A personalized network framework reveals predictive axis of anti-TNF response across diseases

Personalized treatment of complex diseases has been mostly predicated on biomarker identification of one drug-disease combination at a time. Here, we use a computational approach termed Disruption Networks to generate a data type, contextualized by cell-centered individual-level networks, that captures biology otherwise overlooked when performing standard statistics. This data type extends beyond the "feature level space", to the "relations space", by quantifying individual-level breaking or rewiring of cross-feature relations. Applying Disruption Networks to dissect high-dimensional blood data, we discover and validate that the RAC1-PAK1 axis is predictive of anti-TNF response in inflammatory bowel disease. Intermediate monocytes, which correlate with the inflammatory state, play a key role in the RAC1-PAK1 responses, supporting their modulation as a therapeutic target. This axis also predicts response in rheumatoid arthritis, validated in three public cohorts. Our findings support blood-based drug response diagnostics across immune-mediated diseases, implicating common mechanisms of non-response.

B-cell-derived cfDNA after primary BNT162b2 mRNA vaccination anticipates memory B-cells and SARS-CoV-2 neutralizing antibodies

Background

Methods

Findings

Conclusions

Funding

To understand the turnover of immune cells following SARS-CoV-2 vaccination, Fox-Fisher et al. analyzed fragments of cell-free DNA (cfDNA) that are released from dying immune cells to blood. The levels of B cell cfDNA after the primary dose correlated with neutralizing antibodies and memory B cells after the booster, revealing that early B cell turnover—potentially reflecting affinity maturation—affects later development of effective antibodies. They also observed co-elevation of lymphocyte and monocyte cfDNA after the booster, underscoring the involvement of innate immune cell turnover in the development of humoral and cellular adaptive immunity. cfDNA biomarkers open a new window into human immune cell dynamics in response to perturbations.

Third Trimester Structural and Diffusion Brain Imaging after Single Intrauterine Fetal Death in Monochorionic Twins: MRI-Based Cohort Study

BACKGROUND AND PURPOSE

Single intrauterine fetal death increases the risk of antenatal brain lesions in the surviving twin. We evaluated the prevalence of structural brain lesions, biometry, and diffusivity on routine third trimester MR imaging performed following single intrauterine fetal death.

MATERIALS AND METHODS

In a retrospective MR imaging-based cohort study, we compared 29 monochorionic twins complicated with single intrauterine fetal death (14 following laser ablation treatment for twin-to-twin transfusion syndrome, 8 following selective fetal reduction, and 7 spontaneous) with 2 control cohorts (49 singleton fetuses and 28 uncomplicated twin fetuses). All fetuses in the single intrauterine fetal death group underwent fetal brain MR imaging as a routine third trimester evaluation. Structural brain lesions were analyzed. Cerebral biometry and diffusivity were measured and compared.

RESULTS

Brain lesions consistent with the evolution of prior ischemic injury were found in 1 of 29 fetuses, not detected by ultrasound. No acute brain infarction, hemorrhage, or cortical abnormalities were found. Supratentorial biometric measurements in the single intrauterine fetal death group were significantly smaller than those in the singleton group, but not significantly different from those in the uncomplicated twin group. There were no significant differences in ADC values of the cerebral hemispheres, basal ganglia, and pons between the single intrauterine fetal death group and either control group.

CONCLUSIONS

Although smaller brain biometry was found, normal diffusivity in surviving twins suggests normal parenchymal microstructure. The rate of cerebral structural injury was relatively low in our cohort, arguing against the routine use of fetal brain MR imaging in twin pregnancies complicated with single intrauterine fetal death. Larger prospective studies are necessary to guide appropriate surveillance protocol and parental counseling in twin pregnancies complicated by single intrauterine fetal death.

Improving techniques for diagnostics of laser pulses by compact representations

We propose and demonstrate, numerically and experimentally, use of sparsity as prior information for extending the capabilities and performance of techniques and devices for laser pulse diagnostics. We apply the concept of sparsity in three different applications. First, we improve a photodiode-oscilloscope system's resolution for measuring the intensity structure of laser pulses. Second, we demonstrate the intensity profile reconstruction of ultrashort laser pulses from intensity autocorrelation measurements. Finally, we use a sparse representation of pulses (amplitudes and phases) to retrieve measured pulses from incomplete spectrograms of cross-correlation frequency-resolved optical gating traces.

Sequence variation in PPP1R13L results in a novel form of cardio-cutaneous syndrome

Dilated cardiomyopathy (DCM) is a life-threatening disorder whose genetic basis is heterogeneous and mostly unknown. Five Arab Christian infants, aged 4-30 months from four families, were diagnosed with DCM associated with mild skin, teeth, and hair abnormalities. All passed away before age 3. A homozygous sequence variation creating a premature stop codon at PPP1R13L encoding the iASPP protein was identified in three infants and in the mother of the other two. Patients' fibroblasts and PPP1R13L-knocked down human fibroblasts presented higher expression levels of pro-inflammatory cytokine genes in response to lipopolysaccharide, as well as Ppp1r13l-knocked down murine cardiomyocytes and hearts of Ppp1r13l-deficient mice. The hypersensitivity to lipopolysaccharide was NF-κB-dependent, and its inducible binding activity to promoters of pro-inflammatory cytokine genes was elevated in patients' fibroblasts. RNA sequencing of Ppp1r13l-knocked down murine cardiomyocytes and of hearts derived from different stages of DCM development in Ppp1r13l-deficient mice revealed the crucial role of iASPP in dampening cardiac inflammatory response. Our results determined PPP1R13L as the gene underlying a novel autosomal-recessive cardio-cutaneous syndrome in humans and strongly suggest that the fatal DCM during infancy is a consequence of failure to regulate transcriptional pathways necessary for tuning cardiac threshold response to common inflammatory stressors.

Topologically protected bound states in photonic parity-time-symmetric crystals

Parity-time (PT)-symmetric crystals are a class of non-Hermitian systems that allow, for example, the existence of modes with real propagation constants, for self-orthogonality of propagating modes, and for uni-directional invisibility at defects. Photonic PT-symmetric systems that also support topological states could be useful for shaping and routing light waves. However, it is currently debated whether topological interface states can exist at all in PT-symmetric systems. Here, we show theoretically and demonstrate experimentally the existence of such states: states that are localized at the interface between two topologically distinct PT-symmetric photonic lattices. We find analytical closed form solutions of topological PT-symmetric interface states, and observe them through fluorescence microscopy in a passive PT-symmetric dimerized photonic lattice. Our results are relevant towards approaches to localize light on the interface between non-Hermitian crystals.

Accelerating diffraction-free beams in photonic lattices

We study nondiffracting accelerating paraxial optical beams in periodic potentials, in both the linear and the nonlinear domains. In particular, we show that only a unique class of z-dependent lattices can support a true accelerating diffractionless beam. Accelerating lattice solitons, autofocusing beams and accelerating bullets in optical lattices are systematically examined.

Sparsity-based single-shot subwavelength coherent diffractive imaging

Coherent Diffractive Imaging (CDI) is an algorithmic imaging technique where intricate features are reconstructed from measurements of the freely diffracting intensity pattern. An important goal of such lensless imaging methods is to study the structure of molecules that cannot be crystallized. Ideally, one would want to perform CDI at the highest achievable spatial resolution and in a single-shot measurement such that it could be applied to imaging of ultrafast events. However, the resolution of current CDI techniques is limited by the diffraction limit, hence they cannot resolve features smaller than one half the wavelength of the illuminating light. Here, we present sparsity-based single-shot subwavelength resolution CDI: algorithmic reconstruction of subwavelength features from far-field intensity patterns, at a resolution several times better than the diffraction limit. This work paves the way for subwavelength CDI at ultrafast rates, and it can considerably improve the CDI resolution with X-ray free-electron lasers and high harmonics.

Optical transitions and Rabi oscillations in waveguide arrays

It is theoretically demonstrated that Rabi interband oscillations are possible in waveguide arrays. Such transitions can take place in optical lattices when the unit-cell is periodically modulated along the propagation direction. Under phase-matching conditions, direct power transfer between two Floquet-Bloch modes can occur. In the nonlinear domain, periodic oscillations between two different lattice solitons are also possible.

Optical beam instabilities in nonlinear nanosuspensions

We investigate the modulation instability of plane waves and the transverse instabilities of soliton stripe beams propagating in nonlinear nanosuspensions. We show that in these systems the process of modulational instability depends on the input beam conditions. On the other hand, the transverse instability of soliton stripes can exhibit new features as a result of 1D collapse caused by the exponential nonlinearity.

Soliton dynamics and self-induced transparency in nonlinear nanosuspensions

We study spatial soliton dynamics in nano-particle suspensions. Starting from the Nernst-Planck and Smoluchowski equations, we demonstrate that in these systems the underlying nonlinearities as well as the nonlinear Rayleigh losses depend exponentially on optical intensity. Two different nonlinear regimes are identified depending on the refractive index contrast of the nanoparticles involved and the interesting prospect of self-induced transparency is demonstrated. Soliton stability is systematically analyzed for both 1D and 2D configurations and their propagation dynamics in the presence of Rayleigh losses is examined. The possibility of synthesizing artificial nonlinearities using mixtures of nanosuspensions is also considered.

Incoherent white-light solitons in nonlinear periodic lattices

We predict the existence of lattice solitons made of incoherent white light: lattice solitons made of light originating from an ordinary incandescent light bulb. We find that the intensity structure and spatial power spectra associated with different temporal frequency constituents of incoherent white-light lattice solitons (IWLLSs) arrange themselves in a characteristic fashion, with the intensity structure more localized at higher frequencies, and the spatial power spectrum more localized at lower frequencies; the spatial correlation distance is larger at lower frequency constituents of IWLLSs. This characteristic shape of incoherent white-light lattice solitons reflects the fact that diffraction is stronger for lower temporal frequency constituents, while higher frequencies experience stronger effective nonlinearity and deeper lattice structure.

Incoherent matter-wave solitons and pairing instability in an attractively interacting Bose-Einstein condensate

The dynamics of matter-wave solitons in Bose-Einstein condensates (BEC) is considerably affected by the presence of a thermal cloud and the dynamical depletion of the condensate. Our numerical results, based on the time-dependent Hartree-Fock-Bogoliubov theory, demonstrate the collapse of the attractively interacting BEC via collisional emission of atom pairs into the thermal cloud, which splits the (quasi-one-dimensional) BEC soliton into two partially coherent solitonic structures of opposite momenta. These incoherent matter waves are analogous to optical random-phase solitons.

Random-phase solitons in nonlinear periodic lattices

We predict the existence of random phase solitons in nonlinear periodic lattices. These solitons exist when the nonlinear response time is much longer than the characteristic time of random phase fluctuations. The intensity profiles, power spectra, and statistical (coherence) properties of these stationary waves conform to the periodicity of the lattice. The general phenomenon of such solitons is analyzed in the context of nonlinear photonic lattices.

Incoherent white light solitons in logarithmically saturable noninstantaneous nonlinear media

We analytically demonstrate the existence of white light solitons in logarithmically saturable noninstantaneous nonlinear media. This incoherent soliton has elliptic Gaussian intensity profile, and elliptic Gaussian spatial correlation statistics. The existence curve of the soliton connects the strength of the nonlinearity, the spatial correlation distance as a function of frequency, and the characteristic width of the soliton. For this soliton to exist, the spatial correlation distance must be smaller for larger temporal frequency constituents of the beam.

Mathematical frontiers in optical solitons

Solitons are localized concentrations of field energy, resulting from a balance of dispersive and nonlinear effects. They are ubiquitous in the natural sciences. In recent years optical solitons have arisen in new and exciting contexts that differ in many ways from the original context of coherent propagation in a uniform medium. We review recent developments in incoherent spatial solitons and in gap solitons in periodic structures.

Theory of self-focusing in photorefractive InP

We present a theory of self-focusing and solitons in photorefractive InP, including the previously unexplained intensity resonance and the resonant enhancement of the space-charge field.

Collisions between (2+1)D rotating propeller solitons

We study theoretically the collisions between (2+1)D rotating-dipole-type bimodal solitons and find that such interactions exhibit many interesting exchanges of angular momentum.

Rotating propeller solitons

We demonstrate experimentally and theoretically (both analytically and numerically) a new type of spatial soliton: a rotating "propeller" soliton. This is a composite soliton made of a rotating dipole component jointly trapped with a bell-shaped component. We observe as much as 239 degrees of rotation over 13 mm of propagation (6.5 diffraction lengths).