Weight vs magnetization enumerator for Gallager codes

We propose a method to determine the critical noise level for decoding Gallager type low density parity check error correcting codes. The method is based on the magnetization enumerator (¸M), rather than on the weight enumerator (¸W) presented recently in the information theory literature. The interpretation of our method is appealingly simple, and the relation between the different decoding schemes such as typical pairs decoding, MAP, and finite temperature decoding (MPM) becomes clear. Our results are more optimistic than those derived via the methods of information theory and are in excellent agreement with recent results from another statistical physics approach.

Magnetization enumerator for real-valued symmetric channels in Gallager error-correcting codes

Using the magnetization enumerator method, we evaluate the practical and theoretical limitations of symmetric channels with real outputs. Results are presented for several regular Gallager code constructions.

Magnetization enumerator for LDPC codes - a statistical physics approach

We propose a method based on the magnetization enumerator to determine the critical noise level for Gallager type low density parity check error correcting codes (LDPC). Our method provides an appealingly simple interpretation to the relation between different decoding schemes, and provides more optimistic critical noise levels than those reported in the information theory literature.

Carrier lifetime and exciton saturation in a strain-balanced InGaAs/InAsP multiple-quantum-well

The bleaching of the n = 1 heavy-hole and light-hole exciton absorption has been studied at room temperature and zero bias in a strain-balanced InGaAs/InAsP multiple quantum well. Pump-probe spectroscopy was used to measure the decay of the light-hole absorption saturation, giving a hole lifetime of only 280 ps. As only 16 meV separates the light- and heavy-hole bands, the short escape time can be explained by thermalization between these bands followed by thermionic emission over the heavy-hole barrier. The saturation density was estimated to be 1 × 1016 cm-3; this is much lower than expected for tensile-strained wells where both heavy and light holes have large in-plane masses. © 1998 American Institute of Physics.

Regional differences in oxygen saturation in retinal arterioles and venules

BACKGROUND: Retinal vessel oxygenation saturation measurements have been the focus of much attention in recent years as a potential diagnostic parameter in a number of ocular and systemic pathologies. This interest has been heightened by the ability to measure oxygen saturation in vivo using a photographic technique. METHODS: Retinal vessel oxygenation in venules and arterioles of 279 retinal vessels of 12 healthy Caucasian participants (mean age: 30 SD (+/- 6) years) were measured consecutively three times to evaluate short-term variation in oxygen saturation and regional variability of retinal vessel oxygen saturation using dual-wavelength technology (Oxymetry Modul, Imedos, Germany). All subjects underwent standard optometric assessment including non-contact intra-ocular pressure assessment as well as having their systemic blood pressure measured. RESULTS: Vessels were grouped as either near-macula or peripheral, depending on their location. Peripheral arterioles and venules exhibited significantly lower oxygen saturation compared to their near-macula counterparts (arterioles: 94.7% (SD 3.9) vs. 99.7% (SD 3.2); venules: 65.1% (SD 7.2) vs. 90.3% (SD 6.7)). Both arterioles and venules, main branches, and those feeding and draining the retina near the macula and periphery showed low short-term variability of oxygen saturation (arterioles: COV 1.2-1.8%; venules: COV 2.9-4.9%). CONCLUSIONS: Retinal arterioles and venules exhibit low short-term variation of oxygen saturation in healthy subjects. Regional differences in oxygen saturation could be a potential useful marker for risk stratification and diagnostic purposes of area-specific retinal pathology such as age-related macula degeneration and diabetic maculopathy.

Analysis of nocturnal oxygen saturation recordings using kernel entropy to assist in sleep apnea-hypopnea diagnosis

In this study, a new entropy measure known as kernel entropy (KerEnt), which quantifies the irregularity in a series, was applied to nocturnal oxygen saturation (SaO 2) recordings. A total of 96 subjects suspected of suffering from sleep apnea-hypopnea syndrome (SAHS) took part in the study: 32 SAHS-negative and 64 SAHS-positive subjects. Their SaO 2 signals were separately processed by means of KerEnt. Our results show that a higher degree of irregularity is associated to SAHS-positive subjects. Statistical analysis revealed significant differences between the KerEnt values of SAHS-negative and SAHS-positive groups. The diagnostic utility of this parameter was studied by means of receiver operating characteristic (ROC) analysis. A classification accuracy of 81.25% (81.25% sensitivity and 81.25% specificity) was achieved. Repeated apneas during sleep increase irregularity in SaO 2 data. This effect can be measured by KerEnt in order to detect SAHS. This non-linear measure can provide useful information for the development of alternative diagnostic techniques in order to reduce the demand for conventional polysomnography (PSG). © 2011 IEEE.

ProxiMAX randomisation:a new technology for non-degenerate saturation mutagenesis of contiguous codons

Back in 2003, we published ‘MAX’ randomisation, a process of non-degenerate saturation mutagenesis using exactly 20 codons (one for each amino acid) or else any required subset of those 20 codons. ‘MAX’ randomisation saturates codons located in isolated positions within a protein, as might be required in enzyme engineering, or else on one face of an alpha-helix, as in zinc finger engineering. Since that time, we have been asked for an equivalent process that can saturate multiple, contiguous codons in a non-degenerate manner. We have now developed ‘ProxiMAX’ randomisation, which does just that: generating DNA cassettes for saturation mutagenesis without degeneracy or bias. Offering an alternative to trinucleotide phosphoramidite chemistry, ProxiMAX randomisation uses nothing more sophisticated than unmodified oligonucleotides and standard molecular biology reagents. Thus it requires no specialised chemistry, reagents nor equipment and simply relies on a process of saturation cycling comprising ligation, amplification and digestion for each cycle. The process can encode both unbiased representation of selected amino acids or else encode them in pre-defined ratios. Each saturated position can be defined independently of the others. We demonstrate accurate saturation of up to 11 contiguous codons. As such, ProxiMAX randomisation is particularly relevant to antibody engineering.

ProxiMAX Randomisation:a new technology for non-degenerate saturation mutagenesis of contiguous codons

ProxiMAX randomisation achieves saturation mutagenesis of contiguous codons without degeneracy or bias. Offering an alternative to trinucleotide phosphoramidite chemistry, it uses nothing more sophisticated than unmodified oligonucleotides and standard molecular biology reagents and as such, requires no specialised chemistry, reagents nor equipment. When particular residues are known to affect protein activity/specificity, their combinatorial replacement with all 20 amino acids, or a subset thereof, can provide a rapid route to generating proteins with desirable characteristics. Conventionally, saturation mutagenesis replaced key codons with degenerate ones. Although simple to perform, that procedure resulted in unnecessarily large libraries, termination codons and inherent uneven amino acid representation. ProxiMAX randomisation is an enzyme-based technique that can encode unbiased representation of all or selected amino acids or else can provide required codons in pre-defined ratios. Each saturated position can be defined independently of the others. ProxiMAX randomisation is achieved via saturation cycling: an iterative process comprising blunt end ligation, amplification and digestion with a Type IIS restriction enzyme. We demonstrate both unbiased saturation of a short 6-mer peptide and saturation of a hypervariable region of a scfv antibody fragment, where 11 contiguous codons are saturated with selected codons, in pre-defined ratios. As such, ProxiMAX randomisation is particularly relevant to antibody engineering. The development of ProxiMAX randomisation from concept to reality is described.

ProxiMAX randomisation:a new technology for non-degenerate saturation mutagenesis of contiguous codons

Back in 2003, we published ‘MAX’ randomisation, a process of non-degenerate saturation mutagenesis using exactly 20 codons (one for each amino acid) or else any required subset of those 20 codons. ‘MAX’ randomisation saturates codons located in isolated positions within a protein, as might be required in enzyme engineering, or else on one face of an alpha-helix, as in zinc finger engineering. Since that time, we have been asked for an equivalent process that can saturate multiple, contiguous codons in a non-degenerate manner. We have now developed ‘ProxiMAX’ randomisation, which does just that: generating DNA cassettes for saturation mutagenesis without degeneracy or bias. Offering an alternative to trinucleotide phosphoramidite chemistry, ProxiMAX randomisation uses nothing more sophisticated than unmodified oligonucleotides and standard molecular biology reagents. Thus it requires no specialised chemistry, reagents nor equipment and simply relies on a process of saturation cycling comprising ligation, amplification and digestion for each cycle. The process can encode both unbiased representation of selected amino acids or else encode them in pre-defined ratios. Each saturated position can be defined independently of the others. We demonstrate accurate saturation of up to 11 contiguous codons. As such, ProxiMAX randomisation is particularly relevant to antibody engineering.

The impact of flash intensity on retinal vessel oxygen saturation measurements using dual wavelength oximetry

PURPOSE. To establish the optimal flash settings for retinal vessel oxygen saturation parameters using dual-wavelength imaging in a multiethnic group. METHODS. Twelve healthy young subjects (mean age 32 years [SD 7]; three Mediterranean, two South Asian, and seven Caucasian individuals) underwent retinal vessel oxygen saturation measurements using dual-wavelength oximetry, noncontact tonometry, and manual sphygmomanometry. In order to evaluate the impact of flash intensity, we obtained three images (fundus camera angle 30°, ONH centered) per flash setting. Flash settings of the fundus camera were increased in steps of 2 (initial setting of 6 and the final of 22), which reflect logarithmic increasing intensities from 13.5 to 214 Watt seconds (Ws). RESULTS. Flash settings below 27 Ws were too low to obtain saturation measurements, whereas flash settings of more than 214 Ws resulted in overexposed images. Retinal arteriolar and venular oxygen saturation was comparable at flash settings of 27 to 76 Ws (arterioles' range: 85%-92%; venules' range: 45%-53%). Higher flash settings lead to increased saturation measurements in both retinal arterioles (up to 110%) and venules (up to 92%), with a more pronounced increase in venules. CONCLUSIONS. Flash intensity has a significant impact on retinal vessel oxygen saturation measurements using dual-wavelength retinal oximetry. High flash intensities lead to supranormal oxygen saturation measurements with a magnified effect in retinal venules compared with arteries. In addition to even retinal illumination, the correct flash setting is of paramount importance for clinical acquisition of images in retinal oximetry. We recommend flash settings between 27 to 76 Ws. © 2013 The Association for Research in Vision and Ophthalmology, Inc.

Anisotropia magnética em nanofilmes com assimetria cristalográfica

This Thesis comprises a theoretical study about the influence of the magnetocrystalline anisotropy on the static and dynamic magnetic properties of nanofilms: monolayers and trilayers coupled through the bilinear and biquadratic exchange fields, for situations in which the systems are grown in unusual [hkl] asymmetric directions. Using a theory based on a realistic phenomenological model for description of nanometric systems, we consider the total free magnetic energy including the Zeeman interaction, cubic and uniaxial anisotropies, demagnetizing and surface anysotropy energies, as well as the exchange terms. Numerical calculations are conducted by minimizing the total magnetic energy from the determination of equilibrium static configurations. We consider experimental parameters found in the literature to illustrate our results for Fe/Cr/Fe trilayer systems. In particular, a total of six different magnetic scenarios are analyzed for three regimens of exchange fields and the [211] and [321] asymmetric growth directions. After numerically minimize the total energy, we use the equilibrium configurations to calculate magnetization and magnetoresistance curves with the respective magnetic phases and corresponding critical fields. These results are also used to establish the boundary for occurrence of saturated states. Within the context of the spin waves, we solve the equation of motion for these systems in order to find the respective associated dispersion relations. The results show similar magnetization and magnetoresistance curves for both [211] and [321] growth scenarios, including an equivalent magnetic transition behavior. However, the combination of those peculiar symmetries and influence of the exchange energies results in attractive properties, including the generation of magnetic states as a function of the asymmetric degree imposed in the [hkl] growth orientations. There is also an increasing incompatibility between the values of saturation fields of magnetization and magnetoresistance for the cases in which a magnetic field acts along intermediate cubic anisotropic axes, particularly in the situations where the bilinear and biquadratic exchange fields are comparable. The dispersion relations and static results are consistent, the corresponding magnetic states are also present in both acoustic and optical modes. Furthermore, Goldstone excitations are also observed for that particular cases of a magnetic field acting in the intermediate axes, an effect related to transitions of second order and to the spontaneous symmetry breaking imposed by the combination of the biquadratic energy with the cubic and uniaxial anisotropies.

Downcore rock-magnetic properties of ICDP Core 5045-1, Lake Ohrid

The bulk magnetic mineral record from Lake Ohrid, spanning the past 637 kyr, reflects large-scale shifts in hydrological conditions, and, superimposed, a strong signal of environmental conditions on glacial-interglacial and millennial timescales. A shift in the formation of early diagenetic ferrimagnetic iron sulfides to siderites is observed around 320 ka. This change is probably associated with variable availability of sulfide in the pore water. We propose that sulfate concentrations were significantly higher before ~320 ka, due to either a higher sulfate flux or lower dilution of lake sulfate due to a smaller water volume. Diagenetic iron minerals appear more abundant during glacials, which are generally characterized by higher Fe/Ca ratios in the sediments. While in the lower part of the core the ferrimagnetic sulfide signal overprints the primary detrital magnetic signal, the upper part of the core is dominated by variable proportions of high- to low-coercivity iron oxides. Glacial sediments are characterized by high concentration of high-coercivity magnetic minerals (hematite, goethite), which relate to enhanced erosion of soils that had formed during preceding interglacials. Superimposed on the glacial-interglacial behavior are millennial-scale oscillations in the magnetic mineral composition that parallel variations in summer insolation. Like the processes on glacial-interglacial timescales, low summer insolation and a retreat in vegetation resulted in enhanced erosion of soil material. Our study highlights that rock-magnetic studies, in concert with geochemical and sedimentological investigations, provide a multi-level contribution to environmental reconstructions, since the magnetic properties can mirror both environmental conditions on land and intra-lake processes.

Experimental data of CO2, CO3, Omega calcite saturation, pH values, alpha and epsilon fractionation factors, and Dd18O calctite-water

The oxygen isotopic composition (d18O) of calcium carbonate of planktonic calcifying organisms is a key tool for reconstructing both past seawater temperature and salinity. The calibration of paloeceanographic proxies relies in general on empirical relationships derived from field experiments on extant species. Laboratory experiments have more often than not revealed that variables other than the target parameter influence the proxy signal, which makes proxy calibration a challenging task. Understanding these secondary or "vital" effects is crucial for increasing proxy accuracy. We present data from laboratory experiments showing that oxygen isotope fractionation during calcification in the coccolithophore Calcidiscus leptoporus and the calcareous dinoflagellate Thoracosphaera heimii is dependent on carbonate chemistry of seawater in addition to its dependence on temperature. A similar result has previously been reported for planktonic foraminifera, supporting the idea that the [CO3]2- effect on d18O is universal for unicellular calcifying planktonic organisms. The slopes of the d18O/[CO3]2- relationships range between -0.0243 per mil/(µmol/kg) (calcareous dinoflagellate T. heimii) and the previously published -0.0022 per mil/(µmol/kg) (non-symbiotic planktonic foramifera Orbulina universa), while C. leptoporus has a slope of -0.0048 per mil/(µmol/kg). We present a simple conceptual model, based on the contribution of d18O-enriched [HCO3]- to the [CO3]2- pool in the calcifying vesicle, which can explain the [CO3]2- effect on d18O for the different unicellular calcifiers. This approach provides a new insight into biological fractionation in calcifying organisms. The large range in d18O/[CO3]2- slopes should possibly be explored as a means for paleoreconstruction of surface [CO3]2-, particularly through comparison of the response in ecologically similar planktonic organisms.