suggest the need of an improvement of the MCT equations for polymer melts. Concerning the relaxation of the chain degrees of freedom, MCT provides a microscopic basis for time scales from chain reorientation down to the caging regime. It rationalizes, from first principles, the observed deviations from the Rouse model on increasing the barrier strength. These include anomalous scaling of relaxation times, long-time plateaux, and nonmonotonous wavelength dependence of the mode correlators.

Stochastic inversion of tracer test and electrical geophysical data to estimate hydraulic conductivities.

Quantifying the spatial configuration of hydraulic conductivity (K) in heterogeneous geological environments is essential for accurate predictions of contaminant transport, but is difficult because of the inherent limitations in resolution and coverage associated with traditional hydrological measurements. To address this issue, we consider crosshole and surface-based electrical resistivity geophysical measurements, collected in time during a saline tracer experiment. We use a Bayesian Markov-chain-Monte-Carlo (McMC) methodology to jointly invert the dynamic resistivity data, together with borehole tracer concentration data, to generate multiple posterior realizations of K that are consistent with all available information. We do this within a coupled inversion framework, whereby the geophysical and hydrological forward models are linked through an uncertain relationship between electrical resistivity and concentration. To minimize computational expense, a facies-based subsurface parameterization is developed. The Bayesian-McMC methodology allows us to explore the potential benefits of including the geophysical data into the inverse problem by examining their effect on our ability to identify fast flowpaths in the subsurface, and their impact on hydrological prediction uncertainty. Using a complex, geostatistically generated, two-dimensional numerical example representative of a fluvial environment, we demonstrate that flow model calibration is improved and prediction error is decreased when the electrical resistivity data are included. The worth of the geophysical data is found to be greatest for long spatial correlation lengths of subsurface heterogeneity with respect to wellbore separation, where flow and transport are largely controlled by highly connected flowpaths.

Specific inhibition of HCN channels slows rhythm differently in atria, ventricle and outflow tract and stabilizes conduction in the anoxic-reoxygenated embryonic heart model.

The hyperpolarization-activated cyclic nucleotide-gated (HCN) channels are expressed in pacemaker cells very early during cardiogenesis. This work aimed at determining to what extent these channels are implicated in the electromechanical disturbances induced by a transient oxygen lack which may occur in utero. Spontaneously beating hearts or isolated ventricles and outflow tracts dissected from 4-day-old chick embryos were exposed to a selective inhibitor of HCN channels (ivabradine 0.1-10microM) to establish a dose-response relationship. The effects of ivabradine on electrocardiogram, excitation-contraction coupling and contractility of hearts submitted to anoxia (30min) and reoxygenation (60min) were also determined. The distribution of the predominant channel isoform, HCN4, was established in atria, ventricle and outflow tract by immunoblotting. Intrinsic beating rate of atria, ventricle and outflow tract was 164+/-22 (n=10), 78+/-24 (n=8) and 40+/-12bpm (n=23, mean+/-SD), respectively. In the whole heart, ivabradine (0.3microM) slowed the firing rate of atria by 16% and stabilized PR interval. These effects persisted throughout anoxia-reoxygenation, whereas the variations of QT duration, excitation-contraction coupling and contractility, as well as the types and duration of arrhythmias were not altered. Ivabradine (10microM) reduced the intrinsic rate of atria and isolated ventricle by 27% and 52%, respectively, whereas it abolished activity of the isolated outflow tract. Protein expression of HCN4 channels was higher in atria and ventricle than in the outflow tract. Thus, HCN channels are specifically distributed and control finely atrial, ventricular and outflow tract pacemakers as well as conduction in the embryonic heart under normoxia and throughout anoxia-reoxygenation.

The branch-site test of positive selection is surprisingly robust but lacks power under synonymous substitution saturation and variation in GC

Positive selection is widely estimated from protein coding sequence alignments by the nonsynonymous-to-synonymous ratio omega. Increasingly elaborate codon models are used in a likelihood framework for this estimation. Although there is widespread concern about the robustness of the estimation of the omega ratio, more efforts are needed to estimate this robustness, especially in the context of complex models. Here, we focused on the branch-site codon model. We investigated its robustness on a large set of simulated data. First, we investigated the impact of sequence divergence. We found evidence of underestimation of the synonymous substitution rate for values as small as 0.5, with a slight increase in false positives for the branch-site test. When dS increases further, underestimation of dS is worse, but false positives decrease. Interestingly, the detection of true positives follows a similar distribution, with a maximum for intermediary values of dS. Thus, high dS is more of a concern for a loss of power (false negatives) than for false positives of the test. Second, we investigated the impact of GC content. We showed that there is no significant difference of false positives between high GC (up to similar to 80%) and low GC (similar to 30%) genes. Moreover, neither shifts of GC content on a specific branch nor major shifts in GC along the gene sequence generate many false positives. Our results confirm that the branch-site is a very conservative test.

Development of a Subgrade Drainage Model for Unpaved Roads, TR-654, 2015

With over 68 thousand miles of gravel roads in Iowa and the importance of these roads within the farm-to-market transportation system, proper water management becomes critical for maintaining the integrity of the roadway materials. However, the build-up of water within the aggregate subbase can lead to frost boils and ultimately potholes forming at the road surface. The aggregate subbase and subgrade soils under these gravel roads are produced with material opportunistically chosen from local sources near the site and, many times, the compositions of these sublayers are far from ideal in terms of proper water drainage with the full effects of this shortcut not being fully understood. The primary objective of this project was to provide a physically-based model for evaluating the drainability of potential subbase and subgrade materials for gravel roads in Iowa. The Richards equation provided the appropriate framework to study the transient unsaturated flow that usually occurs through the subbase and subgrade of a gravel road. From which, we identified that the saturated hydraulic conductivity, Ks, was a key parameter driving the time to drain of subgrade soils found in Iowa, thus being a good proxy variable for accessing roadway drainability. Using Ks, derived from soil texture, we were able to identify potential problem areas in terms of roadway drainage . It was found that there is a threshold for Ks of 15 cm/day that determines if the roadway will drain efficiently, based on the requirement that the time to drain, Td, the surface roadway layer does not exceed a 2-hr limit. Two of the three highest abundant textures (loam and silty clay loam), which cover nearly 60% of the state of Iowa, were found to have average Td values greater than the 2-hr limit. With such a large percentage of the state at risk for the formation of boils due to the soil with relatively low saturated hydraulic conductivity values, it seems pertinent that we propose alternative design and/or maintenance practices to limit the expensive repair work in Iowa. The addition of drain tiles or French mattresses my help address drainage problems. However, before pursuing this recommendation, a comprehensive cost-benefit analysis is needed.

Measurement of the whole body clearance of infused glycerol as a test of liver function after major hepatectomy.

Major liver resection can be used in the treatment of liver cancer. The functional capacity of liver parenchyma needs to be evaluated preoperatively because it conditions the outcome. We assessed whether the whole body clearance of glycerol, a substrate essentially metabolized in liver cells, may be suitable as a simple test of liver function. Seven patients after major hepatectomy, six patients after colectomy and 12 healthy subjects were studied. Patients were investigated on the first day after surgery. All participants were studied during a 150-min basal period followed by a 120-min infusion of 16 mumol kg-1 min-1 13C-labelled glycerol. Whole body glycerol clearance was calculated from the change in plasma glycerol concentration. Whole body glucose production was measured with 6,6 2H2 glucose infused as a tracer in the basal state and during glycerol infusion. In addition, 13C glucose synthesis was monitored to quantitate gluconeogenesis from glycerol. Patients after liver resection had higher plasma glycerol concentrations and lower whole body glycerol clearance than healthy subjects and patients after colectomy. They also had higher plasma glucagon concentrations. Their fasting glucose production was mildly elevated in the fasting state and did not change after glycerol infusion, indicating a normal hepatic autoregulation of glucose production. These results indicate that whole body glycerol clearance can be simply determined from plasma glycerol concentrations during exogenous glycerol infusion. It is significantly reduced in patients after major hepatectomy, suggesting that it constitutes a sensitive test of hepatic function. Its use as a preoperative testing procedure remains to be evaluated.

Safety Analysis of Low-Volume Rural Roads in Iowa, 2010

Iowa features an extensive surface transportation system, with more than 110,000 miles of roadway, most of which is under the jurisdiction of local agencies. Given that Iowa is a lower-population state, most of this mileage is located in rural areas that exhibit low traffic volumes of less than 400 vehicles per day. However, these low-volume rural roads also account for about half of all recorded traffic crashes in Iowa, including a high percentage of fatal and major injury crashes. This study was undertaken to examine these crashes, identify major contributing causes, and develop low-cost strategies for reducing the incidence of these crashes. Iowa’s extensive crash and roadway system databases were utilized to obtain needed data. Using descriptive statistics, a test of proportions, and crash modeling, various classes of rural secondary roads were compared to similar state of Iowa controlled roads in crash frequency, severity, density, and rate for numerous selected factors that could contribute to crashes. The results of this study allowed the drawing of conclusions as to common contributing factors for crashes on low-volume rural roads, both paved and unpaved. Due to identified higher crash statistics, particular interest was drawn to unpaved rural roads with traffic volumes greater than 100 vehicles per day. Recommendations for addressing these crashes with low-cost mitigation are also included. Because of the isolated nature of traffic crashes on low-volume roads, a systemic or mass action approach to safety mitigation was recommended for an identified subset of the entire system. In addition, future development of a reliable crash prediction model is described.

Selective inhibition of JNK with a peptide inhibitor attenuates pain hypersensitivity and tumor growth in a mouse skin cancer pain model.

Cancer pain significantly affects the quality of cancer patients, and current treatments for this pain are limited. C-Jun N-terminal kinase (JNK) has been implicated in tumor growth and neuropathic pain sensitization. We investigated the role of JNK in cancer pain and tumor growth in a skin cancer pain model. Injection of luciferase-transfected B16-Fluc melanoma cells into a hindpaw of mouse induced robust tumor growth, as indicated by increase in paw volume and fluorescence intensity. Pain hypersensitivity in this model developed rapidly (<5 days) and reached a peak in 2 weeks, and was characterized by mechanical allodynia and heat hyperalgesia. Tumor growth was associated with JNK activation in tumor mass, dorsal root ganglion (DRG), and spinal cord and a peripheral neuropathy, such as loss of nerve fibers in the hindpaw skin and induction of ATF-3 expression in DRG neurons. Repeated systemic injections of D-JNKI-1 (6 mg/kg, i.p.), a selective and cell-permeable peptide inhibitor of JNK, produced an accumulative inhibition of mechanical allodynia and heat hyperalgesia. A bolus spinal injection of D-JNKI-1 also inhibited mechanical allodynia. Further, JNK inhibition suppressed tumor growth in vivo and melanoma cell proliferation in vitro. In contrast, repeated injections of morphine (5 mg/kg), a commonly used analgesic for terminal cancer, produced analgesic tolerance after 1 day and did not inhibit tumor growth. Our data reveal a marked peripheral neuropathy in this skin cancer model and important roles of the JNK pathway in cancer pain development and tumor growth. JNK inhibitors such as D-JNKI-1 may be used to treat cancer pain.

L'adopció internacional amb nens de Nepal: estudi amb el test projectiu Pota Negra

A Espanya i, especialment a Catalunya, la primera dècada del segle xxi ha estat marcada per un increment excepcional de les adopcions internacionals, configurant així un nou model de famílies i una nova realitat social. Des de la perspectiva de salut mental, s’inicia ara una etapa postadoptiva molt necessitada d’investigacions teòriques i empíriques. Amb aquest treball, volem apropar-nos a la realitat interna del nen adoptat, utilitzant el Test Projectiu temàtic Pota Negra (Corman 1961) i conèixer així les repercussions que té, en el seu desenvolupament emocional, el fet d’ésser un nen adoptat. L’estudi es realitza amb una mostra de 10 nens (5 nenes i 5 nens) d’edats compreses entre 6 i 12 anys, que formen part del grup de nens d’adopció internacional d’Espanya (país d’origen: Nepal). En els criteris d’inclusió per als nens, a més de l’edat i el país ja citats, hi ha també el de fer més de dos anys que s’hagi realitzat l’adopció. El criteri d’inclusió, per a les famílies, és no tenir fills biològics, és a dir, només tenir fills adoptius. Els resultats mostren que les variables afectives pròpies de l’adopció dificulten el desenvolupament emocional. Però, igual que en els altres àmbits, el nen adoptat necessitarà més temps, i possiblement suports específics, per a culminar la seva evolució. D’altra banda, es constata que l’ús de Tècniques Projectives facilita el coneixement del món intern del nen adoptat, possibilitant així una anàlisi holística i global de la persona.

Work Zone Simulation Model, 1999

To support the analysis of driver behavior at rural freeway work zone lane closure merge points, Center for Transportation Research and Education staff collected traffic data at merge areas using video image processing technology. The collection of data and the calculation of the capacity of lane closures are reported in a companion report, "Traffic Management Strategies for Merge Areas in Rural Interstate Work Zones". These data are used in the work reported in this document and are used to calibrate a microscopic simulation model of a typical, Iowa rural freeway lane closure. The model developed is a high fidelity computer simulation with an animation interface. It simulates traffic operations at a work zone lane closure. This model enables traffic engineers to visually demonstrate the forecasted delay that is likely to result when freeway reconstruction makes it necessary to close freeway lanes. Further, the model is also sensitive to variations in driver behavior and is used to test the impact of slow moving vehicles and other driver behaviors. This report consists of two parts. The first part describes the development of the work zone simulation model. The simulation analysis is calibrated and verified through data collected at a work zone in Interstate Highway 80 in Scott County, Iowa. The second part is a user's manual for the simulation model, which is provided to assist users with its set up and operation. No prior computer programming skills are required to use the simulation model.

Factors associated with 56-day non-return rate in dairy cattle

The objective of this work was to identify factors associated with the 56-day non-return rate (56-NRR) in dairy herds in the Galician region, Spain, and to estimate it for individual Holstein bulls. The experiment was carried out in herds originated from North-West Spain, from September 2008 to August 2009. Data of the 76,440 first inseminations performed during this period were gathered. Candidate factors were tested for their association with the 56-NRR by using a logistic model (binomial). Afterwards, 37 sires with a minimum of 150 first performed inseminations were individually evaluated. Logistic models were also estimated for each bull, and predicted individual 56-NRR rate values were calculated as a solution for the model parameters. Logistic regression found four major factors associated with 56-NRR in lactating cows: age at insemination, days from calving to insemination, milk production level at the time of insemination, and herd size. First-service conception rate, when a particular sire was used, was higher for heifers (0.71) than for lactating cows (0.52). Non-return rates were highly variable among bulls. Asignificant part of the herd-level variation of 56-NRR of Holstein cattle seems attributable to the service sire. High correlation level between observed and predicted 56-NRR was found.

Carcinoembryonic antigen expression, antibody localisation and immunophotodetection of human colon cancer liver metastases in nude mice: a model for radioimmunotherapy.

Colorectal cancer frequently disseminates through the portal vein into the liver. In this study, outbred Swiss nude mice were adapted to facilitate the induction of liver metastases by a pre-grafting treatment with 6 Gy total body irradiation and i.v. injection of anti-asialo GM1 antibody. One day later, cultured LS 174T human colon cancer cells were injected into the surgically exposed spleen, which was resected 3 min later. In 48 of 65 mice, a few to several hundred liver metastases were macroscopically observed at dissection 3 to 4 weeks after transplantation. Ten of 10 mice, followed-up for survival, died with multiple large confluent liver metastases. By reducing the radiation dose to 4 or 0 Gy, or omitting the anti-asialo GM1 antibody injection, only 60%, 37% or 50% of mice, respectively, had visible metastases 3 weeks after transplantation. Carcinoembryonic antigen (CEA) measured in tumour extracts was in the mean 25.6 micrograms/g in liver metastases compared with 9.2 micrograms/g in s.c. tumours. Uptake of radiolabelled anti-CEA monoclonal antibody (MAb) in the metastases 12, 24 and 48 hr after injection gave a mean value of 39% of the injected dose per gram of tissue (ID/g). In comparison, MAb uptake in s.c. and intrasplenic tumours or lung metastases gave a mean percentage ID/g of 20, 18 and 15, respectively. Laser-induced fluorescence after injection of indocyanin-MAb conjugate allowed direct visual detection of small liver metastases, including some that were not visible under normal light. Preliminary results showed that mice, pre-treated with 4 Gy irradiation and the anti-asialo GM1 injection, were tolerant to radioimmunotherapy with a total dose of 500 muCi 131I labeled anti-CEA intact MAbs given in 3 injections.

The Alcohol Use Disorders Identification Test (AUDIT) as a screening tool for excessive drinking in primary care: reliability and validity of a French version.

BACKGROUND: Excessive drinking is a major problem in Western countries. AUDIT (Alcohol Use Disorders Identification Test) is a 10-item questionnaire developed as a transcultural screening tool to detect excessive alcohol consumption and dependence in primary health care settings. OBJECTIVES: The aim of the study is to validate a French version of the Alcohol Use Disorders Identification Test (AUDIT). METHODS: We conducted a validation cross-sectional study in three French-speaking areas (Paris, Geneva and Lausanne). We examined psychometric properties of AUDIT as its internal consistency, and its capacity to correctly diagnose alcohol abuse or dependence as defined by DSM-IV and to detect hazardous drinking (defined as alcohol intake >30 g pure ethanol per day for men and >20 g of pure ethanol per day for women). We calculated sensitivity, specificity, positive and negative predictive values and Receiver Operator Characteristic curves. Finally, we compared the ability of AUDIT to accurately detect "alcohol abuse/dependence" with that of CAGE and MAST. RESULTS: 1207 patients presenting to outpatient clinics (Switzerland, n = 580) or general practitioners' (France, n = 627) successively completed CAGE, MAST and AUDIT self-administered questionnaires, and were independently interviewed by a trained addiction specialist. AUDIT showed a good capacity to discriminate dependent patients (with AUDIT > or =13 for males, sensitivity 70.1%, specificity 95.2%, PPV 85.7%, NPV 94.7% and for females sensitivity 94.7%, specificity 98.2%, PPV 100%, NPV 99.8%); and hazardous drinkers (with AUDIT > or =7, for males sensitivity 83.5%, specificity 79.9%, PPV 55.0%, NPV 82.7% and with AUDIT > or =6 for females, sensitivity 81.2%, specificity 93.7%, PPV 64.0%, NPV 72.0%). AUDIT gives better results than MAST and CAGE for detecting "Alcohol abuse/dependence" as showed on the comparative ROC curves. CONCLUSIONS: The AUDIT questionnaire remains a good screening instrument for French-speaking primary care.