julilili42/papers huggingface dataset:
The START domain potentiates HD-ZIPIII transcriptional activity
2023-03-02

Abstract The CLASS III HOMEODOMAIN-LEUCINE ZIPPER (HD-ZIPIII) transcription factors (TFs) were repeatedly deployed over 725 million years of evolution to regulate central developmental innovations. The START domain of this pivotal class of developmental regulators was recognized over 20 years ago, but its putative ligands and functional contributions remain unknown. Here, we demonstrate that the START domain promotes HD-ZIPIII TF homodimerization and increases transcriptional potency. Effects on transcriptional output can be ported onto heterologous TFs, consistent with principles of evolution via domain capture. We also show the START domain binds several species of phospholipids, and that mutations in conserved residues perturbing ligand binding and/or its downstream conformational readout abolish HD-ZIPIII DNA-binding competence. Our data present a model in which the START domain potentiates transcriptional activity and uses ligand-induced conformational change to render HD-ZIPIII dimers competent to bind DNA. These findings resolve a long-standing mystery in plant development and highlight the flexible and diverse regulatory potential coded within this widely distributed evolutionary module.
Combined statistical-biophysical modeling links ion channel genes to physiology of cortical neuron types
2023-03-02

ABSTRACT Neural cell types have classically been characterized by their anatomy and electrophysiology. More recently, single-cell transcriptomics has enabled an increasingly fine genetically defined taxonomy of cortical cell types, but the link between the gene expression of individual cell types and their physiological and anatomical properties remains poorly understood. Here, we develop a hybrid modeling approach to bridge this gap. Our approach combines statistical and mechanistic models to predict cells’ electrophysiological activity from their gene expression pattern. To this end, we fit biophysical Hodgkin-Huxley-based models for a wide variety of cortical cell types using simulation-based inference, while overcoming the challenge posed by the mismatch between the mathematical model and the data. Using multimodal Patch-seq data, we link the estimated model parameters to gene expression using an interpretable sparse linear regression model. Our approach recovers specific ion channel gene expressions as predictive of biophysical model parameters including ion channel densities, directly implicating their mechanistic role in determining neural firing.
Three-Dimensional Plotted Calcium Phosphate Scaffolds for Bone Defect Augmentation—A New Method for Regeneration
2023-03-02

For sinus grafting, different methods and materials are available. One possible shortcoming of particulate bone grafts is either overfilling or augmenting the planned implant area insufficiently. To overcome this risk and to determine the implant position prior augmentation, we present an approach using three-dimensional printed scaffolds. A patient with a remaining anterior dentition and bilateral severely atrophied posterior maxilla was seeking oral rehabilitation. The cone beam computed tomography (CBCT) showed residual bone heights between one and two millimeters. Following the three-dimensional reconstruction of the CBCT data, the positions of the implants were determined in areas 16 and 26. Three-dimensional scaffolds adapted to the topography of the sinus were virtually designed and printed using a calcium phosphate cement paste. Bilateral sinus floor augmentation applying the printed scaffolds with an interconnecting porosity followed. After nine months, a satisfying integration of the scaffolds was obvious. At the re-entry, vital bone with sufficient blood supply was found. One implant could be placed in positions 16 and 26, respectively. After five months, the implants could be uncovered and were provided with a temporary denture. The application of three-dimensionally printed scaffolds from calcium phosphate cement paste seems to be a promising technique to graft the severely atrophied posterior maxilla for the placement of dental implants.
Structural MRI predicts clinical progression in presymptomatic genetic frontotemporal dementia: findings from the GENetic Frontotemporal dementia Initiative cohort
2023-03-02

Abstract Biomarkers that can predict disease progression in individuals with genetic frontotemporal dementia are urgently needed. We aimed to identify whether baseline MRI-based grey and white matter abnormalities are associated with different clinical progression profiles in presymptomatic mutation carriers in the GENetic Frontotemporal dementia Initiative. Three hundred eighty-seven mutation carriers were included (160 GRN, 160 C9orf72, 67 MAPT), together with 240 non-carrier cognitively normal controls. Cortical and subcortical grey matter volumes were generated using automated parcellation methods on volumetric 3T T1-weighted MRI scans, while white matter characteristics were estimated using diffusion tensor imaging. Mutation carriers were divided into two disease stages based on their global CDR®+NACC-FTLD score: presymptomatic (0 or 0.5) and fully symptomatic (1 or greater). The w-scores in each grey matter volumes and white matter diffusion measures were computed to quantify the degree of abnormality compared to controls for each presymptomatic carrier, adjusting for their age, sex, total intracranial volume, and scanner type. Presymptomatic carriers were classified as ‘normal’ or ‘abnormal’ based on whether their grey matter volume and white matter diffusion measure w-scores were above or below the cut point corresponding to the 10th percentile of the controls. We then compared the change in disease severity between baseline and one year later in both the ‘normal’ and ‘abnormal’ groups within each genetic subtype, as measured by the CDR®+NACC-FTLD sum-of-boxes score and revised Cambridge Behavioural Inventory total score. Overall, presymptomatic carriers with normal regional w-scores at baseline did not progress clinically as much as those with abnormal regional w-scores. Having abnormal grey or white matter measures at baseline was associated with a statistically significant increase in the CDR®+NACC-FTLD of up to 4 points in C9orf72 expansion carriers, and 5 points in the GRN group as well as a statistically significant increase in the revised Cambridge Behavioural Inventory of up to 11 points in MAPT, 10 points in GRN, and 8 points in C9orf72 mutation carriers. Baseline regional brain abnormalities on MRI in presymptomatic mutation carriers are associated with different profiles of clinical progression over time. These results may be helpful to inform stratification of participants in future trials.
Adhesive Strength and Rupture Behaviour of Birch Tars Made with Different Stone Age Methods
2023-03-02

Abstract Birch tar is the earliest adhesive produced by Neanderthals in the European Palaeolithic. Experimental studies have proposed a number of aceramic (i.e. without the use of ceramics) birch tar–making techniques, but to date, no archaeological evidence for any of these techniques has been brought forward. The likelihood of one of those methods being actually used in the Stone Age may be investigated by evaluating the method’s complexity, efficiency and the performance of the tar obtained. In this study, we experimentally produce birch tar with four common experimental aceramic techniques. These tars are tested for their mechanical properties using lap-shear tests. We found that tar made with the aboveground condensation method is strongest in terms of its adhesive strength. The tar also shows the most consistent behaviour throughout our test series. The weakest adhesive was observed in tar made with an underground (i.e. oxygen-depleted) technique resembling double-pot distillation (raised structure). Two supplementary methods yielded intermediate values: the recently proposed cobble-groove method produces tar with plastic behaviour. Tar made with another underground technique (pit roll) is almost as strong as condensation method tar. This study adds to our understanding of adhesive performance of birch tar made with different aceramic techniques. It also allows understanding the potential use of one method instead of another.
Surgical management of spinal arachnoid web in case of syringomyelia: Strategies and outcomes
2023-03-02

Abstract Spinal arachnoid web (SAW) is a rare disease entity characterized as band-like arachnoid tissue that can cause spinal cord compression and syringomyelia. This study aimed to analyze the surgical management of spinal arachnoid web in patients with syringomyelia, focusing on surgical strategies and outcomes. A total of 135 patients with syringomyelia underwent surgery at our department between November 2003 and December 2022. All patients underwent magnetic resonance imaging (MRI), with a special syringomyelia protocol (including TrueFISP and cine), and electrophysiology. Among these patients, we searched for patients with SAW with syringomyelia following careful analysis of neuroradiological data and surgical reports. The criteria for SAW were as follows: displacement of the spinal cord, disturbed but preserved CSF flow, and intraoperative arachnoid web. Patients were evaluated for initial symptoms, surgical strategies, and complications by reviewing surgical reports, patient documents, neuroradiological data, and follow-up data. Of the 135 patients, 3 (2.22%) fulfilled the SAW criteria. The mean patient age was 51.67 ± 8.33 years. Two patients were male, and one was female. The affected levels were TH2/3, TH6, and TH8. Excision of arachnoid web was performed in all cases. No significant change in intraoperative monitoring was noted. Postoperatively, none of the patients presented new neurological symptoms. The MRI 3 months after surgery revealed that the syringomyelia improved in all cases, and caliber variation of the spinal cord could not be detected anymore. All clinical symptoms improved. In summary SAW can be safely treated by surgery. Even syringomyelia usually improves inMRI and symptoms also improves, residual symptoms might be observed.
Left Atrioventricular Transvalvular Pressure Gradients Derived from Intraoperative and Postoperative Echocardiograms following Atrioventricular Septal Defect Repair
2023-03-02

Background: Left atrioventricular valve (LAVV) stenosis following an atrioventricular septal defect (AVSD) repair is a rare but potentially life-threatening complication. While echocardiographic quantification of diastolic transvalvular pressure gradients is paramount in the evaluation of a newly corrected valve function, it is hypothesized that these measured gradients are overestimated immediately following a cardiopulmonary bypass (CPB) due to the altered hemodynamics when compared to postoperative valve assessments using awake transthoracic echocardiography (TTE) upon recovery after surgery. Methods: Out of the 72 patients screened for inclusion at a tertiary center, 39 patients undergoing an AVSD repair with both intraoperative transesophageal echocardiograms (TEE, performed immediately after a CPB) and an awake TTE (performed prior to hospital discharge) were retrospectively selected. The mean (MPGs) and peak pressure gradients (PPGs) were quantified using a Doppler echocardiography and other measures of interest were recorded (e.g., a non-invasive surrogate of the cardiac output and index (CI), left ventricular ejection fraction, blood pressures and airway pressures). The variables were analyzed using the paired Student’s t-tests and Spearman’s correlation coefficients. Results: The MPGs were significantly higher in the intraoperative measurements when compared to the awake TTE (3.0 ± 1.2 vs. 2.3 ± 1.1 mmHg; p &lt; 0.01); however, the PPGs did not significantly differ (6.6 ± 2.7 vs. 5.7 ± 2.8 mmHg; p = 0.06). Although the assessed intraoperative heart rates (HRs) were also higher (132 ± 17 vs. 114 ± 21 bpm; p &lt; 0.001), there was no correlation found between the MPG and the HR, or any other parameter of interest, at either time-point. In a further analysis, a moderate to strong correlation was observed in the linear relationship between the CI and the MPG (r = 0.60; p &lt; 0.001). During the in-hospital follow-up period, no patients died or required an intervention due to LAVV stenosis. Conclusions: The Doppler-based quantification of diastolic transvalvular LAVV mean pressure gradients using intraoperative transesophageal echocardiography seems to be prone to overestimation due to altered hemodynamics immediately after an AVSD repair. Thus, the current hemodynamic state should be taken into consideration during the intraoperative interpretation of these gradients.
Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations
2023-03-03

Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic datasets remains a major obstacle. Today, more realistic simulations are possible thanks to large increases in the quantity and quality of available genetic data, and the sophistication of inference and simulation software. However, implementing these simulations still requires substantial time and specialized knowledge. These challenges are especially pronounced for simulating genomes for species that are not well-studied, since it is not always clear what information is required to produce simulations with a level of realism sufficient to confidently answer a given question. The community-developed framework stdpopsim seeks to lower this barrier by facilitating the simulation of complex population genetic models using up-to-date information. The initial version of stdpopsim focused on establishing this framework using six well-characterized model species (Adrion et al., 2020). Here, we report on major improvements made in the new release of stdpopsim (version 0.2), which includes a significant expansion of the species catalog and substantial additions to simulation capabilities. Features added to improve the realism of the simulated genomes include non-crossover recombination and provision of species-specific genomic annotations. Through community-driven efforts, we expanded the number of species in the catalog more than threefold and broadened coverage across the tree of life. During the process of expanding the catalog, we have identified common sticking points and developed the best practices for setting up genome-scale simulations. We describe the input data required for generating a realistic simulation, suggest good practices for obtaining the relevant information from the literature, and discuss common pitfalls and major considerations. These improvements to stdpopsim aim to further promote the use of realistic whole-genome population genetic simulations, especially in non-model organisms, making them available, transparent, and accessible to everyone.
Scorpionfish rapidly change colour in response to their background
2023-03-03

Abstract Background To facilitate background matching in heterogenous environments, some animals rapidly change body colouration. Marine predatory fishes might use this ability to hide from predators and prey. Here, we focus on scorpionfishes (Scorpaenidae), well-camouflaged, bottom-dwelling sit-and-wait predators. We tested whether Scorpaena maderensis and Scorpaena porcus adjust body luminance and hue in response to three artificial backgrounds and thereby achieve background matching. Both scorpionfish species are also red fluorescent, which could contribute to background matching at depth. Therefore, we tested whether red fluorescence is also regulated in response to different backgrounds. The darkest and the lightest backgrounds were grey, while the third background was orange of intermediate luminance. Scorpionfish were placed on all three backgrounds in a randomised repeated measures design. We documented changes in scorpionfish luminance and hue with image analysis and calculated contrast to the backgrounds. Changes were quantified from the visual perspective of two potential prey fishes, the triplefin Tripterygion delaisi and the goby Pomatoschistus flavescens . Additionally, we measured changes in the area of scorpionfish red fluorescence. Because scorpionfish changed quicker than initially expected, we measured luminance change at a higher temporal resolution in a second experiment. Results Both scorpionfish species rapidly adjusted luminance and hue in response to a change of background. From prey visual perspective, scorpionfishes’ body achromatic and chromatic contrasts against the background were high, indicating imperfect background matching. Chromatic contrasts differed considerably between the two observer species, highlighting the importance of choosing natural observers with care when studying camouflage. Scorpionfish displayed larger areas of red fluorescence with increasing luminance of the background. With the second experiment, we showed that about 50% of the total luminance change observed after one minute is achieved very rapidly, in five to ten seconds. Conclusion Both scorpionfish species change body luminance and hue in response to different backgrounds within seconds. While the achieved background matching was suboptimal for the artificial backgrounds, we propose that the observed changes were intended to reduce detectability, and are an essential strategy to camouflage in the natural environment.
RT-PCR-based assessment of the SD Bioline Rota/Adeno Antigen-based test in infants with and without diarrhea
2023-03-03

Abstract Background Rotavirus A (RVA) infections remain a major cause of severe acute diarrhea affecting children worldwide. To date, rapid diagnostic tests (RDT) are widely used to detect RVA. However, paediatricians question whether the RDT can still detect the virus accurately. Therefore, this study aimed to evaluate the performance of the rapid rotavirus test in comparison to the one-step RT-qPCR method. Methods A cross-sectional study was conducted in Lambaréné, Gabon, from April 2018 to November 2019. Stool samples were collected from children under 5 years of age with diarrhoea or a history of diarrhoea within the last 24 h, and from asymptomatic children from the same communities. All stool samples were processed and analysed using the SD BIOLINE Rota/Adeno Ag RDT against a quantitative reverse transcription PCR (RT-qPCR), which is considered the gold standard. Results For a total of 218 collected stool samples, the overall sensitivity of the RDT was 46.46% (confidence interval (CI) 36.38–56.77), with a specificity of 96.64% (CI 91.62–99.08) compared to one-step RT-qPCR. After confirming the presence or absence of RVA gastroenteritis, the RDT showed suitable results in detecting rotavirus A-associated disease, with a 91% concordance with the RT-qPCR. Furthermore, the performance of this test varied when correlated with seasonality, symptoms, and rotavirus genotype. Conclusion This RDT showed high sensitivity and was suitable for the detection of RVA in patients with RVA gastroenteritis, although some asymptomatic RVA shedding was missed by RT-qPCR. It could be a useful diagnostic tool, especially in low-income countries.
What is behind partial repetition costs? Event-files do not fully occupy bound feature codes
2023-03-03

Abstract Feature binding accounts state that features of perceived and produced events are bound into event-files. Performance while responding to an event is impaired when some, as opposed to all or none, of this event's features already belong to a previous event-file. While these partial repetition costs are generally considered to be indicators of feature binding, their cause is still unclear. Possibly, features are fully occupied when bound in an event-file and must be unbound in a time-consuming process before they can enter a novel event-file. In this study, we tested this code occupation account. Participants responded to the font color (target) of a word (distractor) by pressing one of three keys (response) while ignoring the word meaning. We measured partial repetition costs from prime to probe while introducing an intermediate trial. We compared sequences in which this intermediate trial did not repeat any prime features and sequences in which it repeated either the prime response or distractor. Partial repetition costs occurred in the probe, even when one (vs. none) of the prime features repeated in the intermediate trial, although significantly reduced. Thus, single bindings do not fully occupy feature codes. By ruling out a possible mechanism behind partial repetition costs, the present study contributes to the further specification of feature binding accounts.
Reinforcement learning of adaptive control strategies
2023-03-03

Humans can up- or downregulate the degree to which they rely on task information for goal directed behaviour, a process often referred to as cognitive control. Adjustments in cognitive control are traditionally studied in response to experienced or expected task-rule conflict. However, recent theories suggest that people can also learn to adapt control settings through reinforcement. Across three preregistered task switching experiments (n=415), we selectively rewarded correct performance on trials with either more (incongruent) or less (congruent) task-rule conflict. Results confirmed the hypothesis that people rewarded more on incongruent trials showed smaller task-rule congruency effects, thus optimally adapting their control settings to the reward scheme. Using drift diffusion modelling, we further show that this reinforcement of cognitive control may occur through conflict-dependent within-trial adjustments of response thresholds after conflict detection. Together, our findings suggest that, while people remain more efficient at learning stimulus-response associations through rewards, they can similarly learn cognitive control strategies through reinforcement.
A multilab investigation into the N2pc as an indicator of attentional selectivity: Direct replication of Eimer (1996).
2023-03-03

The N2pc is widely employed as an electrophysiological marker of an attention allocation. This interpretation was in no small part driven by the observation of an N2pc elicited by an isolated relevant target object, which was reported as Experiment 2 in Eimer (1996; The N2pc component as an indicator of attentional selectivity. Electroencephalography and Clinical Neurophysiology, 99, 225-234). All subsequent refined interpretations of the N2pc had to take this crucial finding into account. Despite its central role for neurocognitive attention research, there have been no direct replications and only few conceptual replications of this seminal work. Within the context of #EEGManyLabs, an international community-driven effort to replicate the most influential EEG studies ever published, the present study was selected due to its impact on the study of selective attention. We propose to provide a high-powered direct replication, carefully following all the steps laid out in Pavlov et al. (2021; #EEGManyLabs: Investigating the replicability of influential EEG experiments. Cortex, 144, 213–229) to assure a high-quality direct replication of the original study. In doing so, we expect to shed further light on the functional significance of the N2pc as an electrophysiological marker of attentional selectivity.