State Preparation in Quantum Algorithms for Fragment-Based Quantum Chemistry.

State preparation for quantum algorithms is crucial for achieving high accuracy in quantum chemistry and competing with classical algorithms. The localized active space-unitary coupled cluster (LAS-UCC) algorithm iteratively loads a fragment-based multireference wave function onto a quantum computer. In this study, we compare two state preparation methods, quantum phase estimation (QPE) and direct initialization (DI), for each fragment. We test the two state preparation methods on three systems, ranging from a model system, a set of interacting hydrogen molecules, to more realistic chemical problems, like the C-C double bond breaking in transbutadiene and the spin ladder in a bimetallic system. We analyze the impact of QPE parameters, such as the number of ancilla qubits and Trotter steps, on the prepared state. We find a trade-off between the methods, where DI requires fewer resources for smaller fragments, while QPE is more efficient for larger fragments. Our resource estimates highlight the benefits of system fragmentation in state preparation for subsequent quantum chemical calculations. These findings have broad applications for preparing multireference quantum chemical wave functions on quantum circuits that can be used for realistic chemical applications.

Emergence of a Low-Energy Peak in the Smoothed Absolute Value Circular Dichroism Spectra of Small Helical Gold Nanorods.

We calculate, using time-dependent density functional theory, absorption and circular dichroism (CD) spectra for a series of small helical gold nanorod structures with a width of 0.6 nm and length increasing from 0.7 nm for Au24 to 1.9 nm for Au56. For a low-energy window, ranging from 1.7 to 4.1 eV, broadening the lines in the absorption spectra results in a low energy peak which previous studies have identified as the (localized) plasmon resonance. As expected, the absorption peak position of the plasmon resonance systematically redshifts as the length of the nanorod increases. However, trends in the CD and straightforwardly broadened CD spectra are more difficult to discern. We introduce the idea of an absolute value CD spectrum and show that broadening the lines results in a low energy peak that has not previously been reported. The peak position systematically redshifts as the length of the nanorod increases but over a significantly smaller range than that for the absorption spectrum.

Artificial intelligence-based clinical decision support for liver transplant evaluation and considerations about fairness: A qualitative study.

BACKGROUND: The use of large-scale data and artificial intelligence (AI) to support complex transplantation decisions is in its infancy. Transplant candidate decision-making, which relies heavily on subjective assessment (ie, high variability), provides a ripe opportunity for AI-based clinical decision support (CDS). However, AI-CDS for transplant applications must consider important concerns regarding fairness (ie, health equity). The objective of this study was to use human-centered design methods to elicit providers' perceptions of AI-CDS for liver transplant listing decisions. METHODS: In this multicenter qualitative study conducted from December 2020 to July 2021, we performed semistructured interviews with 53 multidisciplinary liver transplant providers from 2 transplant centers. We used inductive coding and constant comparison analysis of interview data. RESULTS: Analysis yielded 6 themes important for the design of fair AI-CDS for liver transplant listing decisions: (1) transparency in the creators behind the AI-CDS and their motivations; (2) understanding how the AI-CDS uses data to support recommendations (ie, interpretability); (3) acknowledgment that AI-CDS could mitigate emotions and biases; (4) AI-CDS as a member of the transplant team, not a replacement; (5) identifying patient resource needs; and (6) including the patient's role in the AI-CDS. CONCLUSIONS: Overall, providers interviewed were cautiously optimistic about the potential for AI-CDS to improve clinical and equitable outcomes for patients. These findings can guide multidisciplinary developers in the design and implementation of AI-CDS that deliberately considers health equity.

Biomechanical determinants of endothelial permeability assessed in standard and modified hollow-fibre bioreactors.

Effects of mechanical stress on the permeability of vascular endothelium are important to normal physiology and in the development of atherosclerosis. Here we elucidate novel effects using commercially available and modified hollow-fibre bioreactors, in which endothelial cells form confluent monolayers lining plastic capillaries with porous walls, contained in a cartridge. The capillaries were perfused with a near-aortic waveform, and permeability was assessed by the movement of rhodamine-labelled albumin from the intracapillary to the extracapillary space. Permeability was increased by acute application of shear stress and decreased by chronic shear stress compared with a static control: this has previously been shown only for multidirectional flows. Increasing viscosity reduced permeability under both acute and chronic shear; since shear rate remained unchanged, these effects resulted from altered shear stress. Reducing pulsatility increased permeability, contrary to the widely held assumption that flow which is highly oscillatory causes endothelial dysfunction. Chronic convection across the monolayer increased effective permeability more than could be explained by the addition of advective transport, contrary to results from previous acute experiments. The off-the-shelf and modified bioreactors provide an excellent tool for investigating the biomechanics of endothelial permeability and have revealed novel effects of flow duration, viscosity, pulsatility and transmural flow.

Recombinase-independent chromosomal rearrangements between dispersed inverted repeats in Saccharomyces cerevisiae meiosis.

DNA double-strand break (DSB) repair by homologous recombination (HR) uses a DNA template with similar sequence to restore genetic identity. Allelic DNA repair templates can be found on the sister chromatid or homologous chromosome. During meiotic recombination, DSBs preferentially repair from the homologous chromosome, with a proportion of HR events generating crossovers. Nevertheless, regions of similar DNA sequence exist throughout the genome, providing potential DNA repair templates. When DSB repair occurs at these non-allelic loci (termed ectopic recombination), chromosomal duplications, deletions and rearrangements can arise. Here, we characterize in detail ectopic recombination arising between a dispersed pair of inverted repeats in wild-type Saccharomyces cerevisiae at both a local and a chromosomal scale-the latter identified via gross chromosomal acentric and dicentric chromosome rearrangements. Mutation of the DNA damage checkpoint clamp loader Rad24 and the RecQ helicase Sgs1 causes an increase in ectopic recombination. Unexpectedly, additional mutation of the RecA orthologues Rad51 and Dmc1 alters-but does not abolish-the type of ectopic recombinants generated, revealing a novel class of inverted chromosomal rearrangement driven by the single-strand annealing pathway. These data provide important insights into the role of key DNA repair proteins in regulating DNA repair pathway and template choice during meiosis.

Dynamic regulatory phosphorylation of mouse CDK2 occurs during meiotic prophase I.

During prophase I of meiosis, DNA double-strand breaks form throughout the genome, with a subset repairing as crossover events, enabling the accurate segregation of homologous chromosomes during the first meiotic division. The mechanism by which DSBs become selected to repair as crossovers is unknown, although the crossover positioning and levels in each cell indicate it is a highly regulated process. One of the proteins that localises to crossover sites is the serine/threonine cyclin-dependent kinase CDK2. Regulation of CDK2 occurs via phosphorylation at tyrosine 15 (Y15) and threonine 160 (T160) inhibiting and activating the kinase, respectively. In this study we use a combination of immunofluorescence staining on spread spermatocytes and fixed testis sections, and STA-PUT gravitational sedimentation to isolate cells at different developmental stages to further investigate the temporal phospho regulation of CDK2 during prophase I. Western blotting reveals differential levels of the two CDK2 isoforms (CDK233kDa and CDK239kDa) throughout prophase I, with inhibitory phosphorylation of CDK2 at Y15 occurring early in prophase I, localising to telomeres and diminishing as cells enter pachynema. Conversely, the activatory phosphorylation on T160 occurs later, specifically the CDK233kDa isoform, and T160 signal is detected in spermatogonia and pachytene spermatocytes, where it co-localises with the Class I crossover protein MLH3. Taken together, our data reveals intricate control of CDK2 both with regards to levels of the two CDK2 isoforms, and differential regulation via inhibitory and activatory phosphorylation.

A chemical credit framework to predict the removal performance of organic chemicals of concern from water through an ozonation process.

Ozonation is an effective barrier for removing a wide spectrum of organic Chemicals of Concern (CoC) in a water treatment process. In this study, bench- and full-scale tests were conducted on a secondary treated effluent at the Eastern Treatment Plant (ETP) of Melbourne Water to probe the performance of ozonation in removing CoC in a wastewater discharge. From the secondary treated effluent as the feed to the ozone process, 58 organic chemicals were measured out of a possible 949 compounds by using the AIQS-DB analytical method. A chemical credit framework for the ozonation process has been established according to the bench-scale results. Chemical classifications based on the chemical structures (aromatics, aliphatic and halogenated aliphatic compounds) and reaction rate constants with O3 (KO3) and the ∙OH radical (K∙OH) and a combined O3/TOC ratio and O3 CT value as operating parameters were confirmed to be useful and important in determining whether a chemical would be removed by ozone. It is shown that an O3/TOC ratio of >0.404 was shown to be necessary to overcome the instantaneous ozone demand (IOD) to guarantee enough ozone to oxidise CoC. For CoC with KO3 >105M - 1s - 1 and K∙OH >109M - 1s - 1, an O3/TOC ratio of ≥0.461 or a measurable O3 CT of ≥0.063 mg min/L can achieve log reduction values (LRVs) of ≥1, these are chemicals with aromatic structures; For CoC with low KO3 and high KOH, a combined O3/TOC ratio and O3 CT value inclusive of a chemical structure classification is indicated as necessary criteria to evaluate the removal. UV254 and TOC were demonstrated to be good online surrogates of ozone barrier performance in the absence of continuous O3/TOC ratio and O3 CT value measurements. Full-scale operational results confirm the effective predictions of the chemical credit framework, which highlights the necessity and importance of monitoring both the O3/TOC ratio and O3 CT values to predict the removal efficiency of a given chemical with a known response to O3 or a known chemical structure.

Review of influence of critical operation conditions on by-product/intermediate formation during thermal destruction of PFAS in solid/biosolids.

Poly- and perfluoroalkyl substances (PFAS) are a large group of synthetic organofluorine compounds. Over 4700 PFAS compounds have been produced and used in our daily life since the 1940s. PFAS have received considerable interest because of their toxicity, environmental persistence, bioaccumulation and wide existence in the environment. Various treatment methods have been developed to overcome these issues. Thermal treatment such as combustion and pyrolysis/gasification have been employed to treat PFAS contaminated solids and soils. However, short-chain PFAS and/or volatile organic fluorine is produced and emitted via exhaust gas during the thermal treatment. Combustion can achieve complete mineralisation of PFAS at large scale operation using temperatures >1000 °C. Pyrolysis has been used in treatment of biosolids and has demonstrated that it could remove PFAS completely from the generated biochar by evaporation and degradation. Although pyrolysis partially degrades PFAS to short-chain fluorine containing organics in the syngas, it could not efficiently mineralise PFAS. Combustion of PFAS containing syngas at 1000 °C can achieve complete mineralisation of PFAS. Furthermore, the by-product of mineralisation, HF, should also be monitored due to its low regulated atmospheric discharge values. Alkali scrubbing is normally required to lower the HF concentration in the exhaust gas to acceptable discharge concentrations.

Localized Quantum Chemistry on Quantum Computers.

Quantum chemistry calculations of large, strongly correlated systems are typically limited by the computation cost that scales exponentially with the size of the system. Quantum algorithms, designed specifically for quantum computers, can alleviate this, but the resources required are still too large for today's quantum devices. Here, we present a quantum algorithm that combines a localization of multireference wave functions of chemical systems with quantum phase estimation (QPE) and variational unitary coupled cluster singles and doubles (UCCSD) to compute their ground-state energy. Our algorithm, termed "local active space unitary coupled cluster" (LAS-UCC), scales linearly with the system size for certain geometries, providing a polynomial reduction in the total number of gates compared with QPE, while providing accuracy above that of the variational quantum eigensolver using the UCCSD ansatz and also above that of the classical local active space self-consistent field. The accuracy of LAS-UCC is demonstrated by dissociating (H2)2 into two H2 molecules and by breaking the two double bonds in trans-butadiene, and resource estimates are provided for linear chains of up to 20 H2 molecules.

Combined effects of emitter-emitter and emitter-plasmonic surface separations dictate photoluminescence enhancement in a plasmonic field.

The brightness of an emitter can be enhanced by metal-enhanced fluorescence, wherein the excitonic dipole couples with the electromagnetic field of the surface plasmon. Herein, we experimentally map the landscape of photoluminescence enhancement (EFexp) of emitters in a plasmonic field as a function of the emitter-emitter separation, s, and the emitter-plasmon distance, t. We use Au nanoparticles overcoated with inert spacers as plasmonic systems and CdSe/ZnS quantum dots (QDs) as an emitter bearing opposite surface charges. The t and s are varied by changing the spacer thickness and number density of QDs on the plasmonic surface, respectively. The electrostatic binding of emitters on the plasmonic surface and their number density are established by following the variation of zeta-potential. EFexp is high, when t is short and s is large; nevertheless, it decreases when the emitter-emitter interaction dominates due to plasmon assisted nonradiative processes. In the absence of a plasmonic field, the enhancement observed is attributed to environmental effects and is independent of s, confirming the role of the electric field. Indeed, the distance dependence of EFexp closely follows the decay of the plasmonic field upon dilution of the emitter concentration on nanoparticles' surface (s = 18 nm). The QD-plasmon system is visualized in the framework of the Thomson problem, and classical electrodynamics calculations give the trends in t and s dependence of the photoluminescence. Being the first report on the simultaneous dependence of t and s on plasmon-enhanced photoluminescence, the results presented herein will open newer opportunities in the design of hybrid systems with a high brightness.

Role of EXO1 nuclease activity in genome maintenance, the immune response and tumor suppression in Exo1D173A mice.

DNA damage response pathways rely extensively on nuclease activity to process DNA intermediates. Exonuclease 1 (EXO1) is a pleiotropic evolutionary conserved DNA exonuclease involved in various DNA repair pathways, replication, antibody diversification, and meiosis. But, whether EXO1 facilitates these DNA metabolic processes through its enzymatic or scaffolding functions remains unclear. Here, we dissect the contribution of EXO1 enzymatic versus scaffolding activity by comparing Exo1DA/DA mice expressing a proven nuclease-dead mutant form of EXO1 to entirely EXO1-deficient Exo1-/- and EXO1 wild type Exo1+/+ mice. We show that Exo1DA/DA and Exo1-/- mice are compromised in canonical DNA repair processing, suggesting that the EXO1 enzymatic role is important for error-free DNA mismatch and double-strand break repair pathways. However, in non-canonical repair pathways, EXO1 appears to have a more nuanced function. Next-generation sequencing of heavy chain V region in B cells showed the mutation spectra of Exo1DA/DA mice to be intermediate between Exo1+/+ and Exo1-/- mice, suggesting that both catalytic and scaffolding roles of EXO1 are important for somatic hypermutation. Similarly, while overall class switch recombination in Exo1DA/DA and Exo1-/- mice was comparably defective, switch junction analysis suggests that EXO1 might fulfill an additional scaffolding function downstream of class switching. In contrast to Exo1-/- mice that are infertile, meiosis progressed normally in Exo1DA/DA and Exo1+/+ cohorts, indicating that a structural but not the nuclease function of EXO1 is critical for meiosis. However, both Exo1DA/DA and Exo1-/- mice displayed similar mortality and cancer predisposition profiles. Taken together, these data demonstrate that EXO1 has both scaffolding and enzymatic functions in distinct DNA repair processes and suggest a more composite and intricate role for EXO1 in DNA metabolic processes and disease.

Multicenter study of racial and ethnic inequities in liver transplantation evaluation: Understanding mechanisms and identifying solutions.

Racial and ethnic disparities persist in access to the liver transplantation (LT) waiting list; however, there is limited knowledge about underlying system-level factors that may be responsible for these disparities. Given the complex nature of LT candidate evaluation, a human factors and systems engineering approach may provide insights. We recruited participants from the LT teams (coordinators, advanced practice providers, physicians, social workers, dieticians, pharmacists, leadership) at two major LT centers. From December 2020 to July 2021, we performed ethnographic observations (participant-patient appointments, committee meetings) and semistructured interviews (N = 54 interviews, 49 observation hours). Based on findings from this multicenter, multimethod qualitative study combined with the Systems Engineering Initiative for Patient Safety 2.0 (a human factors and systems engineering model for health care), we created a conceptual framework describing how transplant work system characteristics and other external factors may improve equity in the LT evaluation process. Participant perceptions about listing disparities described external factors (e.g., structural racism, ambiguous national guidelines, national quality metrics) that permeate the LT evaluation process. Mechanisms identified included minimal transplant team diversity, implicit bias, and interpersonal racism. A lack of resources was a common theme, such as social workers, transportation assistance, non-English-language materials, and time (e.g., more time for education for patients with health literacy concerns). Because of the minimal data collection or center feedback about disparities, participants felt uncomfortable with and unadaptable to unwanted outcomes, which perpetuate disparities. We proposed transplant center-level solutions (i.e., including but not limited to training of staff on health equity) to modifiable barriers in the clinical work system that could help patient navigation, reduce disparities, and improve access to care. Our findings call for an urgent need for transplant centers, national societies, and policy makers to focus efforts on improving equity (tailored, patient-centered resources) using the science of human factors and systems engineering.

Cost and efficiency perspectives of ceramic membranes for water treatment.

More robust ceramic membranes with tailorable structures and functions are increasingly employed for water treatment, particularly in some harsh applications for their ultra-long service lifespan due to their high mechanical, structural, chemical and thermal stability and anti-fouling properties. Decreasing cost and enhancing efficiency are two key but quite challenging application-oriented issues for broader and larger-scale engineering application of current ceramic membranes, and are required to make ceramic membranes a highly efficient and economic water treatment technique. In this review, we critically discuss these two significant concerns of both cost and efficiency for water treatment ceramic membranes, focusing on an overview of various advanced strategies and mechanism insights. A brief up-to-date discussion is first introduced about recent developments of ceramic membranes covering the major advances of novel membranes and applications. Then some promising strategies for decreasing the cost of ceramic membranes are discussed, including membrane material cost and processing cost. To fully address the issue of moderate efficiency with single separation function, valuable and considerable insights are provided into recent major progress and mechanism understandings in application with other unit processes, such as advanced oxidation and electrochemistry techniques, to significantly enhance treatment efficiency. Subsequently, a review of recent ceramic membrane applications emphasizing harsh operating environments is presented, such as oil-water separation, saline water, refractory organic and emerging contaminant wastewater treatment. Finally, engineering application, conclusions, and future perspectives of ceramic membrane for water treatment applications are critically discussed offering new insight based on understanding the issues of cost and efficiency.

Clinical Practice Issues for Liver Transplantation in COVID-19 Recovered Recipients.

The ongoing burden of COVID-19 in persons with end stage liver failure necessitates the development of sound and rational policies for organ transplantation in this population. Following our initial experience with two COVID-19 recovered recipients who died shortly after transplant, we adjusted our center policies, re-evaluated outcomes, and retrospectively analyzed the clinical course of the subsequent seven COVID-19 recovered recipients. There were two early deaths and 5 successful outcomes. Both deceased patients shared common characteristics in that they had positive SARS-CoV2 PCR tests proximal to transplant (7-17 days), had acute on chronic liver failure, and suffered thromboembolic phenomena. After a careful review of clinical and virological outcome predictors, we instituted policy changes to avoid transplantation in these circumstances. We believe that our series offers useful insights into the unique challenges that confront transplant centers in the COVID-19 era and could guide future discussions regarding this important area.

Remediation of poly-and perfluoroalkyl substances (PFAS) contaminated soil using gas fractionation enhanced technology.

This study investigated a gas fractionation enhanced soil washing method for poly-and perfluoroalkyl substances (PFAS) removal from contaminated soil. With the assistance of gas fractionation, PFAS removal was increased by a factor of 9, compared to the conventional soil washing method. Pre-extraction (pre-treatment) of the soil with water before gas fractionation enhanced PFAS removal from soil. The optimum extraction time varied based on the soil particle size, since it will change the swelling time of the soil. The influence of various operational conditions such as water to soil mass ratio (W:S ratio), gas type in fractionation, gas flowrate, fractionation time and soil pre-treatment condition have been studied to identify the critical influencing factors. Among various W:S ratios (2, 4, 5, 6, 8, and 10) studied, higher W:S ratio resulted in better PFAS removals, but PFAS removal began to plateau as the W:S ratio increased. PFAS removal could be improved by repeated treatment with low water consumption. Air, oxygen, and ozone generated by air and oxygen were used, in which ozone generated by oxygen achieved the highest PFAS removals of 55.9%. Among different fractionation times (10 min, 20 min and 30 min), a fractionation time of 20 min achieved better total PFAS removal for studied soil, because PFOS was the dominant species in the total PFAS. However, the removal of some PFAS species, such as PFHxS, would be increased with extended fractionation time. With constant fractionation time (10 min), PFAS removal performance improved with the increasing gas flowrate.

Treatment of oily wastewaters by highly porous whisker-constructed ceramic membranes: Separation performance and fouling models.

Efficient treatment of challenging oily emulsion wastewater can alleviate water pollution to provide more chances for water reuse and resource recovery. Despite their promising application potential, conventional porous ceramic membranes have challenging bottleneck issues such as high cost and insufficient permeance. This study presents a new strategy for highly efficient treatment of not only synthetic but real oily emulsions via unexpensive whisker-constructed ceramic membranes, exhibiting exceptional permeance and less energy input. Compared with common ceramic membranes, such lower-cost mullite membranes with a novel whisker-constructed structure show higher porosity and water permeance, and better surface oleophobicity in water. Treatment performance such as permeate flux and oil rejection was explored for the oily emulsions with different properties under key operating parameters. Furthermore, classical Hermia models were used to reveal membrane fouling mechanism to well understand the microscopic interactions between emulsion droplets and membrane interface. Even for real acidic oily wastewater, such membranes also exhibit high permeance and less energy consumption, outperforming most state-of-the-art ceramic membranes. This work provides a new structure concept of highly permeably whisker-constructed porous ceramic membranes that can efficiently enable more water separation applications.

Learning in continuous action space for developing high dimensional potential energy models.

Reinforcement learning (RL) approaches that combine a tree search with deep learning have found remarkable success in searching exorbitantly large, albeit discrete action spaces, as in chess, Shogi and Go. Many real-world materials discovery and design applications, however, involve multi-dimensional search problems and learning domains that have continuous action spaces. Exploring high-dimensional potential energy models of materials is an example. Traditionally, these searches are time consuming (often several years for a single bulk system) and driven by human intuition and/or expertise and more recently by global/local optimization searches that have issues with convergence and/or do not scale well with the search dimensionality. Here, in a departure from discrete action and other gradient-based approaches, we introduce a RL strategy based on decision trees that incorporates modified rewards for improved exploration, efficient sampling during playouts and a "window scaling scheme" for enhanced exploitation, to enable efficient and scalable search for continuous action space problems. Using high-dimensional artificial landscapes and control RL problems, we successfully benchmark our approach against popular global optimization schemes and state of the art policy gradient methods, respectively. We demonstrate its efficacy to parameterize potential models (physics based and high-dimensional neural networks) for 54 different elemental systems across the periodic table as well as alloys. We analyze error trends across different elements in the latent space and trace their origin to elemental structural diversity and the smoothness of the element energy surface. Broadly, our RL strategy will be applicable to many other physical science problems involving search over continuous action spaces.