Unravelling differential Hes1 dynamics during axis elongation of mouse embryos through single-cell tracking.

The intricate dynamics of Hes expression across diverse cell types in the developing vertebrate embryonic tail have remained elusive. To address this, we have developed an endogenously tagged Hes1-Achilles mouse line, enabling precise quantification of dynamics at the single-cell resolution across various tissues. Our findings reveal striking disparities in Hes1 dynamics between presomitic mesoderm (PSM) and preneural tube (pre-NT) cells.

Deciphering lineage specification during early embryogenesis in mouse gastruloids using multilayered proteomics.

Gastrulation is a critical stage in embryonic development during which the germ layers are established. Advances in sequencing technologies led to the identification of gene regulatory programs that control the emergence of the germ layers and their derivatives. However, proteome-based studies of early mammalian development are scarce.

Fine-tuning TrailMap: The utility of transfer learning to improve the performance of deep learning in axon segmentation of light-sheet microscopy images.

Light-sheet microscopy has made possible the 3D imaging of both fixed and live biological tissue, with samples as large as the entire mouse brain. However, segmentation and quantification of that data remains a time-consuming manual undertaking. Machine learning methods promise the possibility of automating this process.

DEIMoS GUI: An Open-Source User Interface for a High-Dimensional Mass Spectrometry Data Processing Tool.

We report here the creation of a graphical user interface (GUI) for the Data Extraction for Integrated Multidimensional Spectrometry (DEIMoS) tool. DEIMoS is a Python package that processes data from high-dimensional mass spectrometry measurements. It is divided into several modules, each representing a data processing step such as peak detection, alignment, and tandem mass spectra extraction and deconvolution.

Fine-tuning TrailMap: The utility of transfer learning to improve the performance of deep learning in axon segmentation of light-sheet microscopy images.

Light-sheet microscopy has made possible the 3D imaging of both fixed and live biological tissue, with samples as large as the entire mouse brain. However, segmentation and quantification of that data remains a time-consuming manual undertaking. Machine learning methods promise the possibility of automating this process.

Classifying metal-binding sites with neural networks.

To advance our ability to predict impacts of the protein scaffold on catalysis, robust classification schemes to define features of proteins that will influence reactivity are needed. One of these features is a protein's metal-binding ability, as metals are critical to catalytic conversion by metalloenzymes. As a step toward realizing this goal, we used convolutional neural networks (CNNs) to enable the classification of a metal cofactor binding pocket within a protein scaffold.

An Automated Scanning Transmission Electron Microscope Guided by Sparse Data Analytics.

Artificial intelligence (AI) promises to reshape scientific inquiry and enable breakthrough discoveries in areas such as energy storage, quantum computing, and biomedicine. Scanning transmission electron microscopy (STEM), a cornerstone of the study of chemical and materials systems, stands to benefit greatly from AI-driven automation. However, present barriers to low-level instrument control, as well as generalizable and interpretable feature detection, make truly automated microscopy impractical.

Building bridges between fields: bringing together development and homeostasis.

Despite striking parallels between the fields of developmental biology and adult tissue homeostasis, these are disconnected in contemporary research. Although development describes tissue generation and homeostasis describes tissue maintenance, it is the balance between stem cell proliferation and differentiation that coordinates both processes. Upstream signalling regulates this balance to achieve the required outcome at the population level.

A Microfluidics Approach for the Functional Investigation of Signaling Oscillations Governing Somitogenesis.

Periodic segmentation of the presomitic mesoderm of a developing mouse embryo is controlled by a network of signaling pathways. Signaling oscillations and gradients are thought to control the timing and spacing of segment formation, respectively. While the involved signaling pathways have been studied extensively over the last decades, direct evidence for the function of signaling oscillations in controlling somitogenesis has been lacking.

Cre/lox-controlled spatiotemporal perturbation of FGF signaling in zebrafish.

Background: Spatiotemporal perturbation of signaling pathways in vivo remains challenging and requires precise transgenic control of signaling effectors. Fibroblast growth factor (FGF) signaling guides multiple developmental processes, including body axis formation and cell fate patterning. In zebrafish, mutants and chemical perturbations affecting FGF signaling have uncovered key developmental processes; however, these approaches cause embryo-wide perturbations, rendering assessment of cell-autonomous vs.

Evaluation of deep vadose zone contaminant flux into groundwater: Approach and case study.

For sites with a contaminant source located in the vadose zone, the nature and extent of groundwater contaminant plumes are a function of the contaminant flux from the vadose zone to groundwater. Especially for thick vadose zones, transport may be relatively slow making it difficult to directly measure contaminant flux. An integrated assessment approach, supported by site characterization and monitoring data, is presented to explain current vadose zone contaminant distributions and to estimate future contaminant flux to groundwater in support of remediation decisions.

Effects of shear-thinning fluids on residual oil formation in microfluidic pore networks.

Two-phase immiscible displacement in porous media is controlled by capillary and viscous forces when gravitational effects are negligible. The relative importance of these forces is quantified through the dimensionless capillary number Ca and the viscosity ratio M between fluid phases. When the displacing fluid is Newtonian, the effects of Ca and M on the displacement patterns can be evaluated independently.

Injectable silica-permanganate gel as a slow-release MnO4(-) source for groundwater remediation: rheological properties and release dynamics.

Injectable slow-release permanganate gels (ISRPGs), formed by mixing aqueous KMnO4 solution with fumed silica powders, may have potential applications in remediating chlorinated solvent plumes in groundwater. A series of batch, column, and two-dimensional (2-D) flow cell experiments has been completed to characterize the ISRPG and study the release of permanganate (MnO4(-)) under a variety of conditions. The experiments have provided information on ISRPG rheology, MnO4(-) release dynamics and distribution in porous media, and trichloroethene (TCE) destruction by the ISRPG-released oxidant.

Effect of aspirin intake at bedtime versus on awakening on circadian rhythm of platelet reactivity. A randomised cross-over trial.

The risk of acute cardiovascular events is highest during morning hours, and platelet activity peaks during morning hours. The effect of timing of aspirin intake on circadian rhythm and morning peak of platelet reactivity is not known. It was our objective to evaluate the effect of timing of aspirin intake on circadian rhythm and morning peak of platelet reactivity.

Measuring spatial variability of vapor flux to characterize vadose-zone VOC sources: flow-cell experiments.

A method termed vapor-phase tomography has recently been proposed to characterize the distribution of volatile organic contaminant mass in vadose-zone source areas, and to measure associated three-dimensional distributions of local contaminant mass discharge. The method is based on measuring the spatial variability of vapor flux, and thus inherent to its effectiveness is the premise that the magnitudes and temporal variability of vapor concentrations measured at different monitoring points within the interrogated area will be a function of the geospatial positions of the points relative to the source location. A series of flow-cell experiments was conducted to evaluate this premise.

Rheological behavior of xanthan gum solution related to shear thinning fluid delivery for subsurface remediation.

Xanthan gum solutions are shear thinning fluids which can be used as delivery media to improve the distribution of remedial amendments injected into heterogeneous subsurface environments. The rheological behavior of the shear thinning solution needs to be known to develop an appropriate design for field injection. In this study, the rheological properties of xanthan gum solutions were obtained under various chemical and environmental conditions relevant to delivery of remedial amendments to groundwater.

Experimental study of crossover from capillary to viscous fingering for supercritical CO2-water displacement in a homogeneous pore network.

Carbon sequestration in saline aquifers involves displacing brine from the pore space by supercritical CO(2) (scCO(2)). The displacement process is considered unstable due to the unfavorable viscosity ratio between the invading scCO(2) and the resident brine. The mechanisms that affect scCO(2)-water displacement under reservoir conditions (41 °C, 9 MPa) were investigated in a homogeneous micromodel.

Leptin-sensitive neurons in the arcuate nuclei contribute to endogenous feeding rhythms.

Neural sites that interact with the suprachiasmatic nuclei (SCN) to generate rhythms of unrestricted feeding remain unknown. We used the targeted toxin, leptin conjugated to saporin (Lep-SAP), to examine the importance of leptin receptor-B (LepR-B)-expressing neurons in the arcuate nucleus (Arc) for generation of circadian feeding rhythms. Rats given Arc Lep-SAP injections were initially hyperphagic and rapidly became obese (the "dynamic phase" of weight gain).

Correlation of oil-water and air-water contact angles of diverse silanized surfaces and relationship to fluid interfacial tensions.

The use of air-water, θ(wa), or air-liquid contact angles is customary in surface science, while oil-water contact angles, θ(ow), are of paramount importance in subsurface multiphase flow phenomena including petroleum recovery, nonaqueous phase liquid fate and transport, and geological carbon sequestration. In this paper we determine both the air-water and oil-water contact angles of silica surfaces modified with a diverse selection of silanes, using hexadecane as the oil. The silanes included alkylsilanes, alkylarylsilanes, and silanes with alkyl or aryl groups that are functionalized with heteroatoms such as N, O, and S.

Assessing performance and closure for soil vapor extraction: integrating vapor discharge and impact to groundwater quality.

Soil vapor extraction (SVE) is typically effective for removal of volatile contaminants from higher-permeability portions of the vadose zone. However, contamination in lower-permeability zones can persist due to mass transfer processes that limit the removal effectiveness. After SVE has been operated for a period of time and the remaining contamination is primarily located in lower-permeability zones, the remedy performance needs to be evaluated to determine whether the SVE system should be optimized, terminated, or transitioned to another technology to replace or augment SVE.

Liquid CO2 displacement of water in a dual-permeability pore network micromodel.

Permeability contrasts exist in multilayer geological formations under consideration for carbon sequestration. To improve our understanding of heterogeneous pore-scale displacements, liquid CO(2) (LCO(2))-water displacement was evaluated in a pore network micromodel with two distinct permeability zones. Due to the low viscosity ratio (logM = -1.

Enhanced remedial amendment delivery to subsurface using shear thinning fluid and aqueous foam.

A major issue with in situ subsurface remediation is the ability to achieve an even spatial distribution of remedial amendments to the contamination zones in an aquifer or vadose zone. Amendment delivery to the aquifer using shear thinning fluid and to the vadose zone using aqueous foam has the potential to enhance the distribution. 2-D saturated flow cell experiments were conducted to evaluate the enhanced fluid sweeping over heterogeneous system, improved contaminant removal, and extended amendment presence in low-permeability zones achieved by shear thinning fluid delivery.

Demonstration of combined zero-valent iron and electrical resistance heating for in situ trichloroethene remediation.

The effectiveness of in situ treatment using zero-valent iron (ZVI) for nonaqueous phase or significant sediment-associated contaminant mass can be limited by relatively low rates of mass transfer to bring contaminants in contact with the reactive media. For a field test in a trichloroethene (TCE) source area, combining moderate-temperature subsurface electrical resistance heating with in situ ZVI treatment was shown to accelerate TCE treatment by a factor of about 4 based on organic daughter products and a factor about 8 based on chloride concentrations. A mass-discharge-based analysis was used to evaluate reaction, dissolution, and volatilization processes at ambient groundwater temperature (~10 °C) and as temperature was increased up to about 50 °C.

Pore-scale study of transverse mixing induced CaCO₃ precipitation and permeability reduction in a model subsurface sedimentary system.

A microfluidic pore structure etched into a silicon wafer was used as a two-dimensional model subsurface sedimentary system (i.e., micromodel) to study mineral precipitation and permeability reduction relevant to groundwater remediation and geological carbon sequestration.

A review of non-invasive imaging methods and applications in contaminant hydrogeology research.

Contaminant hydrogeological processes occurring in porous media are typically not amenable to direct observation. As a result, indirect measurements (e.g.