MR image reconstruction using deep density priors

Algorithms for Magnetic Resonance (MR) image reconstruction from undersampled measurements exploit prior information to compensate for missing k-space data. Deep learning (DL) provides a powerful framework for extracting such information from existing image datasets, through learning, and then using it for reconstruction. Leveraging this, recent methods employed DL to learn mappings from undersampled to fully sampled images using paired datasets, including undersampled and corresponding fully sampled images, integrating prior knowledge implicitly. In this article, we propose an alternative approach that learns the probability distribution of fully sampled MR images using unsupervised DL, specifically Variational Autoencoders (VAE), and use this as an explicit prior term in reconstruction, completely decoupling the encoding operation from the prior. The resulting reconstruction algorithm enjoys a powerful image prior to compensate for missing k-space data without requiring paired datasets for training nor being prone to associated sensitivities, such as deviations in undersampling patterns used in training and test time or coil settings. We evaluated the proposed method with T1 weighted images from a publicly available dataset, multi-coil complex images acquired from healthy volunteers (N=8) and images with white matter lesions. The proposed algorithm, using the VAE prior, produced visually high quality reconstructions and achieved low RMSE values, outperforming most of the alternative methods on the same dataset. On multi-coil complex data, the algorithm yielded accurate magnitude and phase reconstruction results. In the experiments on images with white matter lesions, the method faithfully reconstructed the lesions. Keywords: Reconstruction, MRI, prior probability, machine learning, deep learning, unsupervised learning, density estimationComment: Published in IEEE TMI. Main text and supplementary material, 19 pages tota

Synthesis and viscosity behavior of poly(γ-p-biphenylmethyl-L-glutamate) in benzene/dichloroacetic acid mixtures, a comparison with poly(γ-benzyl-L-glutamate)

The synthesis of poly(γ-p-biphenylmethyl-L-glutamate), PBPLG, (poly{L-imino-1-[2-(4-biphenylylmethoxycarbonyl)ethyl]-2-oxoethylene}), (1d) is described. The viscosity behavior of this polymer in benzene/dichloroacetic acid mixtures (c=0,2.10 -3 - 1,4.10 -3 g/cm3) at 25°CC is investigated. The results are compared with measurements on poly(γ-benzyl-L-glutamate), PBLG, (poly[L-imino-1-(2-benzyloxycarbonylethyl)-2-oxoethylene]), (1c) under the same conditions. A transition from a rigid hydrogen bonded helix to a random solvated coil occurs in two stages for both: PBPLG (first stage 0-55%, second stage 55-100% dichloroacetic acid) and PBLG (first stage 0-70%, second stage 70-100% dichloroacetic acid). \ud Therefore, the introduction of a p-phenyl substituent in PBLG leads to a less stable helix in benzene/dichloroacetic acid mixtures. \ud The stability and viscosity behavior of PBLG in benzene/dichloroacetic acid mixtures (c=0,2.10 - 3 - 1,4.10 - 3g/cm3) is quite similar to the behavior of PBLG in m-cresol/dichloroacetic acid mixtures (c=1,0.10 - 3 - 4,0.10 - 3 g/cm3)

Photo-excited Carrier Dynamics and Impact Excitation Cascade in Graphene

Photo-excitation in solids can trigger a cascade in which multiple particle-hole excitations are generated. We analyze the carrier multiplication cascade of impact excitation processes in graphene and show that the number of pair excitations has a strong dependence on doping, which makes carrier multiplication gate-tunable. We also predict that the number of excited pairs as well as the characteristic time of the cascade scale linearly with photo-excitation energy. These dependences, as well as sharply peaked angular distribution of pair excitations, provide clear experimental signatures of carrier multiplication

Phonon-like hydrogen-bond modes in protic ionic liquids

Gigahertz- to terahertz-frequency infrared and Raman spectra contain a wealth of information concerning the structure, intermolecular forces, and dynamics of ionic liquids. However, these spectra generally have a large number of contributions ranging from slow diffusional modes to underdamped librations and intramolecular vibrational modes. This makes it difficult to isolate effects such as the role of Coulombic and hydrogen-bonding interactions. We have applied far-infrared and ultrafast optical Kerr effect spectroscopies on carefully selected ions with a greater or lesser degree of symmetry in order to isolate spectral signals of interest. This has allowed us to demonstrate the presence of longitudinal and transverse optical phonon modes and a great similarity of alkylammonium-based protic ionic liquids to liquid water. The data show that such phonon modes will be present in all ionic liquids, requiring a reinterpretation of their spectra

Shocked Molecular Hydrogen in the 3C 326 Radio Galaxy System

The Spitzer spectrum of the giant FR II radio galaxy 3C 326 is dominated by very strong molecular hydrogen emission lines on a faint IR continuum. The H2 emission originates in the northern component of a double-galaxy system associated with 3C 326. The integrated luminosity in H2 pure-rotational lines is 8.0E41 erg/s, which corresponds to 17% of the 8-70 micron luminosity of the galaxy. A wide range of temperatures (125-1000 K) is measured from the H2 0-0 S(0)-S(7) transitions, leading to a warm H2 mass of 1.1E9 Msun. Low-excitation ionic forbidden emission lines are consistent with an optical LINER classification for the active nucleus, which is not luminous enough to power the observed H2 emission. The H2 could be shock-heated by the radio jets, but there is no direct indication of this. More likely, the H2 is shock-heated in a tidal accretion flow induced by interaction with the southern companion galaxy. The latter scenario is supported by an irregular morphology, tidal bridge, and possible tidal tail imaged with IRAC at 3-9 micron. Unlike ULIRGs, which in some cases exhibit H2 line luminosities of comparable strength, 3C 326 shows little star-formation activity (~0.1 Msun/yr). This may represent an important stage in galaxy evolution. Starburst activity and efficient accretion onto the central supermassive black hole may be delayed until the shock-heated H2 can kinematically settle and coolComment: 27 pages, 7 figures, accepted for publication in the Astrophysical Journa

Lameness detection challenges in automated milking systems addressed with partial least squares discriminant analysis

AbstractLameness causes decreased animal welfare and leads to higher production costs. This study explored data from an automatic milking system (AMS) to model on-farm gait scoring from a commercial farm. A total of 88 cows were gait scored once per week, for 2 5-wk periods. Eighty variables retrieved from AMS were summarized week-wise and used to predict 2 defined classes: nonlame and clinically lame cows. Variables were represented with 2 transformations of the week summarized variables, using 2-wk data blocks before gait scoring, totaling 320 variables (2×2×80). The reference gait scoring error was estimated in the first week of the study and was, on average, 15%. Two partial least squares discriminant analysis models were fitted to parity 1 and parity 2 groups, respectively, to assign the lameness class according to the predicted probability of being lame (score 3 or 4/4) or not lame (score 1/4). Both models achieved sensitivity and specificity values around 80%, both in calibration and cross-validation. At the optimum values in the receiver operating characteristic curve, the false-positive rate was 28% in the parity 1 model, whereas in the parity 2 model it was about half (16%), which makes it more suitable for practical application; the model error rates were, 23 and 19%, respectively. Based on data registered automatically from one AMS farm, we were able to discriminate nonlame and lame cows, where partial least squares discriminant analysis achieved similar performance to the reference method

Homogeneity density scores of quarter milk in automatic milking systems

Milk quality and clinical mastitis in dairy cows are monitored by detecting visually abnormal milk. A standardized method to evaluate clots in milk and studies of the incidence and dynamics of clots in milk at the quarter level are lacking. We validated a method to score clot density in quarter milk samples and describe the prevalence and dynamics of the density scores between consecutive samplings and periods in 4 farms with automatic milking systems. Using in-line filters, we collected quarter milk samples at each milking during 3 periods of 30 h each in each farm. Clot density was scored based on coverage of the filter area as 0 (negative), 1 (trace), 2 (mild), 3 (moderate), 4 (heavy), and 5 (very heavy). The score for a specific quarter and milking is referred to as the quarter milking score (QMS). Three assessors independently scored 902 images of filter samples with a Fleiss kappa value of 0.72. In total, 21,202 quarter milk samples from 5,398 milkings of 621 cows were collected. Of the quarter filter samples, 2.4% had visible clots, distributed as mild (1.4%), moderate (0.6%), heavy (0.3%), and very heavy (= 4, corresponding to 9.4% of all periods, harbored 86% and 94% of all QMS of 2 to 5 and 3 to 5, respectively. Of these cases, cows sampled in all 3 periods and clots in only 1 period had a quarter period sum score >= 1 in 1.8 different quarters in average. Corresponding numbers for the cows with clots or traces in 2 or 3 periods were 2.2 and 2.5 different quarters, respectively. A QMS of 2 to 5 in the preceding milking increased the chance of a QMS >1 in the following milking, with an average chance of 38%. The probability of a QMS > 1 increased with increasing previous QMS, a higher sum of QMS during the milking period, longer milking interval, and higher lactation number, but decreased with increasing days in milk. Our study showed that the method of clot-density scoring is feasible to perform and reproducible for investigating the occurrence and dynamics of clots in milk. Elevated clot-density scores clustered within certain cows and cow periods and appeared in new quarters of the cows over time. The low recurrence of QMS of 1 and 2 within quarters indicated that QMS 3 could be a reasonable threshold for detecting quarters with abnormal milk that require further attention

Multi-wavelength Observations of Dusty Star Formation at Low and High Redshift

This paper examines what can be learned about high-redshift star formation from the small fraction of high-redshift galaxies' luminosities that is emitted at accessible wavelengths. We review and quantify empirical correlations between bolometric luminosities produced by star formation and the UV, mid-IR, sub-mm, and radio luminosities of galaxies in the local universe. These correlations suggest that observations of high-redshift galaxies at any of these wavelengths should constrain their star-formation rates to within 0.2--0.3 dex. We assemble the limited evidence that high-redshift galaxies obey these locally calibrated correlations. The characteristic luminosities and dust obscurations of galaxies at z ~ 0, z ~ 1, and z ~ 3 are reviewed. After discussing the relationship between the high-redshift populations selected in surveys at different wavelengths, we calculate the contribution to the 850um background from each. The available data show that a correlation between star-formation rate and dust obscuration L_dust/L_UV exists at low and high redshift. This correlation plays a central role in the major conclusion of this paper: most star formation at high redshift occurred in galaxies with 1 < L_dust/L_UV < 100 similar to those that host the majority of star formation in the local universe and to those that are detected in UV-selected surveys. (abridged)Comment: Scheduled for publication in ApJ v544 Dec 2000. Significant changes to section 4. Characteristic UV and dust luminosities of star-forming galaxies at redshifts z~0, z~1, and z~3 presented. Existence of extremely obscured galaxies more clearly acknowledged. Original conclusions reinforced by the observed correlation between bolometric luminosity and dust obscuration at 0<z<