bluuebunny/crossref_metadata_2025_split huggingface dataset:
Numerical study of the radio-frequency biased accelerating system in ion thrusters
Authors: BAI Jinwei , CAO Yong , LI Yang , WANG Kaifa , TIAN Bin , HU Yuan 
Published: February 2023

Abstract
A 2D-3V implicit immersed-finite-element particle-in-cell (IFE-PIC) model is introduced to investigate the radio-frequency (RF) self-bias accelerating system applied in the RF ion thruster. A set of holes in a two-grid system with slit apertures is simulated in Cartesian coordinates. The characteristics of the plasma plume, such as the ion density, the neutralization rate and the ion and electron current density were investigated for different RF voltage amplitudes (600−1200 V) and frequencies (6−30 MHz). Furthermore, the performance of the thruster was also carefully studied. The simulation results show that a well-focused plasma beam can be formed when the voltage amplitude is larger than 900 V and the frequency exceeds the reciprocal of ion transit time (≥12 MHz) in our simulation cases. The performance of the system can be evidently improved by increasing the voltage amplitude and the frequency, and the losses of the particle and thrust are reduced correspondingly. The bulk region of the plasma beam downstream shows good quasi-neutrality, and the ions are dominant in the peripheral region when a well-focused state is achieved. The high ion density beamlet in the periphery of the ion beam is closer to the axis when the voltage amplitude is increasing, while it is expanded radially when increasing the frequency. Backstream electrons have been observed upstream, and this mainly occurs in the phase in which the electron cannot escape.
Quantum control of tunable-coupling transmons using dynamical invariants of motion
Authors: Espinós H , Panadero I , García-Ripoll J J , Torrontegui E 
Published: February 2023

Abstract
We analyze the implementation of a fast nonadiabatic CZ gate between two transmon qubits with tunable coupling. The gate control method is based on a theory of dynamical invariants which leads to reduced leakage and robustness against decoherence. The gate is based on a description of the resonance between the

|
11
⟩

and

|
20
⟩

using an effective Hamiltonian with the six lowest energy states. A modification of the protocol allows us to take into account the higher-order perturbative corrections of this effective model. This enables a gate fidelity several orders of magnitude higher than other quasiadiabatic protocols, with gate times that approach the theoretical limit.
Optimal control in stochastic thermodynamics
Authors: Blaber Steven , Sivak David A 
Published: February 2023

Abstract
We review recent progress in optimal control in stochastic thermodynamics. Theoretical advances provide in-depth insight into minimum-dissipation control with either full or limited (parametric) control, and spanning the limits from slow to fast driving and from weak to strong driving. Known exact solutions give a window into the properties of minimum-dissipation control, which are reproduced by approximate methods in the relevant limits. Connections between optimal-transport theory and minimum-dissipation protocols under full control give deep insight into the properties of optimal control and place bounds on the dissipation of thermodynamic processes. Since minimum-dissipation protocols are relatively well understood and advanced approximation methods and numerical techniques for estimating minimum-dissipation protocols have been developed, now is an opportune time for application to chemical and biological systems.
Nanoscale direct-write fabrication of superconducting devices for application in quantum technologies
Authors: De Teresa José María 
Published: February 2023

Abstract
In this Perspective article, we evaluate the current state of research on the use of focused electron and ion beams to directly fabricate nanoscale superconducting devices with application in quantum technologies. First, the article introduces the main superconducting devices and their fabrication by means of standard lithography techniques such as optical lithography and electron beam lithography. Then, focused ion beam patterning of superconductors through milling or irradiation is shown, as well as the growth of superconducting devices by means of focused electron and ion beam induced deposition. We suggest that the key benefits of these resist-free direct-growth techniques for quantum technologies include the ability to make electrical nanocontacts and circuit edit, fabrication of high-resolution superconducting resonators, creation of Josephson junctions and superconducting quantum interference device (SQUIDs) for on-tip sensors, patterning of high-Tc SQUIDs and other superconducting circuits, and the exploration of fluxtronics and topological superconductivity.
US power sector carbon capture and storage under the Inflation Reduction Act could be costly with limited or negative abatement potential
Authors: Grubert Emily , Sawyer Frances 
Published: February 2023

Abstract
The United States’ (US) largest-ever investment in expected climate mitigation, through 2022’s Inflation Reduction Act (IRA), relies heavily on subsidies. One major subsidy, the 45Q tax credit for carbon oxide sequestration, incentivizes emitters to maximize production and sequestration of carbon oxides, not abatement. Under IRA’s 45Q changes, carbon capture and storage (CCS) is expected to be profitable for coal- and natural gas-based electricity generator owners, particularly regulated utilities that earn a guaranteed rate of return on capital expenditures, despite being costlier than zero-carbon resources like wind or solar. This analysis explores investment decisions driven by profitability rather than system cost minimization, particularly where investments enhance existing assets with an incumbent workforce, existing supplier relationships, and internal knowledge-base. This analysis introduces a model and investigates six scenarios for lifespan extension and capacity factor changes to show that US CCS fossil power sector retrofits could demand $0.4–$3.6 trillion in 45Q tax credits to alter greenhouse gas emissions by −24% ($0.4 trillion) to +82% ($3.6 trillion) versus business-as-usual for affected generators. Particularly given long lead times, limited experience, and the potential for CCS projects to crowd or defer more effective alternatives, regulators should be extremely cautious about power sector CCS proposals.
A novel strategy for dynamic modeling of genome-scale interaction networks
Authors: Borzou Pooya , Ghaisari Jafar , Izadi Iman , Eshraghi Yasin , Gheisari Yousof 
Published: February 2023

AbstractMotivationThe recent availability of omics data allows the construction of holistic maps of interactions between numerous role-playing biomolecules. However, these networks are often static, ignoring the dynamic behavior of biological processes. On the other hand, dynamic models are commonly constructed on small scales. Hence, the construction of large-scale dynamic models that can quantitatively predict the time-course cellular behaviors remains a big challenge.ResultsIn this study, a pipeline is proposed for the automatic construction of large-scale dynamic models. The pipeline uses a list of biomolecules and their time-course trajectories in a given phenomenon as input. First, the interaction network of the biomolecules is constructed. To state the underlying molecular events of each interaction, it is translated into a map of biochemical reactions. Next, to define the kinetics of the reactions, an ordinary differential equation (ODE) is generated for each involved biomolecule. Finally, the parameters of the ODE system are estimated by a novel large-scale parameter approximation method. The high performance of the pipeline is demonstrated by modeling the response of a colorectal cancer cell line to different chemotherapy regimens. In conclusion, Systematic Protein Association Dynamic ANalyzer constructs genome-scale dynamic models, filling the gap between large-scale static and small-scale dynamic modeling strategies. This simulation approach allows for holistic quantitative predictions which are critical for the simulation of therapeutic interventions in precision medicine.Availability and implementationDetailed information about the constructed large-scale model of colorectal cancer is available in supplementary data. The SPADAN toolbox source code is also available on GitHub (https://github.com/PooyaBorzou/SPADAN).Supplementary informationSupplementary data are available at Bioinformatics online.
scGCL: an imputation method for scRNA-seq data based on graph contrastive learning
Authors: Xiong Zehao , Luo Jiawei , Shi Wanwan , Liu Ying , Xu Zhongyuan , Wang Bo 
Published: February 2023

AbstractMotivationSingle-cell RNA-sequencing (scRNA-seq) is widely used to reveal cellular heterogeneity, complex disease mechanisms and cell differentiation processes. Due to high sparsity and complex gene expression patterns, scRNA-seq data present a large number of dropout events, affecting downstream tasks such as cell clustering and pseudo-time analysis. Restoring the expression levels of genes is essential for reducing technical noise and facilitating downstream analysis. However, existing scRNA-seq data imputation methods ignore the topological structure information of scRNA-seq data and cannot comprehensively utilize the relationships between cells.ResultsHere, we propose a single-cell Graph Contrastive Learning method for scRNA-seq data imputation, named scGCL, which integrates graph contrastive learning and Zero-inflated Negative Binomial (ZINB) distribution to estimate dropout values. scGCL summarizes global and local semantic information through contrastive learning and selects positive samples to enhance the representation of target nodes. To capture the global probability distribution, scGCL introduces an autoencoder based on the ZINB distribution, which reconstructs the scRNA-seq data based on the prior distribution. Through extensive experiments, we verify that scGCL outperforms existing state-of-the-art imputation methods in clustering performance and gene imputation on 14 scRNA-seq datasets. Further, we find that scGCL can enhance the expression patterns of specific genes in Alzheimer’s disease datasets.Availability and implementationThe code and data of scGCL are available on Github: https://github.com/zehaoxiong123/scGCL.Supplementary informationSupplementary data are available at Bioinformatics online.
Equivariant estimation of Fréchet means
Authors: McCormack A , Hoff P D 
Published: February 2023

SummaryThe Fréchet mean generalizes the concept of a mean to a metric space setting. In this work we consider equivariant estimation of Fréchet means for parametric models on metric spaces that are Riemannian manifolds. The geometry and symmetry of such a space are partially encoded by its isometry group of distance-preserving transformations. Estimators that are equivariant under the isometry group take into account the symmetry of the metric space. For some models, there exists an optimal equivariant estimator, which will necessarily perform as well or better than other common equivariant estimators, such as the maximum likelihood estimator or the sample Fréchet mean. We derive the general form of this minimum risk equivariant estimator and in a few cases provide explicit expressions for it. A result for finding the Fréchet mean for distributions with radially decreasing densities is presented and used to find expressions for the minimum risk equivariant estimator. In some models the isometry group is not large enough relative to the parametric family of distributions for there to exist a minimum risk equivariant estimator. In such cases, we introduce an adaptive equivariant estimator that uses the data to select a submodel for which there is a minimum risk equivariant estimator. Simulation results show that the adaptive equivariant estimator performs favourably relative to alternative estimators.
Large-scale transient peri-ictal perfusion magnetic resonance imaging abnormalities detected by quantitative image analysis
Authors: Köstner Manuel , Rebsamen Michael , Radojewski Piotr , Rummel Christian , Jin Baudouin , Meier Raphael , Ahmadli Uzeyir , Schindler Kaspar , Wiest Roland 
Published: February 2023

AbstractEpileptic seizures require a rapid and safe diagnosis to minimize the time from onset to adequate treatment. Some epileptic seizures can be diagnosed clinically with the respective expertise. For more subtle seizures, imaging is mandatory to rule out treatable structural lesions and potentially life-threatening conditions. MRI perfusion abnormalities associated with epileptic seizures have been reported in CT and MRI studies. However, the interpretation of transient peri-ictal MRI abnormalities is routinely based on qualitative visual analysis and therefore reader dependent. In this retrospective study, we investigated the diagnostic yield of visual analysis of perfusion MRI during ictal and postictal states based on comparative expert ratings in 51 patients. We further propose an automated semi-quantitative method for perfusion analysis to determine perfusion abnormalities observed during ictal and postictal MRI using dynamic susceptibility contrast MRI, which we validated on a subcohort of 27 patients. The semi-quantitative method provides a parcellation of 3D T1-weighted images into 32 standardized cortical regions of interests and subcortical grey matter structures based on a recently proposed method, direct cortical thickness estimation using deep learning–based anatomy segmentation and cortex parcellation for brain anatomy segmentation. Standard perfusion maps from a Food and Drug Administration–approved image analysis tool (Olea Sphere 3.0) were co-registered and investigated for region-wise differences between ictal and postictal states. These results were compared against the visual analysis of two readers experienced in functional image analysis in epilepsy. In the ictal group, cortical hyperperfusion was present in 17/18 patients (94% sensitivity), whereas in the postictal cohort, cortical hypoperfusion was present only in 9/33 (27%) patients while 24/33 (73%) showed normal perfusion. The (semi-)quantitative dynamic susceptibility contrast MRI perfusion analysis indicated increased thalamic perfusion in the ictal cohort and hypoperfusion in the postictal cohort. Visual ratings between expert readers performed well on the patient level, but visual rating agreement was low for analysis of subregions of the brain. The asymmetry of the automated image analysis correlated significantly with the visual consensus ratings of both readers. We conclude that expert analysis of dynamic susceptibility contrast MRI effectively discriminates ictal versus postictal perfusion patterns. Automated perfusion evaluation revealed favourable interpretability and correlated well with the classification of the visual ratings. It may therefore be employed for high-throughput, large-scale perfusion analysis in extended cohorts, especially for research questions with limited expert rater capacity.
Caloric restriction for the immunometabolic control of human health
Authors: Procaccini Claudio , de Candia Paola , Russo Claudia , De Rosa Giusy , Lepore Maria Teresa , Colamatteo Alessandra , Matarese Giuseppe 
Published: February 2023

Abstract
Nutrition affects all physiological processes occurring in our body, including those related to the function of the immune system; indeed, metabolism has been closely associated with the differentiation and activity of both innate and adaptive immune cells. While excessive energy intake and adiposity have been demonstrated to cause systemic inflammation, several clinical and experimental evidence show that calorie restriction (CR), not leading to malnutrition, is able to delay aging and exert potent anti-inflammatory effects in different pathological conditions. This review provides an overview of the ability of different CR-related nutritional strategies to control autoimmune, cardiovascular, and infectious diseases, as tested by preclinical studies and human clinical trials, with a specific focus on the immunological aspects of these interventions. In particular, we recapitulate the state of the art on the cellular and molecular mechanisms pertaining to immune cell metabolic rewiring, regulatory T cell expansion, and gut microbiota composition, which possibly underline the beneficial effects of CR. Although studies are still needed to fully evaluate the feasibility and efficacy of the nutritional intervention in clinical practice, the experimental observations discussed here suggest a relevant role of CR in lowering the inflammatory state in a plethora of different pathologies, thus representing a promising therapeutic strategy for the control of human health.
Race Theory versus a Religious World-View: SS–Ustaša Relations and Islam in the Independent State of Croatia
Authors: Bartulin Nevenko 
Published: February 2023

Abstract
This article analyses SS policy toward the Bosnian Muslims of the Independent State of Croatia (NDH) within the context of the ideological and political relationship between the German Reich and the Ustaša regime. As part of its broader aim of mobilising Muslim support for Germany during the Second World War, the SS adopted and pursued a pan-Islamic policy in its effort to recruit Muslim soldiers for the Croatian-Bosnian Waffen-SS Handschar Division. Although the SS officially regarded the Bosnian Muslims as ‘Croats of the Islamic faith’ and Aryans, SS propaganda focused on the appeal to religious sentiments and treated them primarily as members of a global Islamic community. This unique pan-Islamic policy was the product not only of broader geopolitical aims that arose in reaction to wartime exigencies but also a widespread Nazi Islamophilic attitude that was combined with the anti-Catholic ideology characteristic of the SS leadership. The SS’s pro-Islamic policy actually undermined one of the main political-ideological aims of the Ustaša government, namely, the integration of the Bosnian Muslims into the Aryan-Croatian ‘national community’. Contrary to the widespread historiographical view that the Ustaše were a politically Catholic movement, this article highlights the fact that they adhered to a clearly secular racial-nationalist ideology, while the SS exaggerated the influence of clericalism in the NDH. Historiographical accounts of SS policy toward Islam in the Balkans have tended to play down the role of the Ustaše and Nazi anti-Catholicism, even though a more thorough analysis of SS-Ustaša relations can shed more light, as this article shows, on the precise nature of the relationship between race and religion in National Socialist ideology.
The legacies of war for Ukraine
Authors: Munroe Ellen , Nosach Anastasiia , Pedrozo Moisés , Guarnieri Eleonora , Riaño Juan Felipe , Tur-Prats Ana , Valencia Caicedo Felipe 
Published: February 2023

Abstract
This article reviews the literature on the multifaceted consequences of historical conflict. We revisit three key topics, which are especially relevant for the current Ukrainian context. (1) The negative long-term impact of bombing campaigns and political repression against civilians. (2) The interplay between forced migration, refugees and war. (3) The role of gender and war, with a special focus on sex ratios and conflict-related sexual violence. We conclude with an empirical investigation of the Russian war against Ukraine, including aforementioned historical determinants such as ethnic populations, historical political repression and voting outcomes.
Social Security Reform and the Untapped Potential of Human Rights Law
Authors: Rowe Christopher 
Published: February 2023

Abstract
The courts have done little to ameliorate the harsh ‘austerity’ reforms pursued by the government since 2010, adopting a highly deferential approach towards human rights claims in the social security context. This article identifies the two key moves to achieve this result: adopting the manifestly without reasonable foundation standard of justification and treating indirect discrimination claims on suspect grounds as not ‘real’ discrimination claims. It shows nonetheless the untapped potential of Convention rights, since even within this framework strong arguments were still available to the courts, based on the functioning of the social security system, which should have rendered two of the harshest reforms, the two-child limit and especially the benefit cap, Convention incompatible. The cap, which limits the subsistence benefits of unemployed families, is justified as a work-incentive policy, yet through Universal Credit the state also independently assesses families affected by the cap as doing all that they reasonably can to find work.
Bypassing the Incumbent: Leadership Tenure and Foreign Aid Channels
Authors: Allen Susan Hannah , Ferry Lauren Lee , Shammama Obaida 
Published: February 2023

AbstractThe traditional perception is that foreign aid provides leaders in recipient states access to nontax revenue, which incumbents may be able to manipulate in order to provide public or private goods as is required to maintain office. Recognizing this possibility, donors have been shifting away from direct government-to-government aid and toward bypass aid, administered by NGOs and civil society groups rather than the regime directly. Receiving aid through alternative channels is designed to increase aid’s effectiveness, yet it has potential implications for incumbent leaders who may have less ability to manipulate aid receipts to their benefit. In this paper, we argue that bypass aid should negatively affect leaders’ tenure, conditional on the political institutions in place. Using data on bypass aid from 2004 to 2017, we find evidence of a punishing effect and conclude that bypass aid is a particularly acute problem for leaders in authoritarian regimes. The findings imply that efficiency and stability may present a tradeoff for potential donors and that bypass aid may not be the panacea of the aid effectiveness movement.
Development and validation of a one-tube, nested real-time PCR method suitable for routine detection ofMycobacterium bovisin animal tissue
Authors: Morris Rowan P , Montoya Teresa , Price Natasha , Nicklin Babita , Hogarth Philip J , Mayers Jo , Sawyer Jason , McGoldrick Adrian 
Published: February 2023

AbstractAimsDevelopment and validation of a real-time PCR test for high-throughput routine screening of animal tissue for Mycobacterium bovis and other Mycobacterium tuberculosis complex (MTBC) members.Methods and resultsA preliminary study compared the results of a combination of five tissue preparation/DNA extraction methods and nine PCR assays on a panel of 92 cattle tissue samples of known M. bovis culture status (55 positive and 37 negative). The combination of DNA extraction and PCR was found to be important in achieving optimal detection of M. bovis. The optimal combination of a simple tissue preparation/DNA extraction method and a one-tube, nested real-time PCR to maximize the sensitivity of detection of an M. bovis-specific RD4 deletion and an IS1081 MTBC-specific target was selected for further evaluation. In total, tissue samples collected from 981 cattle and 366 non-bovine animals and submitted for routine TB culture were parallel tested with the selected method, as well as tissue samples obtained from 156 animals in certified TB-free cattle herds.ConclusionFor cattle, the optimized RD4-IS1081 PCR test exhibited a diagnostic sensitivity of 96% (95% CI: 94–97%) and specificity of 97% (95% CI: 95–98%) compared to culture. Specificity was 100% when testing the 156 samples from known TB-free cattle. For non-bovine species, the PCR had a diagnostic sensitivity of 93% (95% CI: 83–98%) and a specificity of 99% (95% CI: 97–100%).