Miracle-dz/UniFAR-FTUs huggingface dataset:
A framework for preparing a stochastic nonlinear integrate-and-fire model for integrated information theory

ABSTRACT This paper presents a framework for spiking neural networks to be prepared for the Integrated Information Theory (IIT) analysis, using a stochastic nonlinear integrate-and-fire model. The model includes the crucial dynamics of the all-or-none law and after-spike refractoriness. The noise is modelled as an additive term in the system’s equations. By preparing the model for the IIT analysis, it is meant to determine the length of the analysis time-window and the transition probability distributions required for the IIT 3.0. To this end, a system of differential equations is proposed to estimate the time evolution of the system’s mean and covariance. Assuming the binary Fired/Silent activity as the possible states of each neuron, an algorithm is proposed to calculate the required probability distributions. As long as the Fired/Silent probabilities are only concerned, the Gaussian density assumption with the estimated moments is a reasonable estimate. The synaptic inputs are treated as random variables with low variances to avoid the costs of conditioning on the system’s past activities. The Monte-Carlo simulation is used to validate the estimation methods. To increase the reliability of the inductive inference behind the Monte-Carlo method, various stimulation protocols are applied to evoke the dynamics of the equations.
The COVID-19 vaccine concerns scale: Development and validation of a new measure

ABSTRACT Reasons for COVID-19 hesitancy are multi-faceted and tend to differ from those for general vaccine hesitancy. We developed the COVID-19 Vaccine Concerns Scale (CVCS), a self-report measure intended to better understand individuals’ concerns about COVID-19 vaccines. We validated the scale using data from a convenience sample of 2,281 emergency medical services providers, a group of professionals with high occupational COVID-19 risk. Measures included the CVCS items, an adapted Oxford COVID-19 vaccine hesitancy scale, a general vaccine hesitancy scale, demographics, and self-reported COVID-19 vaccination status. The CVCS had high internal consistency reliability (α = .89). A one-factor structure was determined by exploratory and confirmatory factor analyses (EFA and CFA), resulting in a seven-item scale. The model had good fit (X2[14] = 189.26, p < .001; CFI = .95, RMSEA = .11 [.09, .12], NNFI = .93, SRMR = .03). Moderate Pearson correlations with validated scales of general vaccine hesitancy (r = .71 , p < .001; n = 2144) and COVID-19 vaccine hesitancy (r = .82; p < .001; n = 2279) indicated construct validity. The CVCS predicted COVID-19 vaccination status (B = −2.21, Exp(B) = . 11 [95% CI = . 09, . 13], Nagelkerke R2 = . 55), indicating criterion-related validity. In sum, the 7-item CVCS is a reliable and valid self-report measure to examine fears and concerns about COVID-19 vaccines. The scale predicts COVID-19 vaccination status and can be used to inform efforts to reduce COVID-19 vaccine hesitancy.
How the Interplay among Conformational Disorder, Solvation, Local, and Charge-Transfer Excitations Affects the Absorption Spectrum and Photoinduced Dynamics of Perylene Diimide Dimers: A Molecular Dynamics/Quantum Vibronic Approach

In this contribution we present a mixed quantum-classical dynamical approach for the computation of vibronic absorption spectra of molecular aggregates and their nonadiabatic dynamics, taking into account the coupling between local excitations (LE) and charge-transfer (CT) states. The approach is based on an adiabatic (Ad) separation between the soft degrees of freedom (DoFs) of the system and the stiff vibrations, which are described by the quantum dynamics (QD) of wave packets (WPs) moving on the coupled potential energy surfaces (PESs) of the LE and CT states. These PESs are described with a linear vibronic coupling (LVC) Hamiltonian, parameterized by an overlap-based diabatization on the grounds of time-dependent density functional theory computations. The WPs time evolution is computed with the multiconfiguration time-dependent Hartree method, using effective modes defined through a hierarchical representation of the LVC Hamiltonian. The soft DoFs are sampled with classical molecular dynamics (MD), and the coupling between the slow and fast DoFs is included by recomputing the key parameters of the LVC Hamiltonians, specifically for each MD configuration. This method, named Ad-MD|gLVC, is applied to a perylene diimide (PDI) dimer in acetonitrile and water solutions, and it is shown to accurately reproduce the change in the vibronic features of the absorption spectrum upon aggregation. Moreover, the microscopic insight offered by the MD trajectories allows for a detailed understanding of the role played by the fluctuation of the aggregate structure on the shape of the vibronic spectrum and on the population of LE and CT states. The nonadiabatic QD predicts an extremely fast (∼50 fs) energy transfer between the two LEs. CT states have only a moderate effect on the absorption spectrum, despite the fact that after photoexcitation they are shown to acquire a fast and non-negligible population, highlighting their relevance in dictating the charge separation and transport in PDI-based optical devices.
Improving Breast Tumor Segmentation in PET via Attentive Transformation Based Normalization

Positron Emission Tomography (PET) has become a preferred imaging modality for cancer diagnosis, radiotherapy planning, and treatment responses monitoring. Accurate and automatic tumor segmentation is the fundamental requirement for these clinical applications. Deep convolutional neural networks have become the state-of-the-art in PET tumor segmentation. The normalization process is one of the key components for accelerating network training and improving the performance of the network. However, existing normalization methods either introduce batch noise into the instance PET image by calculating statistics on batch level or introduce background noise into every single pixel by sharing the same learnable parameters spatially. In this paper, we proposed an attentive transformation (AT)-based normalization method for PET tumor segmentation. We exploit the distinguishability of breast tumor in PET images and dynamically generate dedicated and pixel-dependent learnable parameters in normalization via the transformation on a combination of channel-wise and spatial-wise attentive responses. The attentive learnable parameters allow to re-calibrate features pixel-by-pixel to focus on the high-uptake area while attenuating the background noise of PET images. Our experimental results on two real clinical datasets show that the AT-based normalization method improves breast tumor segmentation performance when compared with the existing normalization methods.
The chromosome-level genome assembly of Gentiana dahurica (Gentianaceae) provides insights into gentiopicroside biosynthesis

Abstract Gentiana dahurica Fisch. is a perennial herb of the family Gentianaceae. This species is used as a traditional Tibetan medicine because of its rich gentiopicroside constituents. Here, we generate a high-quality, chromosome-level genome of G. dahurica with a total length of 1,416.54 Mb. Comparative genomic analyses showed that G. dahurica shared one whole-genome duplication (WGD) event with Gelsemium sempervirens of the family Gelsemiaceaei and had one additional species-specific WGD after the ancient whole-genome triplication with other eudicots. Further transcriptome analyses identified numerous enzyme coding genes and the transcription factors related to gentiopicroside biosynthesis. A set of candidate cytochrome P450 genes were identified for being involved in biosynthetic shifts from swertiamarin to gentiopicroside. Both gene expressions and the contents measured by high-performance liquid chromatography indicated that the gentiopicrosides were mainly synthesized in the rhizomes with the highest contents. In addition, we found that two above-mentioned WGDs, contributed greatly to the identified candidate genes involving in gentiopicroside biosynthesis. The first reference genome of Gentianaceae we generated here will definitely accelerate evolutionary, ecological, and pharmaceutical studies of this family.
Effects of Exogenous Ketone Supplementation on Blood Glucose: A Systematic Review and Meta-Analysis.

Recently developed ketone (monoester or salt) supplements acutely elevate blood β-hydroxybutyrate (BHB) exogenously without prolonged periods of fasting or carbohydrate restriction. Previous (small-scale) studies have found a blood glucose-lowering effect of exogenous ketones. This study aimed to systematically review available evidence and conduct meta-analyses of studies reporting on exogenous ketones and blood glucose. We searched 6 electronic databases on December 13, 2021 for randomized and non-randomized trials of any length that reported on the use of exogenous ketones. We calculated raw mean differences (MD) in blood BHB and glucose in two main analyses: (I) after compared to before acute ingestion of exogenous ketones, and (II) following acute ingestion of exogenous ketones compared to a comparator supplement. We pooled effect sizes using random-effects models and performed prespecified subgroup analyses to examine the effect of potential explanatory factors, including study population, exercise, blood BHB, and supplement type, dosing, and timing. Risk of bias was examined using Cochrane's risk-of-bias tools. Studies that could not be meta-analyzed were summarized narratively. Forty-three trials including 586 participants are summarized in this review. Following ingestion, exogenous ketones increased blood BHB (MD = 1.73 mM, 95% CI: 1.26 mM to 2.21 mM, P < 0.001) and decreased mean blood glucose (MD = -0.54 mM, 95% CI: -0.68 mM to -0.40 mM, P < 0.001). Similarly, when compared to placebo, blood BHB increased (MD = 1.98 mM, 95% CI: 1.52 mM to 2.45 mM, P < 0.001) and blood glucose decreased (MD = -0.47 mM, 95% CI: -0.57 mM to -0.36 mM, P < 0.001). Across both analyses, significantly greater effects were seen with ketone monoesters compared to salts (P < 0.001). The available evidence indicates that acute ingestion of exogenous ketones leads to increased blood BHB and decreased blood glucose. Limited evidence on prolonged ketone supplementation was found.
Initial Excited State Dynamics of Lumichrome upon Ultraviolet Excitation

Lumichrome (LC) is the major photodegradation product of biologically important flavin cofactors. Since LC serves as a structural comparison with the flavins; understanding excited states of LC is fundamentally important to establish a connection with photophysics of different flavins, such as lumiflavin (LF), riboflavin (RF), flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD). Herein, we deduce the initial excited state structural dynamics of LC using UV resonance Raman (UVRR) intensity analysis. The UVRR spectra at wavelengths across the 260 nm absorption band of LC were measured and resulting Raman excitation profiles and absorption spectrum were self‐consistently simulated using a time‐dependent wave packet formalism to extract the initial excited state structural and solvent broadening parameters. These results are compared with those obtained for other flavins following UV excitations. We find that LC undergoes a very distinct instantaneous charge redistribution than flavins, which is attributed to the extended π‐conjugation present in flavins but missing in LC. The homogeneous broadening linewidth of LC appears to be lower than that of LF, while the inhomogeneous broadening values are comparable, indicating greater solvent interaction with excited flavin on ultrafast timescale compared with LC, whereas on longer timescale these interactions are almost similar.
Event-related Oscillations to Emotional Faces are Related to a History of Internalizing Disorders

Event-related oscillations (EROs) may represent sensitive biomarkers or endophenotypes for disorders that underlie risk behaviors such as suicidal thoughts and actions. In this study, young adults of American Indian (AI) (n = 821) and Mexican American (MA) (n = 721) ancestry (age 18-30 yrs) were clinically assessed for internalizing and externalizing disorders, and an internalizing scale was generated by extracting core diagnostic items from 6 lifetime DSM5-compatible diagnoses (social phobia, panic disorder, agoraphobia, obsessive compulsive disorder, post-traumatic stress disorder, major depressive episode) and symptoms of suicidality. EROs were generated to sad, happy and neutral faces, and energy and phase locking of delta ERO oscillations were assessed in frontal areas. An increase in delta ERO energy was found in the frontal lead (FZ) following presentation of the sad facial expressions in those with a history of 10 or more internalizing symptoms compared to those with no symptoms. Increases in delta ERO energy in FZ were also associated with a diagnosis of major depressive disorder (MDD), but not with anxiety disorders or antisocial personality disorder/conduct disorders (ASP). Major depression was also associated with increases in cross-cortical phase-locking (FZ-PZ). A decrease in the percentage of correctly identified neutral faces also was seen among those with 10 or more internalizing symptoms compared to those without internalizing symptoms, and in those with anxiety disorders, but not in those with ASP or MDD as compared to their controls. These findings suggest ERO measures may represent important potential biomarkers of depressive disorders as well as risk indicators for suicidal behaviors.
A simple extemporaneous oral suspension of aprepitant yields sufficient pharmacokinetic exposure in children

Introduction Aprepitant is used for the treatment of chemotherapy induced nausea and vomiting. A liquid formulation is needed for treatment of young children. However, the commercial (powder for) suspension was not available worldwide for a prolonged period of time and, therefore, a 10 mg/mL aprepitant oral suspension was extemporarily prepared to prevent suboptimal antiemetic treatment. The current pharmacokinetic study was developed to investigate whether this extemporaneous oral suspension offers an appropriate treatment option. Methods From 49 pediatric patients (0.7–17.9 years) 235 plasma concentrations were collected. Patients were either treated with our extemporaneous oral suspension (n = 26; 53%), commercially available capsules (n = 18; 37%), or the intravenous prodrug formulation of aprepitant (fosaprepitant, n = 5; 10%). Pharmacokinetic analyses were performed using nonlinear mixed effects modelling. Results A one-compartment model adequately described the pharmacokinetics of aprepitant in children. The bioavailability of the extemporaneous oral suspension was not significantly different to that of the capsules (P = 0.26). The observed bioavailability throughout the total population was 83% (95% CI 69%-97%). The absorption of the extemporaneous oral suspension was 39.4% (95%CI 19.5–57.4%) faster than that of capsules (mean absorption time of 1.78 h (95%CI 1.32–2.35), but was comparable to that of the commercial oral suspension. The median area under the curve after (fos)aprepitant was 22.2 mg/L*h (range 8.9–50.3 mg/L*h) on day 1. Conclusion Our extemporaneous oral suspension is an adequate alternative for the commercially (un)available oral suspension in young children. An adequate exposure to aprepitant in children was yielded and the bioavailability of the extemporaneous suspension was comparable to capsules.
Be Our Guest: The Development of the Interpersonal Hospitality Scale

Abstract Despite the ubiquity of hosting others in one’s home, no validated measure of domestic hospitality currently exists. To address this gap, the current paper presents a set of four studies that develop and validate the Interpersonal Hospitality Scale, which seeks to capture the affective, motivational, and behavioral components of this person-place construct. The 12-item scale assesses three core dimensions: responsibility for guests, welcomingness, and a lack of perceived imposition. The analyses reported here provide support for the psychometric adequacy of this new scale, demonstrating strong internal reliability and a consistent factor structure. Moreover, this trait was found to be a unique predictor of several theoretically related constructs, including one’s desired home ambiance, attitudes toward immigration, and willingness/likelihood of hosting others in need. This scale offers a much-needed means of measuring one important aspect of how people conceptualize their home environment relative to others.
Access to period products during the first nation-wide lockdown in Australia: Results from an online survey

ABSTRACT In early 2020, Australia experienced a nation-wide lockdown to help stop the spread of COVID-19. While many aspects of normal life were put on hold, others, like menstruation, did not stop. We examined the impact of the lockdown on the ability of people to access their usual period products. We conducted an online survey open for 2.5 weeks during the lockdown. Here, we report on responses from participants who identified as female, who were of reproductive age, and who answered questions regarding their ability to access their usual products. We fitted univariable and multivariable logistic regression models to explore factors associated with difficulty accessing period products and utilized a conventional content analysis for the free-text qualitative data. Of the 410 participants, nearly one-third reported difficulties accessing their usual period products during lockdown. Women under 25 years were more likely to experience difficulty accessing products. Free-text comments revealed the ways in which women handled this, often purchasing whatever was available regardless of whether it was a product that met their needs or not. Periods do not stop in a pandemic, and it is vital that people are able to access the products they require to manage their periods hygienically and comfortably.
Identification of potential antivirals against 3CLpro enzyme for the treatment of SARS-CoV-2: A multi-step virtual screening study

ABSTRACT The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) outbreak is posing a serious public health threat worldwide in the form of COVD-19. Herein, we have performed two-dimensional quantitative structure–activity relationship (2D-QSAR) and three-dimensional pharmacophore modelling analysis employing inhibitors of 3-chymotrypsin-like protease (3CLpro), the leading protease that is crucial for the replication of SARS-CoV-2. The investigation aims to identify the important structural features responsible for the enzyme inhibition and the search for novel 3CLpro enzyme inhibitors as effective therapeutics for treating SARS-CoV-2. Furthermore, we carried out molecular docking studies using the most and least active compounds in the dataset, aiming to validate the contributions of various features as appeared in the QSAR models. Later, the stringently validated 2D-QSAR model was used to estimate the 3CLpro inhibitory activity of compounds from five chemical databases. Compounds with the significant predicted activity were then subjected to pharmacophore-based virtual screening to screen the top-rated compounds, which were then further subjected to molecular docking analysis, absorption, distribution, metabolism, excretion – toxicity (ADMET) profiling, and molecular dynamics (MD) simulation. The multi-step virtual screening analyses suggested that compounds CASAntiV-865453-58-3, CASAntiV-865453-40-3, and CASAntiV-2043031-84-9 could be used as effective therapeutic agents for the treatment of SARS-CoV-2.
Help-Seeking and Help-Related Experiences of Commercially Sexually Exploited Youth: A Qualitative Meta-Synthesis

This interpretive qualitative meta-synthesis (QMS) aims to systematically review what we know about the help-seeking and help-related experiences of commercially sexually exploited youth (CSEY). A comprehensive search of the relevant databases was conducted to identify published qualitative peer-reviewed papers and research reports about the experiences and perceptions of CSEY. A corpus of 34 qualitative studies was compiled and synthesized, using the conceptual framework of help-seeking and QMS guidelines. The QMS reveals that although help-seeking of CSEY are rarely the focus of the inquiry, the reviewed studies include meaningful information about help-related experiences of CSEY. Thus, the synthesis of the available data yields novel insights about how CSEY perceive their involvement in CSE, define the problems they deal with, decide to seek help, choose the proper help, and engage in helping relations. Particularly, the QMS underscores that CSEY do not always perceive their involvement in CSE as problematic, nor do they identify themselves as victims of exploitation. The findings highlight the significance of developing social services that specialize in helping CSEY, the importance of actively identifying CSEY and reaching out to them, and the need to enable CSEY to be involved in decisions about the extent and type of support they are provided.
Reprogramming and redifferentiation of mucosal-associated invariant T cells reveal tumor inhibitory activity

Mucosal-associated invariant T (MAIT) cells belong to a family of innate-like T cells that bridge innate and adaptive immunities. Although MAIT cells have been implicated in tumor immunity, it currently remains unclear whether they function as tumor-promoting or inhibitory cells. Therefore, we herein used induced pluripotent stem cell (iPSC) technology to investigate this issue. Murine MAIT cells were reprogrammed into iPSCs and redifferentiated towards MAIT-like cells (m-reMAIT cells). m-reMAIT cells were activated by an agonist in the presence and absence of antigen-presenting cells and MR1-tetramer, a reagent to detect MAIT cells. This activation accompanied protein tyrosine phosphorylation and the production of T helper (Th)1, Th2, and Th17 cytokines and inflammatory chemokines. Upon adoptive transfer, m-reMAIT cells migrated to different organs with maturation in mice. Furthermore, m-reMAIT cells inhibited tumor growth in the lung metastasis model and prolonged mouse survival upon tumor inoculation through the NK cell-mediated reinforcement of cytolytic activity. Collectively, the present results demonstrated the utility and role of m-reMAIT cells in tumor immunity and provide insights into the function of MAIT cells in immunity.