Detecting epistasis with restricted response patterns in pairs of biallelic loci.

Well-established examples of genetic epistasis between a pair of loci typically show characteristic patterns of phenotypic distributions in joint genotype tables. However, inferring epistasis given such data is difficult due to the lack of power in commonly used approaches, which decompose the epistatic patterns into main plus interaction effects followed by testing the interaction term. Testing additive-only or all terms may have more power, but they are sensitive to nonepistatic patterns. Alternatively, the epistatic patterns of interest can be enumerated and the best matching one is found by searching through the possibilities. Although this approach requires multiple testing correction over possible patterns, each pattern can be fitted with a regression model with just one degree of freedom and thus the overall power can still be high, if the number of possible patterns is limited. Here we compare the power of the linear decomposition and pattern search methods, by applying them to simulated data generated under several patterns of joint genotype effects with simple biological interpretations. Interaction-only tests are the least powerful; while pattern search approach is the most powerful if the range of possibilities is restricted, but still includes the true pattern.

Effect of Knotting on the Shape of Polymers

Momentary configurations of long polymers at thermal equilibrium usually deviate from spherical symmetry and can be better described, on average, by a prolate ellipsoid. The asphericity and nature of asphericity (or prolateness) that describe these momentary ellipsoidal shapes of a polymer are determined by specific expressions involving the three principal moments of inertia calculated for configurations of the polymer. Earlier theoretical studies and numerical simulations have established that as the length of the polymer increases, the average shape for the statistical ensemble of random configurations asymptotically approaches a characteristic universal shape that depends on the solvent quality. It has been established, however, that these universal shapes differ for linear, circular, and branched chains. We investigate here the effect of knotting on the shape of cyclic polymers modeled as random isosegmental polygons. We observe that random polygons forming different knot types reach asymptotic shapes that are distinct from the ensemble average shape. For the same chain length, more complex knots are, on average, more spherical than less complex knots.

The metaphysics of quantum gravity : a causal approach

The dissertation investigates some relevant metaphysical issues arising in the context of spacetime theories. In particular, the inquiry focuses on general relativity and canonical quantum gravity. A formal definition of spacetime theory is proposed and, against this framework, an analysis of the notions of general covariance, symmetry and background independence is performed. It is argued that many conceptual issues in general relativity and canonical quantum gravity derive from putting excessive emphasis on general covariance as an ontological prin-ciple. An original metaphysical position grounded in scientific essential- ism and causal realism (weak essentialism) is developed and defended. It is argued that, in the context of general relativity, weak essentialism supports spacetime substantivalism. It is also shown that weak essentialism escapes arguments from metaphysical underdetermination by positing a particular kind of causation, dubbed geometric. The proposed interpretive framework is then applied to Bohmian mechanics, pointing out that weak essentialism nicely fits into this theory. In the end, a possible Bohmian implementation of loop quantum gravity is considered, and such a Bohmian approach is interpreted in a geometric causal fashion. Under this interpretation, Bohmian loop quantum gravity straightforwardly commits us to an ontology of elementary extensions of space whose evolution is described by a non-local law. The causal mechanism underlying this evolution clarifies many conceptual issues related to the emergence of classical spacetime from the quantum regime. Although there is as yet no fully worked out physical theory of quantum gravity, it is argued that the proposed approach sets up a standard that proposals for a serious ontology in this field should meet.

Conceiving Comparative Policy Analysis : Implementing Air Quality Improvement Programs

The comparative analysis of air quality control policies provides an interesting field for studies of comparative policy analysis including program formulation and implementation processes. In European countries, the problem is comparable, whereas implementation structures, programs and policy impacts vary to a considerable extent. Analysis testing possibilities and constraints of air control policies under varying conditions are likely to contribute to a further development of a theory of policy analysis. This paper presents the analytical framework applied in a continuing empirical study explaining program formulation and implementation processes with respect to the different actors involved. Concrete emitter behavior can be explained by interaction processes at the very local level, by program elements of national legislation, and by structural constraints under which such programs are produced.

Bilateral sequential nonarteritic anterior ischemic optic neuropathy: a comparison of visual outcomes in fellow eyes using quantitative analysis of goldmann visual fields.

OBJECTIVE To better define the concordance of visual loss in patients with nonarteritic anterior ischemic optic neuropathy (NAION). METHODS The medical records of 86 patients with bilateral sequential NAION were reviewed retrospectively, and visual function was assessed using visual acuity, Goldmann visual fields, color vision, and relative afferent papillary defect. A quantitative total visual field score and score per quadrant were analyzed for each eye using the numerical Goldmann visual field scoring method. RESULTS Outcome measures were visual acuity, visual field, color vision, and relative afferent papillary defect. A statistically significant correlation was found between fellow eyes for multiple parameters, including logMAR visual acuity (P = .01), global visual field (P < .001), superior visual field (P < .001), and inferior visual field (P < .001). The mean deviation of total (P < .001) and pattern (P < .001) deviation analyses was significantly less between fellow eyes than between first and second eyes of different patients. CONCLUSIONS Visual function between fellow eyes showed a fair to moderate correlation that was statistically significant. The pattern of vision loss was also more similar in fellow eyes than between eyes of different patients. These results may help allow better prediction of visual outcome for the second eye in patients with NAION.

Extensive variation at MHC DRB in the New Zealand sea lion (Phocarctos hookeri) provides evidence for balancing selection.

Marine mammals are often reported to possess reduced variation of major histocompatibility complex (MHC) genes compared with their terrestrial counterparts. We evaluated diversity at two MHC class II B genes, DQB and DRB, in the New Zealand sea lion (Phocarctos hookeri, NZSL) a species that has suffered high mortality owing to bacterial epizootics, using Sanger sequencing and haplotype reconstruction, together with next-generation sequencing. Despite this species' prolonged history of small population size and highly restricted distribution, we demonstrate extensive diversity at MHC DRB with 26 alleles, whereas MHC DQB is dimorphic. We identify four DRB codons, predicted to be involved in antigen binding, that are evolving under adaptive evolution. Our data suggest diversity at DRB may be maintained by balancing selection, consistent with the role of this locus as an antigen-binding region and the species' recent history of mass mortality during a series of bacterial epizootics. Phylogenetic analyses of DQB and DRB sequences from pinnipeds and other carnivores revealed significant allelic diversity, but little phylogenetic depth or structure among pinniped alleles; thus, we could neither confirm nor refute the possibility of trans-species polymorphism in this group. The phylogenetic pattern observed however, suggests some significant evolutionary constraint on these loci in the recent past, with the pattern consistent with that expected following an epizootic event. These data may help further elucidate some of the genetic factors underlying the unusually high susceptibility to bacterial infection of the threatened NZSL, and help us to better understand the extent and pattern of MHC diversity in pinnipeds.

Phase-sensitive black-blood coronary vessel wall imaging.

Black-blood MR coronary vessel wall imaging may become a powerful tool for the quantitative and noninvasive assessment of atherosclerosis and positive arterial remodeling. Although dual-inversion recovery is currently the gold standard, optimal lumen-to-vessel wall contrast is sometimes difficult to obtain, and the time window available for imaging is limited due to competing requirements between blood signal nulling time and period of minimal myocardial motion. Further, atherosclerosis is a spatially heterogeneous disease, and imaging at multiple anatomic levels of the coronary circulation is mandatory. However, this requirement of enhanced volumetric coverage comes at the expense of scanning time. Phase-sensitive inversion recovery has shown to be very valuable for enhancing tissue-tissue contrast and for making inversion recovery imaging less sensitive to tissue signal nulling time. This work enables multislice black-blood coronary vessel wall imaging in a single breath hold by extending phase-sensitive inversion recovery to phase-sensitive dual-inversion recovery, by combining it with spiral imaging and yet relaxing constraints related to blood signal nulling time and period of minimal myocardial motion.

Genotyping faeces reveals facultative kin association on capercaillie's leks

The role that kin selection might play in the evolution of lekking in birds remains controversial. Recent molecular data suggest that males displaying on leks are related. Here we investigated the genetic structure and pattern of relatedness on leks of a declining population of capercaillie (Tetrao urogallus) using microsatellite genetic markers. Since the species is highly sensitive to disturbance, we adopted a non-invasive method by using faecal samples collected in the field. Based on a dataset of 50 males distributed in 6 sub-populations, we found significant genetic structuring among sub-populations, and a significant pattern of isolation by distance among leks. Estimates of relatedness showed that males displaying on the same lek were related, even when controlling for the effects of genetical differentiation among sub-populations. In addition, the frequency distribution of relatedness values indicated that leks contain a mixture of close kin and unrelated individuals (34 and 66%, respectively). This pattern is consistent with the hypothesis that leks often contain kin associations, which might be due to very restricted dispersal of some of the males or to joint dispersal of kin. The results are discussed with respect to their implication for the conservation of endangered populations.

Entrained macrocryst minerals as a key to the source region of olivine nephelinites: Humberg, Kaiserstuhl, Germany

Olivine nephelinites commonly contain macrocrysts of olivine and clinopyroxene. Some of these macrocrysts might represent fragments of the source region of the host magma transported to the Earth surface. If this hypothesis is correct these fragments can be used to characterize the composition of the source region and to put constraints on the magma generation process. In this study, we investigate the origin of macrocrysts and mineral aggregates from an olivine nephelinite from the Kaiserstuhl, Germany. We focus on clinopyroxenes (Cpx), which can be divided into three groups. Cpx I is relict Cpx from aggregates with deformed olivine that is depleted in Ca and characterized by strong light rare earth element (LREE) fractionation, low Ti/Eu and negative high field strength element (HFSE) anomalies. Its geochemical signature is consistent with formation by carbonatite metasomatism and with equilibration in the Presence of orthopyroxene. Cpx II is Ca-rich Cpx, forming both aggregates with deformed olivine and individual macrocrysts. The LREE, as for Cpx I, are strongly fractionated. Convex REE patterns may be present. The depletion in HFSE is less pronounced. Cpx III is oscillatory zoned Cpx phenociysis showing enrichment in Ca, convex REE patterns and no HFSE anomalies. The transition in the trace element abundances between the Cpx of the three groups is gradual. However, Cpx I and H did not crystallize from the host magma, as demonstrated by the presence of kink-bands and undulose extinction in the associated olivine and by the composition of alkali aluminosilicate glass inclusions in Cpx H. Based on the Cpx relationships, we interpret the studied suite of macrocrysts and mineral aggregates as a mixture of disintegrated fragments of the source region of the host olivine nephelinite. The process of melt generation was multi-stage. A primary carbonatite melt ascending from deeper levels in the mantle, probably from the dolomite-garnet peridotite stability field, reacted with mantle peridotite along the solidus ledge in the system lherzolite-CO2 (< 20-22 kbar) and started to crystallize carbonate minerals. Because of its low solidus temperature, the resulting carbonate-wehrlite assemblage melted incongruently with the formation of additional clinopyroxene. The carbonatite melt evolved during crystallization of carbonate minerals and concomitant incongruent melting of the carbonate-wehrlite, accompanied by the segregation of incipient alkali aluminosilicate melts. As a consequence of fast reaction rates in the presence of a carbonatite melt, this process probably took place under disequilibrium conditions. Further melting of the assemblage wehrlite + alkali aluminosilicate melt led to the generation of the olivine nephelinite magma. It entrained fragments of the wehrlite and brought them to the surface.

Predicting clinical scores from magnetic resonance scans in Alzheimer's disease.

Machine learning and pattern recognition methods have been used to diagnose Alzheimer's disease (AD) and mild cognitive impairment (MCI) from individual MRI scans. Another application of such methods is to predict clinical scores from individual scans. Using relevance vector regression (RVR), we predicted individuals' performances on established tests from their MRI T1 weighted image in two independent data sets. From Mayo Clinic, 73 probable AD patients and 91 cognitively normal (CN) controls completed the Mini-Mental State Examination (MMSE), Dementia Rating Scale (DRS), and Auditory Verbal Learning Test (AVLT) within 3months of their scan. Baseline MRI's from the Alzheimer's disease Neuroimaging Initiative (ADNI) comprised the other data set; 113 AD, 351 MCI, and 122 CN subjects completed the MMSE and Alzheimer's Disease Assessment Scale-Cognitive subtest (ADAS-cog) and 39 AD, 92 MCI, and 32 CN ADNI subjects completed MMSE, ADAS-cog, and AVLT. Predicted and actual clinical scores were highly correlated for the MMSE, DRS, and ADAS-cog tests (P<0.0001). Training with one data set and testing with another demonstrated stability between data sets. DRS, MMSE, and ADAS-Cog correlated better than AVLT with whole brain grey matter changes associated with AD. This result underscores their utility for screening and tracking disease. RVR offers a novel way to measure interactions between structural changes and neuropsychological tests beyond that of univariate methods. In clinical practice, we envision using RVR to aid in diagnosis and predict clinical outcome.

Scar asymmetry after abdominoplasty: the unexpected role of seroma.

Achievement of symmetry remains one of the goals of cosmetic procedures. Interestingly, scar asymmetry after abdominoplasty has been rarely considered a complication. However, this can have a significant impact on patient and surgeon satisfaction. This study identifies silent seromas as a potential cause of scar asymmetry.Among abdominoplasty procedures in a university hospital institution over a 30 months' period (October 1, 2007 to April 1, 2010), we retrospectively identified 6 patients who developed abdominal scar asymmetry only 3 months postoperatively and without any early warning complications (hematoma, seroma, or infection). Clinical examination was completed by abdominal diagnostic ultrasonography. Seroma capsulectomy under local anesthesia was performed in all cases.In all patients clinically presenting late abdominal scar asymmetry, ultrasonography confirmed the presence of an encapsulated chronic seroma. Surgical capsulectomy under local anesthesia resulted in reestablishment of former symmetry and high patient satisfaction. No complications such as wound infection, dehiscence, hematoma, or recurrence of seroma were detected after revision surgery.In our experience, fibrous capsule due to chronic seromas resulted in abdominal scar deviation and asymmetry. Surgical capsulectomy followed by wearing of compressive garments resulted to be an effective treatment with pleasant aesthetic outcome and no seroma recurrence. Silent seromas should be considered as a possible etiologic factor of scar asymmetries appearing during late follow-up after abdominoplasty.

Evidence of an interannual effect of maternal immunization on the immune response of juveniles in a long-lived colonial bird.

Little is known about the maternal transfer of antibodies in natural host-parasite systems despite its possible evolutionary and ecological implications. In domestic animals, the maternal transfer of antibodies can enhance offspring survival via a temporary protection against parasites, but it can also interfere with the juvenile immune response to antigens. We tested the functional role of maternal antibodies in a natural population of a long-lived colonial seabird, the kittiwake (Rissa tridactyla), using a vaccine (Newcastle disease virus vaccine) to mimic parasite exposure combined with a cross-fostering design. We first investigated the role of prior maternal exposure on the interannual transmission of Ab to juveniles. We then tested the effect of these antibodies on the juvenile immune response to the same antigen. The results show that specific maternal antibodies were transferred to chicks 1 year after maternal exposure and that these antibodies were functional, i.e. they affected juvenile immunity. These results suggest that the role of maternal antibodies may depend on the timing and pattern of offspring exposure to parasites, along with the patterns of maternal exposure and the dynamics of her immune response. Overall, our approach underlines that although the transgenerational transfer of antibodies in natural populations is likely to have broad implications, the nature of these effects may vary dramatically among host-parasite systems, depending on the physiological mechanisms involved and the ecological context.

Fat oxidation kinetics : effect of exercise

ABSTRACT Fat oxidation kinetics: effect of exercise. During graded exercise, absolute whole body fat oxidation rates increase from low to moderate intensities, and then markedly decline at high intensities, implying an exercise intensity (Fatmax) at which the fat oxidation rate is maximal (MFO). The main aim of the present work was to examine the effect of exercise on whole body fat oxidation kinetics. For this purpose, a sinusoidal mathematical model (SIN) has been developped in the first study to provide an accurate description of the shape of fat oxidation kinetics during graded exercise, represented as a function of exercise intensity, and to determine Fatmax and MFO. The SIN model incorporates three independent variables (i.e., dilatation, symmetry, and translation) that correspond to main expected modulations of the basic fat oxidation curve because of factors such as mode of exercise or training status. The results of study 1 showed that the SIN model was a valuable tool to determine Fatmax and MFO, and to precisely characterize and quantify the different shape of fat oxidation kinetics through its three variables. The effectiveness of the SIN model to detect differences in fat oxidation kinetics induced by a specific factor was then confirmed in the second study, which quantitatively described and compared fat oxidation kinetics in two different popular modes of exercise: running and cycling. It was found that the mean fat oxidation kinetics during running was characterized by a greater dilatation and a rightward asymmetry compared with the symmetric parabolic curve in cycling. In the two subsequent studies, the effect of a prior endurance exercise of different intensities and durations on whole body fat oxidation kinetics was examined. Study 3 determined the impact of a 1-h continuous exercise bout at an exercise intensity corresponding to Fatmax on fat oxidation kinetics during a subsequent graded test, while study 4 investigated the effect of an exercise leading to a more pronounced muscle glycogen depletion. The results of these two latter studies showed that fat oxidation rates, MFO, and Fatmax were enhanced following endurance exercise, but were increased to a greater extent with a more severe mucle glycogen depletion, inducing therefore modifications in the postexercise fat oxidation kinetics (i.e., greater dilatation and rightward asymmetry). In perspective, further studies have been suggested 1) to assess physiological meaning of the three independent variables of the SIN model; and 2) to compare the effect of two different training programs on fat oxidation kinetics in obese subjects.

Are the light-harvesting I complexes from Rhodospirillum rubrum arranged around the reaction centre in a square geometry?

The basic photosynthetic unit containing the reaction centre and the light-harvesting I complex (RC-LHI) of the purple non-sulphur bacterium Rhodospirillum rubrum was purified and reconstituted into two-dimensional (2D) membrane crystals. Transmission electron microscopy using conventional techniques and cryoelectron microscopy of the purified single particles and of 2D crystals yielded a projection of the RC-LHI complex at a resolution of at least 1.6 nm. In this projection the LHI ring appears to have a square symmetry and packs in a square crystal lattice. The square geometry of the LHI ring was observed also in images of single isolated particles of the RC-LHI complex. However, although the LHI units are packed identically within the crystal lattice, a new rotational analysis developed here showed that the reaction centres take up one of four possible orientations within the ring. This fourfold disorder supports our interpretation of a square ring symmetry and suggests that a hitherto undetected component may be present within the photosynthetic unit.

Thrombosis in paroxysmal nocturnal hemoglobinuria at a glance: a clinical review.

Paroxysmal nocturnal hemoglobinuria (PNH) is a rare, acquired stem cell disorder, with its primary clinical manifestations being hemolytic anemia, marrow failure and thrombophilia. Chronic hemolysis, failures of the fibrinolytic system, increased leukocyte-derived tissue factor levels in plasma, procoagulant microparticles generated through complement-mediated damage of platelets and venous endothelium are related to the acquired hypercoagulable state. Visceral thrombosis (including hepatic veins and mesenteric veins), cerebrovascular events and pulmonary embolism predict a poor outcome. Thrombosis is also associated with significant morbidity during pregnancy. Depending on the sites of thrombosis, a score-based probability to predict outcome can be assigned. Abdominal vein thromboses account for the majority of morbidity and mortality related to thrombosis, and time-dependent trends suggest that mortality rates tend to decline, with the advent of evolution of therapeutic and diagnostic strategies. In contrast, mortality rates from cerebrovascular events display no significant decline. Prompt diagnosis requires both clinical suspicion and sophisticated imaging techniques, along with multidisciplinary therapeutic intervention. In the eculizumab era, a significant reduction of thrombotic events was observed during therapy, and long-term follow up is needed to establish any benefit in rates and pattern of this complication. However, up to now, only bone marrow transplantation permanently abolishes the coagulation defect.