Exact reconstruction of gene regulatory networks using compressive sensing.

BackgroundWe consider the problem of reconstructing a gene regulatory network structure from limited time series gene expression data, without any a priori knowledge of connectivity. We assume that the network is sparse, meaning the connectivity among genes is much less than full connectivity. We develop a method for network reconstruction based on compressive sensing, which takes advantage of the network's sparseness.ResultsFor the case in which all genes are accessible for measurement, and there is no measurement noise, we show that our method can be used to exactly reconstruct the network. For the more general problem, in which hidden genes exist and all measurements are contaminated by noise, we show that our method leads to reliable reconstruction. In both cases, coherence of the model is used to assess the ability to reconstruct the network and to design new experiments. We demonstrate that it is possible to use the coherence distribution to guide biological experiment design effectively. By collecting a more informative dataset, the proposed method helps reduce the cost of experiments. For each problem, a set of numerical examples is presented.ConclusionsThe method provides a guarantee on how well the inferred graph structure represents the underlying system, reveals deficiencies in the data and model, and suggests experimental directions to remedy the deficiencies

Dark matter halo response to the disk growth

We consider the sensitivity of the circular-orbit adiabatic contraction approximation to the baryon condensation rate and the orbital structure of dark matter halos in the $\Lambda$CDM paradigm. Using one-dimensional hydrodynamic simulations including the dark matter halo mass accretion history and gas cooling, we demonstrate that the adiabatic approximation is approximately valid even though halos and disks may assemble simultaneously. We further demonstrate the validity of the simple approximation for $\Lambda$CDM halos with isotropic velocity distributions using three-dimensional N-body simulations. This result is easily understood: an isotropic velocity distribution in a cuspy halo requires more circular orbits than radial orbits. Conversely, the approximation is poor in the extreme case of a radial orbit halo. It overestimates the response a core dark matter halo, where radial orbit fraction is larger. Because no astronomically relevant models are dominated by low-angular momentum orbits in the vicinity of the disk and the growth time scale is never shorter than a dynamical time, we conclude that the adiabatic contraction approximation is useful in modeling the response of dark matter halos to the growth of a disk.Comment: 7 pages, 6 figures, accepted for publication in MNRA

Evaluation of Die Trim Morphology Made by CAD-CAM Technology

Statement of problem The die contour can affect the emergence profile of prosthetic restorations. However, little information is available regarding the congruency between a stereolithographic (SLA) die and its corresponding natural tooth. Purpose The purpose of this vitro study was to evaluate the shapes of SLA die in comparison with the subgingival contour of a prepared tooth to be restored with a ceramic crown. Material and methods Twenty extracted human teeth, 10 incisors, and 10 molars, were disinfected and mounted in a typodont model. The teeth were prepared for a ceramic restoration. Definitive impressions were made using an intraoral scanner from which 20 SLA casts with removable dies were fabricated. The removable dies and corresponding human teeth were digitized using a 3-dimensional desktop scanner and evaluated with computer-aided design software. The subgingival morphology with regard to angle, length, and volume at the buccolingual and mesiodistal surfaces and at zones A, B, C, and D were compared. Data were first analyzed with repeated measures analysis of variance (ANOVA), using locations (buccolingual and mesiodistal), zones (A, B, C, and D), and model type (SLA and Natural) as within-subject factors and tooth type (molar and incisor) as the between-subject factor. Post hoc analyses were performed to investigate the difference between natural teeth and corresponding SLA models, depending upon the interaction effect from the repeated measures ANOVA (α=.05). Results For angle analysis, the incisor group demonstrated a significant difference between the natural tooth and SLA die on the buccolingual surfaces (PPPPPP Conclusions For the comparison of angles, SLA dies did not replicate the subgingival contour of natural teeth on the buccolingual surfaces of the incisal groups. For the comparison of length and volume, SLA dies were more concave and did not replicate the subgingival contour of natural teeth in the incisal and molar groups

Suboptimal Larval Habitats Modulate Oviposition of the Malaria Vector Mosquito Anopheles coluzzii.

Selection of oviposition sites by gravid females is a critical behavioral step in the reproductive cycle of Anopheles coluzzii, which is one of the principal Afrotropical malaria vector mosquitoes. Several studies suggest this decision is mediated by semiochemicals associated with potential oviposition sites. To better understand the chemosensory basis of this behavior and identify compounds that can modulate oviposition, we examined the generally held hypothesis that suboptimal larval habitats give rise to semiochemicals that negatively influence the oviposition preference of gravid females. Dual-choice bioassays indicated that oviposition sites conditioned in this manner do indeed foster significant and concentration dependent aversive effects on the oviposition site selection of gravid females. Headspace analyses derived from aversive habitats consistently noted the presence of dimethyl disulfide (DMDS), dimethyl trisulfide (DMTS) and 6-methyl-5-hepten-2-one (sulcatone) each of which unitarily affected An. coluzzii oviposition preference. Electrophysiological assays across the antennae, maxillary palp, and labellum of gravid An. coluzzii revealed differential responses to these semiochemicals. Taken together, these findings validate the hypothesis in question and suggest that suboptimal environments for An. coluzzii larval development results in the release of DMDS, DMTS and sulcatone that impact the response valence of gravid females

Collapse transition of a square-lattice polymer with next nearest-neighbor interaction

We study the collapse transition of a polymer on a square lattice with both nearest-neighbor and next nearest-neighbor interactions, by calculating the exact partition function zeros up to chain length 36. The transition behavior is much more pronounced than that of the model with nearest-neighbor interactions only. The crossover exponent and the transition temperature are estimated from the scaling behavior of the first zeros with increasing chain length. The results suggest that the model is of the same universality class as the usual theta point described by the model with only nearest-neighbor interaction.Comment: 14 pages, 5 figure

Holographic Nuclear Matter in AdS/QCD

We study the physics with finite nuclear density in the framework of AdS/QCD with holographic baryon field included. Based on a mean field type approach, we introduce the nucleon density as a bi-fermion condensate of the lowest mode of the baryon field and calculate the density dependence of the chiral condensate and the nucleon mass. We observe that the chiral condensate as well as the mass of nucleon decrease with increasing nuclear density. We also consider the mass splitting of charged vector mesons in iso-spin asymmetric nuclear matter.Comment: 16 pages, 3 figures, two references are added, typo corrected, section 3.3 remove

Multi-kilowatt single-mode ytterbium-doped large-core fiber laser

We have demonstrated a highly efficient cladding-pumped ytterbium-doped fiber laser, generating >2.1 kW of continuous-wave output power at 1.1 µm with 74% slope efficiency with respect to launched pump power. The beam quality factor (M2) was better than 1.2. The maximum output power was only limited by available pump power, showing no evidence of roll-over even at the highest output power. We present data on how the beam quality depends on the fiber parameter, based on our current and past fiber laser developments. We also discuss the ultimate power-capability of our fiber in terms of thermal management, Raman nonlinear scattering, and material damage, and estimate it to 10 k

Cardiac interventions in patients with achondroplasia: a systematic review.

Patients with achondroplasia and other causes of dwarfism suffer from increased rates of cardiovascular disease relative to the remainder of the population. Few studies have examined these patients when undergoing cardiac surgery or percutaneous intervention. This systematic review examines the literature to determine outcomes following cardiac intervention in this unique population. An electronic search was performed in the English literature to identify all reports of achondroplasia, dwarfism, and cardiac intervention. Of the 5,274 articles identified, 14 articles with 14 cases met inclusion criteria. Patient-level data was extracted and analyzed. Median patient age was 55.5 [interquartile ranges (IQR), 43.8, 59.8] years, median height 102.0 [98.8, 112.5] cm, median BMI 32.1 [27.0, 45.9], and 57.1% (8/14) were male. Of these 14 patients, nine had the following documented skeletal abnormalities: 66.7% (6/9) had scoliosis, 66.7% (6/9) had kyphosis, 11.1% (1/9) had lordosis, 11.1% (1/9) pectus carinatum and 11.1% (1/9) spinal stenosis. Coronary artery disease was present in 53.8% (7/13), and 30.8% (4/13) patients previously suffered a myocardial infarction. Of the eight patients who underwent cardiac surgery, 37.5% (3/8) underwent multivessel coronary artery bypass grafting, 37.5% (3/8) underwent aortic valve replacement, 25.0% (2/8) underwent type A aortic dissection repair, and the remaining 12.5% (1/8) underwent pulmonary thromboendarterectomy. Six patients underwent percutaneous intervention. Median cardiopulmonary bypass time was 136.5 [110.0, 178.8] minutes. Median arterial cannula size was 20.0 [20.0, 24.0] Fr. Bicaval cannulation was performed in all cases describing cannulation strategy (5/5). Median superior vena cava cannula size was 28.0 [28.0, 28.0] Fr, and inferior vena cava cannula size was 28.0 [28.0, 28.0] Fr. No mortality was reported with a median follow up time of 6.0 [6.0, 10.5] months. In conclusion, Common cardiac procedures can be performed with reasonable safety in this patient population. Operative adjustments may need to be made with respect to equipment to accommodate patient-specific needs