Probing single electrons across 300-mm spin qubit wafers.

Building a fault-tolerant quantum computer will require vast numbers of physical qubits. For qubit technologies based on solid-state electronic devices1-3, integrating millions of qubits in a single processor will require device fabrication to reach a scale comparable to that of the modern complementary metal-oxide-semiconductor (CMOS) industry. Equally important, the scale of cryogenic device testing must keep pace to enable efficient device screening and to improve statistical metrics such as qubit yield and voltage variation. Spin qubits1,4,5 based on electrons in Si have shown impressive control fidelities6-9 but have historically been challenged by yield and process variation10-12. Here we present a testing process using a cryogenic 300-mm wafer prober13 to collect high-volume data on the performance of hundreds of industry-manufactured spin qubit devices at 1.6 K. This testing method provides fast feedback to enable optimization of the CMOS-compatible fabrication process, leading to high yield and low process variation. Using this system, we automate measurements of the operating point of spin qubits and investigate the transitions of single electrons across full wafers. We analyse the random variation in single-electron operating voltages and find that the optimized fabrication process leads to low levels of disorder at the 300-mm scale. Together, these results demonstrate the advances that can be achieved through the application of CMOS-industry techniques to the fabrication and measurement of spin qubit devices.

Quantitative evaluation of 90Y-PET/CT and 90Y-SPECT/CT-based dosimetry following Yttrium-90 radioembolization.

BACKGROUND: Following yttrium-90 radioembolization (90Y-RE), 90Y-PET/CT and 90Y-SPECT/CT imaging provide the means to calculate the voxelized absorbed dose distribution. Given the widespread use of the two imaging modalities and lack of well-established standardized dosimetry protocols for 90Y-RE, there is a clinical need to systematically investigate and evaluate differences in the performance of voxel-based dosimetry between 90Y-PET/CT and 90Y-SPECT/CT. PURPOSE: To quantitatively analyze and compare 90Y-PET/CT and 90Y-SPECT/CT-based dosimetry following 90Y-RE. METHODS: 90Y-PET/CT and 90Y-SPECT/CT imaging was acquired for 35 patients following 90Y-RE with TheraSphere for the treatment of unresectable hepatocellular carcinoma. Dosimetry was performed using the local deposition method with known activity and the mean dose (Dmean) was calculated for perfused liver volumes (PV), tumors (T), and perfused normal livers (NL). Additionally, the absorbed dose to x% of the volume (Dx, x ∈ $ \in $ [5%, 10%, …, 90%, 95%]) and the volume receiving y Gy (Vy, y ∈ $ \in $ [10 Gy, 20 Gy, …, 190 Gy, 200 Gy]) were calculated for T and NL, respectively. Dose metrics were compared using linear regression, Bland-Altman analysis, and statistical testing. RESULTS: Both 90Y-SPECT/CT and 90Y-PET/CT-based tumor Dmean were strongly correlated (R2 ≥ 0.90) with Dx, excluding metrics on the extrema. Intra-modality comparisons of various Dx and Vy metrics yielded statistically significant differences (ANOVA, p < 0.001) for both90Y-PET/CT and 90Y-SPECT/CT. Based on statistical testing, only Dx metrics separated by greater than 20%-30% coverage, and only Vy metrics separated by greater than 40-70 Gy, reported significant differences. For PV, there was a strong correlation (R2 ≥ 0.99) between Dmean derived separately from 90Y-PET/CT and 90Y-SPECT/CT imaging. The strength of the correlation was slightly reduced for T and NL with R2 = 0.91 and R2 = 0.95, respectively. For PV, the mean bias ± standard error (SE) and 95% limits of agreement (LOA) between Dmean from the two modalities was effectively zero with -0.8 ± 0.4% (± 2.5%). For T and NL, the mean bias ± SE (± LOA) was -14.5 ± 3.7% (± 24%) and 9.4 ± 4.7% (± 27%), respectively. CONCLUSION: The strong correlation between Dmean and Dx suggests information from multiple dose metrics (e.g., D70 and Dmean) is largely redundant when establishing dose-response relationships in 90Y-RE. Dmean is highly correlated between 90Y-PET/CT and 90Y-SPECT/CT-based dosimetry, for all liver VOIs. Relative to 90Y-SPECT/CT, 90Y-PET/CT, on average, yielded higher Dmean to tumors (14%) and lower Dmean to perfused normal livers (9%). Absorbed dose differences for perfused liver volumes between 90Y-SPECT/CT and 90Y-PET/CT were negligible.

A comparison of methods for in vivo activity and absorbed dose quantification with PET/CT following yttrium-90 radioembolization.

BACKGROUND: Yttrium-90 (90Y) positron emission tomography (PET)/computed tomography (CT) imaging is increasingly being used to perform tumor (T) and normal liver (NL) voxel dosimetry after 90Y-radioembolization (90Y-RE). Yet, the accuracy of in vivo 90Y-PET/CT imaging, subject to motion blur and co-registration inaccuracies, and 90Y-PET/CT dose quantification, subject to availability of different voxel dosimetry algorithms, are not well understood. PURPOSE: The purpose of this study was to investigate the accuracy of 90Y-PET/CT-based activity estimates following 90Y-RE and characterize differences between 90Y-PET/CT-based voxel dosimetry algorithms. METHODS: Thirty-five patients underwent 90Y-PET/CT imaging after 90Y-RE with TheraSphere. The net administered 90Y activity (Aadmin) was determined using a dose calibrator and pre- and post-procedure exposure rate measurements. The summation of image-based activity (Aimage) was extracted from perfused volume (PV) and 3D-isotropically 2-cm expanded PV contour (PV+2 cm). Absorbed doses were calculated using voxel S-value (VSV), local deposition method (LDM), and LDM with known activity (LDMKA) dosimetry algorithms. Linear regression and Bland-Altman analysis quantified the relationship between Aimage and Aadmin and between mean dose estimates (DLDM, DVSV, DLDM-KA) for PV, T, and perfused NL volumes. RESULTS: While Aadmin and Aimage in PV were highly correlated (R2 > 0.95), the mean bias ± standard error (SE) and (95% limits of agreement, LOA) was significantly non-zero with -22.7 ± 4.7% (± 28.4%). In PV+2 cm, the mean bias ± SE (± LOA) decreased to 1.3 ± 3.4% (± 18.0%) consistent with zero mean error. DLDM and DVSV were highly correlated (R2 > 0.99) for all volumes of interest (VOIs) and the mean bias ± SE (± LOA) was 2.2 ± 0.2% (± 1.0%), 0.7 ± 0.4% (± 2.8%), and 3.2 ± 0.5% (± 2.8%) for PV, T, and NL, respectively. DLDM-KA and DVSV were correlated with R2 = 0.86, 0.80, and 0.86 for PV, T, and NL, respectively. The mean bias ± SE (± LOA) between DLDM-KA and DVSV was significantly non-zero with -19.6 ± 5.1% (± 31.0%), -20.8 ± 4.4% (± 29.0%), and -18.1 ± 5.3% (± 31.1%) for PV, T, and NL, respectively. CONCLUSIONS: The summation of Aimage in PV was underestimated relative to Aadmin. Only by accounting for respiratory motion, limited spatial resolution, and PET/CT co-registration errors through VOI expansion was Aimage, on average, equal to Aadmin. The differences between DLDM and DVSV were not clinically relevant, though DLDM-KA was approximately 20% greater than DVSV. Given the high quantitative accuracy of dose calibrators and challenges associated with accurate 90Y-PET/CT quantification, LDMKA is the preferred algorithm for accurate 90Y-PET/CT-based dosimetry following 90Y-RE.

Incorporating the benefits of vegetative filter strips into risk assessment and risk management of pesticides.

The pesticide registration process in North America, including the USA and Canada, involves conducting a risk assessment based on relatively conservative modeling to predict pesticide concentrations in receiving waterbodies. The modeling framework does not consider some commonly adopted best management practices that can reduce the amount of pesticide that may reach a waterbody, such as vegetative filter strips (VFS). Currently, VFS are being used by growers as an effective way to reduce off-site movement of pesticides, and they are being required or recommended on pesticide labels as a mitigation measure. Given the regulatory need, a pair of multistakeholder workshops were held in Raleigh, North Carolina, to discuss how to incorporate VFS into pesticide risk assessment and risk management procedures within the North American regulatory framework. Because the risk assessment process depends heavily on modeling, one key question was how to quantitatively incorporate VFS into the existing modeling approach. Key outcomes from the workshops include the following: VFS have proven effective in reducing pesticide runoff to surface waterbodies when properly located, designed, implemented, and maintained; Vegetative Filter Strip Modeling System (VFSMOD), a science-based and widely validated mechanistic model, is suitable for further vetting as a quantitative simulation approach to pesticide mitigation with VFS in current regulatory settings; and VFSMOD parametrization rules need to be developed for the North American aquatic exposure assessment. Integr Environ Assess Manag 2024;20:454-464. © 2023 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC).

Predicting the net administered activity in 90 Y-radioembolization patients from post-procedure 90 Y-SPECT/CT.

BACKGROUND: The calculation of the net administered activity (Aadmin ) in patients undergoing 90 Y-radioembolization is essential for dosimetry and radiation safety, yet current methods for measuring residual 90 Y activity are often associated with high uncertainty. Therefore, an accurate, robust, and clinically viable method for the determination of Aadmin across approved 90 Y microsphere devices is desirable. PURPOSE: We report on a novel method to determine Aadmin by leveraging the quantitative capabilities of SPECT/CT to measure 90 Y-emission in vivo from patients following 90 Y-radioembolization with glass or resin microspheres. METHODS: 90 Y-SPECT/CT attenuation-corrected count data from 147 sequential 90 Y-radioembolization patients was used for this analysis. Aadmin was calculated as part of routine clinical practice via the exposure rate differences between the initial 90 Y-vial and the 90 Y-residual jar. This served as our gold standard measure of Aadmin . Patient data for each microsphere device were separated into training and testing cohorts to first develop regression models and then to independently assess model performance. The training cohorts were divided into four groups: first, based on the microsphere device (glass or resin), and second, based on the SPECT volume used to calculate counts (the full SPECT field of view (FOV) or liver only (VOIliver )). Univariate linear regression models were generated for each group to predict Aadmin based on 90 Y-SPECT data from the training cohorts. Leave-one-out cross validation was implemented to estimate variability in model parameters. To assess performance, linear models derived from the training cohort were applied to 90 Y-SPECT data from the testing cohort. A comparison of the models between microspheres devices was also performed. RESULTS: Linear models derived from the glass and resin training cohorts demonstrated a strong, positive correlation between 90 Y-SPECT image counts and Aadmin for VOIliver and FOV with R2  > 0.98 in all cases. In the glass training cohort, model accuracy (100%-absolute mean prediction error) and precision (95% prediction intervals of mean prediction error) were 99.0% and 15.4% for the VOIliver and 99.7% and 17.5% for the FOV models, respectively. In the resin training cohort, the corresponding values were 98.6% and 16.7% for VOIliver and > 99.9% and 11.4% for the FOV models, respectively. The application of these linear models to 90 Y-SPECT data from the testing cohort showed Aadmin prediction errors to have high accuracy and precision for both microsphere devices. For the glass testing cohort, accuracy (precision) was 96.9% (19.6%) and 98.8% (21.1%) for the VOIliver and FOV models, respectively. The corresponding values for the resin training cohort were 97.3% (26.2%) and 98.5% (25.7%) for the VOIliver and FOV models, respectively. The slope of the linear models between the two microsphere devices was observed to be significantly different with resin microspheres generating 48%-49% more SPECT counts for equivalent 90 Y activity based on each device manufacturer's activity calibration process. CONCLUSION: 90 Y-SPECT image counts can reliably predict (accuracy > 95% and precision < 18%) Aadmin after 90 Y-radioembolization, with performance characteristics essentially equivalent for both glass and resin microspheres. There is a clear indication that activity calibrations are fundamentally different between the two microsphere devices.

Phenotypic screening of the ReFRAME drug repurposing library to discover new drugs for treating sickle cell disease.

Stem cell transplantation and genetic therapies offer potential cures for patients with sickle cell disease (SCD), but these options require advanced medical facilities and are expensive. Consequently, these treatments will not be available for many years to the majority of patients suffering from this disease. What is urgently needed now is an inexpensive oral drug in addition to hydroxyurea, the only drug approved by the FDA that inhibits sickle-hemoglobin polymerization. Here, we report the results of the first phase of our phenotypic screen of the 12,657 compounds of the Scripps ReFRAME drug repurposing library using a recently developed high-throughput assay to measure sickling times following deoxygenation to 0% oxygen of red cells from sickle trait individuals. The ReFRAME library is a very important collection because the compounds are either FDA-approved drugs or have been tested in clinical trials. From dose-response measurements, 106 of the 12,657 compounds exhibit statistically significant antisickling at concentrations ranging from 31 nM to 10 µM. Compounds that inhibit sickling of trait cells are also effective with SCD cells. As many as 21 of the 106 antisickling compounds emerge as potential drugs. This estimate is based on a comparison of inhibitory concentrations with free concentrations of oral drugs in human serum. Moreover, the expected therapeutic potential for each level of inhibition can be predicted from measurements of sickling times for cells from individuals with sickle syndromes of varying severity. Our results should motivate others to develop one or more of these 106 compounds into drugs for treating SCD.

Efficient 3-hydroxypropionic acid production by Acetobacter sp. CIP 58.66 through a feeding strategy based on pH control.

Acetic acid bacteria (AAB) can selectively oxidize diols into their corresponding hydroxyacids. Notably, they can convert 1,3-propanediol (1,3-PDO) into 3-hydroxypropionic acid (3-HP), which is a promising building-block. Until now, 3-HP production with AAB is carried out in batch and using resting cells at high cell densities (up to 10 g L-1 of cell dry weight). This approach is likely limited by detrimental accumulation of the intermediate 3-hydroxypropanal (3-HPA). Herein, we investigate an alternative implementation that allows highly efficient 3-HP production with lower cell densities of growing cells and that prevents 3-HPA accumulation. First, growth and 3-HP production of Acetobacter sp. CIP 58.66 were characterized with 1,3-PDO or glycerol as growth substrate. The strain was then implemented in a bioreactor, during a sequential process where it was first cultivated on glycerol, then the precursor 1,3-PDO was continuously supplied at a varying rate, easily controlled by the pH control. Different pH set points were tested (5.0, 4.5, and 4.0). This approach used the natural resistance of acetic acid bacteria to acidic conditions. Surprisingly, when pH was controlled at 5.0, the performances achieved in terms of titer (69.76 g3-HP L-1), mean productivity (2.80 g3-HP L-1 h-1), and molar yield (1.02 mol3-HP mol-11,3-PDO) were comparable to results obtained with genetically improved strains at neutral pH. The present results were obtained with comparatively lower cell densities (from 0.88 to 2.08 g L-1) than previously reported. This feeding strategy could be well-suited for future scale-up, since lower cell densities imply lower process costs and energy needs.

Treatment of sickle cell disease by increasing oxygen affinity of hemoglobin.

The issue of treating sickle cell disease with drugs that increase hemoglobin oxygen affinity has come to the fore with the US Food and Drug Administration approval in 2019 of voxelotor, the only antisickling drug approved since hydroxyurea in 1998. Voxelotor reduces sickling by increasing the concentration of the nonpolymerizing, high oxygen affinity R (oxy) conformation of hemoglobin S (HbS). Treatment of sickle cell patients with voxelotor increases Hb levels and decreases indicators of hemolysis, but with no indication as yet that it reduces the frequency of pain episodes. In this study, we used the allosteric model of Monod, Wyman, and Changeux to simulate whole-blood oxygen dissociation curves and red cell sickling in the absence and presence of voxelotor under the in vivo conditions of rapid oxygen pressure decreases. Our modeling agrees with results of experiments using a new robust assay, which shows the large, expected decrease in sickling from the drug. The modeling indicates, however, that the increase in oxygen delivery from reduced sickling is largely offset by the increase in oxygen affinity. The net result is that the drug increases overall oxygen delivery only at the very lowest oxygen pressures. However, reduction of sickling mitigates red cell damage and explains the observed decrease in hemolysis. More importantly, our modeling of in vivo oxygen dissociation, sickling, and oxygen delivery suggests that drugs that increase fetal Hb or decrease mean corpuscular hemoglobin concentration (MCHC) should be more therapeutically effective than drugs that increase oxygen affinity.

MWC allosteric model explains unusual hemoglobin-oxygen binding curves from sickle cell drug binding.

An oxygen-affinity-modifying drug, voxelotor, has very recently been approved by the FDA for treatment of sickle cell disease. The proposed mechanism of action is by preferential binding of the drug to the R quaternary conformation, which cannot copolymerize with the T conformation to form sickle fibers. Here, we report widely different oxygen dissociation and oxygen association curves for normal blood in the presence of voxelotor and interpret the results in terms of the allosteric model of Monod, Wyman, and Changeux with the addition of drug binding. The model does remarkably well in quantitatively explaining a complex data set with just the addition of drug binding and dissociation rates for the R and T conformations. Whereas slow dissociation of the drug from R results in time-independent dissociation curves, the changing association curves result from slow dissociation of the drug from T, as well as extremely slow binding of the drug to T. By calculating true equilibrium curves from the model parameters, we show that there would be a smaller decrease in oxygen delivery from the left shift in the dissociation curve caused by drug binding if drug binding and dissociation for both R and T were rapid. Our application of the Monod, Wyman, and Changeux model demonstrates once more its enormous power in explaining many different kinds of experimental results for hemoglobin. It should also be helpful in analyzing oxygen binding and in vivo delivery in future investigations of oxygen-affinity-modifying drugs for sickle cell disease.

Allosteric control of hemoglobin S fiber formation by oxygen and its relation to the pathophysiology of sickle cell disease.

The pathology of sickle cell disease is caused by polymerization of the abnormal hemoglobin S upon deoxygenation in the tissues to form fibers in red cells, causing them to deform and occlude the circulation. Drugs that allosterically shift the quaternary equilibrium from the polymerizing T quaternary structure to the nonpolymerizing R quaternary structure are now being developed. Here we update our understanding on the allosteric control of fiber formation at equilibrium by showing how the simplest extension of the classic quaternary two-state allosteric model of Monod, Wyman, and Changeux to include tertiary conformational changes provides a better quantitative description. We also show that if fiber formation is at equilibrium in vivo, the vast majority of cells in most tissues would contain fibers, indicating that it is unlikely that the disease would be survivable once the nonpolymerizing fetal hemoglobin has been replaced by adult hemoglobin S at about 1 y after birth. Calculations of sickling times, based on a recently discovered universal relation between the delay time prior to fiber formation and supersaturation, show that in vivo fiber formation is very far from equilibrium. Our analysis indicates that patients survive because the delay period allows the majority of cells to escape the small vessels of the tissues before fibers form. The enormous sensitivity of the duration of the delay period to intracellular hemoglobin composition also explains why sickle trait, the heterozygous condition, and the compound heterozygous condition of hemoglobin S with pancellular hereditary persistence of fetal hemoglobin are both relatively benign conditions.

Interactions of an Anti-Sickling Drug with Hemoglobin in Red Blood Cells from a Patient with Sickle Cell Anemia.

The pathophysiology associated with sickle cell disease (SCD) includes hemolytic anemia, vaso-occlusive events, and ultimately end organ damage set off by the polymerization of deoxygenated hemoglobin S (HbS) into long fibers and sickling of red blood cells (RBCs). One approach toward mitigating HbS polymerization is to pharmacologically stabilize the oxygenated (R) conformation of HbS and thereby reduce sickling frequency and SCD pathology. GBT440 is an α-subunit-specific modifying agent that has recently been reported to increase HbS oxygen binding affinity and consequently delay in vitro polymerization. In addition, animal model studies have demonstrated the potential for GBT440 to be a suitable therapeutic for daily oral dosing in humans. Here, we report an optimized method for detecting GBT440 intermediates in human patient hemolysate using a combination of HPLC and mass spectrometry analysis. First, oxygen dissociation curves (ODCs) analyzed from patient blood showed that oxygen affinity increased in a dose dependent manner. Second, HPLC and integrated mass spectrometric analysis collectively confirmed that GBT440 labeling was specific to the α N-terminus thereby ruling out other potential ligand binding sites. Finally, the results from this optimized analytical approach allowed us to detect a stable α-specific GBT440 adduct in the patient's hemolysate in a dose dependent manner. The results and methods presented in this report could therefore potentially help therapeutic monitoring of GBT440 induced oxygen affinity and reveal critical insight into the biophysical properties of GBT440 Hb complexes.

Theoretical Simulation of Red Cell Sickling Upon Deoxygenation Based on the Physical Chemistry of Sickle Hemoglobin Fiber Formation.

The polymerization of the mutant hemoglobin S upon deoxygenation to form fibers in red blood cells of patients suffering from sickle-cell anemia results in changes in cell shape and rigidity, also known as sickling, which underlie the pathology of the disease. While much has been learned about the fundamental physical chemistry of the polymerization process, transferring these insights to sickling of red cells under in vivo conditions requires being able to monitor, and ultimately predict, the time course of cellular sickling under physiological conditions of deoxygenation. To this end, we have developed an experimental technique for tracking the temporal evolution of the sickling of red blood cells under laboratory deoxygenation conditions, based on the automated analysis of sequences of microscope images and machine-learning analysis to characterize cell morphology. As an aid in the quantitative understanding of these experiments, we have developed a computational framework for simulating the time dependence of sickling in populations of red blood cells which incorporates the current theoretical and empirical understanding of the physical chemistry of the sickling process. In order to apply these techniques to our experiments, we have theoretically determined the time course of deoxygenation by solving the diffusion equation for oxygen in our experimental geometry. With this combined description, we are able to reproduce our experimentally observed kinetics of sickling, suggesting that our theoretical approach should be applicable to physiological deoxygenation scenarios.

Process engineering for microbial production of 3-hydroxypropionic acid.

Due to concerns about the unsustainability and predictable shortage of fossil feedstocks, research efforts are currently being made to develop new processes for production of commodities using alternative feedstocks. 3-Hydroxypropionic acid (CAS 503-66-2) was recognised by the US Department of Energy as one of the most promising value-added chemicals that can be obtained from biomass. This article aims at reviewing the various strategies implemented thus far for 3-hydroxypropionic acid bioproduction. Special attention is given here to process engineering issues. The variety of possible metabolic pathways is also described in order to highlight how process design can be guided by their understanding. The most recent advances are described here in order to draw up a panorama of microbial 3-hydroxypropionic acid production: best performances to date, remaining hurdles and foreseeable developments. Important milestones have been achieved, and process metrics are getting closer to commercial relevance. New strategies are continuously being developed that involve new microbial strains, new technologies, or new carbon sources in order to overcome the various hurdles inherent to the different microbial routes.

Effect of dairy matrices on the survival of Streptococcus thermophilus, Brevibacterium aurantiacum and Hafnia alvei during digestion.

This study evaluated the ability of dairy matrices, different in composition (with and without fat) and structure (liquid and gel), to enhance microorganisms survival through digestion. The viability of three dairy microorganisms Streptococcus thermophilus, Brevibacterium aurantiacum and Hafnia alvei was measured during in vitro and in vivo digestion. S. thermophilus was highly sensitive to gastric stress, and was not found in the duodenal compartment. B. auranticum was moderately sensitive to gastric stress but resistant to duodenal stress. H. alvei was highly resistant to both stresses. LIVE/DEAD confocal microscopy's images, probed the effect of low pH on microorganisms survival. However, in vivo analyses (16S rRNA gene metabarcoding) failed to confirm in vitro observations since tested microorganisms were not detected. Despite of the different evolutions during digestion on buffer capacity, lipolysis, and rheological characteristics, we did not observe any protective effect of the dairy matrices on microorganisms survival.

Kinetic assay shows that increasing red cell volume could be a treatment for sickle cell disease.

Although it has been known for more than 60 years that the cause of sickle cell disease is polymerization of a hemoglobin mutant, hydroxyurea is the only drug approved for treatment by the US Food and Drug Administration. This drug, however, is only partially successful, and the discovery of additional drugs that inhibit fiber formation has been hampered by the lack of a sensitive and quantitative cellular assay. Here, we describe such a method in a 96-well plate format that is based on laser-induced polymerization in sickle trait cells and robust, automated image analysis to detect the precise time at which fibers distort ("sickle") the cells. With this kinetic method, we show that small increases in cell volume to reduce the hemoglobin concentration can result in therapeutic increases in the delay time prior to fiber formation. We also show that, of the two drugs (AES103 and GBT440) in clinical trials that inhibit polymerization by increasing oxygen affinity, one of them (GBT440) also inhibits sickling in the absence of oxygen by two additional mechanisms.

Surfactant-induced flow compromises determination of air-water interfacial areas by surfactant miscible-displacement.

Surfactant miscible-displacement (SMD) column experiments are used to measure air-water interfacial area (AI) in unsaturated porous media, a property that influences solute transport and phase-partitioning. The conventional SMD experiment results in surface tension gradients that can cause water redistribution and/or net drainage of water from the system ("surfactant-induced flow"), violating theoretical foundations of the method. Nevertheless, the SMD technique is still used, and some suggest that experimental observations of surfactant-induced flow represent an artifact of improper control of boundary conditions. In this work, we used numerical modeling, for which boundary conditions can be perfectly controlled, to evaluate this suggestion. We also examined the magnitude of surfactant-induced flow and its impact on AI measurement during multiple SMD flow scenarios. Simulations of the conventional SMD experiment showed substantial surfactant-induced flow and consequent drainage of water from the column (e.g., from 75% to 55% SW) and increases in actual AI of up to 43%. Neither horizontal column orientation nor alternative boundary conditions resolved surfactant-induced flow issues. Even for simulated flow scenarios that avoided surfactant-induced drainage of the column, substantial surfactant-induced internal water redistribution occurred and was sufficient to alter surfactant transport, resulting in up to 23% overestimation of AI. Depending on the specific simulated flow scenario and data analysis assumptions used, estimated AI varied by nearly 40% and deviated up to 36% from the system's initial AI. We recommend methods for AI determination that avoid generation of surface-tension gradients and urge caution when relying on absolute AI values measured via SMD.

The Complete and Updated "Rotifer Polyculture Method" for Rearing First Feeding Zebrafish.

The zebrafish (Danio rerio) is a model organism of increasing importance in many fields of science. One of the most demanding technical aspects of culture of this species in the laboratory is rearing first-feeding larvae to the juvenile stage with high rates of growth and survival. The central management challenge of this developmental period revolves around delivering highly nutritious feed items to the fish on a nearly continuous basis without compromising water quality. Because larval zebrafish are well-adapted to feed on small zooplankton in the water column, live prey items such as brachionid rotifers, Artemia, and Paramecium are widely recognized as the feeds of choice, at least until the fish reach the juvenile stage and are able to efficiently feed on processed diets. This protocol describes a method whereby newly hatched zebrafish larvae are cultured together with live saltwater rotifers (Brachionus plicatilis) in the same system. This polyculture approach provides fish with an "on-demand", nutrient-rich live food source without producing chemical waste at levels that would otherwise limit performance. Importantly, because the system harnesses both the natural high productivity of the rotifers and the behavioral preferences of the fish, the labor involved with maintenance is low. The following protocol details an updated, step-by-step procedure that incorporates rotifer production (scalable to any desired level) for use in a polyculture of zebrafish larvae and rotifers that promotes maximal performance during the first 5 days of exogenous feeding.

Rapid and Efficient Production of Coronary Artery Ligation and Myocardial Infarction in Mice Using Surgical Clips.

AIMS: The coronary artery ligation model in rodents mimics human myocardial infarction (MI). Normally mechanical ventilation and prolonged anesthesia period are needed. Recently, a method has been developed to create MI by popping-out the heart (without ventilation) followed by immediate suture ligation. Mortality is high due to the time-consuming suture ligation process while the heart is exposed. We sought to improve this method and reduce mortality by rapid coronary ligation using a surgical clip instead of a suture. METHODS AND RESULTS: Mice were randomized into 3 groups: clip MI (CMI), suture MI (SMI), or sham (SHAM). In all groups, heart was manually exposed without intubation through a small incision on the chest wall. Unlike the conventional SMI method, mice in the CMI group received a metal clip on left anterior descending artery (LAD), quickly dispensed by an AutoSuture Surgiclip™. The CMI method took only 1/3 of ligation time of the standard SMI method and improved post-MI survival rate. TTC staining and Masson's trichrome staining revealed a similar degree of infarct size in the SMI and CMI groups. Echocardiograph confirmed that both SMI and CMI groups had a similar reduction of ejection fraction and fraction shortening over the time. Histological analysis showed that the numbers of CD68+ macrophages and apoptotic cells (TUNEL-positive) are indistinguishable between the two groups. CONCLUSION: This new method, taking only less than 3 minutes to complete, represents an efficient myocardial infarction model in rodents.

Relationships between the use of Embden Meyerhof pathway (EMP) or Phosphoketolase pathway (PKP) and lactate production capabilities of diverse Lactobacillus reuteri strains.

The aims of this study is to compare the growth and glucose metabolism of three Lactobacillus reuteri strains (i.e. DSM 20016, DSM 17938, and ATCC 53608) which are lactic acid bacteria of interest used for diverse applications such as probiotics implying the production of biomass, or for the production of valuable chemicals (3-hydroxypropionaldehyde, 3-hydroxypropionic acid, 1,3-propanediol). However, the physiological diversity inside the species, even for basic metabolisms, like its capacity of acidification or glucose metabolism, has not been studied yet. In the present work, the growth and metabolism of three strains representative of the species diversity have been studied in batch mode. The strains were compared through characterization of growth kinetics and evaluation of acidification kinetics, substrate consumption and product formation. The results showed significant differences between the three strains which may be explained, at least in part, by variations in the distribution of carbon source between two glycolytic pathways during the bacterial growth: the phosphoketolase or heterolactic pathway (PKP) and the Embden-Meyerhof pathway (EMP). It was also shown that, in the context of obtaining a large amount of biomass, DSM 20016 and DSM 17938 strains were the most effective in terms of growth kinetics. The DSM 17938 strain, which shows the more significant metabolic shift from EMP to PKP when the pH decreases, is more effective for lactate production.