bluuebunny/crossref_metadata_2025 huggingface dataset:
Perceived Corona virus exposure as a function of interpersonal distance and time of a conversation
Authors: Svenson Ola
Published: December 2022

Background

During the COVID-19 pandemic people were asked to keep interpersonal distance, wash their hands and avoid gatherings of people. But, do people understand how much a change of the distance to a virus infected person means for the exposure to that person’s virus? To answer this question, we studied how people perceive virus exposure from an infected person at different distances and lengths of a conversation.

Method

An online questionnaire was distributed to 101 participants drawn from the general US population. Participants judged perceived virus exposure at different interpersonal distances to an infected person in a face to face conversation of different lengths of time. A model based on empirical and theoretical studies of dispersion of particles in the air was used to estimate a person’s objective virus exposure during different times and distances from a virus source. The model and empirical data show that exposure changes with the square of the distance and linearly with time.

Results

A majority (78%) of the participants underestimated the effects on virus exposure following a change of interpersonal distance. The dominating bias was assuming that exposure varies linearly with distance. To illustrate, an approach to a virus source from 6 to 2 feet was judged to give a 3 times higher exposure but, objectively it is 9 times. By way of contrast, perceptions of exposure as a function of the duration of a conversation were unbiased. The COVID-19 pandemic caused by the SARS-CoV2 virus is likely to be followed by other pandemics also caused by airborne Corona or other viruses. Therefore, the results are important for administrators when designing risk communications to the general public and workers in the health care sector about social distancing and infection risks.

Conclusions

People quite drastically underestimate the increase in virus exposure following an approach to a virus infected person. They also overestimate exposure after a move away from an infected person. For public health reasons, the correct function connecting distance with virus exposure should be communicated to the general public to avoid deliberate violations of recommended interpersonal distances.
Verification and validation procedure for high-definition maps in Taiwan
Authors: Chiang Kai-Wei , Wang Chi-Kuei , Hong Jung-Hong , Li Pei-Ling , Yang Chin-Sung , Tsai Meng-Lun , Lee Jeffrey , Lin Sean
Published: December 2022

Producing high-definition maps (HD maps) is critical for achieving the goal of safe autonomous vehicles. These maps must have sufficient quality to ensure safety in self-driving applications. In this paper, a procedure for the verifying the accuracy of HD maps and validating the maps is proposed. Maps meeting the standards should have horizontal and vertical accuracy of 20 and 30 cm, respectively. Moreover, the HD maps must include attributes that can be used by autonomous vehicles.
Magnetic field enhanced critical current and subharmonic structures in dissipative superconducting gold nanowires
Authors: Wang Jian , Wang Ziqiao , Wang Pinyuan
Published: December 2022

Quantum breakdown of superconductivity in low-dimensional superconducting systems has attracted enormous attention due to the underlying fluctuation. Here we report exotic phenomena observed during the current-induced breakdown of superconductivity in gold nanowires contacted by superconducting electrodes. In a 1.0 μm-long nanowire, the resistance as a function of current exhibits a random resistance switching at 1.8 K and tail-like metallic state at higher temperatures, indicating phase slips in proximity-induced superconducting nanowire. Additionally, the upper critical current is enhanced under low magnetic field, which may be attributed to the formation of spin-triplet pairing in superconducting gold nanowire. In a 1.2 μm-long gold nanowire, unexpected subharmonic structures with characteristic energy smaller than superconducting gap are superimposed on tail-like structures. The signal might be related to the axions-triggered process in phase slip center Josephson junction and thus stimulate further studies in dissipative superconducting nanowires.
An investigation on the mechanical behaviour of sandwich composite structures with circular honeycomb bamboo core
Authors: de Oliveira Lívia Ávila , Vieira Matheus Milagres , dos Santos Júlio Cesar , Freire Rodrigo Teixeira Santos , Tonatto Maikson Luiz Passaia , Panzera Túlio Hallak , Zamani Pedram , Scarpa Fabrizio
Published: December 2022

Sandwich panels made with a bamboo core of different dimensions, packing geometries and facing materials are subjected to three-point bending tests and assessed through statistical and failure analysis. In addition to promoting a circular economy, this architecture holds great promise for replacing secondary structural components in sustainable construction and transportation facilities. The statistical analysis responses are associated with the equivalent density of the panels, flexural strength and modulus of the panels, skin stress and core shear strength and modulus. Individual bamboo rings are also characterised using physic mechanical and interfacial bonding tests. Treated aluminium face sheets provide the best mechanical performance compared to glass fibre-reinforced composite (GFRP) ones by increasing the overall properties of the sandwich panels. The specific face sheet material and void percentage affect the equivalent density, with lower values (~ 0.48 g/cm3) when using GFRP skins, larger bamboo rings and cubic packing. Sandwich panels with 30 mm bamboo rings and hexagonal packing provide higher flexural properties, i.e. ~ 43 MPa strength and ~ 7.6 GPa modulus, and skin stress (~ 288 MPa), while those with 20 mm bamboo rings have higher shear stiffness (~ 132 MPa) and resistance (~ 3.33 MPa). Sandwich panels made with aluminium skins show evident skin-polymer debonding, while those with GFRP have premature skin failure and lower structural performance. The proposed sandwich panels present remarkable and competitive mechanical performance concerning commercial analogous structures, generally used in the aeronautical and automotive industries.
Multiple roles of dissolved organic matter on typical engineered nanomaterials: environmental behaviors, pollutants removal and potential risks
Authors: Zheng Xianyao , Xu Zhixiang , Liu Jun , Luo Yu , Gu Lipeng , Zhao Dimeng , Hu Siyuan , Pan Xuejun
Published: December 2022

With the rapid development of nanotechnology, engineered nanomaterials (ENMs) have been produced and widely used in various fields, especially in environmental protection. ENMs would be released into the environmental media, particularly natural water, and then they exert great risks to ecosystem safety and human health. Dissolved organic matter (DOM) commonly exists in water environments. As a result, the interactions between DOM and ENMs are bound to occur. Herein, the multiple roles of DOM on ENMs are summarized. DOM can often interact with ENMs to positively or negatively influence nanomaterials-mediated pollutant removal through adsorption and catalytic degradation processes. On the other hand, DOM also regulates the potential ecotoxic effects of ENMs on organisms, either mitigation or enhancement. ENMs in turn would alter the physicochemical properties of DOM along with their environmental behaviors and risks. The present review aims to provide insight into DOM's influence on environmental behaviors, environmental applications, and potential risks of ENMs.

Graphical Abstract
Can we trust trust-based data governance models?
Authors: van der Sloot Bart , Keymolen Esther
Published: December 2022

Fiduciary agents and trust-based institutions are increasingly proposed and considered in legal, regulatory, and ethical discourse as an alternative or addition to a control-based model of data management. Instead of leaving it up to the citizen to decide what to do with her data and to ensure that her best interests are met, an independent person or organization will act on her behalf, potentially also taking into account the general interest. By ensuring that these interests are protected, the hope is that citizens’ willingness to share data will increase, thereby allowing for more data-driven projects. Thus, trust-based models are presented as a win–win scenario. It is clear, however, that there are also apparent dangers entailed with trust-based approaches. Especially one model, that of data trusts, may have far-reaching consequences.
A dependent multimodel approach to climate prediction with Gaussian processes
Authors: Thompson Marten , Braverman Amy , Chatterjee Snigdhansu
Published: December 2022

Simulations of future climate contain variability arising from a number of sources, including internal stochasticity and external forcings. However, to the best of our abilities climate models and the true observed climate depend on the same underlying physical processes. In this paper, we simultaneously study the outputs of multiple climate simulation models and observed data, and we seek to leverage their mean structure as well as interdependencies that may reflect the climate’s response to shared forcings. Bayesian modeling provides a fruitful ground for the nuanced combination of multiple climate simulations. We introduce one such approach whereby a Gaussian process is used to represent a mean function common to all simulated and observed climates. Dependent random effects encode possible information contained within and between the plurality of climate model outputs and observed climate data. We propose an empirical Bayes approach to analyze such models in a computationally efficient way. This methodology is amenable to the CMIP6 model ensemble, and we demonstrate its efficacy at forecasting global average near-surface air temperature. Results suggest that this model and the extensions it engenders may provide value to climate prediction and uncertainty quantification.
Affective Reason
Authors: McMartin Jason , Pickavance Timothy
Published: December 2022

This paper contributes to the recent explosion of literature on the epistemological role of emotions and other affective states by defending two claims. First, affective states might do more than position us to receive evidence or function as evidence. Affective states might be thought to appraise evidence, in the sense that affective states influence what doxastic state is rational for someone given a body of evidence. The second claim is that affective evidentialism, the view that affective states function rationally in this way, is not just possible but plausible and fruitful. We offer two arguments in favor of affective evidentialism.
Diode-pumped high-power continuous-wave intracavity frequency-doubled Pr3+:YLF ultraviolet lasers around 349 nm
Authors: Lin Xiuji , Zhang Zheng , Ji Shuaihao , Fang Run , Xiao Bo , Xu Huiying , Cai Zhiping
Published: December 2022

High-power continuous-wave ultraviolet lasers are useful for many applications. As ultraviolet laser sources, the wavelength switching capability and compact structure are very important to extend the applicability and improve the flexibility in practical applications. In this work, we present two simple and relatively compact schemes by laser diode pumping to obtain a watt-level single-wavelength 348.7-nm laser and discrete wavelength tunable ultraviolet lasers around 349 nm (from 334.7 to 364.5 nm) by intracavity frequency doubling based on Pr3+:YLF and

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-BBO crystals. The maximum output power of the single-wavelength 348.7-nm laser is 1.033 W. The output powers of the discrete wavelength tunable lasers are at the level of tens of milliwatts, except for two peaks at 348.7 and 360.3 nm with output powers of approximately 500 mW. In addition, simulations are carried out to explain the experimental results and clarify the tuning mechanisms.
American Religious Liberty without (Much) Theory - Discussed: Religion and the American Constitutional Experiment, 5th ed. By John WitteJr. , Joel A. Nichols, and Richard W. Garnett. Oxford: Oxford University Press, 2022. Pp. 464. $150.00 (cloth); $39.95 (paper); $26.99 (digital). ISBN: 9780197587614.
Authors: Chapman Nathan S.
Published: December 2022

The author first presents an uncritical user’s guide to the book, then discusses why Witte, Nichols, and Garnett should consider including key chapters of the story of US religious liberty in the next edition. The author then deconstructs the normative and methodological assumptions of the book.
Leading voices: dialogue semantics, cognitive science and the polyphonic structure of multimodal interaction
Authors: Lücking Andy , Ginzburg Jonathan
Published: December 2022

The neurocognition of multimodal interaction – the embedded, embodied, predictive processing of vocal and non-vocal communicative behaviour – has developed into an important subfield of cognitive science. It leaves a glaring lacuna, however, namely the dearth of a precise investigation of the meanings of the verbal and non-verbal communication signals that constitute multimodal interaction. Cognitively construable dialogue semantics provides a detailed and context-aware notion of meaning, and thereby contributes content-based identity conditions needed for distinguishing syntactically or form-based defined multimodal constituents. We exemplify this by means of two novel empirical examples: dissociated uses of negative polarity utterances and head shaking, and attentional clarification requests addressing speaker/hearer roles. On this view, interlocutors are described as co-active agents, thereby motivating a replacement of sequential turn organisation as a basic organising principle with notions of leading and accompanying voices. The Multimodal Serialisation Hypothesis is formulated: multimodal natural language processing is driven in part by a notion of vertical relevance – relevance of utterances occurring simultaneously – which we suggest supervenes on sequential (‘horizontal’) relevance – relevance of utterances succeeding each other temporally.
Different trajectories of depression, anxiety and anhedonia symptoms in the first 12 months of the COVID-19 pandemic in a UK longitudinal sample
Authors: Parsons Christine E. , Purves Kirstin L. , Skelton Megan , Peel Alicia J. , Davies Molly R. , Rijsdijk Fruhling , Bristow Shannon , Eley Thalia C. , Breen Gerome , Hirsch Colette R. , Young Katherine S.
Published: December 2022

Background

While studies from the start of the COVID-19 pandemic have described initial negative effects on mental health and exacerbating mental health inequalities, longer-term studies are only now emerging.

Method

In total, 34 465 individuals in the UK completed online questionnaires and were re-contacted over the first 12 months of the pandemic. We used growth mixture modelling to identify trajectories of depression, anxiety and anhedonia symptoms using the 12-month data. We identified sociodemographic predictors of trajectory class membership using multinomial regression models.

Results

Most participants had consistently low symptoms of depression or anxiety over the year of assessments (60%, 69% respectively), and a minority had consistently high symptoms (10%, 15%). We also identified participants who appeared to show improvements in symptoms as the pandemic progressed, and others who showed the opposite pattern, marked symptom worsening, until the second national lockdown. Unexpectedly, most participants showed stable low positive affect, indicating anhedonia, throughout the 12-month period. From regression analyses, younger age, reporting a previous mental health diagnosis, non-binary, or self-defined gender, and an unemployed or a student status were significantly associated with membership of the stable high symptom groups for depression and anxiety.

Conclusions

While most participants showed little change in their depression and anxiety symptoms across the first year of the pandemic, we highlight the divergent responses of subgroups of participants, who fared both better and worse around national lockdowns. We confirm that previously identified predictors of negative outcomes in the first months of the pandemic also predict negative outcomes over a 12-month period.
Accepting Moral Luck and Taking Responsibility in Public Health Crises
Authors: Tigard Daniel
Published: December 2022

We see cases of moral luck arising in recent times, as we face the uncertainties of provisional rules for navigating the coronavirus pandemic. How should we respond to rule-breakers, and how should they view themselves, when they cause harm inadvertently? Although some argue that guilt is unnecessary for any harm that may result from luck, this paper takes moral luck seriously and encourages consideration of the benefits to be achieved by expressions of self-blame amidst troubling circumstances, from pure accidents to how we live during pandemics. It argues that rule-breakers in public health crises show us the importance of taking responsibility for our actions.
Reluctant Rulers: Policy, Politics, and Assisted Reproduction Technology in Japan
Authors: Croydon Silvia
Published: December 2022

This article puts the spotlight on the world’s largest artificial reproduction technology (ART) industry—that of Japan, seeking to explain the exceptional tardiness of the government there to install a comprehensive legal framework that regulates these practices. By relying on minutes from a conversation with an influential parliamentarian active in this area, as well as official documents, media reports, and an interview conducted with key physicians, the article reconstructs the historical trajectory leading to the enactment in December 2020 of the Assisted Reproduction Technology Act. The author contends that it is only on the background of an overview of what happened in the two decades preceding the promulgation of this Act that a sense can be made of why the latter came to be as scant and evasive as it is in terms of provisions, de facto leaving unaltered the socially and ethically undesirable situation of self-regulation in ART application by the Japanese doctors. This article adds credence to the hypothesis with regard to the issue of regulatory governance of emerging technologies more broadly that the direction of travel is toward soft, as opposed to hard, law.
Negative Sentiment and Congressional Cue-Taking on Social Media
Authors: Macdonald Maggie , Russell Annelise , Hua Whitney
Published: December 2022

Congressional candidates regularly turn their frustration into posts on Facebook, fueling extreme partisanship and “echo-chamber” dialogue with their negative sentiment. In this research, we provide new evidence demonstrating the power of that negative sentiment to elicit more user engagement on Facebook across various metrics, illustrating how congressional candidates’ use of negativity corresponds with greater negativity in public responses. To fully comprehend the impact of these online political messages, we use a dictionary-based computational approach to catalog the tone of US House of Representatives candidates’ messages on Facebook and the user responses they elicit during the 2020 election. This research speaks to the power of elite rhetoric to shape political climates and pairs candidate strategies with user responses—contributing new insights into the mechanisms for voter engagement.
Critical junctures and the crystallization of cosmopolitanism and communitarianism
Authors: de Wilde Pieter , Langsæther Peter Egge , Özdemir Sina
Published: December 2022

A burgeoning literature documents the emergence of a new globalization cleavage in Western Europe, centered around the issues of immigration and European integration. We investigate to what extent the globalization cleavage has crystallized by studying the alignment of preferences regarding open borders, their connection to more fundamental elements in the normative component of cosmopolitanism and communitarianism, and the extent to which this links up to the organizational component through party choice. To do this, we use innovative items tapping into political priorities, values, understandings of democracy, and virtues in a cross-sectional comparative survey in Norway and the UK. We find that the globalization cleavage is significantly more developed in the UK than in Norway but lacks a solidified normative component in both. This implies that considerable opportunities remain for ideological entrepreneurs to either fortify or dilute this cleavage, even in the UK.
Magnetosphere Distortions During the “Satellite Killer” Storm of February 3–4, 2022, as Derived From a Hybrid Empirical Model and Archived Data Mining
Authors: Tsyganenko N. A. , Andreeva V. A. , Sitnov M. I. , Stephens G. K.
Published: December 2022

A pair of relatively mild geomagnetic storms of February 3–4, 2022, resulted in the loss of 38 Starlink satellites. In this work we reconstruct a sequence of magnetospheric configurations during that event, based on the largest ever archive of historical data, a new magnetic field model, and the nearest‐neighbor method of mining the solar wind, magnetosphere, and ground activity data. The model is constructed as a combination of main modular framework, explicitly representing magnetic effects of principal current systems, and a high‐resolution superstructure, based on expanding the field of equatorial currents into a sum of quasi‐orthogonal harmonics, whose purpose is to correct residual inaccuracies of the modular component. In addition, the variable penetration of the interplanetary magnetic field (IMF) into the magnetosphere is taken into account in the form of a potential field, parameterized by the observed IMF components. Despite relatively modest intensity of the event in terms of Sym‐H peak values, surprisingly strong transient distortions of the global magnetic field are found. Whereas under quiet pre‐storm conditions the midnight segment of synchronous orbit and the dayside cusps mapped, respectively, to ∼67° and ∼77° of corrected latitude, at the peak of the storm their footpoints shifted equatorward to as low as ∼63° and ∼67°–68°, with formation of entangled flux‐rope‐like structures and magnetic neutral lines at distances R ∼ 12–15 RE on the nightside. At nearly the same time, a deep magnetic depression and, possibly, an island of reversed field polarity forms even closer, in the post‐dusk sector of geosynchronous orbit.
The Development of an Adherence Measure for Pediatric Failure to Thrive/Faltering Growth
Authors: David Jennie G. , Kiely Jenna R. , Kersten Hans B. , Bennett David S.
Published: December 2022

Objective: Failure to thrive/faltering growth (FTT/FG) is often multiply determined and involves caregiver adherence to various recommendations to optimize child weight gain. The current study at an interdisciplinary FTT/FG clinic (a) documented the taxonomy of treatment recommendations made for children with FTT/FG (Study 1) and (b) developed an adherence measure, which was used by trained clinicians to examine the relationship between adherence and weight gain (Study 2). Methods: In Study 1, all treatment recommendations made to caregivers of 102 children with FTT/FG were recorded and categorized into domains. Based on domains identified in Study 1, a seven-domain adherence measure was developed. Using a new sample in Study 2 ( n = 131, aged 1 to 10 years), clinicians assessed caregiver adherence to recommendations made at the prior clinic visit and examined the association between adherence and weight gain. Results: From Study 1, clinic recommendations fell within seven domains, including the following four that were expected to be associated with weight gain: liquids, food, behavior, and meal structure. Study 2 found that caregiver adherence, overall, was generally high ( M = 3.0, SD = .80, rated on a 0 to 4 scale). Greater overall adherence was associated with greater weight gain ( r = .253, p = .02). Examining specific recommendations, adherence to using high-calorie add-ons and limiting long mealtimes were associated with greater weight gain. Conclusions: The adherence measure developed in this study can be used to assist clinicians in the management of FTT/FG. Future research is needed to further identify specific treatment recommendations whose adherence is most closely associated with children’s weight gain.

Implications for Impact Statement

Failure to thrive/faltering growth (FTT/FG), is complex as clinical presentations may vary depending on the child, with a universal goal of increasing weight and growth. Understanding the role of caregiver adherence to recommendations from interdisciplinary providers for FTT/FG has not been explored in the extant literature, and this study developed an adherence measure for this population in an interdisciplinary clinic setting. Overall adherence and adherence to several specific recommendations were significantly associated with greater weight gain, demonstrating a novel application of adherence assessment for children with FTT/FG.
Clinical Application of a Peer Coaching Intervention to Enhance Self-Management for Adolescents and Young Adults With Inflammatory Bowel Disease
Authors: Pollock McLean D. , Brotkin Samuel M. , Denio Erin , Dave Sneha , Fisher Edwin B. , Docherty Sharron L. , Maslow Gary R.
Published: December 2022

Objective: The purpose of this article is to characterize the current evidence base related to peer support interventions for adolescents and young adults (AYAs) with inflammatory bowel disease (IBD) and to describe a peer support program to enhance self-management for AYAs with IBD through a case study. There is strong theory and compelling evidence suggesting that AYAs with IBD could benefit from and are interested in receiving peer support to enhance self-management; however, literature on peer support interventions for AYAs with IBD is lacking. Methods: This study (a) presents a topical review describing qualitative factors AYAs with IBD would seek in a peer support program as well as existing peer support programs for this population, (b) presents an innovative one-to-one peer support program targeting self-management through a case study, and (c) discusses clinical implications and directions for future research. Results: Peer support offers a promising approach for AYAs with IBD that is feasible and acceptable to patient populations. However, results from the present topical review identified only two studies that examined peer support interventions for AYAs with IBD. The case study demonstrates how a theoretically driven program uses peer support to promote self-management and adaptive behavioral change. Conclusions: The paucity of literature in this area reveals a critical opportunity for future research and clinical programming to improve existing practices by leveraging peer support. We present the application of an innovative mobile-based peer coaching intervention that has the potential to support AYAs with IBD in their self-management.

Implications for Impact Statement

The purpose of this article is to present the current evidence base related to peer support for adolescents and young adults (AYAs) with inflammatory bowel disease (IBD) and to describe a peer support program to enhance self-management for AYAs with IBD through a case study. Peer support, such as the one-to-one peer coaching model presented in this article, offers a promising approach for AYAs with IBD that is feasible, developmentally appropriate, and acceptable to patient populations. Given the nascent nature of the literature on peer support interventions for AYAs with IBD, further research is needed to develop this area and inform clinical practice, which should consider opportunities to intentionally leverage peer support in settings in which AYAs with IBD currently engage.
U-IMPACT: a universal 3D microfluidic cell culture platform
Authors: Lee Seung-Ryeol , Kim Youngtaek , Kim Suryong , Kim Jiho , Park Seonghyuk , Rhee Stephen , Park Dohyun , Lee Byungjun , Baek Kyusuk , Kim Ho-Young , Jeon Noo Li
Published: December 2022

The development of organs-on-a-chip has resulted in advances in the reconstruction of 3D cellular microenvironments. However, there remain limitations regarding applicability and manufacturability. Here, we present an injection-molded plastic array 3D universal culture platform (U-IMPACT) for various biological applications in a single platform, such as cocultures of various cell types, and spheroids (e.g., tumor spheroids, neurospheres) and tissues (e.g., microvessels). The U-IMPACT consists of three channels and a spheroid zone with a 96-well plate form factor. Specifically, organoids or spheroids (~500 μm) can be located in designated areas, while cell suspensions or cell-laden hydrogels can be selectively placed in three channels. For stable multichannel patterning, we developed a new patterning method based on capillary action, utilizing capillary channels and the native contact angle of the materials without any modification. We derived the optimal material hydrophilicity (contact angle of the body, 45–90°; substrate, <30°) for robust patterning through experiments and theoretical calculations. We demonstrated that the U-IMPACT can implement 3D tumor microenvironments for angiogenesis, vascularization, and tumor cell migration. Furthermore, we cultured neurospheres from induced neural stem cells. The U-IMPACT can serve as a multifunctional organ-on-a-chip platform for high-content and high-throughput screening.
Many-body quantum chaos and space-time translational invariance
Authors: Chan Amos , Shivam Saumya , Huse David A. , De Luca Andrea
Published: December 2022

We study the consequences of having translational invariance in space and time in many-body quantum chaotic systems. We consider ensembles of random quantum circuits as minimal models of translational invariant many-body quantum chaotic systems. We evaluate the spectral form factor as a sum over many-body Feynman diagrams in the limit of large local Hilbert space dimension q. At sufficiently large t, diagrams corresponding to rigid translations dominate, reproducing the random matrix theory (RMT) behaviour. At finite t, we show that translational invariance introduces additional mechanisms via two novel Feynman diagrams which delay the emergence of RMT. Our analytics suggests the existence of exact scaling forms which describe the approach to RMT behavior in the scaling limit where both t and L are large while the ratio between L and LTh(t), the many-body Thouless length, is fixed. We numerically demonstrate, with simulations of two distinct circuit models, that the resulting scaling functions are universal in the scaling limit.
Self-assembling nanofibrous bacteriophage microgels as sprayable antimicrobials targeting multidrug-resistant bacteria
Authors: Tian Lei , He Leon , Jackson Kyle , Saif Ahmed , Khan Shadman , Wan Zeqi , Didar Tohid F. , Hosseinidoust Zeinab
Published: December 2022

Nanofilamentous bacteriophages (bacterial viruses) are biofunctional, self-propagating, and monodisperse natural building blocks for virus-built materials. Minifying phage-built materials to microscale offers the promise of expanding the range function for these biomaterials to sprays and colloidal bioassays/biosensors. Here, we crosslink half a million self-organized phages as the sole structural component to construct each soft microgel. Through an in-house developed, biologics-friendly, high-throughput template method, over 35,000 phage-built microgels are produced from every square centimetre of a peelable microporous film template, constituting a 13-billion phage community. The phage-exclusive microgels exhibit a self-organized, highly-aligned nanofibrous texture and tunable auto-fluorescence. Further preservation of antimicrobial activity was achieved by making hybrid protein-phage microgels. When loaded with potent virulent phages, these microgels effectively reduce heavy loads of multidrug-resistant Escherichia coli O157:H7 on food products, leading to up to 6 logs reduction in 9 hours and rendering food contaminant free.
High-fidelity qutrit entangling gates for superconducting circuits
Authors: Goss Noah , Morvan Alexis , Marinelli Brian , Mitchell Bradley K. , Nguyen Long B. , Naik Ravi K. , Chen Larry , Jünger Christian , Kreikebaum John Mark , Santiago David I. , Wallman Joel J. , Siddiqi Irfan
Published: December 2022

Ternary quantum information processing in superconducting devices poses a promising alternative to its more popular binary counterpart through larger, more connected computational spaces and proposed advantages in quantum simulation and error correction. Although generally operated as qubits, transmons have readily addressable higher levels, making them natural candidates for operation as quantum three-level systems (qutrits). Recent works in transmon devices have realized high fidelity single qutrit operation. Nonetheless, effectively engineering a high-fidelity two-qutrit entanglement remains a central challenge for realizing qutrit processing in a transmon device. In this work, we apply the differential AC Stark shift to implement a flexible, microwave-activated, and dynamic cross-Kerr entanglement between two fixed-frequency transmon qutrits, expanding on work performed for the ZZ interaction with transmon qubits. We then use this interaction to engineer efficient, high-fidelity qutrit CZ† and CZ gates, with estimated process fidelities of 97.3(1)% and 95.2(3)% respectively, a significant step forward for operating qutrits on a multi-transmon device.
Single-shot self-supervised object detection in microscopy
Authors: Midtvedt Benjamin , Pineda Jesús , Skärberg Fredrik , Olsén Erik , Bachimanchi Harshith , Wesén Emelie , Esbjörner Elin K. , Selander Erik , Höök Fredrik , Midtvedt Daniel , Volpe Giovanni
Published: December 2022

Object detection is a fundamental task in digital microscopy, where machine learning has made great strides in overcoming the limitations of classical approaches. The training of state-of-the-art machine-learning methods almost universally relies on vast amounts of labeled experimental data or the ability to numerically simulate realistic datasets. However, experimental data are often challenging to label and cannot be easily reproduced numerically. Here, we propose a deep-learning method, named LodeSTAR (Localization and detection from Symmetries, Translations And Rotations), that learns to detect microscopic objects with sub-pixel accuracy from a single unlabeled experimental image by exploiting the inherent roto-translational symmetries of this task. We demonstrate that LodeSTAR outperforms traditional methods in terms of accuracy, also when analyzing challenging experimental data containing densely packed cells or noisy backgrounds. Furthermore, by exploiting additional symmetries we show that LodeSTAR can measure other properties, e.g., vertical position and polarizability in holographic microscopy.
Predicting European cities’ climate mitigation performance using machine learning
Authors: Hsu Angel , Wang Xuewei , Tan Jonas , Toh Wayne , Goyal Nihit
Published: December 2022

Although cities have risen to prominence as climate actors, emissions’ data scarcity has been the primary challenge to evaluating their performance. Here we develop a scalable, replicable machine learning approach for evaluating the mitigation performance for nearly all local administrative areas in Europe from 2001-2018. By combining publicly available, spatially explicit environmental and socio-economic data with self-reported emissions data from European cities, we predict annual carbon dioxide emissions to explore trends in city-scale mitigation performance. We find that European cities participating in transnational climate initiatives have likely decreased emissions since 2001, with slightly more than half likely to have achieved their 2020 emissions reduction target. Cities who report emissions data are more likely to have achieved greater reductions than those who fail to report any data. Despite its limitations, our model provides a replicable, scalable starting point for understanding city-level climate emissions mitigation performance.
Cannabinoid non-cannabidiol site modulation of TRPV2 structure and function
Authors: Zhang Liying , Simonsen Charlotte , Zimova Lucie , Wang Kaituo , Moparthi Lavanya , Gaudet Rachelle , Ekoff Maria , Nilsson Gunnar , Hellmich Ute A. , Vlachova Viktorie , Gourdon Pontus , Zygmunt Peter M.
Published: December 2022

TRPV2 is a ligand-operated temperature sensor with poorly defined pharmacology. Here, we combine calcium imaging and patch-clamp electrophysiology with cryo-electron microscopy (cryo-EM) to explore how TRPV2 activity is modulated by the phytocannabinoid Δ9-tetrahydrocannabiorcol (C16) and by probenecid. C16 and probenecid act in concert to stimulate TRPV2 responses including histamine release from rat and human mast cells. Each ligand causes distinct conformational changes in TRPV2 as revealed by cryo-EM. Although the binding for probenecid remains elusive, C16 associates within the vanilloid pocket. As such, the C16 binding location is distinct from that of cannabidiol, partially overlapping with the binding site of the TRPV2 inhibitor piperlongumine. Taken together, we discover a new cannabinoid binding site in TRPV2 that is under the influence of allosteric control by probenecid. This molecular insight into ligand modulation enhances our understanding of TRPV2 in normal and pathophysiology.
Structural basis of sequence-specific RNA recognition by the antiviral factor APOBEC3G
Authors: Yang Hanjing , Kim Kyumin , Li Shuxing , Pacheco Josue , Chen Xiaojiang S.
Published: December 2022

An essential step in restricting HIV infectivity by the antiviral factor APOBEC3G is its incorporation into progeny virions via binding to HIV RNA. However, the mechanism of APOBEC3G capturing viral RNA is unknown. Here, we report crystal structures of a primate APOBEC3G bound to different types of RNAs, revealing that APOBEC3G specifically recognizes unpaired 5’-AA-3’ dinucleotides, and to a lesser extent, 5’-GA-3’ dinucleotides. APOBEC3G binds to the common 3’A in the AA/GA motifs using an aromatic/hydrophobic pocket in the non-catalytic domain. It binds to the 5’A or 5’G in the AA/GA motifs using an aromatic/hydrophobic groove conformed between the non-catalytic and catalytic domains. APOBEC3G RNA binding property is distinct from that of the HIV nucleocapsid protein recognizing unpaired guanosines. Our findings suggest that the sequence-specific RNA recognition is critical for APOBEC3G virion packaging and restricting HIV infectivity.
Tissue and liquid biopsy profiling reveal convergent tumor evolution and therapy evasion in breast cancer
Authors: Sivakumar Smruthy , Jin Dexter X. , Tukachinsky Hanna , Murugesan Karthikeyan , McGregor Kimberly , Danziger Natalie , Pavlick Dean , Gjoerup Ole , Ross Jeffrey S. , Harmon Robert , Chung Jon , Decker Brennan , Dennis Lucas , Frampton Garrett M. , Molinero Luciana , Oesterreich Steffi , Venstrom Jeffrey M. , Oxnard Geoffrey R. , Hegde Priti S. , Sokol Ethan S.
Published: December 2022

Pathological and genomic profiling have transformed breast cancer care by matching patients to targeted treatments. However, tumors evolve and evade therapeutic interventions often through the acquisition of genomic mutations. Here we examine patients profiled with tissue (TBx) and liquid biopsy (LBx) as part of routine clinical care, to characterize the tumor evolutionary landscape and identify potential vulnerabilities in the relapsed setting. Real-world evidence demonstrates that LBx is utilized later in care and identifies associations with intervening therapy. While driver events are frequently shared, acquired LBx alterations are detected in a majority of patients, with the highest frequency in ER+ disease and in patients with longer biopsy intervals. Acquired mutations are often polyclonal and present at lower allelic fractions, suggesting multi-clonal convergent evolution. In addition to well-characterized resistance mutations (e.g.,ESR1,NF1,RB1,ERBB2), we observe a diversity of rarer but potentially targetable mutations (e.g.,PIK3CA, HRAS/NRAS/KRAS,FGFR1/2/3,BRAF) and fusions (e.g.,FGFR1/2,ERBB2,RET), as well asBRCA1/2reversions through a variety of mechanisms, including splice alterations and structural deletions. This study provides insights on treatment and selection-driven tumor evolution and identifies potential combinatorial treatment options in advanced breast cancer.
Targeting endogenous kidney regeneration using anti-IL11 therapy in acute and chronic models of kidney disease
Authors: Widjaja Anissa A. , Viswanathan Sivakumar , Shekeran Shamini G. , Adami Eleonora , Lim Wei-Wen , Chothani Sonia , Tan Jessie , Goh Joyce Wei Ting , Chen Hui Mei , Lim Sze Yun , Boustany-Kari Carine M. , Hawkins Julie , Petretto Enrico , Hübner Norbert , Schafer Sebastian , Coffman Thomas M. , Cook Stuart A.
Published: December 2022

The kidney has large regenerative capacity, but this is compromised when kidney damage is excessive and renal tubular epithelial cells (TECs) undergo SNAI1-driven growth arrest. Here we investigate the role of IL11 in TECs, kidney injury and renal repair. IL11 stimulation of TECs induces ERK- and p90RSK-mediated GSK3β inactivation, SNAI1 upregulation and pro-inflammatory gene expression. Mice with acute kidney injury upregulate IL11 in TECs leading to SNAI1 expression and kidney dysfunction, which is not seen inIl11deleted mice or in mice administered a neutralizing IL11 antibody in either preemptive or treatment modes. In acute kidney injury, anti-TGFβ reduces renal fibrosis but exacerbates inflammation and tubule damage whereas anti-IL11 reduces all pathologies. Mice with TEC-specific deletion ofIl11ra1have reduced pathogenic signaling and are protected from renal injury-induced inflammation, fibrosis, and failure. In a model of chronic kidney disease, anti-IL11 therapy promotes TEC proliferation and parenchymal regeneration, reverses fibroinflammation and restores renal mass and function. These data highlight IL11-induced mesenchymal transition of injured TECs as an important renal pathology and suggest IL11 as a therapeutic target for restoring stalled endogenous regeneration in the diseased kidney.
Local striatal volume and motor reserve in drug-naïve Parkinson’s disease
Authors: Jeong Seong Ho , Lee Eun-Chong , Chung Seok Jong , Lee Hye Sun , Jung Jin Ho , Sohn Young H. , Seong Joon-Kyung , Lee Phil Hyu
Published: December 2022

Motor reserve (MR) may explain why individuals with similar pathological changes show marked differences in motor deficits in Parkinson’s disease (PD). In this study, we investigated whether estimated individual MR was linked to local striatal volume (LSV) in PD. We analyzed data obtained from 333 patients with drug naïve PD who underwent dopamine transporter scans and high-resolution 3-tesla T1-weighted structural magnetic resonance images. Using a residual model, we estimated individual MRs on the basis of initial UPDRS-III score and striatal dopamine depletion. We performed a correlation analysis between MR estimates and LSV. Furthermore, we assessed the effect of LSV, which is correlated with MR estimates, on the longitudinal increase in the levodopa-equivalent dose (LED) during the 4-year follow-up period using a linear mixed model. After controlling for intracranial volume, there was a significant positive correlation between LSV and MR estimates in the bilateral caudate, anterior putamen, and ventro-posterior putamen. The linear mixed model showed that the large local volume of anterior and ventro-posterior putamen was associated with the low requirement of LED initially and accelerated LED increment thereafter. The present study demonstrated that LSV is crucial to MR in early-stage PD, suggesting LSV as a neural correlate of MR in PD.
A library of base editors for the precise ablation of all protein-coding genes in the mouse mitochondrial genome
Authors: Silva-Pinheiro Pedro , Mutti Christian D. , Van Haute Lindsey , Powell Christopher A. , Nash Pavel A. , Turner Keira , Minczuk Michal
Published: December 2022

The development of curative treatments for mitochondrial diseases, which are often caused by mutations in mitochondrial DNA (mtDNA) that impair energy metabolism and other aspects of cellular homoeostasis, is hindered by an incomplete understanding of the underlying biology and a scarcity of cellular and animal models. Here we report the design and application of a library of double-stranded-DNA deaminase-derived cytosine base editors optimized for the precise ablation of every mtDNA protein-coding gene in the mouse mitochondrial genome. We used the library, which we named MitoKO, to produce near-homoplasmic knockout cells in vitro and to generate a mouse knockout with high heteroplasmy levels and no off-target edits. MitoKO should facilitate systematic and comprehensive investigations of mtDNA-related pathways and their impact on organismal homoeostasis, and aid the generation of clinically meaningful in vivo models of mtDNA dysfunction.
Mechanical Unloading of Engineered Human Meniscus Models Under Simulated Microgravity: A Transcriptomic Study
Authors: Ma Zhiyao , Li David Xinzheyang , Chee Ryan K. W. , Kunze Melanie , Mulet-Sierra Aillette , Sommerfeldt Mark , Westover Lindsey , Graf Daniel , Adesida Adetola B.
Published: December 2022

Osteoarthritis (OA) primarily affects mechanical load-bearing joints, with the knee being the most common. The prevalence, burden and severity of knee osteoarthritis (KOA) are disproportionately higher in females, but hormonal differences alone do not explain the disproportionate incidence of KOA in females. Mechanical unloading by spaceflight microgravity has been implicated in OA development in cartilaginous tissues. However, the mechanisms and sex-dependent differences in OA-like development are not well explored. In this study, engineered meniscus constructs were generated from healthy human meniscus fibrochondrocytes (MFC) seeded onto type I collagen scaffolds and cultured under normal gravity and simulated microgravity conditions. We report the whole-genome sequences of constructs from 4 female and 4 male donors, along with the evaluation of their phenotypic characteristics. The collected data could be used as valuable resources to further explore the mechanism of KOA development in response to mechanical unloading, and to investigate the molecular basis of the observed sex differences in KOA.