Computational problems in perfect phylogeny haplotyping: typing without calling the allele.

A haplotype is an m-long binary vector. The XOR-genotype of two haplotypes is the m-vector of their coordinate-wise XOR. We study the following problem: Given a set of XOR-genotypes, reconstruct their haplotypes so that the set of resulting haplotypes can be mapped onto a perfect phylogeny (PP) tree. The question is motivated by studying population evolution in human genetics, and is a variant of the perfect phylogeny haplotyping problem that has received intensive attention recently. Unlike the latter problem, in which the input is "full" genotypes, here we assume less informative input, and so may be more economical to obtain experimentally. Building on ideas of Gusfield, we show how to solve the problem in polynomial time, by a reduction to the graph realization problem. The actual haplotypes are not uniquely determined by that tree they map onto, and the tree itself may or may not be unique. We show that tree uniqueness implies uniquely determined haplotypes, up to inherent degrees of freedom, and give a sufficient condition for the uniqueness. To actually determine the haplotypes given the tree, additional information is necessary. We show that two or three full genotypes suffice to reconstruct all the haplotypes, and present a linear algorithm for identifying those genotypes.

Poison without antidote for the historical Socrates and french classical tragedy in El verí del teatre (The Poison of the Theatre) by Rodolf Sirera. (An extreme dose of sadism to put a stop to the excesses of theatrical fiction).

Socrates' serene attitude before his death -although this is questioned-, as described by Xenophon in his Apologia Socratis becomes for the playwright Rodolf Sirera a useful reference in an effort to reflect boldly on the limits of theatrical fiction in another clear example of the Classical Tradition, including that derived from Baroque Tragedy. However, in this case, it is judged severely to make us more conscious of the risk of turning life into a mere theatrical performance and human beings into actors and actresses in a play they did not write.

Daytime sleepiness with and without cataplexy in Chinese-Taiwanese patients.

BACKGROUND AND PURPOSE: Investigation of Chinese-Taiwanese patients with excessive sleepiness, but no association with other sleep disorders, and with the presence or absence of cataplexy. PATIENTS AND METHODS: Thirty-five patients, successively referred between 2002 and 2004, underwent polysomnography (PSG), repeat multiple sleep latency test (MSLT), and human leukocyte antigen (HLA) typing. Three patients without cataplexy also had cerebrospinal fluid (CSF) hypocretin measurements. RESULTS: DQB1*0602 was associated with cataplexy in over 90% of Chinese-Taiwanese cases. Absence of cataplexy and <2 sleep-onset REM periods (SOREMPs) was seen in only two subjects, but presence of two SOREMPs did not dissociate DQB1*0602 positive and negative or cataplexy positive and negative subjects. As a group, narcoleptics with cataplexy had a higher number of SOREMPs, and the mean sleep latency was much shorter in narcoleptics with cataplexy than in the non-cataplectic patients, independent of the number of SOREMPs. CONCLUSIONS: Chinese-Taiwanese patients with cataplexy present with similar HLA findings as Black and Caucasian patients, but the presence of two or more SOREMPs in Chinese-Taiwanese patients is not a sufficient diagnostic tool to identify narcolepsy. When cataplexy is not present, description of PSG nd HLA findings may be a better approach than using a label with little scientific significance, allowing for better collection of patients' phenotype.

Microstructure of highly oriented, hexagonal, boron nitride thin films grown on crystalline silicon by radio frequency plasma-assisted chemical vapor deposition

We present a high‐resolution electron microscopy study of the microstructure of boron nitride thin films grown on silicon (100) by radio‐frequency plasma‐assisted chemical vapor deposition using B2H6 (1% in H2) and NH3 gases. Well‐adhered boron nitride films grown on the grounded electrode show a highly oriented hexagonal structure with the c‐axis parallel to the substrate surface throughout the film, without any interfacial amorphous layer. We ascribed this textured growth to an etching effect of atomic hydrogen present in the gas discharge. In contrast, films grown on the powered electrode, with compressive stress induced by ion bombardment, show a multilayered structure as observed by other authors, composed of an amorphous layer, a hexagonal layer with the c‐axis parallel to the substrate surface and another layer oriented at random

Photosynthesis rate, chlorophyll content and initial development of physic nut without micronutrient fertilization

Few studies in Brazil have addressed the need for micronutrients of physic nut focusing on physiological responses, especially in terms of photosynthesis. The objective of this study was to evaluate the effects of omission of boron (B), copper (Cu), iron (Fe), manganese (Mn) and zinc (Zn) on Jatropha curcas L.. The experimental design was a randomized block with four replications. The treatments were complete solution (control) and solution without B, Cu, Fe, Mn, and Zn. We evaluated the chlorophyll content (SPAD units), photosynthetic rate, dry matter production and accumulation of micronutrients in plants, resulting from different treatments. The first signs of deficiency were observed for Fe and B, followed by Mn and Zn, while no symptoms were observed for Cu deficiency. The micronutrient omission reduced the dry matter yield, chlorophyll content and photosynthetic rate of the plants differently for each omitted nutrient. It was, however, the omission of Fe that most affected the development of this species in all parameters evaluated. The treatments negatively affected the chlorophyll content, evaluated in SPAD units, and the photosynthetic rate, except for the omission of B. However this result was probably due to the concentration effect, since there was a significant reduction in the dry matter production of B-deficient plants.

Gas collisions and pressure quenching of the photoluminescence of silicon nanopowder grown by plasma-enhanced chemical vapor deposition

The quenching of the photoluminescence of Si nanopowder grown by plasma-enhanced chemical vapor deposition due to pressure was measured for various gases ( H2, O2, N2, He, Ne, Ar, and Kr) and at different temperatures. The characteristic pressure, P0, of the general dependence I(P) = I0¿exp(¿P/P0) is gas and temperature dependent. However, when the number of gas collisions is taken as the variable instead of pressure, then the quenching is the same within a gas family (mono- or diatomic) and it is temperature independent. So it is concluded that the effect depends on the number of gas collisions irrespective of the nature of the gas or its temperature.

Plasma-enhanced chemical vapor deposition of boron nitride thin films from B2H6-H2-NH3 and B2H6-N2 gas mixtures

Highly transparent and stoichiometric boron nitride (BN) films were deposited on both electrodes (anode and cathode) of a radio-frequency parallel-plate plasma reactor by the glow discharge decomposition of two gas mixtures: B2H6-H2-NH3 and B2H6-N2. The chemical, optical, and structural properties of the films, as well as their stability under long exposition to humid atmosphere, were analyzed by x-ray photoelectron, infrared, and Raman spectroscopies; scanning and transmission electron microscopies; and optical transmittance spectrophotometry. It was found that the BN films grown on the anode using the B2H6-H2-NH3 mixture were smooth, dense, adhered well to substrates, and had a textured hexagonal structure with the basal planes perpendicular to the film surface. These films were chemically stable to moisture, even after an exposition period of two years. In contrast, the films grown on the anode from the B2H6-N2 mixture showed tensile stress failure and were very unstable in the presence of moisture. However, the films grown on the cathode from B2H6-H2-NH3 gases suffered from compressive stress failure on exposure to air; whereas with B2H6-N2 gases, adherent and stable cathodic BN films were obtained with the same crystallographic texture as anodic films prepared from the B2H6-H2-NH3 mixture. These results are discussed in terms of the origin of film stress, the effects of ion bombardment on the growing films, and the surface chemical effects of hydrogen atoms present in the gas discharge.

Ion assisted deposition of thin films by substrate tuned radio frequency magnetron sputtering

The substrate tuning technique was applied to a radio frequency magnetron sputtering system to obtain a variable substrate bias without an additional source. The dependence of the substrate bias on the value of the external impedance was studied for different values of chamber pressure, gas composition and rf input power. A qualitative explanation of the results is given, based on a simple model, and the role of the stray capacitance is clearly disclosed. Langmuir probe measurements show that this system allows independent control of the ion flux and the ion energy bombarding the growing film. For an argon flow rate of 2.8 sccm and a radio frequency power of 300 W (intermediate values of the range studied) the ion flux incident on the substrate was 1.3 X 1020-m-2-s-1. The maximum ion energy available in these conditions can be varied in the range 30-150 eV. As a practical application of the technique, BN thin films were deposited under different ion bombardment conditions. An ion energy threshold of about 80 eV was found, below which only the hexagonal phase was present in the films, while for higher energies both hexagonal and cubic phase were present. A cubic content of about 60% was found for an ion energy of 120 V.

Dreaming without REM sleep.

To test whether mental activities collected from non-REM sleep are influenced by REM sleep, we suppressed REM sleep using clomipramine 50mg (an antidepressant) or placebo in the evening, in a double blind cross-over design, in 11 healthy young men. Subjects were awakened every hour and asked about their mental activity. The marked (81%, range 39-98%) REM-sleep suppression induced by clomipramine did not substantially affect any aspects of dream recall (report length, complexity, bizarreness, pleasantness and self-perception of dream or thought-like mentation). Since long, complex and bizarre dreams persist even after suppressing REM sleep either partially or totally, it suggests that the generation of mental activity during sleep is independent of sleep stage.

Glassiness in a model without energy barriers

We propose a microscopic model without energy barriers in order to explain some generic features observed in structural glasses. The statics can be exactly solved while the dynamics has been clarified using Monte Carlo calculations. Although the model has no thermodynamic transition, it captures some of the essential features of real glasses, i.e., extremely slow relaxation, time dependent hysteresis effects, anomalous increase of the relaxation time, and aging. This suggests that the effect of entropy barriers can be an important ingredient to account for the behavior observed in real glasses.

Water Heating, 2011

Although there are many ways to cut you water heating bills, the all fall into two broad categories: reducing the amount of hot water you use and making your water heating system more efficient. Fortunately, there are several strategies that can help you consume less energy and save money - and still meet you hot water needs without sacrificing comfort or practicality. The booklet was designed to answer common questions about hot water systems and to provide you with the information necessary to make informed decision about a wide variety of topics, ranging from repairing hot water faucet leaks an insulation water supply pipes to installing low-flow shower heads and tuning you your existing water heather. You'll also find details on what to consider when it's time to go comparison shopping for a new water heater-including an evaluation of the alternatives to the common gas or electric storage tank unit that's found in the majority of homes in Iowa and across the country.

Continuous phase transition in a spin-glass model without time-reversal symmetry

We investigate the phase transition in a strongly disordered short-range three-spin interaction model characterized by the absence of time-reversal symmetry in the Hamiltonian. In the mean-field limit the model is well described by the Adam-Gibbs-DiMarzio scenario for the glass transition; however, in the short-range case this picture turns out to be modified. The model presents a finite temperature continuous phase transition characterized by a divergent spin-glass susceptibility and a negative specific-heat exponent. We expect the nature of the transition in this three-spin model to be the same as the transition in the Edwards-Anderson model in a magnetic field, with the advantage that the strong crossover effects present in the latter case are absent.

Greenhouse Gas and Nitrogen Fertilizer Scenarios for U.S. Agriculture and Global Biofuels, June 2011

This analysis uses the 2011 FAPRI-CARD (Food and Agricultural Policy Research Institute–Center for Agricultural and Rural Development) baseline to evaluate the impact of four alternative scenarios on U.S. and world agricultural markets, as well as on world fertilizer use and world agricultural greenhouse gas emissions. A key assumption in the 2011 baseline is that ethanol support policies disappear in 2012. The baseline also assumes that existing biofuel mandates remain in place and are binding. Two of the scenarios are adverse supply shocks, the first being a 10% increase in the price of nitrogen fertilizer in the United States, and the second, a reversion of cropland into forestland. The third scenario examines how lower energy prices would impact world agriculture. The fourth scenario reintroduces biofuel tax credits and duties. Given that the baseline excludes these policies, the fourth scenario is an attempt to understand the impact of these policies under the market conditions that prevail in early 2011. A key to understanding the results of this fourth scenario is that in the absence of tax credits and duties, the mandate drives biofuel use. Therefore, when the tax credits and duties are reintroduced, the impacts are relatively small. In general, the results show that the entire international commodity market system is remarkably robust with respect to policy changes in one country or in one sector. The policy implication is that domestic policy changes implemented by a large agricultural producer like the United States can have fairly significant impacts on the aggregate world commodity markets. A second point that emerges from the results is that the law of unintended consequences is at work in world agriculture. For example, a U.S. nitrogen tax that might presumably be motivated for environmental benefit results in an increase in world greenhouse gas emissions. A similar situation occurs in the afforestation scenario in which crop production shifts from high-yielding land in the United States to low-yielding land and probably native vegetation in the rest of the world, resulting in an unintended increase in global greenhouse gas emissions.

Thermogenesis and fructose metabolism in humans.

Resting metabolic rate was measured in 10 healthy volunteers (25 yr, 73 kg, 182 cm) for 1 h before and 4 h during intravenous (iv) fructose administration (20% at 50 mumol.kg-1.min-1) with (+P) or without (-P) propranolol (100 micrograms/kg, 1 microgram.kg-1.min-1) during the last 2 h. Some subjects were studied a further 2 h with fructose infusion and +P or -P in hyperinsulinemic (2.9 pmol.kg-1.min-1) euglycemic conditions. Glucose turnover ([3-3H]glucose, 20 muCi bolus and 0.2 muCi/min) was calculated over 30 min at 0, 2, 4, and 6 h. The thermic effect of iv fructose was approximately 7.5% and decreased to 4.9 +/- 0.4% (P less than 0.01) +P. During the euglycemic clamp the thermic effect was 6.2 +/- 0.9% (-P) and 5.3 +/- 0.9% (+P). Hepatic glucose production (HGP) was 11.7 mumol.kg-1.min-1 (0 h) and did not change after 2 h iv fructose (11.8 +/- 0.5 and 9.8 +/- 0.6 mumol.kg-1.min-1 -P and +P, respectively) but increased to 13.8 +/- 0.9 (-P) and 12.9 +/- 0.8 mumol.kg-1.min-1 (+P) (P less than 0.01) after 4 h. HGP was suppressed to varying degrees during the euglycemic clamp. It is concluded that 1) the greater thermic effect of fructose compared with glucose is probably due to continued gluconeogenesis (which is suppressed by glucose or glucose-insulin) and the energy cost of fructose metabolism to glucose in the liver. 2) There is a sympathetically mediated component to the thermic effect of fructose (approximately 30%) that is not mediated by elevated plasma insulin concentrations similar to those observed with iv glucose.