bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dark loops: contagion effects, consistency and chemosocial matrices in psychedelic-assisted therapy trials
Authors: Noorani Tehseen , Bedi Gillinder , Muthukumaraswamy Suresh 
Published: July 2023

AbstractWhat happens when an emerging programme of medical research overlaps with a surging social movement? In this article we draw on the anthropological term ‘chemosociality’ to describe forms of sociality born of shared chemical exposure. Psychedelic administration in the context of recent clinical trials appears to have been particularly chemosocial in nature. We argue that one consequence is that psychedelic-assisted therapy (PAT) clinical research trials tend to breach key assumptions underlying the logic of causal inference used to establish efficacy. We propose the concept of dark loops to describe forms of sociality variously emerging from, and impacting participant experiences in, PAT trials. These dark loops are not recorded, let alone incorporated into the causal pathways in the interpretation of psychedelic trial data to date. We end with three positions which researchers might adopt in response to these issues: chemosocial minimisation where research is designed to attenuate or eliminate the effects of dark loops in trials; chemosocial description where dark loops (and their impacts) are openly and candidly documented and chemosocial valorisation where dark loops are hypothesised to contribute to trial outcomes and actively drawn upon for positive effect. Our goal is to fold in an appreciation of how the increasingly-discussed hype surrounding psychedelic research and therapeutics continues to shape the phenomena under study in complex ways, even as trials become larger and more rigorous in their design.
A New Four‐Component L*‐Dependent Model for Radial Diffusion Based on Solar Wind and Magnetospheric Drivers of ULF Waves
Authors: Murphy Kyle R. , Sandhu Jasmine , Rae I. Jonathan , Daggitt Thomas , Glauert Sarah , Horne Richard B. , Watt Clare E. J. , Bentley Sarah , Kellerman Adam , Ozeke Louis , Halford Alexa J. , Tian Sheng , Breneman Aaron , Olifer Leonid , Mann Ian R. , Angelopoulos Vassilis , Wygant John 
Published: July 2023

AbstractWaves which couple to energetic electrons are particularly important in space weather, as they drive rapid changes in the topology and intensity of Earth's outer radiation belt during geomagnetic storms. This includes Ultra Low Frequency (ULF) waves that interact with electrons via radial diffusion which can lead to electron dropouts via outward transport and rapid electron acceleration via inward transport. In radiation belt simulations, the strength of this interaction is specified by ULF wave radial diffusion coefficients. In this paper we detail the development of new models of electric and magnetic radial diffusion coefficients derived from in‐situ observations of the azimuthal electric field and compressional magnetic field. The new models use as it accounts for adiabatic changes due to the dynamic magnetic field coupled with an optimized set of four components of solar wind and geomagnetic activity, , , , and , as independent variables (inputs). These independent variables are known drivers of ULF waves and offer the ability to calculate diffusion coefficients at a higher cadence then existing models based on Kp. We investigate the performance of the new models by characterizing the model residuals as a function of each independent variable and by comparing to existing radial diffusion models during a quiet geomagnetic period and through a geomagnetic storm. We find that the models developed here perform well under varying levels of activity and have a larger slope or steeper gradient as a function of as compared to existing models (higher diffusion at higher values).
Early and intensive Motor Training for people with spinal cord injuries (the SCI-MT Trial): description of the intervention
Authors: Ben M. , Glinsky J. V. , Chu J. , Spooren A. I. , Roberts S. , Chen L. W. , Denis S. , Lorusso M. , Jorgensen V. , Gollan E. J. , Agostinello J. , Van Laake-Geelen C. C. M. , Lincoln C. , Stolwijk J. M. , Bell C. , Paddison S. , Rainey D. , Tranter K. , Ilha J. , Oostra K. , Sherrington C. , Harvey L. A. 
Published: July 2023

Abstract
Study design
Descriptive.

Objectives
The primary objective is to describe the intervention that will be provided in a large multi-centre randomised controlled trial titled: Early and Intensive Motor Training for people with Spinal Cord Injuries (the SCI-MT Trial). The secondary objective is to describe the strategies that will be used to operationalise and standardise the Motor Training provided to participants while keeping the intervention person-centred.

Methods
The paper focuses on the rationale and principles of Motor Training for people with spinal cord injuries (SCI). The description of the intervention is based on the Template for Intervention Description and Replication (TIDieR) checklist. Specifically, it addresses the following 6 criteria of the TIDieR checklist: why the effectiveness of Motor Training is being examined; what, how, where and when the Motor Training will be administered; and how much Motor Training will be provided.

Results
A detailed intervention manual has been developed to help standardise the delivery of the intervention.

Conclusions
This paper describes the details of a complex intervention administered as part of a large randomised controlled trial. It will facilitate the subsequent interpretation of the trial results and enable the intervention to be reproduced in clinical practice and future trials.
Pulcherrimin protects Bacillus subtilis against oxidative stress during biofilm development
Authors: Angelini Leticia Lima , dos Santos Renato Augusto Corrêa , Fox Gabriel , Paruthiyil Srinand , Gozzi Kevin , Shemesh Moshe , Chai Yunrong 
Published: July 2023

AbstractPulcherrimin is an iron-binding reddish pigment produced by various bacterial and yeast species. In the soil bacterium Bacillus subtilis, this pigment is synthesized intracellularly as the colorless pulcherriminic acid by using two molecules of tRNA-charged leucine as the substrate; pulcherriminic acid molecules are then secreted and bind to ferric iron extracellularly to form the red-colored pigment pulcherrimin. The biological importance of pulcherrimin is not well understood. A previous study showed that secretion of pulcherrimin caused iron depletion in the surroundings and growth arrest on cells located at the edge of a B. subtilis colony biofilm. In this study, we identified that pulcherrimin is primarily produced under biofilm conditions and provides protection to cells in the biofilm against oxidative stress. We presented molecular evidence on how pulcherrimin lowers the level of reactive oxygen species (ROS) and alleviates oxidative stress and DNA damage caused by ROS accumulation in a mature biofilm. We also performed global transcriptome profiling to identify differentially expressed genes in the pulcherrimin-deficient mutant compared with the wild type, and further characterized the regulation of genes by pulcherrimin that are related to iron homeostasis, DNA damage response (DDR), and oxidative stress response. Based on our findings, we propose pulcherrimin as an important antioxidant that modulates B. subtilis biofilm development.
Mixing of moiré-surface and bulk states in graphite
Authors: Mullan Ciaran , Slizovskiy Sergey , Yin Jun , Wang Ziwei , Yang Qian , Xu Shuigang , Yang Yaping , Piot Benjamin A. , Hu Sheng , Taniguchi Takashi , Watanabe Kenji , Novoselov Kostya S. , Geim A. K. , Fal’ko Vladimir I. , Mishchenko Artem 
Published: July 2023

AbstractVan der Waals assembly enables the design of electronic states in two-dimensional (2D) materials, often by superimposing a long-wavelength periodic potential on a crystal lattice using moiré superlattices1–9. This twistronics approach has resulted in numerous previously undescribed physics, including strong correlations and superconductivity in twisted bilayer graphene10–12, resonant excitons, charge ordering and Wigner crystallization in transition-metal chalcogenide moiré structures13–18 and Hofstadter’s butterfly spectra and Brown–Zak quantum oscillations in graphene superlattices19–22. Moreover, twistronics has been used to modify near-surface states at the interface between van der Waals crystals23,24. Here we show that electronic states in three-dimensional (3D) crystals such as graphite can be tuned by a superlattice potential occurring at the interface with another crystal—namely, crystallographically aligned hexagonal boron nitride. This alignment results in several Lifshitz transitions and Brown–Zak oscillations arising from near-surface states, whereas, in high magnetic fields, fractal states of Hofstadter’s butterfly draw deep into the bulk of graphite. Our work shows a way in which 3D spectra can be controlled using the approach of 2D twistronics.
A cell-type-specific error-correction signal in the posterior parietal cortex
Authors: Green Jonathan , Bruno Carissa A. , Traunmüller Lisa , Ding Jennifer , Hrvatin Siniša , Wilson Daniel E. , Khodadad Thomas , Samuels Jonathan , Greenberg Michael E. , Harvey Christopher D. 
Published: July 2023

AbstractNeurons in the posterior parietal cortex contribute to the execution of goal-directed navigation1 and other decision-making tasks2–4. Although molecular studies have catalogued more than 50 cortical cell types5, it remains unclear what distinct functions they have in this area. Here we identified a molecularly defined subset of somatostatin (Sst) inhibitory neurons that, in the mouse posterior parietal cortex, carry a cell-type-specific error-correction signal for navigation. We obtained repeatable experimental access to these cells using an adeno-associated virus in which gene expression is driven by an enhancer that functions specifically in a subset of Sst cells6. We found that during goal-directed navigation in a virtual environment, this subset of Sst neurons activates in a synchronous pattern that is distinct from the activity of surrounding neurons, including other Sst neurons. Using in vivo two-photon photostimulation and ex vivo paired patch-clamp recordings, we show that nearby cells of this Sst subtype excite each other through gap junctions, revealing a self-excitation circuit motif that contributes to the synchronous activity of this cell type. These cells selectively activate as mice execute course corrections for deviations in their virtual heading during navigation towards a reward location, for both self-induced and experimentally induced deviations. We propose that this subtype of Sst neurons provides a self-reinforcing and cell-type-specific error-correction signal in the posterior parietal cortex that may help with the execution and learning of accurate goal-directed navigation trajectories.
Organ Mapping Antibody Panels: a community resource for standardized multiplexed tissue imaging
Authors: Quardokus Ellen M. , Saunders Diane C. , McDonough Elizabeth , Hickey John W. , Werlein Christopher , Surrette Christine , Rajbhandari Presha , Casals Anna Martinez , Tian Hua , Lowery Lisa , Neumann Elizabeth K. , Björklund Frida , Neelakantan Taruna V. , Croteau Josh , Wiblin Anne E. , Fisher Jeremy , Livengood April J. , Dowell Karen G. , Silverstein Jonathan C. , Spraggins Jeffrey M. , Pryhuber Gloria S. , Deutsch Gail , Ginty Fiona , Nolan Garry P. , Melov Simon , Jonigk Danny , Caldwell Michael A. , Vlachos Ioannis S. , Muller Werner , Gehlenborg Nils , Stockwell Brent R. , Lundberg Emma , Snyder Michael P. , Germain Ronald N. , Camarillo Jeannie M. , Kelleher Neil L. , Börner Katy , Radtke Andrea J. 
Published: July 2023

AbstractMultiplexed antibody-based imaging enables the detailed characterization of molecular and cellular organization in tissues. Advances in the field now allow high-parameter data collection (>60 targets); however, considerable expertise and capital are needed to construct the antibody panels employed by these methods. Organ mapping antibody panels are community-validated resources that save time and money, increase reproducibility, accelerate discovery and support the construction of a Human Reference Atlas.
Viral kinetics, stability and sensitivity analysis of the within-host COVID-19 model
Authors: Elbaz Islam M. , El-Metwally H. , Sohaly M. A. 
Published: July 2023

AbstractThis paper delves into the investigation of the COVID-19 dynamics within a host using the Target-Latent-Infected-Virus (TLIV) model, presenting a fresh approach compared to previous studies. Our model introduces a latent class and explores sensitivity analysis, aspects that have received limited attention in prior research. A significant contribution of this study is the analysis of both local and global stability of equilibrium states, subject to specific sufficient conditions based on the basic reproduction number $$R_0$$

R
0

. By examining these stability properties, we aim to gain insights into the factors underlying variations observed in the findings of different studies. Additionally, we identify the death rate of infected cells as the parameter most susceptible to influence in our model. To minimize its impact and facilitate recovery, it is crucial to implement appropriate medical therapies and consume immune-boosting foods. Some computer simulations are carried out to strengthen the theoretical results.
Development and external validation of a pretrained deep learning model for the prediction of non-accidental trauma
Authors: Huang David , Cogill Steven , Hsia Renee Y. , Yang Samuel , Kim David 
Published: July 2023

AbstractNon-accidental trauma (NAT) is deadly and difficult to predict. Transformer models pretrained on large datasets have recently produced state of the art performance on diverse prediction tasks, but the optimal pretraining strategies for diagnostic predictions are not known. Here we report the development and external validation of Pretrained and Adapted BERT for Longitudinal Outcomes (PABLO), a transformer-based deep learning model with multitask clinical pretraining, to identify patients who will receive a diagnosis of NAT in the next year. We develop a clinical interface to visualize patient trajectories, model predictions, and individual risk factors. In two comprehensive statewide databases, approximately 1% of patients experience NAT within one year of prediction. PABLO predicts NAT events with area under the receiver operating characteristic curve (AUROC) of 0.844 (95% CI 0.838–0.851) in the California test set, and 0.849 (95% CI 0.846–0.851) on external validation in Florida, outperforming comparator models. Multitask pretraining significantly improves model performance. Attribution analysis shows substance use, psychiatric, and injury diagnoses, in the context of age and racial demographics, as influential predictors of NAT. As a clinical decision support system, PABLO can identify high-risk patients and patient-specific risk factors, which can be used to target secondary screening and preventive interventions at the point-of-care.
Fast detection of slender bodies in high density microscopy data
Authors: Alonso Albert , Kirkegaard Julius B. 
Published: July 2023

AbstractComputer-aided analysis of biological microscopy data has seen a massive improvement with the utilization of general-purpose deep learning techniques. Yet, in microscopy studies of multi-organism systems, the problem of collision and overlap remains challenging. This is particularly true for systems composed of slender bodies such as swimming nematodes, swimming spermatozoa, or the beating of eukaryotic or prokaryotic flagella. Here, we develop a end-to-end deep learning approach to extract precise shape trajectories of generally motile and overlapping slender bodies. Our method works in low resolution settings where feature keypoints are hard to define and detect. Detection is fast and we demonstrate the ability to track thousands of overlapping organisms simultaneously. While our approach is agnostic to area of application, we present it in the setting of and exemplify its usability on dense experiments of swimming Caenorhabditis elegans. The model training is achieved purely on synthetic data, utilizing a physics-based model for nematode motility, and we demonstrate the model’s ability to generalize from simulations to experimental videos.
Parvalbumin neurons enhance temporal coding and reduce cortical noise in complex auditory scenes
Authors: Nocon Jian Carlo , Gritton Howard J. , James Nicholas M. , Mount Rebecca A. , Qu Zhili , Han Xue , Sen Kamal 
Published: July 2023

AbstractCortical representations supporting many cognitive abilities emerge from underlying circuits comprised of several different cell types. However, cell type-specific contributions to rate and timing-based cortical coding are not well-understood. Here, we investigated the role of parvalbumin neurons in cortical complex scene analysis. Many complex scenes contain sensory stimuli which are highly dynamic in time and compete with stimuli at other spatial locations. Parvalbumin neurons play a fundamental role in balancing excitation and inhibition in cortex and sculpting cortical temporal dynamics; yet their specific role in encoding complex scenes via timing-based coding, and the robustness of temporal representations to spatial competition, has not been investigated. Here, we address these questions in auditory cortex of mice using a cocktail party-like paradigm, integrating electrophysiology, optogenetic manipulations, and a family of spike-distance metrics, to dissect parvalbumin neurons’ contributions towards rate and timing-based coding. We find that suppressing parvalbumin neurons degrades cortical discrimination of dynamic sounds in a cocktail party-like setting via changes in rapid temporal modulations in rate and spike timing, and over a wide range of time-scales. Our findings suggest that parvalbumin neurons play a critical role in enhancing cortical temporal coding and reducing cortical noise, thereby improving representations of dynamic stimuli in complex scenes.
Unusual crossover from Bardeen-Cooper-Schrieffer to Bose-Einstein-condensate superconductivity in iron chalcogenides
Authors: Mizukami Yuta , Haze Masahiro , Tanaka Ohei , Matsuura Kohei , Sano Daiki , Böker Jakob , Eremin Ilya , Kasahara Shigeru , Matsuda Yuji , Shibauchi Takasada 
Published: July 2023

AbstractThe BCS-BEC (Bardeen-Cooper-Schrieffer–Bose-Einstein-condensate) crossover from strongly overlapping Cooper pairs to non-overlapping composite bosons in the strong coupling limit has been a long-standing issue of interacting many-body fermion systems. Recently, FeSe semimetal with hole and electron bands emerged as a high-transition-temperature (high-Tc) superconductor located in the BCS-BEC crossover regime, owing to its very small Fermi energies. In FeSe, however, an ordinary BCS-like heat-capacity jump is observed at Tc, posing a fundamental question on the characteristics of the BCS-BEC crossover. Here we report on high-resolution heat capacity, magnetic torque, and scanning tunneling spectroscopy measurements in FeSe1−xSx. Upon entering the tetragonal phase at x > 0.17, where nematic order is suppressed, Tc discontinuously decreases. In this phase, highly non-mean-field behaviours consistent with BEC-like pairing are found in the thermodynamic quantities with giant superconducting fluctuations extending far above Tc, implying the change of pairing nature. Moreover, the pseudogap formation, which is expected in BCS-BEC crossover of single-band superconductors, is not observed in the tunneling spectra. These results illuminate highly unusual features of the superconducting states in the crossover regime with multiband electronic structure and competing electronic instabilities.
Influence of high‐order electromagnetic force on vibration characteristics of induction motor
Authors: Liu Xiaopeng , Hong Jianfeng , Sun Bingxiang , Zhang Weige , Jiang Jiuchun 
Published: July 2023

AbstractThe exploration of electromagnetic vibration sources is very important for the vibroacoustic reduction of a squirrel‐cage induction motor. However, the influence of high‐order electromagnetic force on the electromagnetic vibration of induction motor has not been studied before. The influence of high‐order electromagnetic force on motor vibration is investigated in detail. Firstly, the Maxwell stress tensor method is applied to calculate the electromagnetic force. Next, the force transfer function is introduced to describe the phenomenon that the high‐order electromagnetic force induces the low‐mode motor vibration. Then, the high‐order forces in the air gap of the induction motor are analysed in detail and their effects on motor vibration are simulated. Finally, an experiment is conducted to verify the correctness of the analytical scheme.
A power quality‐based framework for optimal siting and sizing of wind turbines by search space reduction via power losses and flicker emission sensitivity indices
Authors: Ghaffari Abolfazl , Askarzadeh Alireza , Fadaeinedjad Roohollah 
Published: July 2023

AbstractAs a well‐established renewable energy resource, wind energy is being widely used in distribution networks. However, flicker emission produced by wind turbines (WTs) is one of the main disadvantages which may cause serious problems during the system operation. Power quality‐based optimal allocation (siting and sizing) of WTs is an appropriate way to mitigate the flicker emission. Since the planning issue is a high dimensional and complex optimization problem and optimization methods suffer from premature convergence, search space reduction may be an effective approach to optimally solve the allocation problem. Here, to determine the importance of the network buses, two indices, namely, power loss index (PLI) and flicker emission index (FEI) are introduced to determine the sensitivity of the network losses and flicker emission to allocate WT on each bus. Then, based on the proposed indices, a number of important buses are identified and the allocation problem is solved with respect to these buses. Over the case study, it can be drawn that optimal allocation of WTs considerably affects the flicker emission. Moreover, search space reduction is an efficient way to optimally solve the allocation problem.
Deep sequencing of circulating miRNAs and target mRNAs level in deep venous thrombosis patients
Authors: Wang Qingxian , Chang Yunhe , Yang Xuqing , Han Ziwang 
Published: July 2023

AbstractDeep venous thrombosis is one of the most common peripheral vascular diseases that lead to major morbidity and mortality. The authors aimed to identify potential differentially expressed miRNAs and target mRNAs, which were helpful in understanding the potential molecule mechanism of deep venous thrombosis. The plasma samples of patients with deep venous thrombosis were obtained for the RNA sequencing. Differentially expressed miRNAs were identified, followed by miRNA‐mRNA target analysis. Enrichment analysis was used to analyze the potential biological function of target mRNAs. GSE19151 and GSE173461 datasets were used for expression validation of mRNAs and miRNAs. 131 target mRNAs of 21 differentially expressed miRNAs were identified. Among which, 8 differentially expressed miRNAs including hsa‐miR‐150‐5p, hsa‐miR‐326, hsa‐miR‐144‐3p, hsa‐miR‐199a‐5p, hsa‐miR‐199b‐5p, hsa‐miR‐125a‐5p, hsa‐let‐7e‐5p and hsa‐miR‐381‐3p and their target mRNAs (PRKCA, SP1, TP53, SLC27A4, PDE1B, EPHB3, IRS1, HIF1A, MTUS1 and ZNF652) were found associated with deep venous thrombosis for the first time. Interestingly, PDE1B and IRS1 had a potential diagnostic value for patients. Additionally, 3 important signaling pathways including p53, PI3K‐Akt and MAPK were identified in the enrichment analysis of target mRNAs (TP53, PRKCA and IRS1). Identified circulating miRNAs and target mRNAs and related signaling pathways may be involved in the process of deep venous thrombosis.