last updated by Pluto on 2024-07-26 08:12:19 UTC on behalf of the NeuroFedora SIG.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science on 2024-07-26 07:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science on 2024-07-26 07:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science on 2024-07-26 07:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science on 2024-07-26 07:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
Brain Sciences, Vol. 14, Pages 749: Effect of Spatial and Temporal Prediction on Tactile Sensitivity
Brain Sciences doi: 10.3390/brainsci14080749
Authors: Hiroshi Kunimura Hitoshi Oda Taku Kawasaki Han Gao Shiho Fukuda Koichi Hiraoka
The purpose of the present study was to examine whether spatial or temporal prediction of the tactile stimulus contributes to tactile sensitivity. To investigate the effect of spatial prediction on tactile sensitivity, electrical stimuli were provided for the digit nerve in one of five fingers, and advanced notice of the stimulating finger was provided before the stimulus in some trials but not in others. There was no significant effect of spatial prediction on the intensity at the perceptual threshold of the digit nerve stimulus. This indicates that spatial prediction of the tactile stimulus does not influence tactile sensitivity. To examine the effect of temporal prediction, an auditory warning cue was provided 0, 1, or 10 s before the electrical stimulus to the digit nerve. The stimulus intensity at the perceptual threshold in the trials with the 1 s warning cue was lower than those with the 0 s warning cue. This indicates that temporal prediction enhances tactile sensitivity. The stimulus intensity at the perceptual threshold in the trials with the 1 s warning cue was lower than those with the 10 s warning cue. This means that the contribution of temporal prediction to the tactile sensitivity is greater as the warning cue is closer to the time of the stimulus. This finding may be explained by a defense mechanism activated when humans predict that a tactile stimulus is coming soon.
in Brain Sciences on 2024-07-26 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
Brain Sciences, Vol. 14, Pages 748: Neuromodulation Treatments Targeting Pathological Synchrony for Tinnitus in Adults: A Systematic Review
Brain Sciences doi: 10.3390/brainsci14080748
Authors: Derek J. Hoare Gillian W. Shorter Giriraj S. Shekhawat Amr El Refaie Bas Labree Magdalena Sereda
(1) Background: Tinnitus involves the conscious awareness of a tonal or composite noise for which there is no identifiable corresponding external acoustic source. For many people, tinnitus is a disorder associated with symptoms of emotional distress, cognitive dysfunction, autonomic arousal, behavioural changes, and functional disability. Many symptoms can be addressed effectively using education or cognitive behavioural therapy. However, there is no treatment that effectively reduces or alters tinnitus-related neurophysiological activity and thus the tinnitus percept. In this systematic review, we evaluated the effectiveness of neuromodulation therapies for tinnitus that explicitly target pathological synchronous neural activity. (2) Methods: Multiple databases were searched for randomised controlled trials of neuromodulation interventions for tinnitus in adults, with 24 trials included. The risk of bias was assessed, and where appropriate, meta-analyses were performed. (3) Results: Few trials used acoustic, vagal nerve, or transcranial alternating current stimulation, or bimodal stimulation techniques, with limited evidence of neuromodulation or clinical effectiveness. Multiple trials of transcranial direct current stimulation (tDCS) were identified, and a synthesis demonstrated a significant improvement in tinnitus symptom severity in favour of tDCS versus control, although heterogeneity was high. (4) Discussion: Neuromodulation for tinnitus is an emerging but promising field. Electrical stimulation techniques are particularly interesting, given recent advances in current flow modelling that can be applied to future studies.
in Brain Sciences on 2024-07-26 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
The role of gamma rhythm (30–80 Hz) in visual processing is debated; stimuli like gratings and hue patches generate strong gamma, but many natural images do not. Could image gamma responses be predicted by approximating images as gratings or hue patches? Surprisingly, this question remains unanswered, since the joint dependence of gamma on multiple features is poorly understood. We recorded local field potentials and electrocorticogram from two female monkeys while presenting natural images and parametric stimuli varying along several feature dimensions. Gamma responses to different grating/hue features were separable, allowing for a multiplicative model based on individual features. By fitting a hue patch to the image around the receptive field, this simple model could predict gamma responses to chromatic images across scales with reasonably high accuracy. Our results provide a simple "baseline" model to predict gamma from local image properties, against which more complex models of natural vision can be tested.
in eNeuro on 2024-07-25 16:30:41 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
Chronic neuropathic pain can result from nervous system injury and can persist in the absence of external stimuli. Although ongoing pain characterizes the disorder, in many individuals, the intensity of this ongoing pain fluctuates dramatically. Previously, it was identified that functional magnetic resonance imaging signal covariations between the midbrain periaqueductal gray (PAG) matter, rostral ventromedial medulla (RVM), and spinal trigeminal nucleus are associated with moment-to-moment fluctuations in pain intensity in individuals with painful trigeminal neuropathy (PTN). Since this brainstem circuit is modulated by higher brain input, we sought to determine which cortical sites might be influencing this brainstem network during spontaneous fluctuations in pain intensity. Over 12 min, we recorded the ongoing pain intensity in 24 PTN participants and classified them as fluctuating (n = 13) or stable (n = 11). Using a PAG seed, we identified connections between the PAG and emotional-affective sites such as the hippocampal and posterior cingulate cortices, the sensory-discriminative posterior insula, and cognitive-affective sites such as the dorsolateral prefrontal (dlPFC) and subgenual anterior cingulate cortices that were altered dependent on spontaneous high and low pain intensity. Additionally, sliding-window functional connectivity analysis revealed that the dlPFC–PAG connection anticorrelated with perceived pain intensity over the entire 12 min period. These findings reveal cortical systems underlying moment-to-moment changes in perceived pain in PTN, which likely cause dysregulation in the brainstem circuits previously identified, and consequently alter the appraisal of pain across time.
in eNeuro on 2024-07-25 16:30:41 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
by Patrick Bryant, Frank Noé
Structure prediction of protein complexes has improved significantly with AlphaFold2 and AlphaFold-multimer (AFM), but only 60% of dimers are accurately predicted. Here, we learn a bias to the MSA representation that improves the predictions by performing gradient descent through the AFM network. We demonstrate the performance on seven difficult targets from CASP15 and increase the average MMscore to 0.76 compared to 0.63 with AFM. We evaluate the procedure on 487 protein complexes where AFM fails and obtain an increased success rate (MMscore>0.75) of 33% on these difficult targets. Our protocol, AFProfile, provides a way to direct predictions towards a defined target function guided by the MSA. We expect gradient descent over the MSA to be useful for different tasks.in PLoS Computational Biology on 2024-07-25 14:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
by David Moreau, Kristina Wiebels
Open science principles are revolutionizing the transparency, reproducibility, and accessibility of research. Meta-analysis has become a key technique for synthesizing data across studies in a principled way; however, its impact is contingent on adherence to open science practices. Here, we outline 9 quick tips for open meta-analyses, aimed at guiding researchers to maximize the reach and utility of their findings. We advocate for outlining preregistering clear protocols, opting for open tools and software, and the use of version control systems to ensure transparency and facilitate collaboration. We further emphasize the importance of reproducibility, for example, by sharing search syntax and analysis scripts, and discuss the benefits of planning for dynamic updating to enable living meta-analyses. We also recommend publication in open-access formats, as well as open data, open code, and open access publication. We close by encouraging active promotion of research findings to bridge the gap between complex syntheses and public discourse, and provide a detailed submission checklist to equip researchers, reviewers and journal editors with a structured approach to conducting and reporting open meta-analyses.in PLoS Computational Biology on 2024-07-25 14:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
by Hoda Jaffal, Mounia Kortebi, Pauline Misson, Paulo Tavares, Malika Ouldali, Hervé Leh, Sylvie Lautru, Virginia S. Lioy, François Lecointe, Stéphanie G. Bury-Moné
Streptomyces are renowned for their prolific production of specialized metabolites with applications in medicine and agriculture. These multicellular bacteria present a sophisticated developmental cycle and play a key role in soil ecology. Little is known about the impact of Streptomyces phage on bacterial physiology. In this study, we investigated the conditions governing the expression and production of “Samy,” a prophage found in Streptomyces ambofaciens ATCC 23877. This siphoprophage is produced simultaneously with the activation of other mobile genetic elements. Remarkably, the presence and production of Samy increases bacterial dispersal under in vitro stress conditions. Altogether, this study unveiled a new property of a bacteriophage infection in the context of multicellular aggregate dynamics.in PLoS Biology on 2024-07-25 14:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
by Thi Tuong Vi Dang, Corinne Maufrais, Jessie Colin, Frédérique Moyrand, Isabelle Mouyna, Jean-Yves COPPEE, Chinaemerem U. Onyishi, Joanna Lipecka, Ida Chiara Guerrera, Robin C. May, Guilhem Janbon
Alternative transcription start site (TSS) usage regulation has been identified as a major means of gene expression regulation in metazoans. However, in fungi, its impact remains elusive as its study has thus far been restricted to model yeasts. Here, we first re-analyzed TSS-seq data to define genuine TSS clusters in 2 species of pathogenic Cryptococcus. We identified 2 types of TSS clusters associated with specific DNA sequence motifs. Our analysis also revealed that alternative TSS usage regulation in response to environmental cues is widespread in Cryptococcus, altering gene expression and protein targeting. Importantly, we performed a forward genetic screen to identify a unique transcription factor (TF) named Tur1, which regulates alternative TSS (altTSS) usage genome-wide when cells switch from exponential phase to stationary phase. ChiP-Seq and DamID-Seq analyses suggest that at some loci, the role of Tur1 might be direct. Tur1 has been previously shown to be essential for virulence in C. neoformans. We demonstrated here that a tur1Δ mutant strain is more sensitive to superoxide stress and phagocytosed more efficiently by macrophages than the wild-type (WT) strain.in PLoS Biology on 2024-07-25 14:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
Despite therapeutic suppression of relapses, multiple sclerosis (MS) patients often experience subtle deterioration, which extends beyond the definition of “progression independent of relapsing activity.” We propose the concept of smouldering-associated-worsening (SAW), encompassing physical and cognitive symptoms, resulting from smouldering pathological processes, which remain unmet therapeutic targets. We provide a consensus-based framework of possible pathological substrates and manifestations of smouldering MS, and we discuss clinical, radiological, and serum/cerebrospinal fluid biomarkers for potentially monitoring SAW. Finally, we share considerations for optimizing disease surveillance and implications for clinical trials to promote the integration of smouldering MS into routine practice and future research efforts. ANN NEUROL 2024
in Annals of Neurology on 2024-07-25 10:55:44 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science on 2024-07-25 07:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science on 2024-07-25 07:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science on 2024-07-25 05:58:05 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science on 2024-07-25 05:58:05 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science on 2024-07-25 05:58:05 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science on 2024-07-25 05:58:05 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science on 2024-07-25 05:58:05 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science on 2024-07-25 05:58:05 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science on 2024-07-25 05:58:05 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science on 2024-07-25 05:58:05 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science on 2024-07-25 05:58:05 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science on 2024-07-25 05:58:05 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science on 2024-07-25 05:58:05 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science on 2024-07-25 05:58:05 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science on 2024-07-25 05:58:05 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science on 2024-07-25 05:58:05 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science on 2024-07-25 05:58:05 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science on 2024-07-25 05:58:05 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science on 2024-07-25 05:58:05 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science on 2024-07-25 05:58:05 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science on 2024-07-25 05:58:05 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science on 2024-07-25 05:58:05 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science on 2024-07-25 05:58:05 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science on 2024-07-25 05:58:05 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science on 2024-07-25 05:58:05 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science on 2024-07-25 05:58:05 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science on 2024-07-25 05:58:05 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science on 2024-07-25 05:58:05 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science on 2024-07-25 05:58:05 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science on 2024-07-25 05:58:05 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science on 2024-07-25 05:58:05 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science on 2024-07-25 05:58:05 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science on 2024-07-25 05:58:05 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science on 2024-07-25 05:58:05 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science on 2024-07-25 05:58:05 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science on 2024-07-25 05:58:05 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science on 2024-07-25 05:58:05 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science on 2024-07-25 05:58:05 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Journal of Neurophysiology on 2024-07-25 03:18:47 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Journal of Neurophysiology on 2024-07-25 03:18:47 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Neuron: In press on 2024-07-25 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Neuron: In press on 2024-07-25 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Cell Reports: Current Issue on 2024-07-25 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Cell Reports: Current Issue on 2024-07-25 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Cell Reports: Current Issue on 2024-07-25 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Cell Reports: Current Issue on 2024-07-25 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Cell Reports: Current Issue on 2024-07-25 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Cell Reports: Current Issue on 2024-07-25 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Cell Reports: Current Issue on 2024-07-25 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Cell Reports: Current Issue on 2024-07-25 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in eLife on 2024-07-25 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in eLife on 2024-07-25 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in eLife on 2024-07-25 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in eLife on 2024-07-25 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in eLife on 2024-07-25 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in bioRxiv: Neuroscience on 2024-07-25 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in bioRxiv: Neuroscience on 2024-07-25 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in bioRxiv: Neuroscience on 2024-07-25 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in bioRxiv: Neuroscience on 2024-07-25 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in bioRxiv: Neuroscience on 2024-07-25 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in bioRxiv: Neuroscience on 2024-07-25 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in bioRxiv: Neuroscience on 2024-07-25 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in bioRxiv: Neuroscience on 2024-07-25 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in bioRxiv: Neuroscience on 2024-07-25 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in bioRxiv: Neuroscience on 2024-07-25 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in bioRxiv: Neuroscience on 2024-07-25 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in bioRxiv: Neuroscience on 2024-07-25 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in bioRxiv: Neuroscience on 2024-07-25 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in bioRxiv: Neuroscience on 2024-07-25 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in bioRxiv: Neuroscience on 2024-07-25 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in bioRxiv: Neuroscience on 2024-07-25 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
Brain Sciences, Vol. 14, Pages 747: Do Psoriasis and Atopic Dermatitis Affect Memory, Attention, Stress and Emotions?
Brain Sciences doi: 10.3390/brainsci14080747
Authors: Kuryłło Mojs Woźniak Wiśniewska-Szeplewicz
Background: Psoriasis and atopic dermatitis are chronic skin diseases found all over the world that cause a lot of suffering to patients. Objectives: The aim of this study was to answer the following questions: whether people suffering from psoriasis and AD have greater problems with recognizing emotions, the effectiveness of attention and memory processes, and whether they use different strategies of coping with stress than healthy people. Methods: This study involved 90 patients, including 30 patients with psoriasis, 30 patients with AD and 30 healthy patients, aged 21 to 63 years, including 54 women and 36 men. This study used a battery of the CANTAB Cognitive Tests, Mini-COPE Questionnaire Inventory, Toronto Alexithymia Scale TAS Questionnaire, Psoriasis Area and Severity Index, and Eczema Area and Severity Index. Results: People with psoriasis and AD had higher total scores on the alexithymia scale and had greater difficulty in identifying and verbalizing emotions. People with psoriasis and AD are less likely to choose the correct stimulus and achieve a shorter length of the sequence that should be remembered. Psoriasis patients with more severe symptoms are less likely to use the strategy of a sense of humor in stressful situations. AD patients with more severe symptoms are less likely to use strategies of operative thinking, denial and self-blame, and the strategy of seeking instrumental support is used more often. Conclusion: Patients with psoriasis and AD require a holistic approach; in addition to dermatological treatment, psychological support, psychotherapeutic support and possible psychiatric treatment are recommended.
in Brain Sciences on 2024-07-25 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
Brain Sciences, Vol. 14, Pages 746: A Meta-Analysis of the Reliability of Second Language Listening Tests (1991–2022)
Brain Sciences doi: 10.3390/brainsci14080746
Authors: Yuxin Shang Vahid Aryadoust Zhuohan Hou
To investigate the reliability of L2 listening tests and explore potential factors affecting the reliability, a reliability generalization (RG) meta-analysis was conducted in the present study. A total number of 122 alpha coefficients of L2 listening tests from 92 published articles were collected and submitted to a linear mixed effects RG analysis. The papers were coded based on a coding scheme consisting of 16 variables classified into three categories: study features, test features, and statistical results. The results showed an average reliability of 0.818 (95% CI: 0.803 to 0.833), with 40% of reliability estimates falling below the lower bound of CI. The presence of publication bias and heterogeneity was found in the reliability of L2 listening tests, indicating that low reliability coefficients were likely omitted from some published studies. In addition, two factors predicting the reliability of L2 listening tests were the number of items and test type (standardized and researcher- or teacher-designed tests). The study also found that reliability is not a moderator of the relationship between L2 listening scores and theoretically relevant constructs. Reliability induction was identified in reporting the reliability of L2 listening tests, too. Implications for researchers and teachers are discussed.
in Brain Sciences on 2024-07-25 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
Brain Sciences, Vol. 14, Pages 745: Gruppo Otologico’s Experience in Managing the So-Called Inoperable Tympanojugular Paraganglioma
Brain Sciences doi: 10.3390/brainsci14080745
Authors: Mario Sanna Mohammed Al-Khateeb Melcol Hailu Yilala Mohanad Almashhadani Giuseppe Fancello
Objective: to identify advanced or “so-called inoperable” cases of tympanojugular paragangliomas (PGLs) and analyze how each case is surgically managed and followed afterward. Study Design: a retrospective case series study. Methods: Out of 262 type C and D TJPs and more than 10 cases of advanced or so-called inoperable cases, files of 6 patients with a diagnosis of advanced tympanojugular PGLs who were referred to an otology and skull-base center between 1996 and 2021 were reviewed to analyze management and surgical outcomes. The criteria for choosing these cases involve having one or more of the following features: (1) a large-sized tumor; (2) a single ipsilateral internal carotid artery (ICA); (3) involvement of the vertebral artery; (4) a considerable involvement of the ICA; (5) an extension to the clivus, foramen magnum, and cavernous sinus; (6) large intradural involvement (IDE); and (7) bilateral or multiple PGLs. Results: The age range at presentation was 25–43 years old, with a mean of 40.5 years: two females and four males. The presenting symptoms were glossal atrophy, hearing loss, pulsatile tinnitus, dysphonia, shoulder weakness, and diplopia. The modified Infratemporal Fossa Approach (ITFA) with a transcondylar–transtubercular extension is the principal approach in most cases, with additional approaches being used accordingly. Conclusions: The contemporary introduction of carotid artery stenting with the direct and indirect embolization of PGLs has made it possible to operate on many cases, which was otherwise considered impossible to treat surgically. Generally, the key is to stage the removal of the tumor in multiple stages during the management of complex PGLs to decrease surgical morbidities. A crucial aspect is to centralize the treatment of PGLs in referral centers with experienced surgeons who are trained to plan the stages and manage possible surgical complications.
in Brain Sciences on 2024-07-25 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
Brain Sciences, Vol. 14, Pages 744: The Interplay between Gender and Duration of Hospitalization Modulates Psychiatric Symptom Severity in Subjects with Long COVID-19
Brain Sciences doi: 10.3390/brainsci14080744
Authors: Alessio Simonetti Antonio Restaino Claudia Calderoni Emanuela De Chiara Antonio Maria D’Onofrio Salvatore Lioniello Giovanni Camardese Delfina Janiri Matteo Tosato Francesco Landi Gabriele Sani
Long COVID-19 is characterized by ongoing symptoms or prolonged or long-term complications of SARS-CoV-2 contraction which persist beyond 4 weeks from the initial onset of symptoms. Gender and duration of hospitalization (DH) are key risk factors for developing long COVID-19 syndrome, but their impact and interplay need further study. This research involved 996 long COVID-19 patients, and we compared the levels of general psychopathology, depression, agitated depression, anxiety, and medication use between hospitalized and non-hospitalized males and females. In the hospitalized patients, multivariate regressions assessed the impact of gender, DH, and the interaction of these variables. The females had higher levels of long COVID-19 symptoms, psychotropic drug use, depression, anxiety, and general psychopathology than the males. The non-hospitalized females exhibited more severe agitated depression than the non-hospitalized males. In females, DH was more strongly correlated with the number of psychotropic medications used during long COVID-19. A negative correlation was found between DH and severity of agitated depression in the female patients only. These results highlight that the gender-specific relationship between DH and agitated depression severity should be explored further.
in Brain Sciences on 2024-07-25 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
Brain Sciences, Vol. 14, Pages 743: Multiple Types of Developmental Dyslexias in a Shallow Orthography: Principles for Diagnostic Screening in Italian
Brain Sciences doi: 10.3390/brainsci14080743
Authors: Daniela Traficante Claudio Luzzatti Naama Friedmann
A new dyslexia screening test for Italian, Tiltan-IT, is presented. The test was developed based on an integrated dual-route model of reading, which describes in detail specific mechanisms underpinning early visual processes as well as the lexical and the sublexical routes. The principle according to which the test was developed is that each dyslexia type is manifested in different kinds of errors and in different kinds of stimuli, and we therefore included stimuli sensitive to each dyslexia type in the test. Tiltan-IT is a reading aloud test that includes word, nonword, and word pair lists. The test was administered to 618 Italian-speaking children (2nd–8th grade). Each error produced by the children was classified through the coding scheme developed to detect the different types of dyslexias described by the reading model. The Tiltan-IT was able to identify 110 children with dyslexia. The identified dyslexia types included letter position dyslexia, attentional dyslexia, letter identity dyslexia, surface dyslexia, vowel dyslexia, consonant conversion dyslexia, multi-letter phonological dyslexia, voicing dyslexia. The results confirm that the selection of items in the Tiltan-IT enabled the detection of the wide variety of dyslexias in Italian, some of them for the first time, adding evidence for the cross-linguistic validity of multiple types of developmental dyslexias and for the dual-route model of reading.
in Brain Sciences on 2024-07-25 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
Brain Sciences, Vol. 14, Pages 742: Resting-State Functional Connectivity Profile of Insular Subregions
Brain Sciences doi: 10.3390/brainsci14080742
Authors: Jimmy Ghaziri Phillip Fei Alan Tucholka Sami Obaid Olivier Boucher Isabelle Rouleau Dang K. Nguyen
The insula is often considered the fifth lobe of the brain and is increasingly recognized as one of the most connected regions in the brain, with widespread connections to cortical and subcortical structures. As a follow-up to our previous tractography work, we investigated the resting-state functional connectivity (rsFC) profiles of insular subregions and assessed their concordance with structural connectivity. We used the CONN toolbox to analyze the rsFC of the same 19 insular regions of interest (ROIs) we used in our prior tractography work and regrouped them into six subregions based on their connectivity pattern similarity. Our analysis of 50 healthy participants confirms the known broad connectivity of the insula and shows novel and specific whole-brain and intra-connectivity patterns of insular subregions. By examining such subregions, our findings provide a more detailed pattern of connectivity than prior studies that may prove useful for comparison between patients.
in Brain Sciences on 2024-07-25 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
Brain Sciences, Vol. 14, Pages 741: The Role of the Thalamus in Nociception: Important but Forgotten
Brain Sciences doi: 10.3390/brainsci14080741
Authors: Giovane Galdino Flavio Protasio Veras Tayllon dos Anjos-Garcia
Pain is a complex response to noxious stimuli. Upon detection of the nociceptive stimulus by first-order neurons or nociceptors, an action potential ascends to the spinal dorsal horn, a crucial site for synapsing with second-order neurons. These second-order neurons carry the nociceptive stimulus to supraspinal regions, notably the thalamus. Although extensive research has focused on spinal-level nociceptive mechanisms (e.g., neurotransmitters, receptors, and glial cells), the thalamus is still poorly elucidated. The role of the thalamus in relaying sensory and motor responses to the cortex is well known. However, a comprehensive understanding of the mechanisms in the synapse between the second-order and third-order neurons that transmit this impulse to the somatosensory cortex, where the response is processed and interpreted as pain, is still lacking. Thus, this review investigated the thalamus’s role in transmitting nociceptive impulses. Current evidence indicates the involvement of the neurotransmitters glutamate and serotonin, along with NMDA, P2X4, TLR4, FGR, and NLRP3 receptors, as well as signaling pathways including ERK, P38, NF-κB, cytokines, and glial cells at nociceptive synapses within the thalamus.
in Brain Sciences on 2024-07-25 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
Many neurons including vasopressin (VP) magnocellular neurosecretory cells (MNCs) of the hypothalamic supraoptic nucleus (SON) generate afterhyperpolarizations (AHPs) during spiking to slow firing, a phenomenon known as spike frequency adaptation. The AHP is underlain by Ca2+-activated K+ currents, and while slow component (sAHP) features are well described, its mechanism remains poorly understood. Previous work demonstrated that Ca2+ influx through N-type Ca2+ channels is a primary source of sAHP activation in SON oxytocin neurons, but no obvious channel coupling was described for VP neurons. Given this, we tested the possibility of an intracellular source of sAHP activation, namely, the Ca2+-handling organelles endoplasmic reticulum (ER) and mitochondria in male and female Wistar rats. We demonstrate that ER Ca2+ depletion greatly inhibits sAHPs without a corresponding decrease in Ca2+ signal. Caffeine sensitized AHP activation by Ca2+. In contrast to ER, disabling mitochondria with CCCP or blocking mitochondria Ca2+ uniporters (MCUs) enhanced sAHP amplitude and duration, implicating mitochondria as a vital buffer for sAHP-activating Ca2+. Block of mitochondria Na+-dependent Ca2+ release via triphenylphosphonium (TPP+) failed to affect sAHPs, indicating that mitochondria Ca2+ does not contribute to sAHP activation. Together, our results suggests that ER Ca2+-induced Ca2+ release activates sAHPs and mitochondria shape the spatiotemporal trajectory of the sAHP via Ca2+ buffering in VP neurons. Overall, this implicates organelle Ca2+, and specifically ER–mitochondria-associated membrane contacts, as an important site of Ca2+ microdomain activity that regulates sAHP signaling pathways. Thus, this site plays a major role in influencing VP firing activity and systemic hormonal release.
in Journal of Neuroscience on 2024-07-24 16:30:24 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Journal of Neuroscience on 2024-07-24 16:30:24 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
Representing the probability and uncertainty of outcomes facilitates adaptive behavior by allowing organisms to prepare in advance and devote attention to relevant events. Probability and uncertainty are often studied only for valenced (appetitive or aversive) outcomes, raising the question of whether the identified neural machinery also processes the probability and uncertainty of motivationally neutral outcomes. Here, we aimed to dissociate valenced from valence-independent (i.e., generic) probability (p; maximum at p = 1) and uncertainty (maximum at p = 0.5) signals using human neuroimaging. In a Pavlovian task (n = 41; 19 females), different cues predicted appetitive, aversive, or neutral liquids with different probabilities (p = 0, p = 0.5, p = 1). Cue-elicited motor responses accelerated, and pupil sizes increased primarily for cues that predicted valenced liquids with higher probability. For neutral liquids, uncertainty rather than probability tended to accelerate cue-induced responding and decrease pupil size. At the neural level, generic uncertainty signals were limited to the occipital cortex, while generic probability also activated the anterior ventromedial prefrontal cortex. These generic probability and uncertainty signals contrasted with cue-induced responses that only encoded the probability and uncertainty of valenced liquids in medial prefrontal, insular, and occipital cortices. Our findings show a behavioral and neural dissociation of generic and valenced signals. Thus, some parts of the brain keep track of motivational charge while others do not, highlighting the need and usefulness of characterizing the exact nature of learned representations.
in Journal of Neuroscience on 2024-07-24 16:30:24 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
During nervous system development, Sonic hedgehog (Shh) guides developing commissural axons toward the floor plate of the spinal cord. To guide axons, Shh binds to its receptor Boc and activates downstream effectors such as Smoothened (Smo) and Src family kinases (SFKs). SFK activation requires Smo activity and is also required for Shh-mediated axon guidance. Here we report that β-arrestin1 and β-arrestin2 (β-arrestins) serve as scaffolding proteins that link Smo and SFKs in Shh-mediated axon guidance. We found that β-arrestins are expressed in rat commissural neurons. We also found that Smo, β-arrestins, and SFKs form a tripartite complex, with the complex formation dependent on β-arrestins. β-arrestin knockdown blocked the Shh-mediated increase in Src phosphorylation, demonstrating that β-arrestins are required to activate Src kinase downstream of Shh. β-arrestin knockdown also led to the loss of Shh-mediated attraction of rat commissural axons in axon turning assays. Expression of two different dominant-negative β-arrestins, β-arrestin1 V53D which blocks the internalization of Smo and β-arrestin1 P91G-P121E which blocks its interaction with SFKs, also led to the loss of Shh-mediated attraction of commissural axons. In vivo, the expression of these dominant-negative β-arrestins caused defects in commissural axon guidance in the spinal cord of chick embryos of mixed sexes. Thus we show that β-arrestins are essential scaffolding proteins that connect Smo to SFKs and are required for Shh-mediated axon guidance.
in Journal of Neuroscience on 2024-07-24 16:30:24 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Journal of Neuroscience on 2024-07-24 16:30:24 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Journal of Neuroscience on 2024-07-24 16:30:24 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
Music, like spoken language, is often characterized by hierarchically organized structure. Previous experiments have shown neural tracking of notes and beats, but little work touches on the more abstract question: how does the brain establish high-level musical structures in real time? We presented Bach chorales to participants (20 females and 9 males) undergoing electroencephalogram (EEG) recording to investigate how the brain tracks musical phrases. We removed the main temporal cues to phrasal structures, so that listeners could only rely on harmonic information to parse a continuous musical stream. Phrasal structures were disrupted by locally or globally reversing the harmonic progression, so that our observations on the original music could be controlled and compared. We first replicated the findings on neural tracking of musical notes and beats, substantiating the positive correlation between musical training and neural tracking. Critically, we discovered a neural signature in the frequency range ~0.1 Hz (modulations of EEG power) that reliably tracks musical phrasal structure. Next, we developed an approach to quantify the phrasal phase precession of the EEG power, revealing that phrase tracking is indeed an operation of active segmentation involving predictive processes. We demonstrate that the brain establishes complex musical structures online over long timescales (>5 s) and actively segments continuous music streams in a manner comparable to language processing. These two neural signatures, phrase tracking and phrasal phase precession, provide new conceptual and technical tools to study the processes underpinning high-level structure building using noninvasive recording techniques.
in Journal of Neuroscience on 2024-07-24 16:30:24 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
Fragile X syndrome (FXS) is a genetic cause of intellectual disability and autism spectrum disorder. The mesocorticolimbic system, which includes the prefrontal cortex (PFC), basolateral amygdala (BLA), and nucleus accumbens core (NAcC), is essential for regulating socioemotional behaviors. We employed optogenetics to compare the functional properties of the BLA->NAcC, PFC->NAcC, and reciprocal PFCBLA pathways in Fmr1–/y::Drd1a-tdTomato male mice. In FXS mice, the PFCBLA reciprocal pathway was unaffected, while significant synaptic modifications occurred in the BLA/PFC->NAcC pathways. We observed distinct changes in D1 striatal projection neurons (SPNs) and separate modifications in D2 SPNs. In FXS mice, the BLA/PFC->NAcC-D2 SPN pathways demonstrated heightened synaptic strength. Focusing on the BLA->NAcC pathway, linked to autistic symptoms, we found increased AMPAR and NMDAR currents and elevated spine density in D2 SPNs. Conversely, the amplified firing probability of BLA->NAcC-D1 SPNs was not accompanied by increased synaptic strength, AMPAR and NMDAR currents, or spine density. These pathway-specific alterations resulted in an overall enhancement of excitatory-to-spike coupling, a physiologically relevant index of how efficiently excitatory inputs drive neuronal firing, in both BLA->NAcC-D1 and BLA->NAcC-D2 pathways. Finally, the absence of fragile X messenger ribonucleoprotein 1 (FMRP) led to impaired long-term depression specifically in BLA->D1 SPNs. These distinct alterations in synaptic transmission and plasticity within circuits targeting the NAcC highlight the potential role of postsynaptic mechanisms in selected SPNs in the observed circuit-level changes. This research underscores the heightened vulnerability of the NAcC in the context of FMRP deficiency, emphasizing its pivotal role in the pathophysiology of FXS.
in Journal of Neuroscience on 2024-07-24 16:30:24 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
Magnetogenetics was developed to remotely control genetically targeted neurons. A variant of magnetogenetics uses magnetic fields to activate transient receptor potential vanilloid (TRPV) channels when coupled with ferritin. Stimulation with static or RF magnetic fields of neurons expressing these channels induces Ca2+ transients and modulates behavior. However, the validity of ferritin-based magnetogenetics has been questioned due to controversies surrounding the underlying mechanisms and deficits in reproducibility. Here, we validated the magnetogenetic approach Ferritin-iron Redistribution to Ion Channels (FeRIC) using electrophysiological (Ephys) and imaging techniques. Previously, interference from RF stimulation rendered patch-clamp recordings inaccessible for magnetogenetics. We solved this limitation for FeRIC, and we studied the bioelectrical properties of neurons expressing TRPV4 (nonselective cation channel) and transmembrane member 16A (TMEM16A; chloride-permeable channel) coupled to ferritin (FeRIC channels) under RF stimulation. We used cultured neurons obtained from the rat hippocampus of either sex. We show that RF decreases the membrane resistance (Rm) and depolarizes the membrane potential in neurons expressing TRPV4FeRIC. RF does not directly trigger action potential firing but increases the neuronal basal spiking frequency. In neurons expressing TMEM16AFeRIC, RF decreases the Rm, hyperpolarizes the membrane potential, and decreases the spiking frequency. Additionally, we corroborated the previously described biochemical mechanism responsible for RF-induced activation of ferritin-coupled ion channels. We solved an enduring problem for ferritin-based magnetogenetics, obtaining direct Ephys evidence of RF-induced activation of ferritin-coupled ion channels. We found that RF does not yield instantaneous changes in neuronal membrane potentials. Instead, RF produces responses that are long-lasting and moderate, but effective in controlling the bioelectrical properties of neurons.
in Journal of Neuroscience on 2024-07-24 16:30:24 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
Linking sensory input and its consequences is a fundamental brain operation. During behavior, the neural activity of neocortical and limbic systems often reflects dynamic combinations of sensory and task-dependent variables, and these "mixed representations" are suggested to be important for perception, learning, and plasticity. However, the extent to which such integrative computations might occur outside of the forebrain is less clear. Here, we conduct cellular-resolution two-photon Ca2+ imaging in the superficial "shell" layers of the inferior colliculus (IC), as head-fixed mice of either sex perform a reward-based psychometric auditory task. We find that the activity of individual shell IC neurons jointly reflects auditory cues, mice's actions, and behavioral trial outcomes, such that trajectories of neural population activity diverge depending on mice's behavioral choice. Consequently, simple classifier models trained on shell IC neuron activity can predict trial-by-trial outcomes, even when training data are restricted to neural activity occurring prior to mice's instrumental actions. Thus, in behaving mice, auditory midbrain neurons transmit a population code that reflects a joint representation of sound, actions, and task-dependent variables.
in Journal of Neuroscience on 2024-07-24 16:30:24 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
It has been suggested that, prior to a saccade, visual neurons predictively respond to stimuli that will fall in their receptive fields after completion of the saccade. This saccadic remapping process is thought to compensate for the shift of the visual world across the retina caused by eye movements. To map the timing of this predictive process in the brain, we recorded neural activity using electroencephalography during a saccade task. Human participants (male and female) made saccades between two fixation points while covertly attending to oriented gratings briefly presented at various locations on the screen. Data recorded during trials in which participants maintained fixation were used to train classifiers on stimuli in different positions. Subsequently, data collected during saccade trials were used to test for the presence of remapped stimulus information at the post-saccadic retinotopic location in the peri-saccadic period, providing unique insight into when remapped information becomes available. We found that the stimulus could be decoded at the remapped location ~180 ms post-stimulus onset, but only when the stimulus was presented 100–200 ms before saccade onset. Within this range, we found that the timing of remapping was dictated by stimulus onset rather than saccade onset. We conclude that presenting the stimulus immediately before the saccade allows for optimal integration of the corollary discharge signal with the incoming peripheral visual information, resulting in a remapping of activation to the relevant post-saccadic retinotopic neurons.
in Journal of Neuroscience on 2024-07-24 16:30:24 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
Light plays an essential role in a variety of physiological processes, including vision, mood, and glucose homeostasis. However, the intricate relationship between light and an animal's feeding behavior has remained elusive. Here, we found that light exposure suppresses food intake, whereas darkness amplifies it in male mice. Interestingly, this phenomenon extends its reach to diurnal male Nile grass rats and healthy humans. We further show that lateral habenula (LHb) neurons in mice respond to light exposure, which in turn activates 5-HT neurons in the dorsal Raphe nucleus (DRN). Activation of the LHb->5-HTDRN circuit in mice blunts darkness-induced hyperphagia, while inhibition of the circuit prevents light-induced anorexia. Together, we discovered a light-responsive neural circuit that relays the environmental light signals to regulate feeding behavior in mice.
in Journal of Neuroscience on 2024-07-24 16:30:24 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
Completely ignoring a salient distractor presented concurrently with a target is difficult, and sometimes attention is involuntarily attracted to the distractor's location (attentional capture). Employing the N2ac component as a marker of attention allocation toward sounds, in this study we investigate the spatiotemporal dynamics of auditory attention across two experiments. Human participants (male and female) performed an auditory search task, where the target was accompanied by a distractor in two-third of the trials. For a distractor more salient than the target (Experiment 1), we observe not only a distractor N2ac (indicating attentional capture) but the full chain of attentional dynamics implied by the notion of attentional capture, namely, (1) the distractor captures attention before the target is attended, (2) allocation of attention to the target is delayed by distractor presence, and (3) the target is attended after the distractor. Conversely, for a distractor less salient than the target (Experiment 2), although responses were delayed, no attentional capture was observed. Together, these findings reveal two types of spatial attentional dynamics in the auditory modality (distraction with and without attentional capture).
in Journal of Neuroscience on 2024-07-24 16:30:24 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
Mature vertebrates maintain posture using vestibulospinal neurons that transform sensed instability into reflexive commands to spinal motor circuits. Postural stability improves across development. However, due to the complexity of terrestrial locomotion, vestibulospinal contributions to postural refinement in early life remain unexplored. Here we leveraged the relative simplicity of underwater locomotion to quantify the postural consequences of losing vestibulospinal neurons during development in larval zebrafish of undifferentiated sex. By comparing posture at two timepoints, we discovered that later lesions of vestibulospinal neurons led to greater instability. Analysis of thousands of individual swim bouts revealed that lesions disrupted movement timing and corrective reflexes without impacting swim kinematics, and that this effect was particularly strong in older larvae. Using a generative model of swimming, we showed how these disruptions could account for the increased postural variability at both timepoints. Finally, late lesions disrupted the fin/trunk coordination observed in older larvae, linking vestibulospinal neurons to postural control schemes used to navigate in depth. Since later lesions were considerably more disruptive to postural stability, we conclude that vestibulospinal contributions to balance increase as larvae mature. Vestibulospinal neurons are highly conserved across vertebrates; we therefore propose that they are a substrate for developmental improvements to postural control.
in Journal of Neuroscience on 2024-07-24 16:30:24 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
by Noah B. Herrington, Yan Chak Li, David Stein, Gaurav Pandey, Avner Schlessinger
Protein kinase function and interactions with drugs are controlled in part by the movement of the DFG and ɑC-Helix motifs that are related to the catalytic activity of the kinase. Small molecule ligands elicit therapeutic effects with distinct selectivity profiles and residence times that often depend on the active or inactive kinase conformation(s) they bind. Modern AI-based structural modeling methods have the potential to expand upon the limited availability of experimentally determined kinase structures in inactive states. Here, we first explored the conformational space of kinases in the PDB and models generated by AlphaFold2 (AF2) and ESMFold, two prominent AI-based protein structure prediction methods. Our investigation of AF2’s ability to explore the conformational diversity of the kinome at various multiple sequence alignment (MSA) depths showed a bias within the predicted structures of kinases in DFG-in conformations, particularly those controlled by the DFG motif, based on their overabundance in the PDB. We demonstrate that predicting kinase structures using AF2 at lower MSA depths explored these alternative conformations more extensively, including identifying previously unobserved conformations for 398 kinases. Ligand enrichment analyses for 23 kinases showed that, on average, docked models distinguished between active molecules and decoys better than random (average AUC (avgAUC) of 64.58), but select models perform well (e.g., avgAUCs for PTK2 and JAK2 were 79.28 and 80.16, respectively). Further analysis explained the ligand enrichment discrepancy between low- and high-performing kinase models as binding site occlusions that would preclude docking. The overall results of our analyses suggested that, although AF2 explored previously uncharted regions of the kinase conformational space and select models exhibited enrichment scores suitable for rational drug discovery, rigorous refinement of AF2 models is likely still necessary for drug discovery campaigns.in PLoS Computational Biology on 2024-07-24 14:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
by Virgile Andreani, Eric J. South, Mary J. Dunlop
Dense arrangements of binding sites within nucleotide sequences can collectively influence downstream transcription rates or initiate biomolecular interactions. For example, natural promoter regions can harbor many overlapping transcription factor binding sites that influence the rate of transcription initiation. Despite the prevalence of overlapping binding sites in nature, rapid design of nucleotide sequences with many overlapping sites remains a challenge. Here, we show that this is an NP-hard problem, coined here as the nucleotide String Packing Problem (SPP). We then introduce a computational technique that efficiently assembles sets of DNA-protein binding sites into dense, contiguous stretches of double-stranded DNA. For the efficient design of nucleotide sequences spanning hundreds of base pairs, we reduce the SPP to an Orienteering Problem with integer distances, and then leverage modern integer linear programming solvers. Our method optimally packs sets of 20–100 binding sites into dense nucleotide arrays of 50–300 base pairs in 0.05–10 seconds. Unlike approximation algorithms or meta-heuristics, our approach finds provably optimal solutions. We demonstrate how our method can generate large sets of diverse sequences suitable for library generation, where the frequency of binding site usage across the returned sequences can be controlled by modulating the objective function. As an example, we then show how adding additional constraints, like the inclusion of sequence elements with fixed positions, allows for the design of bacterial promoters. The nucleotide string packing approach we present can accelerate the design of sequences with complex DNA-protein interactions. When used in combination with synthesis and high-throughput screening, this design strategy could help interrogate how complex binding site arrangements impact either gene expression or biomolecular mechanisms in varied cellular contexts.in PLoS Computational Biology on 2024-07-24 14:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
by Pierre Le Denmat, Tom Verguts, Kobe Desender
Human decision making is accompanied by a sense of confidence. According to Bayesian decision theory, confidence reflects the learned probability of making a correct response, given available data (e.g., accumulated stimulus evidence and response time). Although optimal, independently learning these probabilities for all possible data combinations is computationally intractable. Here, we describe a novel model of confidence implementing a low-dimensional approximation of this optimal yet intractable solution. This model allows efficient estimation of confidence, while at the same time accounting for idiosyncrasies, different kinds of biases and deviation from the optimal probability correct. Our model dissociates confidence biases resulting from the estimate of the reliability of evidence by individuals (captured by parameter α), from confidence biases resulting from general stimulus independent under and overconfidence (captured by parameter β). We provide empirical evidence that this model accurately fits both choice data (accuracy, response time) and trial-by-trial confidence ratings simultaneously. Finally, we test and empirically validate two novel predictions of the model, namely that 1) changes in confidence can be independent of performance and 2) selectively manipulating each parameter of our model leads to distinct patterns of confidence judgments. As a tractable and flexible account of the computation of confidence, our model offers a clear framework to interpret and further resolve different forms of confidence biases.in PLoS Computational Biology on 2024-07-24 14:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
by Wentao Li, Han Chen, Xiaoqian Jiang, Arif Harmanci
Increasing genetic and phenotypic data size is critical for understanding the genetic determinants of diseases. Evidently, establishing practical means for collaboration and data sharing among institutions is a fundamental methodological barrier for performing high-powered studies. As the sample sizes become more heterogeneous, complex statistical approaches, such as generalized linear mixed effects models, must be used to correct for the confounders that may bias results. On another front, due to the privacy concerns around Protected Health Information (PHI), genetic information is restrictively protected by sharing according to regulations such as Health Insurance Portability and Accountability Act (HIPAA). This limits data sharing among institutions and hampers efforts around executing high-powered collaborative studies. Federated approaches are promising to alleviate the issues around privacy and performance, since sensitive data never leaves the local sites. Motivated by these, we developed FedGMMAT, a federated genetic association testing tool that utilizes a federated statistical testing approach for efficient association tests that can correct for confounding fixed and additive polygenic random effects among different collaborating sites. Genetic data is never shared among collaborating sites, and the intermediate statistics are protected by encryption. Using simulated and real datasets, we demonstrate FedGMMAT can achieve the virtually same results as pooled analysis under a privacy-preserving framework with practical resource requirements.in PLoS Computational Biology on 2024-07-24 14:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
by Ben Ewen-Campen, Norbert Perrimon
Despite the deep conservation of the DNA damage response (DDR) pathway, cells in different contexts vary widely in their susceptibility to DNA damage and their propensity to undergo apoptosis as a result of genomic lesions. One of the cell signaling pathways implicated in modulating the DDR is the highly conserved Wnt pathway, which is known to promote resistance to DNA damage caused by ionizing radiation in a variety of human cancers. However, the mechanisms linking Wnt signal transduction to the DDR remain unclear. Here, we use a genetically encoded system in Drosophila to reliably induce consistent levels of DNA damage in vivo, and demonstrate that canonical Wnt signaling in the wing imaginal disc buffers cells against apoptosis in the face of DNA double-strand breaks. We show that Wg, the primary Wnt ligand in Drosophila, activates epidermal growth factor receptor (EGFR) signaling via the ligand-processing protease Rhomboid, which, in turn, modulates the DDR in a Chk2-, p53-, and E2F1-dependent manner. These studies provide mechanistic insight into the modulation of the DDR by the Wnt and EGFR pathways in vivo in a highly proliferative tissue. Furthermore, they reveal how the growth and patterning functions of Wnt signaling are coupled with prosurvival, antiapoptotic activities, thereby facilitating developmental robustness in the face of genomic damage.in PLoS Biology on 2024-07-24 14:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
Author(s): Aakanksha Gubbala, Daniel P. Arnold, Anika Jena, Stephanie Anujarerat, and Sho C. Takatori
We study the dynamic structure of lipid domain inclusions embedded within a phase-separated reconstituted lipid bilayer in contact with a swarming flow of gliding filamentous actin. Passive circular domains transition into highly deformed morphologies that continuously elongate, rotate, and pinch of…
[Phys. Rev. E 110, 014410] Published Wed Jul 24, 2024
in Physical Review E: Biological physics on 2024-07-24 10:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science Advances on 2024-07-24 07:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science Advances on 2024-07-24 07:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science Advances on 2024-07-24 07:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science Advances on 2024-07-24 07:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science Advances on 2024-07-24 07:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science Advances on 2024-07-24 07:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science Advances on 2024-07-24 07:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science Advances on 2024-07-24 07:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science Advances on 2024-07-24 07:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science Advances on 2024-07-24 07:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science Advances on 2024-07-24 07:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science Advances on 2024-07-24 07:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science Advances on 2024-07-24 07:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science Advances on 2024-07-24 07:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science Advances on 2024-07-24 07:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science Advances on 2024-07-24 07:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science Advances on 2024-07-24 07:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science Advances on 2024-07-24 07:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science Advances on 2024-07-24 07:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science Advances on 2024-07-24 07:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science Advances on 2024-07-24 07:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science Advances on 2024-07-24 07:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science Advances on 2024-07-24 07:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science Advances on 2024-07-24 07:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Science Advances on 2024-07-24 07:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Journal of Neurophysiology on 2024-07-24 04:22:42 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Trends in Neurosciences: In press on 2024-07-24 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Trends in Neurosciences: In press on 2024-07-24 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Cell Reports: Current Issue on 2024-07-24 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Cell Reports: Current Issue on 2024-07-24 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Cell Reports: Current Issue on 2024-07-24 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Cell Reports: Current Issue on 2024-07-24 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Cell Reports: Current Issue on 2024-07-24 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Cell Reports: Current Issue on 2024-07-24 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Cell Reports: In press on 2024-07-24 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in eLife on 2024-07-24 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in eLife on 2024-07-24 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in eLife on 2024-07-24 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in eLife on 2024-07-24 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in eLife on 2024-07-24 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in eLife on 2024-07-24 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in eLife on 2024-07-24 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in eLife on 2024-07-24 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in eLife on 2024-07-24 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in bioRxiv: Neuroscience on 2024-07-24 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in bioRxiv: Neuroscience on 2024-07-24 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in bioRxiv: Neuroscience on 2024-07-24 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in bioRxiv: Neuroscience on 2024-07-24 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in bioRxiv: Neuroscience on 2024-07-24 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in bioRxiv: Neuroscience on 2024-07-24 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in bioRxiv: Neuroscience on 2024-07-24 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in bioRxiv: Neuroscience on 2024-07-24 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in bioRxiv: Neuroscience on 2024-07-24 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in bioRxiv: Neuroscience on 2024-07-24 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in bioRxiv: Neuroscience on 2024-07-24 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in bioRxiv: Neuroscience on 2024-07-24 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in bioRxiv: Neuroscience on 2024-07-24 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in bioRxiv: Neuroscience on 2024-07-24 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
Brain Sciences, Vol. 14, Pages 740: Exploring Pathways for Pain Relief in Treatment and Management of Lumbar Foraminal Stenosis: A Review of the Literature
Brain Sciences doi: 10.3390/brainsci14080740
Authors: Renat Nurmukhametov Manuel De Jesus Encarnacion Ramirez Medet Dosanov Abakirov Medetbek Stepan Kudryakov Gervith Reyes Soto Claudia B. Ponce Espinoza Jeff Natalaja Mukengeshay Tshiunza Mpoyi Cherubin Vladimir Nikolenko Artem Gushcha Salman Sharif Nicola Montemurro
Background: Lumbar foraminal stenosis (LFS) involves the narrowing of neural foramina, leading to nerve compression, significant lower back pain and radiculopathy, particularly in the aging population. Management includes physical therapy, medications and potentially invasive surgeries such as foraminotomy. Advances in diagnostic and treatment strategies are essential due to LFS’s complexity and prevalence, which underscores the importance of a multidisciplinary approach in optimizing patient outcomes. Method: This literature review on LFS employed a systematic methodology to gather and synthesize recent scientific data. A comprehensive search was conducted across PubMed, Scopus and Cochrane Library databases using specific keywords related to LFS. The search, restricted to English language articles from 1 January 2000 to 31 December 2023, focused on peer-reviewed articles, clinical trials and reviews. Due to the heterogeneity among the studies, data were qualitatively synthesized into themes related to diagnosis, treatment and pathophysiology. Results: This literature review on LFS analyzed 972 articles initially identified, from which 540 remained after removing duplicates. Following a rigorous screening process, 20 peer-reviewed articles met the inclusion criteria and were reviewed. These studies primarily focused on evaluating the diagnostic accuracy, treatment efficacy and pathophysiological insights into LFS. Conclusion: The comprehensive review underscores the necessity for precise diagnostic and management strategies for LFS, highlighting the role of a multidisciplinary approach and the utility of a unified classification system in enhancing patient outcomes in the face of this condition’s increasing prevalence.
in Brain Sciences on 2024-07-24 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
Brain Sciences, Vol. 14, Pages 739: You’re Beautiful When You Smile: Event-Related Brain Potential (ERP) Evidence of Early Opposite-Gender Bias in Happy Faces
Brain Sciences doi: 10.3390/brainsci14080739
Authors: Jonas Schmuck Emely Voltz Henning Gibbons
Studies of social cognition have shown gender differences regarding human face processing. One interesting finding is the enhanced processing of opposite-gender faces at different time stages, as revealed by event-related brain potentials. Crucially, from an evolutionary perspective, such a bias might interact with the emotional expression of the face. To investigate this, 100 participants (50 female, 50 male) completed an expression-detection task while their EEG was recorded. In three blocks, fearful, happy and neutral faces (female and male) were randomly presented, with participants instructed to respond to only one predefined target expression level in each block. Using linear mixed models, we observed both faster reaction times as well as larger P1 and late positive potential (LPP) amplitudes for women compared to men, supporting a generally greater female interest in faces. Highly interestingly, the analysis revealed an opposite-gender bias at P1 for happy target faces. This suggests that participants’ attentional templates may include more opposite-gender facial features when selectively attending to happy faces. While N170 was influenced by neither the face nor the participant gender, LPP was modulated by the face gender and specific combinations of the target status, face gender and expression, which is interpreted in the context of gender-emotion stereotypes. Future research should further investigate this expression and attention dependency of early opposite-gender biases.
in Brain Sciences on 2024-07-24 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
Brain Sciences, Vol. 14, Pages 738: Individual Deviation-Based Functional Hypergraph for Identifying Subtypes of Autism Spectrum Disorder
Brain Sciences doi: 10.3390/brainsci14080738
Authors: Jialong Li Weihao Zheng Xiang Fu Yu Zhang Songyu Yang Ying Wang Zhe Zhang Bin Hu Guojun Xu
Heterogeneity has been one of the main barriers to understanding and treatment of autism spectrum disorder (ASD). Previous studies have identified several subtypes of ASD through unsupervised clustering analysis. However, most of them primarily depicted the pairwise similarity between individuals through second-order relationships, relying solely on patient data for their calculation. This leads to an underestimation of the complexity inherent in inter-individual relationships and the diagnostic information provided by typical development (TD). To address this, we utilized an elastic net model to construct an individual deviation-based hypergraph (ID-Hypergraph) based on functional MRI data. We then conducted a novel community detection clustering algorithm to the ID-Hypergraph, with the aim of identifying subtypes of ASD. By applying this framework to the Autism Brain Imaging Data Exchange repository data (discovery: 147/125, ASD/TD; replication: 134/132, ASD/TD), we identified four reproducible ASD subtypes with roughly similar patterns of ALFF between the discovery and replication datasets. Moreover, these subtypes significantly varied in communication domains. In addition, we achieved over 80% accuracy for the classification between these subtypes. Taken together, our study demonstrated the effectiveness of identifying subtypes of ASD through the ID-hypergraph, highlighting its potential in elucidating the heterogeneity of ASD and diagnosing ASD subtypes.
in Brain Sciences on 2024-07-24 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
Psychotic symptoms and delusional beliefs have been linked to dopamine transmission in both healthy and clinical samples and are assumed to result at least in part from perceiving illusory patterns in noise. However, the existing literature on the role of dopamine in detecting patterns in noise is inconclusive. To address this issue, we assessed the effect of manipulating dopaminergic neurotransmission on illusory pattern perception in healthy individuals (n = 48, n = 19 female) in a double-blind placebo-controlled within-subjects design (see preregistration at https://osf.io/a4k9j/). We predicted individuals on versus off ʟ-DOPA to be more likely to perceive illusory patterns, specifically objects in images containing only noise. Using a signal detection model, however, we found no credible evidence that ʟ-DOPA compared with placebo increased false alarm rates. Further, ʟ-DOPA did not reliably modulate measures of accuracy, discrimination sensitivity, and response bias. In all cases, Bayesian statistics revealed strong evidence in favor of the null hypothesis. The task design followed previous work on illusory pattern perception and comprised a limited number of items per condition. The results therefore need to be interpreted with caution, as power was limited. Future studies should address illusory pattern perception using more items and take into account potential dose-dependent effects and differential effects in healthy versus clinical samples.
in eNeuro on 2024-07-23 16:30:30 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
Typical statistical practices in the biological sciences have been increasingly called into question due to difficulties in the replication of an increasing number of studies, many of which are confounded by the relative difficulty of null significance hypothesis testing designs and interpretation of p-values. Bayesian inference, representing a fundamentally different approach to hypothesis testing, is receiving renewed interest as a potential alternative or complement to traditional null significance hypothesis testing due to its ease of interpretation and explicit declarations of prior assumptions. Bayesian models are more mathematically complex than equivalent frequentist approaches, which have historically limited applications to simplified analysis cases. However, the advent of probability distribution sampling tools with exponential increases in computational power now allows for quick and robust inference under any distribution of data. Here we present a practical tutorial on the use of Bayesian inference in the context of neuroscientific studies in both rat electrophysiological and computational modeling data. We first start with an intuitive discussion of Bayes' rule and inference followed by the formulation of Bayesian-based regression and ANOVA models using data from a variety of neuroscientific studies. We show how Bayesian inference leads to easily interpretable analysis of data while providing an open-source toolbox to facilitate the use of Bayesian tools.
in eNeuro on 2024-07-23 16:30:30 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
by Thomas Williams, James M. McCaw, James M. Osborne
The role of direct cell–to–cell spread in viral infections—where virions spread between host and susceptible cells without needing to be secreted into the extracellular environment—has come to be understood as essential to the dynamics of medically significant viruses like hepatitis C and influenza. Recent work in both the experimental and mathematical modelling literature has attempted to quantify the prevalence of cell–to–cell infection compared to the conventional free virus route using a variety of methods and experimental data. However, estimates are subject to significant uncertainty and moreover rely on data collected by inhibiting one mode of infection by either chemical or physical factors, which may influence the other mode of infection to an extent which is difficult to quantify. In this work, we conduct a simulation–estimation study to probe the practical identifiability of the proportion of cell–to–cell infection, using two standard mathematical models and synthetic data that would likely be realistic to obtain in the laboratory. We show that this quantity cannot be estimated using non–spatial data alone, and that the collection of a data which describes the spatial structure of the infection is necessary to infer the proportion of cell–to–cell infection. Our results provide guidance for the design of relevant experiments and mathematical tools for accurately inferring the prevalence of cell–to–cell infection in in vitro and in vivo contexts.in PLoS Computational Biology on 2024-07-23 14:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
by Rikesh M. Rajani, Robert Ellingford, Mariam Hellmuth, Samuel S. Harris, Orjona S. Taso, David Graykowski, Francesca Kar Wey Lam, Charles Arber, Emre Fertan, John S. H. Danial, Matthew Swire, Marcus Lloyd, Tatiana A. Giovannucci, Mathieu Bourdenx, David Klenerman, Robert Vassar, Selina Wray, Carlo Sala Frigerio, Marc Aurel Busche
Reduction of amyloid beta (Aβ) has been shown to be effective in treating Alzheimer’s disease (AD), but the underlying assumption that neurons are the main source of pathogenic Aβ is untested. Here, we challenge this prevailing belief by demonstrating that oligodendrocytes are an important source of Aβ in the human brain and play a key role in promoting abnormal neuronal hyperactivity in an AD knock-in mouse model. We show that selectively suppressing oligodendrocyte Aβ production improves AD brain pathology and restores neuronal function in the mouse model in vivo. Our findings suggest that targeting oligodendrocyte Aβ production could be a promising therapeutic strategy for treating AD.in PLoS Biology on 2024-07-23 14:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
by Malgorzata Lagisz, Joanna Rutkowska, Upama Aich, Robert M. Ross, Manuela S. Santana, Joshua Wang, Nina Trubanová, Matthew J. Page, Andrew Adrian Yu Pua, Yefeng Yang, Bawan Amin, April Robin Martinig, Adrian Barnett, Aswathi Surendran, Ju Zhang, David N. Borg, Jafsia Elisee, James G. Wrightson, Shinichi Nakagawa
Awards can propel academic careers. They also reflect the culture and values of the scientific community. But do awards incentivize greater transparency, inclusivity, and openness in science? Our cross-disciplinary survey of 222 awards for the “best” journal articles across all 27 SCImago subject areas revealed that journals and learned societies administering such awards generally publish little detail on their procedures and criteria. Award descriptions were brief, rarely including contact details or information on the nominations pool. Nominations of underrepresented groups were not explicitly encouraged, and concepts that align with Open Science were almost absent from the assessment criteria. At the same time, 10% of awards, especially the recently established ones, tended to use article-level impact metrics. USA-affiliated researchers dominated the winner’s pool (48%), while researchers from the Global South were uncommon (11%). Sixty-one percent of individual winners were men. Overall, Best Paper awards miss the global calls for greater transparency and equitable access to academic recognition. We provide concrete and implementable recommendations for scientific awards to improve the scientific recognition system and incentives for better scientific practice.in PLoS Biology on 2024-07-23 14:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in The Neuroscientist on 2024-07-23 10:56:10 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in The Neuroscientist on 2024-07-23 10:51:18 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
Author(s): Supravat Dey, Gladys Massiera, and Estelle Pitard
Large groups of active cilia collectively beat in a fluid medium as metachronal waves, essential for some microorganisms motility and for flow generation in mucociliary clearance. Several models can predict the emergence of metachronal waves, but what controls the properties of metachronal waves is …
[Phys. Rev. E 110, 014409] Published Tue Jul 23, 2024
in Physical Review E: Biological physics on 2024-07-23 10:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
One-year-old mice with deletions of malin display robust Lafora body accumulation, astrogliosis, microgliosis, and evidence of cortical circuit dysfunction. Despite these pathologies, malin KO mice exhibited no abnormalities in a wide range of home-cage neurobehavioral endpoints, pointing to a broad window for intervention in this otherwise fatal form of epilepsy.
Lafora disease (LD) is a syndrome of progressive myoclonic epilepsy and cumulative neurocognitive deterioration caused by recessively inherited genetic lesions of EPM2A (laforin) or NHLRC1 (malin). Neuropsychiatric symptomatology in LD is thought to be directly downstream of neuronal and astrocytic polyglucosan aggregates, termed Lafora bodies (LBs), which faithfully accumulate in an age-dependent manner in all mouse models of LD. In this study, we applied home-cage monitoring to examine the extent of neurobehavioral deterioration in a model of malin-deficient LD as a means to identify robust preclinical endpoints that may guide the selection of novel genetic treatments. At 6 weeks, ∼6–7 months, and ∼12 months of age, malin-deficient mice (“KO”) and wild-type (WT) littermates underwent a standardized home-cage behavioral assessment designed to non-obtrusively appraise features of rest/arousal, consumptive behaviors, risk aversion, and voluntary wheel-running. At all timepoints, and over a range of metrics that we report transparently, WT and KO mice were essentially indistinguishable. In contrast, within WT mice compared across the same timepoints, we identified age-related nocturnal hypoactivity, diminished sucrose preference, and reduced wheel-running. Neuropathological examinations in subsets of the same mice revealed expected age-dependent LB accumulation, gliosis, and microglial activation in cortical and subcortical brain regions. At 12 months of age, despite the burden of neocortical LBs, we did not identify spontaneous seizures during an electroencephalographic (EEG) survey, and KO and WT mice exhibited similar spectral EEG features. However, in an in vitro assay of neocortical function, paroxysmal bursts of network activity (UP states) in KO slices were more prolonged at 3 and 6 months of age, but similar to WT at 12 months. KO mice displayed a distinct response to pentylenetetrazole, with a greater incidence of clonic seizures and a more pronounced postictal suppression of movement, feeding, and drinking behavior. Together, these results highlight the clinicopathologic dissociation in a mouse model of LD, where the accrual of LBs may latently modify cortical circuit function and seizure threshold without clinically meaningful changes in home-cage behavior. Our findings allude to a delay between LB accumulation and neurobehavioral decline in LD: one that may provide a window for treatment, and whose precise duration may be difficult to ascertain within the typical lifespan of a laboratory mouse.
in Journal of Comparative Neurology on 2024-07-23 07:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
Endovascular thrombectomy (EVT) safety and efficacy in patients with large core infarcts receiving oral anticoagulants (OAC) are unknown. In the SELECT2 trial (NCT03876457), 29 of 180 (16%; vitamin K antagonists 15, direct OACs 14) EVT, and 18 of 172 (10%; vitamin K antagonists 3, direct OACs 15) medical management (MM) patients reported OAC use at baseline. EVT was not associated with better clinical outcomes in the OAC group (EVT 6 [4–6] vs MM 5 [4–6], adjusted generalized odds ratio 0.89 [0.53–1.50]), but demonstrated significantly better outcomes in patients without OAC (EVT 4 [3–6] vs MM 5 [4–6], adjusted generalized odds ratio 1.87 [1.45–2.40], p = 0.02). The OAC group had higher comorbidities, including atrial fibrillation (70% vs 17%), congestive heart failure (28% vs 10%), and hypertension (87% vs 72%), suggesting increased frailty. However, the results were consistent after adjustment for these comorbidities, and was similar regardless of the type of OACs used. Whereas any hemorrhage rates were higher in the OAC group receiving EVT (86% in OAC vs 70% in no OAC), no parenchymal hemorrhage or symptomatic intracranial hemorrhage were observed with OAC use in both the EVT and MM arms. Although we did not find evidence that the effect was due to excess hemorrhage or confounded by underlying cardiac disease or older age, OAC use alone should not exclude patients from receiving EVT. Baseline comorbidities and ischemic injury extent should be considered while making individualized treatment decisions. ANN NEUROL 2024
in Annals of Neurology on 2024-07-23 04:58:53 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Neuron: In press on 2024-07-23 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Cell Reports: Current Issue on 2024-07-23 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Cell Reports: Current Issue on 2024-07-23 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Cell Reports: Current Issue on 2024-07-23 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Cell Reports: Current Issue on 2024-07-23 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Cell Reports: Current Issue on 2024-07-23 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Cell Reports: Current Issue on 2024-07-23 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Cell Reports: Current Issue on 2024-07-23 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in Cell Reports: Current Issue on 2024-07-23 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in eLife on 2024-07-23 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in eLife on 2024-07-23 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in eLife on 2024-07-23 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in eLife on 2024-07-23 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
in eLife on 2024-07-23 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
Brain Sciences, Vol. 14, Pages 737: DNA Methylation in Autism Spectrum Disorders: Biomarker or Pharmacological Target?
Brain Sciences doi: 10.3390/brainsci14080737
Authors: Hanieh Gholamalizadeh Maedeh Amiri-Shahri Fatemeh Rasouli Arina Ansari Vafa Baradaran Rahimi Vahid Reza Askari
Autism spectrum disorder (ASD) is a group of heterogeneous neurodevelopmental disabilities with persistent impairments in cognition, communication, and social behavior. Although environmental factors play a role in ASD etiopathogenesis, a growing body of evidence indicates that ASD is highly inherited. In the last two decades, the dramatic rise in the prevalence of ASD has interested researchers to explore the etiologic role of epigenetic marking and incredibly abnormal DNA methylation. This review aimed to explain the current understanding of the association between changes in DNA methylation signatures and ASD in patients or animal models. We reviewed studies reporting alterations in DNA methylation at specific genes as well as epigenome-wide association studies (EWASs). Finally, we hypothesized that specific changes in DNA methylation patterns could be considered a potential biomarker for ASD diagnosis and prognosis and even a target for pharmacological intervention.
in Brain Sciences on 2024-07-23 00:00:00 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
The adult turtle spinal cord can generate multiple kinds of limb movements, including swimming, three forms of scratching, and limb withdrawal (flexion reflex), even without brain input and sensory feedback. There are many multifunctional spinal neurons, activated during multiple motor patterns, and some behaviorally specialized neurons, activated during only one. How do multifunctional and behaviorally specialized neurons each contribute to motor output? We analyzed in vivo intracellular recordings of multifunctional and specialized neurons. Neurons tended to spike in the same phase of the hip-flexor (HF) activity cycle during swimming and scratching, though one preferred opposite phases. During both swimming and scratching, a larger fraction of multifunctional neurons than specialized neurons were highly rhythmic. One group of multifunctional neurons was active during the HF-on phase and another during the HF-off phase. Thus, HF–extensor alternation may be generated by a subset of multifunctional spinal neurons during both swimming and scratching. Scratch-specialized neurons and flexion reflex-selective neurons may instead trigger their respective motor patterns, by biasing activity of multifunctional neurons. In phase-averaged membrane potentials of multifunctional neurons, trough phases were more highly correlated between swimming and scratching than peak phases, suggesting that rhythmic inhibition plays a greater role than rhythmic excitation. We also provide the first intracellular recording of a turtle swim-specialized neuron: tonically excited during swimming but inactive during scratching and flexion reflex. It displayed an excitatory postsynaptic potential following each swim-evoking electrical stimulus and thus may be an intermediary between reticulospinal axons and the swimming CPG they activate.
in eNeuro on 2024-07-22 16:27:57 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
The gaze-following patch (GFP) is located in the posterior temporal cortex and has been described as a cortical module dedicated to processing other people's gaze-direction in a domain-specific manner. Thus, it appears to be the neural correlate of Baron-Cohen's eye direction detector (EDD) which is one of the core modules in his mindreading system—a neurocognitive model for the theory of mind concept. Inspired by Jerry Fodor's ideas on the modularity of the mind, Baron-Cohen proposed that, among other things, the individual modules are domain specific. In the case of the EDD, this means that it exclusively processes eye-like stimuli to extract gaze-direction and that other stimuli, which may carry directional information as well, are processed elsewhere. If the GFP is indeed EDD's neural correlate, it must meet this expectation. To test this, we compared the GFP's BOLD activity during gaze-direction following with the activity during arrow-direction following in the present human fMRI study. Contrary to the expectation based on the assumption of domain specificity, we did not find a differentiation between gaze- and arrow-direction following. In fact, we were not able to reproduce the GFP as presented in the previous studies. A possible explanation is that in the present study—unlike the previous work—the gaze stimuli did not contain an obvious change of direction that represented a visual motion. Hence, the critical stimulus component responsible for the identification of the GFP in the previous experiments might have been visual motion.
in eNeuro on 2024-07-22 16:27:57 UTC.
- Wallabag.it! - Save to Instapaper - Save to Pocket -
by Hsun Chiang, Chih-Ang Chung
Capillary plexus cultivation is crucial in tissue engineering and regenerative medicine. Theoretical simulations have been conducted to supplement the expensive experimental works. However, the mechanisms connecting mechanical and chemical stimuli remained undefined, and the functions of the different VEGF forms in the culture environment were still unclear. In this paper, we developed a hybrid model for simulating short-term in vitro capillary incubations. We used the Cellular Potts model to predict individual cell migration, morphology change, and continuum mechanics to quantify biogel deformation and VEGF transport dynamics. By bridging the mechanical regulation and chemical stimulation in the model, the results showed good agreement between the predicted network topology and experiments, in which elongated cells connected, forming the network cords and round cells gathered, creating cobblestone-like aggregates. The results revealed that the capillary-like networks could develop in high integrity only when the mechanical and chemical couplings worked adequately, with the cell morphology and haptotaxis driven by the soluble and bound forms of VEGF, respectively, functioning simultaneously.in PLoS Computational Biology on 2024-07-22 14:00:00 UTC.