bluuebunny/crossref_metadata_2025_split huggingface dataset:
Experimental demonstration of robustness under scaling errors for superadiabatic population transfer in a superconducting circuit
Authors: Dogra Shruti , Vepsäläinen Antti , Paraoanu Gheorghe Sorin 
Published: November 2022

We study experimentally and theoretically the transfer of population between the ground state and the second excited state in a transmon circuit by the use of superadiabatic stimulated Raman adiabatic passage (saSTIRAP). We show that the transfer is remarkably resilient against variations in the amplitudes of the pulses (scaling errors), thus demostrating that the superadiabatic process inherits certain robustness features from the adiabatic one. In particular, we provide new evidence of a plateau that appears at high values of the counterdiabatic pulse strength, which goes beyond the usual framework of saSTIRAP.
This article is part of the theme issue ‘Shortcuts to adiabaticity: theoretical, experimental and interdisciplinary perspectives’.
Non-adiabatic quantum control of quantum dot arrays with fixed exchange using Cartan decomposition
Authors: Kanaar David W. , Güngördü Utkan , Kestner J. P. 
Published: November 2022

In semiconductor spin qubits which typically interact through short-range exchange coupling, shuttling of spin is a practical way to generate quantum operations between distant qubits. Although the exchange is often tunable through voltages applied to gate electrodes, its minimal value can be significantly large, which hinders the applicability of existing shuttling protocols to such devices, requiring a different approach. In this work, we extend our previous results for double- and triple-dot systems, and describe a method for implementing spin state transfer in long chains of singly occupied quantum dots in a non-adiabatic manner. We make use of Cartan decomposition to break down the interacting problem into simpler problems in a systematic way, and use dynamical invariants to design smooth non-adiabatic pulses that can be implemented in devices with modest control bandwidth. Finally, we discuss the extensibility of our results to directed shuttling of spin states on two-dimensional lattices of quantum dots with fixed coupling.
This article is part of the theme issue ‘Shortcuts to adiabaticity: theoretical, experimental and interdisciplinary perspectives’.
Optimizing counterdiabaticity by variational quantum circuits
Authors: Sun Dan , Chandarana Pranav , Xin Zi-Hua , Chen Xi 
Published: November 2022

Using counterdiabatic (CD) driving—aiming at suppression of diabatic transition—in digitized adiabatic evolution has garnered immense interest in quantum protocols and algorithms. However, improving the approximate CD terms with a nested commutator ansatz is a challenging task. In this work, we propose a technique of finding optimal coefficients of the CD terms using a variational quantum circuit. By classical optimization routines, the parameters of this circuit are optimized to provide the coefficients corresponding to the CD terms. Then their improved performance is exemplified in Greenberger–Horne–Zeilinger state preparation on the nearest-neighbour Ising model. Finally, we also show the advantage over the usual quantum approximation optimization algorithm, in terms of fidelity with bounded time.This article is part of the theme issue ‘Shortcuts to adiabaticity: theoretical, experimental and interdisciplinary perspectives’.
Optimal shortcuts of stimulated Raman adiabatic passage in the presence of dissipation
Authors: Stefanatos D. , Paspalakis E. 
Published: November 2022

We use optimal control theory to obtain shortcuts to adiabaticity which maximize population transfer in a three-level stimulated Raman adiabatic passage system, for a given finite duration of the process and a specified dissipation rate at the intermediate state. We fix the sum of the intensities of the pump and Stokes pulses and use the mixing angle of the fields as the sole control variable. We determine the optimal variation of this angle and reveal the role of the singular arc in the optimal trajectory, in order to minimize the effect of dissipation.This article is part of the theme issue ‘Shortcuts to adiabaticity: theoretical, experimental and interdisciplinary perspectives’.
Disproportionate impacts of COVID-19 in a large US city
Authors: Fox Spencer J. , Javan Emily , Pasco Remy , Gibson Graham C. , Betke Briana , Diestra José-Luis Herrera , Woody Spencer , Pierce Kelly , Johnson Kaitlyn E. , Johnson-León Maureen , Lachmann Michael , Meyers Lauren Ancel 
Published: November 2022

AbstractCOVID-19 has disproportionately impacted individuals depending on where they live and work, and based on their race, ethnicity, and socioeconomic status. Studies have documented catastrophic disparities at critical points throughout the pandemic, but have not yet systematically tracked their severity through time. Using anonymized hospitalization data from March 11, 2020 to June 1, 2021, we estimate the time-varying burden of COVID-19 by age group and ZIP code in Austin, Texas. During this 15-month period, we estimate an overall 16.9% (95% CrI: 16.1-17.8%) infection rate and 34.1% (95% CrI: 32.4-35.8%) case reporting rate. Individuals over 65 were less likely to be infected than younger age groups (8.0% [95% CrI: 7.5-8.6%] vs 18.1% [95% CrI: 17.2-19.2%]), but more likely to be hospitalized (1,381 per 100,000 vs 319 per 100,000) and have their infections reported (51% [95% CrI: 48-55%] vs 33% [95% CrI: 31-35%]). Children under 18, who make up 20.3% of the local population, accounted for only 5.5% (95% CrI: 3.8-7.7%) of all infections between March 1 and May 1, 2020 compared with 20.4% (95% CrI: 17.3-23.9%) between December 1, 2020 and February 1, 2021. We compared ZIP codes ranking in the 75th percentile of vulnerability to those in the 25th percentile, and found that the more vulnerable communities had 2.5 (95% CrI: 2.0-3.0) times the infection rate and only 70% (95% CrI: 61%-82%) the reporting rate compared to the less vulnerable communities. Inequality persisted but declined significantly over the 15-month study period. For example, the ratio in infection rates between the more and less vulnerable communities declined from 12.3 (95% CrI: 8.8-17.1) to 4.0 (95% CrI: 3.0-5.3) to 2.7 (95% CrI: 2.0-3.6), from April to August to December of 2020, respectively. Our results suggest that public health efforts to mitigate COVID-19 disparities were only partially effective and that the CDC’s social vulnerability index may serve as a reliable predictor of risk on a local scale when surveillance data are limited.
Fine scale human mobility changes in 26 US cities in 2020 in response to the COVID-19 pandemic were associated with distance and income
Authors: Arambepola Rohan , Schaber Kathryn L , Schluth Catherine , Huang Angkana T , Labrique Alain B , Mehta Shruti H , Solomon Sunil S , Cummings Derek A T , Wesolowski Amy 
Published: November 2022

AbstractHuman mobility patterns changed greatly due to the COVID-19 pandemic. Despite many analyses investigating general mobility trends, there has been less work characterising changes in mobility on a fine spatial scale and developing frameworks to model these changes. We analyse zip code-level mobility data from 26 US cities between February 2 – August 31, 2020. We use Bayesian models to characterise the initial decrease in mobility and mobility patterns between June - August at this fine spatial scale. There were similar temporal trends across cities but large variations in the magnitude of mobility reductions. Long-distance routes and higher-income subscribers, but not age, were associated with greater mobility reductions. At the city level, mobility rates around early April, when mobility was lowest, and over summer showed little association with non-pharmaceutical interventions or case rates. Changes in mobility patterns lasted until the end of the study period, despite overall numbers of trips recovering to near baseline levels in many cities.
Dynamics of Mitochondrial NAD+Import Reveal Preference for Oxidized Ligand and Substrate Led Transport
Authors: Goyal Shivansh , Cambronne Xiaolu A. 
Published: November 2022

AbstractSLC25A51 is a member of the mitochondrial carrier family (MCF) but lacks key residues that have been attributed to the mechanism of other nucleotide MCF transporters. Thus, how SLC25A51 transports NAD+across the inner mitochondrial membrane remains unclear. To elucidate its mechanism, we used Molecular Dynamic simulations to study reconstituted SLC25A51 homology models in lipid bilayers. We observed spontaneous binding of cardiolipin phospholipids to three distinct sites on the exterior of SLC25A51’s central pore and found that mutation of these sites impaired transporter activity. We also observed that stable formation of the required matrix gate was controlled by a single salt bridge. Using simulation data and in-cell activity assays we identified binding sites in SLC25A51 for NAD+and showed that its binding was guided by an electrostatic interaction between NAD+and a negatively charged patch in the pore. In turn, interaction of NAD+with interior residue E132 guided the ligand to dynamically engage and weaken the salt bridge gate, representing a ligand-induced initiation of transport.SignificanceNAD+is an intermediary metabolite whose multiple functions are entwined with respiration, catabolism, and stress responses in cells. Previous sensor measurements had indicated that its continuous biosynthesis was required to sustain mitochondrial matrix levels in respiring cells, and SLC25A51 was identified as the required importer of NAD+across the inner mitochondrial membrane. However, SLC25A51 has little homology to other nucleotide carriers at its substrate binding site. By combining modeling approaches and experimental assays, this work provides mechanistic insight into how human SLC25A51 recognizes its ligand, how the transporter can be regulated by its lipid environment, and an observation of ligand-induced gate opening. This represents the first description of the ligand binding site for an NAD+mitochondrial carrier.
Structural basis of bifunctionality ofSinorhizobium melilotiClr, a cAMP and cGMP receptor protein
Authors: Werel Laura , Farmani Neda , Krol Elizaveta , Serrania Javier , Essen Lars-Oliver , Becker Anke 
Published: November 2022

ABSTRACTIn bacteria, Crp-Fnr superfamily transcription factors are the most ubiquitous receptor proteins of 3’,5’-cyclic adenosine monophosphate (cAMP) and 3’,5’-cyclic guanosine monophosphate (cGMP). The prototypicEscherichia coliCAP protein represents the main CRP subclass and is known to bind cAMP and cGMP, but to mediate transcription activation only in its cAMP-bound state. In contrast, both cyclic nucleotides mediate transcription activation by CRP subclass G protein Clr ofSinorhizobium meliloti. We present crystal structures of apo-Clr, and Clr•cAMP and Clr•cGMP bound to the core motif of the palindromic Clr DNA binding site (CBS). We show that both cyclic nucleotides shift ternary Clr•cNMP•CBS-DNA complexes to almost identical active conformations. Unlike the situation known for theE. coliCAP•cNMP complex, in the Clr•cNMP complex, the nucleobases of cGMP and cAMP are in thesyn-andanti-conformation, respectively, allowing a shift to the active conformations in both cases. Isothermal titration calorimetry measured similar affinities of cAMP and cGMP binding to Clr in presence of CBS core motif DNA (KDcNMP16 μM). However, different affinities were determined in absence of this DNA (KDcGMP24 μM; KDcGMP6 μM). Sequencing of Clr co-immunoprecipitated DNA as well as Electrophoretic Mobility Shift and promoter-probe assays expanded the list of experimentally proven Clr-regulated promoters and CBS. This comprehensive set of CBS features conserved nucleobases, which are in agreement with the sequence readout through interactions of Clr amino acid residues with these nucleobases, as revealed by the Clr•cNMP•CBS-DNA crystal structures.IMPORTANCECyclic 3’,5’-adenosine monophosphate (cAMP) and cyclic 3’,5’-guanosine monophosphate (cGMP) are both long known as important nucleotide second messenger in eukaryotes. This is also the case for cAMP in prokaryotes, whereas a signaling role for cGMP in this domain of life has been recognized only recently. Catabolite repressor proteins (CRPs) are the most ubiquitous bacterial cAMP receptor proteins.Escherichia coliCAP, the prototypic transcription regulator of the main CRP subclass, binds both cyclic mononucleotides, but only the CAP•cAMP complex promotes transcription activation. In contrast, CRP subclass G proteins studied so far, are activated by cGMP, or both by cAMP and cGMP. Here, we report a structural analysis of the bifunctional cAMP- and cGMP-activatable Clr fromSinorhizobium meliloti, how binding of cAMP and cGMP shifts Clr to its active conformation, and the structural basis of its DNA binding site specificity.
Neural Entrainment to Musical Pulse In Naturalistic Music Is Preserved In Aging: Implications for Music-Based Interventions
Authors: Tichko Parker , Page Nicole , Kim Ji Chul , Large Edward , Loui Psyche 
Published: November 2022

AbstractNeural entrainment to musical rhythm is thought to underlie the perception and production of music. In aging populations, the strength of neural entrainment to rhythm has been found to be attenuated, particularly during attentive listening to auditory streams. However, previous studies on neural entrainment to rhythm and aging have often employed artificial auditory rhythms or limited pieces of recorded, naturalistic music, failing to account for the diversity of rhythmic structures found in natural music. As part of larger project assessing a novel music-based intervention for healthy aging, we investigated neural entrainment to musical rhythms in the electroencephalogram (EEG) while participants listened to self-selected musical recordings across a sample of younger and older adults. We specifically measured neural entrainment to the level of musical pulse—quantified here as the phase-locking value (PLV)—after normalizing the PLVs to each musical recording’s detected pulse frequency. As predicted, we observed strong neural phase-locking to musical pulse, and to the sub-harmonic and harmonic levels of musical meter. Overall, PLVs were not significantly different between older and younger adults. This preserved neural entrainment to musical pulse and rhythm could support the design of music-based interventions that aim to modulate endogenous brain activity via self-selected music for healthy cognitive aging.
Functional characterization of cardiac fibroblasts in response to hemodynamic alteration
Authors: Shiraishi Manabu , Suzuki Ken , Yamaguchi Atsushi 
Published: November 2022

AbstractExcess deposition of extracellular matrix in the myocardium is a predictor of reduced left ventricular function. Although reducing the hemodynamic load is known to improve myocardial fibrosis, the mechanisms underlying reversal of the fibrosis have not been elucidated. We modeled normal myocardium, fibrotic myocardium and myocardium with reduced fibrosisin vitro. Fibroblasts differentiated into activated or fibrinolytic types in response to the pericellular environment. Comprehensive gene expression analysis of fibroblasts in eachin vitrocondition showedSelenbp1to be one of the genes responsible for regulating differentiation of fibroblasts.In vitroknockdown ofSelenbp1enhanced fibroblast activation and inhibited conversion to the fibrinolytic form.In vivoknockdown ofSelenbp1resulted in structural changes in the left ventricle associated with progressive tissue fibrosis and left ventricular diastolic failure. Selenbp1 is involved in regulating fibroblast differentiation and appears to be one of the major molecules regulating collagen turnover in cardiac fibrosis.
Complex third-party effects in theDictyostelium-Paraburkholderiasymbiosis: prey bacteria that are eaten, carried, or left behind
Authors: Scott Trey J. , Queller David C. , Strassmann Joan E. 
Published: November 2022

AbstractSymbiotic interactions may change depending on the abundance of third parties like predators, prey, or pathogens. Third-party interactions with prey bacteria are central to the symbiosis betweenDictyostelium discoideumsocial amoeba hosts andParaburkholderiafacultative bacterial symbionts. Symbiosis with inedibleParaburkholderiaallows hostD. discoideumto carry prey bacteria through the dispersal stage where host amoebae aggregate and develop into fruiting bodies that disperse spores. Carrying prey bacteria benefits hosts when prey bacteria are scarce but harms hosts when prey bacteria are plentiful. Symbiont-carrying hosts leave some bacteria behind; this could explain the harm to hosts if left-behind bacteria include uneaten prey bacteria. Thus, understanding both benefits and costs in this symbiosis requires measuring how many prey bacteria are eaten, carried, and left behind by infected hosts. We found thatParaburkholderiainfection makes hosts leave behind both symbionts and prey bacteria. However, the number of prey bacteria left uneaten was small and did not explain why infected hosts produced fewer spores than uninfected hosts. Turning to the bacteria that are carried, we found that hosts carry more prey bacteria after developing in prey- poor environments than in prey-rich ones. This suggests that carriage is actively modified to ensure hosts have prey in the harshest conditions. Our results show that multifaceted interactions with third parties shape the evolution of symbioses in complex ways.
A novel antidepressant actingviaallosteric inhibition of GluN2D-incorporated NMDA receptors at GABAergic interneurons
Authors: Zhang Jilin , Duan Jinjin , Ye Luyu , Li Wei , Zhou Haitao , Liu Fang , Xiaoting Tian , Xie Yang , Huang Yiming , Sun Yidi , Zhou Hu , Huang Chenggang , Li Yang , Zhu Shujia , Guo Fei 
Published: November 2022

AbstractN-methyl-D-aspartate receptors (NMDARs) are glutamate-gated calcium-permeable excitatory channels. They have attracted great interest as potential targets for the treatment of depression in recent years. NMDARs typically assemble as heterotetramers composed of two GluN1 and two alternative GluN2 (2A-2D) subunits, the latter of which endow various subtypes with diverse gating and pharmacological properties. To date, limited molecules with GluN2 specificity have been identified to show antidepressant effects. Here, we identify a compound termed YY-23 extracted fromRhizoma Anemarrhenaeallosterically inhibited the channel activities of GluN2C- or GluN2D-incorporated NMDARs, an effect that was presumably influenced by the S2 segment in the ligand-binding domain of the GluN2 subunit. We found that prefrontal GluN2D-containing NMDARs were predominantly expressed at GABAergic interneurons rather than pyramidal neurons. Furthermore, we revealed that YY-23 suppressed the activity of GluN2D-containing NMDARs and GABAergic neurotransmission in the medial prefrontal cortex (mPFC). As a consequence, this GABAergic disinhibition facilitated the excitatory transmission. Behavioural experiments showed that YY-23 acted as a rapid antidepressant in both stress-naïve and stressed animal models, which was abolished inGrin2d-knockoutmice. Together, our findings suggest that GluN2D-incorporated NMDARs on GABAergic interneurons might be promising therapeutic targets for the treatment of depression.
The SspB adaptor drives structural changes in the AAA+ClpXP protease during ssrA-tagged substrate delivery
Authors: Ghanbarpour Alireza , Fei Xue , Baker Tania A. , Davis Joseph H. , Sauer Robert T. 
Published: November 2022

ABSTRACTEnergy-dependent protein degradation by the AAA+ClpXP protease helps maintain protein homeostasis in organisms ranging from simple bacteria to humans. InE. coliand many other proteobacteria, the SspB adaptor assists ClpXP in degrading ssrA-tagged polypeptides produced as a consequence of tmRNA-mediated ribosome rescue. By tethering these incomplete ssrA-tagged proteins to ClpXP, SspB facilitates their efficient degradation at low substrate concentrations. How this process occurs structurally is unknown. Here, we present a cryo-EM structure of the SspB adaptor bound to a GFP-ssrA substrate and to ClpXP. This structure provides evidence for simultaneous contacts of SspB and ClpX with the ssrA tag within the tethering complex, allowing direct substrate handoff concomitant with the initiation of substrate translocation. Furthermore, our structures reveal that binding of the substrate•adaptor complex induces unexpected conformational changes within the spiral structure of the AAA+ClpX hexamer and its interaction with the ClpP tetradecamer.SIGNIFICANCEIntercellular proteases, including ClpXP, degrade damaged or unneeded proteins. Peptide tags allow specific protein substrates to be recognized by the ClpX unfoldase/translocase component of ClpXP and by an adaptor, SspB, which tethers itself to ClpX and enhances ClpXP degradation of the tagged protein. Our cryo-EM structure of ClpXP bound to SspB and a tagged substrate shows that SspB and ClpX simultaneously contact the degradation tag and reveal changes in the structure of ClpX and its interaction with ClpP. These structural changes appear to be a prelude to an initial ClpX translocation step that pulls the substrate away from SspB and initiates degradation by allowing substrate unfolding and further translocation of the unfolded substrate into the proteolytic chamber of ClpP.
Vitamin-B12 enrichment in tempeh by co-culture withPropionibacterium freudenreichiiduring fermentation
Authors: He Meng Tian , Howell Kate S. 
Published: November 2022

AbstractVitamin-B12, or cobalamin, is an essential human vitamin and most commonly acquired in the diet through consumption of animal products. Acquisition of the vitamin for people who follow strict plant-based diets is limited to supplementation via tablets or consumption of fortified foods. Tempeh — an Indonesian food of soybeans fermented with a filamentous fungi,Rhizopussp. is a potential dietary source of cobalamin, but its presence is under question based on difficult quantification of this trace vitamin. This study tested the presence and concentration of vitamin-B12 in commercially available tempeh and tempeh produced with deliberate inoculation of various bacteria and moulds. Vitamin-B12 was not detected in any commercially available tempeh. Tempeh made with filamentous fungi andPropionibacterium freudenreichii(ATCC 9617) consistently produced detectable levels of cobalamin.P. freudenreichiico-fermented withRhizopus oligosporus(ATCC 22959) produced the highest concentration of cobalamin at 8.26 ± 0.13 μg/100g of wet weight of tempeh. Co-fermentation with a different tempeh mould significantly reduced the amount of cobalamin (P= 0.008). Results from this study suggest that incorporating nutrient-enhancing microbes into an existing fermentation stage of a product is an effective method to increase the nutritional density of food. The results of this study suggest that cheap, safe and easily cultured microbes can contribute to the nutritional diversity of people following plant-only diets.