Simplified amino acid alphabets based on deviation of conditional probability from random background

The primitive data for deducing the Miyazawa-Jernigan contact energy or BLOSUM score matrix consists of pair frequency counts. Each amino acid corresponds to a conditional probability distribution. Based on the deviation of such conditional probability from random background, a scheme for reduction of amino acid alphabet is proposed. It is observed that evident discrepancy exists between reduced alphabets obtained from raw data of the Miyazawa-Jernigan's and BLOSUM's residue pair counts. Taking homologous sequence database SCOP40 as a test set, we detect homology with the obtained coarse-grained substitution matrices. It is verified that the reduced alphabets obtained well preserve information contained in the original 20-letter alphabet.Comment: 9 pages,3figure

Wintertime CO2 Emission from Soils of Northeastern Siberia

The emission of C02 from northeastern Siberian soil was estimated for the period December 1989 to February 1990. Concentrations of air CO2 near the ground and 1 m above the snow cover were measured by an infrared gas analyzer. Fluxes of CO2 across the snow cover were calculated from the differences of these two values and the predetermined CO2 transfer coefficients at various flux rates through a layer of snow. Temperature and moisture content of the soil profiles were also observed simultaneously. The average transfer coefficient of CO2 for packed snow measured in the winter of 1989/90 was about 0.28 sq. cm/s. This value was used to estimate the average CO2 flux from soil: 0.26 g C/sq. m/day in December 1989, 0.13 g C/sq. m/day in January 1990 and 0.07 g C/sq. m/day in February 1990. Thus a minimal total of about 13.8 g C/sq. m had been released from the tundra soil during the 90 days from December 1989 to February 1990. Using the study by Kelley et al. (1968) and assuming that the minimal CO2 transfer coefficient is also applicable for the entire tundra and Northern Taiga zones between September and June, the total emission from this region would amount to 0.23 x 10**15 g of carbon. The main source of this CO2 probably originated from microbial oxidation of soil organic matter. This assertion is supported by the existence of a relatively warm layer in the frozen soil at 40-120 cm depth. This warm layer was about 10-40 C higher than the ambient air, or about 5-10 C higher than the soil surface, and its moisture content was also higher than the surrounding layers.Key words: CO2 flux, Siberian tundra, soil temperature, moisture contentOn a évalué l'émission de CO2 provenant du sol dans le nord-est sibérien, durant la période allant de décembre 1989 à février 1990. On a mesuré les concentrations du CO2 ambiant près du sol et à 1 m de la couverture de neige, à l'aide d'un analyseur de gaz infrarouge. On a calculé les flux du CO2 à travers le couvert nival à partir des différences de ces deux valeurs et des coefficients de transfert du CO2 prédéterminés pour divers taux de flux à travers une couche de neige. On a aussi observé simultanément la température et la teneur en humidité des profils pédologiques. Le coefficient de transfert moyen du CO2 pour la neige tassée mesuré durant l'hiver de 1989-90 était d'environ 0,28 cm²/s. Cette valeur a servi à estimer le flux moyen du CO2 provenant du sol: 0,26 g C/m²/jour en décembre 1989, 0,13 g C/m²/jour en janvier 1990 et 0,07 g C/m²/jour en février 1990. Par conséquent, un total minimal d'environ 13,8 g C/m² a été libéré du sol de la toundra au cours des 90 jours allant de décembre à février 1990. En nous servant de l'étude menée précédemment par Kelley et al. (1968) et en supposant que le coefficient minimal de transfert du CO2 s'applique aussi à l'ensemble des zones de toundra et de taïga septentrionale entre septembre et juin, l'émission totale provenant de cette région se monterait à 0,23 x 10**15 g de carbone. La source principale de ce CO2 venait probablement de l'oxydation microbienne de la matière organique contenue dans le sol. Cette assertion est soutenue par l'existence d'une couche de température relativement élevée dans le sol gelé, qui se trouve de 40 à 120 cm de profondeur. La température de cette couche était de 10 à 40 °C plus élevée que l'air ambiant, ou environ de 5 à 10 °C plus élevée que la surface du sol, et sa teneur en eau était aussi plus élevée que les couches adjacentes.Mots clés : flux de CO2, toundra sibérienne, temperature du sol, teneur en ea

Protein Kinase B Regulates T Lymphocyte Survival, Nuclear Factor κb Activation, and Bcl-XL Levels in Vivo

The serine/threonine kinase protein kinase B (PKB)/Akt mediates cell survival in a variety of systems. We have generated transgenic mice expressing a constitutively active form of PKB (gag-PKB) to examine the effects of PKB activity on T lymphocyte survival. Thymocytes and mature T cells overexpressing gag-PKB displayed increased active PKB, enhanced viability in culture, and resistance to a variety of apoptotic stimuli. PKB activity prolonged the survival of CD4+CD8+ double positive (DP) thymocytes in fetal thymic organ culture, but was unable to prevent antigen-induced clonal deletion of thymocytes expressing the major histocompatibility complex class I–restricted P14 T cell receptor (TCR). In mature T lymphocytes, PKB can be activated in response to TCR stimulation, and peptide-antigen–specific proliferation is enhanced in T cells expressing the gag-PKB transgene. Both thymocytes and T cells overexpressing gag-PKB displayed elevated levels of the antiapoptotic molecule Bcl-XL. In addition, the activation of peripheral T cells led to enhanced nuclear factor (NF)-κB activation via accelerated degradation of the NF-κB inhibitory protein IκBα. Our data highlight a physiological role for PKB in promoting survival of DP thymocytes and mature T cells, and provide evidence for the direct association of three major survival molecules (PKB, Bcl-XL, and NF-κB) in vivo in T lymphocytes

SARS Transmission among Hospital Workers in Hong Kong

Despite infection control measures, breakthrough transmission of severe acute respiratory syndrome (SARS) occurred for many hospital workers in Hong Kong. We conducted a case-control study of 72 hospital workers with SARS and 144 matched controls. Inconsistent use of goggles, gowns, gloves, and caps was associated with a higher risk for SARS infection (unadjusted odds ratio 2.42 to 20.54, p < 0.05). The likelihood of SARS infection was strongly associated with the amount of personal protection equipment perceived to be inadequate, having <2 hours of infection control training, and not understanding infection control procedures. No significant differences existed between the case and control groups in the proportion of workers who performed high-risk procedures, reported minor protection equipment problems, or had social contact with SARS-infected persons. Perceived inadequacy of personal protection equipment supply, infection control training <2 hours, and inconsistent use of personal protection equipment when in contact with SARS patients were significant independent risk factors for SARS infection

Quantum Chaos in Open versus Closed Quantum Dots: Signatures of Interacting Particles

This paper reviews recent studies of mesoscopic fluctuations in transport through ballistic quantum dots, emphasizing differences between conduction through open dots and tunneling through nearly isolated dots. Both the open dots and the tunnel-contacted dots show random, repeatable conductance fluctuations with universal statistical proper-ties that are accurately characterized by a variety of theoretical models including random matrix theory, semiclassical methods and nonlinear sigma model calculations. We apply these results in open dots to extract the dephasing rate of electrons within the dot. In the tunneling regime, electron interaction dominates transport since the tunneling of a single electron onto a small dot may be sufficiently energetically costly (due to the small capacitance) that conduction is suppressed altogether. How interactions combine with quantum interference are best seen in this regime.Comment: 15 pages, 11 figures, PDF 2.1 format, to appear in "Chaos, Solitons & Fractals

Viral Load Distribution in SARS Outbreak

Airborne transmission may have resulted in an outbreak of SARS in Hong Kong

Compactification with Flux on K3 and Tori

We study compactifications of Type IIB string theory on a K3 \times T^2/Z_2 orientifold in the presence of RR and NS flux. We find the most general supersymmetry preserving, Poincare invariant, vacua in this model. All the complex structure moduli and some of the Kahler moduli are stabilised in these vacua. We obtain in an explicit fashion the restrictions imposed by supersymmetry on the flux, and the values of the fixed moduli. Some T-duals and Heterotic duals are also discussed, these are non-Calabi-Yau spaces. A superpotential is constructed describing these duals.Comment: Discussion of susy breaking vacua significantly altere

Type IIB Solutions with Interpolating Supersymmetries

We study type IIB supergravity solutions with four supersymmetries that interpolate between two types widely considered in the literature: the dual of Becker and Becker's compactifications of M-theory to 3 dimensions and the dual of Strominger's torsion compactifications of heterotic theory to 4 dimensions. We find that for all intermediate solutions the internal manifold is not Calabi-Yau, but has SU(3) holonomy in a connection with a torsion given by the 3-form flux. All 3-form and 5-form fluxes, as well as the dilaton, depend on one function appearing in the supersymmetry spinor, which satisfies a nonlinear differential equation. We check that the fields corresponding to a flat bound state of D3/D5-branes lie in our class of solutions. The relations among supergravity fields that we derive should be useful in studying new gravity duals of gauge theories, as well as possibly compactifications.Comment: 27pp, v2 REVTeX4, typographical fixes and minor clarifications, v3 added ref, modified discussion of RR axion slightl

New Supersymmetric String Compactifications

We describe a new class of supersymmetric string compactifications to 4d Minkowski space. These solutions involve type II strings propagating on (orientifolds of) non Calabi-Yau spaces in the presence of background NS and RR fluxes. The simplest examples have descriptions as cosets, generalizing the three-dimensional nilmanifold. They can also be thought of as twisted tori. We derive a formula for the (super)potential governing the light fields, which is generated by the fluxes and certain ``twists'' in the geometry. Detailed consideration of an example also gives strong evidence that in some cases, these exotic geometries are related by smooth transitions to standard Calabi-Yau or G2 compactifications of M-theory.Comment: 43 pages, harvmac bi