Scalable spatiotemporal prediction with Bayesian neural fields.

Spatiotemporal datasets, which consist of spatially-referenced time series, are ubiquitous in diverse applications, such as air pollution monitoring, disease tracking, and cloud-demand forecasting. As the scale of modern datasets increases, there is a growing need for statistical methods that are flexible enough to capture complex spatiotemporal dynamics and scalable enough to handle many observations. This article introduces the Bayesian Neural Field (BAYESNF), a domain-general statistical model that infers rich spatiotemporal probability distributions for data-analysis tasks including forecasting, interpolation, and variography.

An open-source alignment method for multichannel infinite-conjugate microscopes using a ray transfer matrix analysis model.

Multichannel, infinite-conjugate optical systems easily allow implementation of multiple image paths and imaging modes into a single microscope. Traditional optical alignment methods which rely on additional hardware are not always simple to implement, particularly in compact open-source microscope designs. We present here an alignment algorithm and process to position the lenses and cameras in a microscope using only image magnification measurements.

Adapting the 3D-printed Openflexure microscope enables computational super-resolution imaging.

We report on a 3D printed microscope, based on a design by the Openflexure project, that uses low cost components to perform fluorescence imaging. The system is sufficiently sensitive and mechanically stable to allow the use of the Super Resolution Radial Fluctuations algorithm to obtain images with resolution better than the diffraction limit. Due to the low-cost components, the entire system can be built for approximately $1200.

Low-cost, open-access quantitative phase imaging of algal cells using the transport of intensity equation.

Phase microscopy allows stain-free imaging of transparent biological samples. One technique, using the transport of intensity equation (TIE), can be performed without dedicated hardware by simply processing pairs of images taken at known spacings within the sample. The resulting TIE images are quantitative phase maps of unstained biological samples.

Nanodiamonds enable adaptive-optics enhanced, super-resolution, two-photon excitation microscopy.

Particles of diamond in the 5-100 nm size range, known as nanodiamond (ND), have shown promise as robust fluorophores for optical imaging. We demonstrate here that, due to their photostability, they are not only suitable for two-photon imaging, but also allow significant resolution enhancement when combined with computational super-resolution techniques. We observe a resolution of 42.

Vector light shift averaging in paraffin-coated alkali vapor cells.

Light shifts are an important source of noise and systematics in optically pumped magnetometers. We demonstrate that the long spin-coherence time in paraffin-coated cells leads to spatial averaging of the vector light shift over the entire cell volume. This renders the averaged vector light shift independent, under certain approximations, of the light-intensity distribution within the sensor cell.

Three-dimensional STED microscopy of aberrating tissue using dual adaptive optics.

When imaging through tissue, the optical inhomogeneities of the sample generate aberrations that can prevent effective Stimulated Emission Depletion (STED) imaging. This is particularly problematic for 3D-enhanced STED. We present here an adaptive optics implementation that incorporates two adaptive optic elements to enable correction in all beam paths, allowing performance improvement in thick tissue samples.

Aberrations and adaptive optics in super-resolution microscopy.

As one of the most powerful tools in the biological investigation of cellular structures and dynamic processes, fluorescence microscopy has undergone extraordinary developments in the past decades. The advent of super-resolution techniques has enabled fluorescence microscopy - or rather nanoscopy - to achieve nanoscale resolution in living specimens and unravelled the interior of cells with unprecedented detail. The methods employed in this expanding field of microscopy, however, are especially prone to the detrimental effects of optical aberrations.

Is phase-mask alignment aberrating your STED microscope?

The performance of a stimulated emission depletion (STED) microscope depends critically upon the pupil plane phase mask that is used to shape the depletion focus. Misalignments of the mask create unwanted distortions of the depletion focus to the detriment of image quality. It is shown how the phase errors introduced by a misplaced mask are similar to coma aberrations.

Solid immersion facilitates fluorescence microscopy with nanometer resolution and sub-ångström emitter localization.

Exploring the maximum spatial resolution achievable in far-field optical imaging, we show that applying solid immersion lenses (SIL) in stimulated emission depletion (STED) microscopy addresses single spins with a resolution down to 2.4 ± 0.3 nm and with a localization precision of 0.

Magnetometry with mesospheric sodium.

Measurement of magnetic fields on the few 100-km length scale is significant for many geophysical applications including mapping of crustal magnetism and ocean circulation measurements, yet available techniques for such measurements are very expensive or of limited accuracy. We propose a method for remote detection of magnetic fields using the naturally occurring atomic sodium-rich layer in the mesosphere and existing high-power lasers developed for laser guide star applications. The proposed method offers a dramatic reduction in cost and opens the way to large-scale, parallel magnetic mapping and monitoring for atmospheric science, navigation, and geophysics.

Femtoliter tunable optical cavity arrays.

Large arrays of uniform, precisely tunable, open-access optical microcavities with mode volumes as small as 2.2 μm(3) are reported. The cavities show clear Hermite-Gauss mode structure and display finesses up to 460, in addition to quality (Q) factors in excess of 10,000.

A high stability beam-scanning confocal optical microscope for low temperature operation.

We report on the design and performance of a high stability scanning confocal microscope for optical microscopy at low temperatures. By scanning the beam in a cold objective lens system, we achieve wide fields of view without compromising image quality. Photoluminescence from single nitrogen-vacancy centers in high purity diamond is used to illustrate the imaging and stability performance of the microscope.

Transient coherent nonlinear spectroscopy of single quantum dots.

We review our recent advances in four-wave mixing spectroscopy of single semiconductor quantum dots using heterodyne spectral interferometry, a novel implementation of transient nonlinear spectroscopy allowing the study of the transient nonlinear polarization emitted from individual electronic transitions in both amplitude and phase. We present experiments on individual excitonic transitions localized in monolayer islands of GaAs/AlAs quantum wells and in self-assembled CdTe/ZnTe quantum dots. We investigate the formation of the photon echo from individual transitions, both with increasing number of transitions in the ensemble, and in the presence of temporal jitter of the energy of a single transition.

Arrhythmia susceptibility and premature death in transgenic mice overexpressing both SUR1 and Kir6.2[DeltaN30,K185Q] in the heart.

Sarcolemmal ATP-sensitive potassium (K(ATP)) channels are activated after pathological depletion of intracellular ATP, unlike their pancreatic beta-cell counterparts, which dynamically regulate membrane excitability in response to changes in blood glucose. We recently engineered a series of transgenic (TG) mice overexpressing an ATP-insensitive inward rectifying K(+) channel protein (Kir)6.2 mutant (Kir6.

Expression of ATP-insensitive KATP channels in pancreatic beta-cells underlies a spectrum of diabetic phenotypes.

Glucose metabolism in pancreatic beta-cells elevates cytoplasmic [ATP]/[ADP], causing closure of ATP-sensitive K(+) channels (K(ATP) channels), Ca(2+) entry through voltage-dependent Ca(2+) channels, and insulin release. Decreased responsiveness of K(ATP) channels to the [ATP]/[ADP] ratio should lead to decreased insulin secretion and diabetes. We generated mice expressing K(ATP) channels with reduced ATP sensitivity in their beta-cells.

Designing 129Xe NMR biosensors for matrix metalloproteinase detection.

Xenon-129 biosensors offer an attractive alternative to conventional MRI contrast agents due to the chemical shift sensitivity and large nuclear magnetic signal of hyperpolarized (129)Xe. Here, we report the first enzyme-responsive (129)Xe NMR biosensor. This compound was synthesized in 13 steps by attaching the consensus peptide substrate for matrix metalloproteinase-7 (MMP-7), an enzyme that is upregulated in many cancers, to the xenon-binding organic cage, cryptophane-A.

Heterodyne spectral interferometry for multidimensional nonlinear spectroscopy of individual quantum systems.

A novel implementation of transient nonlinear spectroscopy is presented that allows the study of the transient nonlinear polarization emitted from individual electronic transitions. Both the amplitude and the phase of the polarization are retrieved, permitting the implementation of multidimensional spectroscopy in the excitation pulse delays. The technique is shown to detect mutual coherent coupling in a group of individual, localized excitonic transitions.

ATP-sensitive K+ channel signaling in glucokinase-deficient diabetes.

As the rate-limiting controller of glucose metabolism, glucokinase represents the primary beta-cell "glucose sensor." Inactivation of both glucokinase (GK) alleles results in permanent neonatal diabetes; inactivation of a single allele causes maturity-onset diabetes of the young type 2 (MODY-2). Similarly, mice lacking both alleles (GK(-/-)) exhibit severe neonatal diabetes and die within a week, whereas heterozygous GK(+/-) mice exhibit markedly impaired glucose tolerance and diabetes, resembling MODY-2.

Microscopic measurement of photon echo formation in groups of individual excitonic transitions.

The third-order polarization emitted from groups of individual localized excitonic transitions after pulsed optical excitation is measured. We observe the evolution of the nonlinear response from the case of a free polarization decay for a single transition, to that of a photon echo for many transitions. The echo is shown to arise from the mutual rephasing of the emission from individual transitions.

Diet-induced glucose intolerance in mice with decreased beta-cell ATP-sensitive K+ channels.

ATP-sensitive K+ channels (K(ATP) channels) control electrical activity in beta-cells and therefore are key players in excitation-secretion coupling. Partial suppression of beta-cell K(ATP) channels in transgenic (AAA) mice causes hypersecretion of insulin and enhanced glucose tolerance, whereas complete suppression of these channels in Kir6.2 knockout (KO) mice leads to hyperexcitability, but mild glucose intolerance.

Increased backbone mobility in beta-barrel enhances entropy gain driving binding of N-TIMP-1 to MMP-3.

The high-affinity inhibition of stromelysin 1 (MMP-3) by tissue inhibitor of metalloproteinases 1 (TIMP-1) helps control tissue remodeling and tumor development. The interaction of N-TIMP-1 with the catalytic domain of MMP-3 has been investigated by titration calorimetry and 15N NMR. Their unfavorable enthalpy of binding of +6.