Pebble to the Metal: A Boulder Approach to Enrichment for Danio rerio.

Zebrafish are an established and widely used animal model, yet there is limited understanding of their welfare needs. Despite an increasing number of studies on zebrafish enrichment, in-tank environmental enrichment remains unpopular among researchers. This is due to perceived concerns over health/hygiene when it comes to introducing enrichment into the tank, although actual evidence for this is sparse. To accommodate this belief, regardless of veracity, we tested the potential benefits of enrichments presented outside the tank. Thus, we investigated the preferences and physiological stress of zebrafish with pictures of pebbles placed underneath the tank. We hypothesized that zebrafish would show a preference for enriched environments and have lower stress levels than barren housed zebrafish. In our first experiment, we housed zebrafish in a standard rack system and recorded their preference for visual access to a pebble picture, with two positive controls: visual access to conspecifics, and group housing. Using a crossover repeated-measures factorial design, we tested if the preference for visual access to pebbles was as strong as the preference for social contact. Zebrafish showed a strong preference for visual access to pebbles, equivalent to that for conspecifics. Then, in a second experiment, tank water cortisol was measured to assess chronic stress levels of zebrafish housed with or without a pebble picture under their tank, with group housing as a positive control. Cortisol levels were significantly reduced in zebrafish housed with pebble pictures, as were cortisol levels in group housed zebrafish. In fact, single housed zebrafish with pebble pictures showed the same cortisol levels as group housed zebrafish without pebble pictures. Thus, the use of an under-tank pebble picture was as beneficial as being group housed, effectively compensating for the stress of single housing. Pebble picture enrichment had an additive effect with group housing, where group housed zebrafish with pebble pictures had the lowest cortisol levels of any treatment group.

They all rock: A systematic comparison of conformational movements in LeuT-fold transporters.

Many membrane transporters share the LeuT fold-two five-helix repeats inverted across the membrane plane. Despite hundreds of structures, whether distinct conformational mechanisms are supported by the LeuT fold has not been systematically determined. After annotating published LeuT-fold structures, we analyzed distance difference matrices (DDMs) for nine proteins with multiple available conformations. We identified rigid bodies and relative movements of transmembrane helices (TMs) during distinct steps of the transport cycle. In all transporters the bundle (first two TMs of each repeat) rotates relative to the hash (third and fourth TMs). Motions of the arms (fifth TM) to close or open the intracellular and outer vestibules are common, as is a TM1a swing, with notable variations in the opening-closing motions of the outer vestibule. Our analyses suggest that LeuT-fold transporters layer distinct motions on a common bundle-hash rock and demonstrate that systematic analyses can provide new insights into large structural datasets.

An End-to-End Platform for Digital Pathology Using Hyperspectral Autofluorescence Microscopy and Deep Learning-Based Virtual Histology.

Conventional histopathology involves expensive and labor-intensive processes that often consume tissue samples, rendering them unavailable for other analyses. We present a novel end-to-end workflow for pathology powered by hyperspectral microscopy and deep learning. First, we developed a custom hyperspectral microscope to nondestructively image the autofluorescence of unstained tissue sections. We then trained a deep learning model to use autofluorescence to generate virtual histologic stains, which avoids the cost and variability of chemical staining procedures and conserves tissue samples. We showed that the virtual images reproduce the histologic features present in the real-stained images using a randomized nonalcoholic steatohepatitis (NASH) scoring comparison study, where both real and virtual stains are scored by pathologists (D.T., A.D.B., R.K.P.). The test showed moderate-to-good concordance between pathologists' scoring on corresponding real and virtual stains. Finally, we developed deep learning-based models for automated NASH Clinical Research Network score prediction. We showed that the end-to-end automated pathology platform is comparable with an independent panel of pathologists for NASH Clinical Research Network scoring when evaluated against the expert pathologist consensus scores. This study provides proof of concept for this virtual staining strategy, which could improve cost, efficiency, and reliability in pathology and enable novel approaches to spatial biology research.

Two state reactivity (TSR) and hydrogen tunneling reaction kinetics measured in the Co+ mediated decomposition of CH3CHO.

The electronic structure of a transition metal atom allows it to act as a catalytic active site by providing lower energy alternative pathways in chemical transformations. We have identified and kinetically characterized three such pathways in the title reaction. One is an adiabatic pathway that occurs on a single potential energy surface described within the Born-Oppenheimer approximation. A second pathway opens microseconds into the reaction as a portion of the reacting population competitively transitions from triplet to singlet multiplicity to circumvent energetic barriers on the triplet surface. These pathways are single- and two-state reactive (SSR and TSR) where the Co+ cation mediates an oxidative addition/reductive elimination sequence of the CH3CHO molecule. The third observed reaction pathway is the aldehyde hydrogen tunneling through an Eyring barrier to form high-spin products. First-order rate constants for the adiabatic and nonadiabatic energy lowered pathways, and the hydrogen tunneling pathway, are each measured using the single photon initiated dissociative rearrangement reaction (SPIDRR) experimental technique. We believe that this is the first experimental study where such disparate dynamic features (SSR, TSR, and H-tunneling) are disentangled in a system's chemistry, attributing specific rate constant values to each effect and quantifying the various competitions. Moreover, multi-reference CASSCF/CASPT2 calculations indicate that structures with covalent Co-H bonds are present exclusively along the excited singlet surface. This phenomenon significantly reduces these structures' energy relative to their triplet counterparts, thus enabling the surface crossing and spin inversion that cause the observed two-state reactivity.

Emergence of a proton exchange-based isomerization and lactonization mechanism in the plant coumarin synthase COSY.

Plants contain rapidly evolving specialized enzymes that support the biosynthesis of functionally diverse natural products. In coumarin biosynthesis, a BAHD acyltransferase-family enzyme COSY was recently discovered to accelerate coumarin formation as the only known BAHD enzyme to catalyze an intramolecular acyl transfer reaction. Here we investigate the structural and mechanistic basis for COSY's coumarin synthase activity. Our structural analyses reveal an unconventional active-site configuration adapted to COSY's specialized activity. Through mutagenesis studies and deuterium exchange experiments, we identify a unique proton exchange mechanism at the α-carbon of the o-hydroxylated trans-hydroxycinnamoyl-CoA substrates during the catalytic cycle of COSY. Quantum mechanical cluster modeling and molecular dynamics further support this key mechanism for lowering the activation energy of the rate-limiting trans-to-cis isomerization step in coumarin production. This study unveils an unconventional catalytic mechanism mediated by a BAHD-family enzyme, and sheds light on COSY's evolutionary origin and its recruitment to coumarin biosynthesis in eudicots.

Measurement of time dependent product branching ratios indicates two-state reactivity in metal mediated chemical reactions.

For several decades, the influence of Two State Reactivity (TSR) has been implicated in a host of reactions, but has lacked a stand-alone, definitive experimental kinetic signature identifying its occurrence. Here, we demonstrate that the measurement of a temporally dependent product branching ratio is indicative of spin inversion and is a kinetic signature of TSR. This is caused by products exiting different hypersurfaces with different rates and relative exothermicities. The composite measurement of product intensities with the same mass but with different multiplicities yield biexponential temporal dependences with the sampled product ratio changing in time. These measurements are made using the single photon initiated dissociative rearrangement reaction (SPIDRR) technique which identifies TSR but further determines the kinetic parameters for reaction along the original ground electronic surface in competition with spin inversion and its consequent TSR.

Sorting droplets into many outlets.

Droplet microfluidics is a commercially successful technology, widely used in single cell sequencing and droplet PCR. Combining droplet making with droplet sorting has also been demonstrated, but so far found limited use, partly due to difficulties in scaling manufacture with injection molded plastics. We introduce a droplet sorting system with several new elements, including: 1) an electrode design combining metallic and ionic liquid parts, 2) a modular, multi-sorting fluidic design with features for keeping inter-droplet distances constant, 3) using timing parameters calculated from fluorescence or scatter signal triggers to precisely actuate dozens of sorting electrodes, 4) droplet collection techniques, including ability to collect a single droplet, and 5) a new emulsion breaking method to collect aqueous samples for downstream analysis. We use these technologies to build a fluorescence based cell sorter that can sort with high (>90%) purity. We also show that these microfluidic designs can be translated into injection molded thermoplastic, suitable for industrial production. Finally, we tally the advantages and limitations of these devices.

Corrigendum to "Data, data flows, and model specifications for linking multi-level contribution margin accounting with multi-level fixed-charge problems" [Data in Brief 35 (2021) 106931].

[This corrects the article DOI: 10.1016/j.dib.2021.106931.].

Erratum to "Making better decisions by applying mathematical optimization to cost accounting: An advanced approach to multi-level contribution margin accounting" [Heliyon 7 (2) (February 2021) e06096].

[This corrects the article DOI: 10.1016/j.heliyon.2021.e06096.].

Data, data flows, and model specifications for linking multi-level contribution margin accounting with multi-level fixed-charge problems.

This article describes the data, data flows, and spreadsheet implementations for linking multi-level contribution margin accounting as a subsystem in cost accounting with several versions of a multi-level fixed-charge problem (MLFCP), the latter based on the optimization approach in operations research. This linkage can reveal previously hidden optimization potentials within the framework of multi-level contribution margin accounting, thus providing better information for decision making in companies and other organizations. For the data, plausible fictitious values have been assumed taking into consideration the calculation principles in cost accounting where applicable. They include resource-related data, market-related data, and data from cost accounting needed to analyze the profitability of a company´s products and organizational entities in the presence of hierarchically structured fixed costs. The data are processed and analyzed by means of mathematical optimization techniques and sensitivity analysis. The linkage between multi-level contribution margin accounting and MLFCP is implemented in three spreadsheet files, including versions for deterministic optimization, stochastic optimization, and robust optimization. This paper provides specifications for compatible solver add-ins and for executing sensitivity analysis. The data and spreadsheet implementations described in this article were used in a research article entitled "Making better decisions by applying mathematical optimization to cost accounting: An advanced approach to multi-level contribution margin accounting" [1]. The data sets and the spreadsheet implementations may be reused a) by researchers in management and cost accounting as well as in operations research and quantitative methods for verification and for further development of the linkage concept and of the underlying optimization models; b) by practitioners for gaining insight into the data requirements, methods, and benefits of the proposed linkage, thus supporting continuing education; and c) by instructors in academia who may find the data and spreadsheets valuable for classroom use in advanced courses. The complete spreadsheet implementations in the form of three ready-to-use Excel files (deterministic, stochastic, and robust version) are available for download at Mendeley Data. They may serve as customizable templates for various use cases in research, practice, and education.

Making better decisions by applying mathematical optimization to cost accounting: An advanced approach to multi-level contribution margin accounting.

The purpose of multi-level contribution margin accounting in cost accounting is to analyze the profitability of products and organizational entities with appropriate allocation of fixed costs and to provide relevant information for short-term, medium- and longer-term decisions. However, the conventional framework of multi-level contribution margin accounting does not usually incorporate a mathematical optimization method that simultaneously integrates variable and fixed costs to determine the best possible product mix within hierarchically structured organizations. This may be surprising in that operations research provides an optimization model in the form of the fixed-charge problem (FCP) that takes into account not only variable costs but also fixed costs of the activities to be planned. This paper links the two approaches by expanding the FCP to a multi-level fixed-charge problem (MLFCP), which maps the hierarchical decomposition of fixed costs in accordance with multi-level contribution margin accounting. In this way, previously hidden optimization potentials can be made visible within the framework of multi-level contribution margin accounting. Applying the linkage to a case study illustrates that the original assessment of profitability gained on the sole basis of a multi-level contribution margin calculation might turn out to be inappropriate or even inverted as soon as mathematical optimization is utilized: products, divisions, and other reference objects for fixed cost allocation, which at first glance seem to be profitable (or unprofitable) might be revealed as actually unprofitable (or profitable), when the multi-level contribution margin calculation is linked to the MLFCP. Furthermore, the proposed concept facilitates assessment of the costs of an increasing variant diversity, which also demonstrates that common rules on how to interpret a multi-level contribution margin calculation may have to be revised in some cases from the viewpoint of optimization. Finally, the impact of changes in the fixed cost structure and other parameters is tested via sensitivity analyses and stochastic optimization.

Preventing and reversing vacuum-induced optical losses in high-finesse tantalum (V) oxide mirror coatings.

High-finesse optical cavities placed under vacuum are foundational platforms in quantum information science with photons and atoms. We study the vacuum-induced degradation of high-finesse optical cavities with mirror coatings composed of SiO2-Ta2O5 dielectric stacks, and present methods to protect these coatings and to recover their initial low loss levels. For separate coatings with reflectivities centered at 370 nm and 422 nm, a vacuum-induced continuous increase in optical loss occurs if the surface-layer coating is made of Ta2O5, while it does not occur if it is made of SiO2. The incurred optical loss can be reversed by filling the vacuum chamber with oxygen at atmospheric pressure, and the recovery rate can be strongly accelerated by continuous laser illumination at 422 nm. Both the degradation and the recovery processes depend strongly on temperature. We find that a 1 nm-thick layer of SiO2 passivating the Ta2O5 surface layer is sufficient to reduce the degradation rate by more than a factor of 10, strongly supporting surface oxygen depletion as the primary degradation mechanism.

Homology modeling of cannabinoid receptors: discovery of cannabinoid analogues for therapeutic use.

Cannabinoids represent a promising class of compounds for developing novel therapeutic agents. Since the isolation and identification of the major psychoactive component Δ(9)-THC in Cannabis sativa in the 1960s, numerous analogues of the classical plant cannabinoids have been synthesized and tested for their biological activity. These compounds primarily target the cannabinoid receptors 1 (CB1) and Cannabinoid receptors 2 (CB2). This chapter focuses on CB1. Despite the lack of crystal structures for CB1, protein-based homology modeling approaches and molecular docking methods can be used in the design and discovery of cannabinoid analogues. Efficient synthetic approaches for therapeutically interesting cannabinoid analogues have been developed to further facilitate the drug discovery process.

Underutilization of beta-adrenoceptor antagonists post-myocardial infarction.

Coronary artery disease continues to be the leading cause of death in the US. Several classes of drugs available today have shown benefit in decreasing the progression of coronary artery disease and its associated symptoms. When a patient experiences an acute coronary syndrome, beta-adrenoceptor antagonists are considered one of the cornerstones of medical therapy. Over the past 25 years, trials have demonstrated morbidity and mortality benefit when this class of drugs was given early in the post-myocardial infarction period. Subsequent substantial data have confirmed their beneficial effect on outcomes in other high-risk populations such as the elderly, those with left ventricular dysfunction, peripheral vascular disease, diabetic patients, and selected patients with reactive airway disease. Several reviews of hospital discharge data revealed that beta-adrenoceptor antagonists remain significantly underutilized in patients with acute, as well as chronic coronary artery disease. Misconceptions about the adverse effects and who would benefit probably account for physician reluctance to prescribe these medications. With rare exception, the overwhelming evidence currently supports the practice of prescribing beta-adrenoceptor antagonists to all patients immediately post-myocardial infarction and therapy to be continued indefinitely.