Miracle-dz/UniFAR-FTUs huggingface dataset:
Temporal–spectral signaling of sensory information and expectations in the cerebral processing of pain

Significance Pain is not only shaped by sensory information but also by an individual’s expectations. Here, we investigated how commonly analyzed electroencephalography (EEG) responses to pain signal sensory information, expectations, and discrepancies thereof (prediction errors) in the processing of pain. Bayesian analysis confirmed that pain perception was shaped by objective sensory information and expectations. In contrast, EEG responses at different latencies (including the N1, N2, and P2 components) and frequencies (including alpha, beta, and gamma oscillations) were shaped by sensory information but not by expectations. Thus, EEG responses to pain are more involved in signaling sensory information than in signaling expectations or prediction errors. Expectation effects are obviously mediated by other brain mechanisms than the effects of sensory information on pain. The perception of pain is shaped by somatosensory information about threat. However, pain is also influenced by an individual’s expectations. Such expectations can result in clinically relevant modulations and abnormalities of pain. In the brain, sensory information, expectations (predictions), and discrepancies thereof (prediction errors) are signaled by an extended network of brain areas which generate evoked potentials and oscillatory responses at different latencies and frequencies. However, a comprehensive picture of how evoked and oscillatory brain responses signal sensory information, predictions, and prediction errors in the processing of pain is lacking so far. Here, we therefore applied brief painful stimuli to 48 healthy human participants and independently modulated sensory information (stimulus intensity) and expectations of pain intensity while measuring brain activity using electroencephalography (EEG). Pain ratings confirmed that pain intensity was shaped by both sensory information and expectations. In contrast, Bayesian analyses revealed that stimulus-induced EEG responses at different latencies (the N1, N2, and P2 components) and frequencies (alpha, beta, and gamma oscillations) were shaped by sensory information but not by expectations. Expectations, however, shaped alpha and beta oscillations before the painful stimuli. These findings indicate that commonly analyzed EEG responses to painful stimuli are more involved in signaling sensory information than in signaling expectations or mismatches of sensory information and expectations. Moreover, they indicate that the effects of expectations on pain are served by brain mechanisms which differ from those conveying effects of sensory information on pain.
Impact of SNP microarray analysis of compromised DNA on kinship classification success in the context of investigative genetic genealogy

Single nucleotide polymorphism (SNP) data generated with microarray technologies have been used to solve murder cases via investigative leads obtained from identifying relatives of the unknown perpetrator included in accessible genomic databases, referred to as investigative genetic genealogy (IGG). However, SNP microarrays were developed for relatively high input DNA quantity and quality, while SNP microarray data from compromised DNA typically obtainable from crime scene stains are largely missing. By applying the Illumina Global Screening Array (GSA) to 264 DNA samples with systematically altered quantity and quality, we empirically tested the impact of SNP microarray analysis of deprecated DNA on kinship classification success, as relevant in IGG. Reference data from manufacturer-recommended input DNA quality and quantity were used to estimate genotype accuracy in the compromised DNA samples and for simulating data of different degree relatives. Although stepwise decrease of input DNA amount from 200 nanogram to 6.25 picogram led to decreased SNP call rates and increased genotyping errors, kinship classification success did not decrease down to 250 picogram for siblings and 1st cousins, 1 nanogram for 2nd cousins, while at 25 picogram and below kinship classification success was zero. Stepwise decrease of input DNA quality via increased DNA fragmentation resulted in the decrease of genotyping accuracy as well as kinship classification success, which went down to zero at the average DNA fragment size of 150 base pairs. Combining decreased DNA quantity and quality in mock casework and skeletal samples further highlighted possibilities and limitations. Overall, GSA analysis achieved maximal kinship classification success from 800-200 times lower input DNA quantities than manufacturer-recommended, although DNA quality plays a key role too, while compromised DNA produced false negative kinship classifications rather than false positive ones. Author Summary Investigative genetic genealogy (IGG), i.e., identifying unknown perpetrators of crime via genomic database-tracing of their relatives by means of microarray-based single nucleotide polymorphism (SNP) data, is a recently emerging field. However, SNP microarrays were developed for much higher DNA quantity and quality than typically available from crime scenes, while SNP microarray data on quality and quantity compromised DNA are largely missing. As first attempt to investigate how SNP microarray analysis of quantity and quality compromised DNA impacts kinship classification success in the context of IGG, we performed systematic SNP microarray analyses on DNA samples below the manufacturer-recommended quantity and quality as well as on mock casework samples and on skeletal remains. In addition to IGG, our results are also relevant for any SNP microarray analysis of compromised DNA, such as for the DNA prediction of appearance and biogeographic ancestry in forensics and anthropology and for other purposes.
Coordination games in cancer

We propose a model of cancer initiation and progression where tumor growth is modulated by an evolutionary coordination game. Evolutionary games of cancer are widely used to model frequency-dependent cell interactions with the most studied games being the Prisoner’s Dilemma and public goods games. Coordination games, by their more obscure and less evocative nature, are left understudied, despite the fact that, as we argue, they offer great potential in understanding and treating cancer. In this paper we present the conditions under which coordination games between cancer cells evolve, we propose aspects of cancer that can be modeled as results of coordination games, and explore the ways through which coordination games of cancer can be exploited for therapy.
Similar neural networks respond to coherence during comprehension and production of discourse

When comprehending discourse, listeners engage default mode regions associated with integrative semantic processing to construct a situation model of its content. We investigated how similar networks are engaged when we produce, as well as comprehend, discourse. During fMRI, participants spoke about a series of specific topics and listened to discourse on other topics. We tested how activation was predicted by natural fluctuations in the global coherence of the discourse, i.e., the degree to which utterances conformed to the expected topic. The neural correlates of coherence were similar across speaking and listening, particularly in default mode regions. This network showed greater activation when less coherent speech was heard or produced, reflecting updating of mental representations when discourse did not conform to the expected topic. In contrast, regions that exert control over semantic activation showed task-specific effects, correlating negatively with coherence during listening but not during production. Participants who showed greater activation in left inferior prefrontal cortex also produced more coherent discourse, suggesting a specific role for this region in goal-directed regulation of speech content. Results suggest strong correspondence of discourse representations during speaking and listening. However, they indicate that the semantic control network plays different roles in comprehension and production.
FMRP regulates experience-dependent maturation of callosal synaptic connections and bilateral cortical synchrony

Reduced structural and functional interhemispheric connectivity correlates with the severity Autism Spectrum Disorder (ASD) behaviors in humans. Little is known of how ASD-risk genes regulate callosal connectivity. Here we show that Fmr1, whose loss-of-function leads to Fragile X Syndrome (FXS), cell autonomously promotes maturation of callosal excitatory synapses between somatosensory barrel cortices. Postnatal, cell-autonomous deletion of Fmr1 in postsynaptic Layer (L) 2/3 or L5 neurons results in a selective weakening of AMPA receptor- (R), but not NMDA receptor-, mediated synaptic function, indicative of increased “silent”, or immature, callosal synapses. Sensory deprivation by contralateral whisker trimming normalizes callosal input strength, suggesting that experience-driven activity of postsynaptic Fmr1 KO L2/3 neurons weakens callosal synapses. In contrast to callosal inputs, synapses originating from local L4 and L2/3 circuits are normal, revealing an input-specific role for postsynaptic Fmr1 in promoting callosal synaptic connectivity. Multielectrode EEG recordings in awake Fmr1 KO mice find reduced coherence of bilateral neural oscillations in beta and gamma frequencies during rest and sensory stimulation, reflecting reduced interhemispheric integration. Our findings reveal the cellular and synaptic mechanisms by which loss of Fmr1 leads to reduced interhemispheric connectivity and suggests a novel biomarker of brain dysfunction in FXS.
Design and Validation of a Multi-Point Injection Technology for MR-Guided Convection Enhanced Delivery in the Brain

Convection enhanced delivery (CED) allows direct intracranial administration of neuro-therapeutics. Success of CED relies on specific targeting and broad volume distributions (VD). However, to prevent off-target delivery and tissue damage, CED is typically conducted with small cannulas and at low flow rates, which critically limit the maximum achievable VD. Furthermore, in applications such as gene therapy requiring injections of large fluid volumes into broad subcortical regions, low flow rates translate into long infusion times and multiple surgical trajectories. The cannula design is a major limiting factor in achieving broad VD, while minimizing infusion time and backflow. Here we present and validate a novel multi-point cannula specifically designed to optimize distribution and delivery time in MR-guided intracranial CED of gene-based therapeutics. First, we evaluated the compatibility of our cannula with MRI and common viral vectors for gene therapy. Then, we conducted CED tests in agarose brain phantoms and benchmarked the results against single-needle delivery. 3T MRI in brain phantoms revealed minimal susceptibility-induced artifacts, comparable to the device dimensions. Benchtop CED of adeno-associated virus demonstrated no viral loss or inactivation. CED in agarose brain phantoms at 3, 6, and 9 μL/min showed >3x increase in volume distribution and 60% time reduction compared to single-needle delivery. This study confirms the validity of a multi-point delivery approach for improving infusate distribution at clinically-compatible timescales and supports the feasibility of our novel cannula design for advancing safety and efficacy of MR-guided CED to the central nervous system.
Functional diversification gave rise to allelic specialization in a rice NLR immune receptor pair

Cooperation between receptors from the NLR superfamily is important for intracellular activation of immune responses. NLRs can function in pairs that, upon pathogen recognition, trigger hypersensitive cell death and stop pathogen invasion. Natural selection drives specialization of host immune receptors towards an optimal response, whilst keeping a tight regulation of immunity in the absence of pathogens. However, the molecular basis of co-adaptation and specialization between paired NLRs remains largely unknown. Here, we describe functional specialization in alleles of the rice NLR pair Pik that confers resistance to strains of the blast fungus Magnaporthe oryzae harbouring AVR-Pik effectors. We revealed that matching pairs of allelic Pik NLRs mount effective immune responses whereas mismatched pairs lead to autoimmune phenotypes, a hallmark of hybrid necrosis in both natural and domesticated plant populations. We further showed that allelic specialization is largely underpinned by a single amino acid polymorphism that determines preferential association between matching pairs of Pik NLRs. These results provide a framework for how functionally linked immune receptors undergo co-adaptation to provide an effective and regulated immune response against pathogens. Understanding the molecular constraints that shape paired NLR evolution has implications beyond plant immunity given that hybrid necrosis can drive reproductive isolation.
Coupling of pupil- and neuronal population dynamics reveals diverse influences of arousal on cortical processing

Fluctuations in arousal, controlled by subcortical neuromodulatory systems, continuously shape cortical state, with profound consequences for information processing. Yet, how arousal signals influence cortical population activity in detail has only been characterized for a few selected brain regions so far. Traditional accounts conceptualize arousal as a homogeneous modulator of neural population activity across the cerebral cortex. Recent insights, however, point to a higher specificity of arousal effects on different components of neural activity and across cortical regions. Here, we provide a comprehensive account of the relationships between fluctuations in arousal and neuronal population activity across the human brain. Exploiting the established link between pupil size and central arousal systems, we performed concurrent magnetoencephalographic (MEG) and pupillographic recordings in a large number of participants, pooled across three laboratories. We found a cascade of effects relative to the peak timing of spontaneous pupil dilations: Decreases in low-frequency (2-8 Hz) activity in temporal and lateral frontal cortex, followed by increased high-frequency (>64 Hz) activity in mid-frontal regions, followed by linear and non-linear relationships with intermediate frequency-range activity (8-32 Hz) in occipito-parietal regions. The non-linearity resembled an inverted U-shape whereby intermediate pupil sizes coincided with maximum 8-32 Hz activity. Pupil-linked arousal also coincided with widespread changes in the structure of the aperiodic component of cortical population activity, indicative of changes in the excitation-inhibition balance in underlying microcircuits. Our results provide a novel basis for studying the arousal modulation of cognitive computations in cortical circuits.
Genetic evidence for environment-dependent hybrid incompatibilities in threespine stickleback

Hybrid incompatibilities occur when interactions between opposite-ancestry alleles at different loci reduce the fitness of hybrids. Most work on incompatibilities has focused on those that are ‘intrinsic’, meaning they affect viability and sterility in the laboratory. Theory predicts that ecological selection can also underlie hybrid incompatibilities, but tests of this hypothesis are scarce. In this article, we compiled genetic data for F2 hybrid crosses between divergent populations of threespine stickleback fish (Gasterosteus aculeatus L.) that were born and raised in either the field (semi-natural experimental ponds) or the laboratory (aquaria). We tested for differences in excess heterozygosity between these two environments at ancestry informative loci—a genetic signature of selection against incompatibilities. We found that excess ancestry heterozygosity was elevated by approximately 3% in crosses raised in ponds compared to those raised in aquaria. Previous results from F1 hybrids in the field suggest that pond-specific (single-locus) heterosis is unlikely to explain this finding. Our study suggests that, in stickleback, a coarse signal of environment-dependent hybrid incompatibilities is reliably detectable and that extrinsic incompatibilities have evolved before intrinsic incompatibilities.
Cardiovascular disease causes proinflammatory microvascular changes in the human right atrium

Ischemic heart disease is globally the leading cause of death. It plays a central role in the electrical and structural remodeling of the right atrium, predisposing to arrhythmias, heart failure, and sudden death. Here, we provide the first dissection of the gene expression changes in the live right atrial tissue, using single-nuclei RNA-seq and spatial transcriptomics. We investigate matched samples of the tissue and pericardial fluid and reveal substantial differences in disease- associated gene expression in all cell types, leading to inflammatory microvascular dysfunction and changes in the tissue composition. Our study demonstrates the importance of creating high- resolution cellular maps and partitioning disease signals beyond epicardial coronary arteries and ischemic left ventricle to identify candidate mechanisms leading to more severe types of human cardiovascular disease. One-Sentence Summary Single-cell dissection of ex vivo heart biopsies and pericardial fluid in ischemic heart disease and heart failure
X-Linked Agammaglobulinemia Presenting as Neutropenia: Case Report and an Overview of Literature

X-linked agammaglobulinemia (XLA) is an inherited immunodeficiency caused by mutations in the Bruton Tyrosine Kinase (BTK) gene. Marked neutropenia can be the initial abnormal laboratory finding in patients with XLA who are presenting with their first illness. The two cases presented herein support early consideration of evaluation for primary humoral immune deficiency in previously healthy male patients under the age of 12 months who present with neutropenia in the setting of infection shortly after passively acquired maternal antibody has sufficiently waned. Initial consideration of XLA (or other humoral immune deficiencies) in this particular population of young male neutropenic patients may afford the opportunity to avoid bone marrow biopsy in otherwise stable cases with similar presentations.
Risk Factors of Venous Thromboembolism in Inflammatory Bowel Disease: A Systematic Review and Meta-Analysis

Background: Patients suffering from chronic inflammatory disorders, such as inflammatory bowel disorder, are at higher risk of developing thromboembolism. The chronic inflammatory nature of inflammatory bowel disease has been identified as a predominant reason for a state of Virchow's triad (i.e., endothelial dysfunction, stasis, and general hypercoagulability), eventually leading to the onset of venous thromboembolism. Recent studies show that certain factors, such as demographics, medication history, and history of surgical intervention may increase thromboembolism risk in patients with inflammatory bowel disease. However, to date, no study has attempted to evaluate the effect of different risk factors associated with the development of venous thromboembolism in inflammatory bowel disease patients. Objective: To evaluate the risk factors that can influence the incidence of venous thromboembolism in patients with inflammatory bowel disease. Methods: Academic literature was systematically searched based on the PRISMA guidelines across five databases: Web of Science, EMBASE, CENTRAL, Scopus, and MEDLINE. A random-effect meta-analysis was conducted to evaluate the hazard ratio for the risk factors (i.e., aging, gender, steroid therapy, surgery, and ulcerative colitis) that can influence the incidence of venous thromboembolism in patients with inflammatory bowel disease. Results: From a total of 963 studies, 18 eligible studies with 1,062,985 (44.59 ± 10.18 years) patients suffering from inflammatory bowel disease were included in the review. A meta-analysis revealed a higher risk of aging (Hazard's ratio: 2.19), steroids (1.87), surgery (1.48), and ulcerative colitis (2.06) on venous thromboembolism in patients with inflammatory bowel disease. We also found that the female gender (0.92) did not increase the incidence of venous thromboembolism in inflammatory bowel disease patients. Conclusion: The study provides preliminary evidence regarding high risks associated with ulcerative colitis, steroid consumption, and aging for the development of venous thromboembolism in patients with inflammatory bowel disease. The findings from this study may contribute to developing awareness among clinicians, better risk stratification and prevention of venous thromboembolic complications in patients with inflammatory bowel disease.
Influence of Feeding Omega-3 Polyunsaturated Fatty Acids to Broiler Breeders on Indices of Immunocompetence, Gastrointestinal, and Skeletal Development in Broiler Chickens

Modern broiler chickens are associated with rapid growth rates and superior feed efficiency. However, they are also susceptible to physiological and metabolic disorders (e.g., skin lesions, lameness, sudden death, enteric diseases, myopathies) that exert substantial economic losses to producers. This is further exacerbated by consumer pressure and mandated cessation of production practices such as indiscriminate use of antimicrobial growth promoters. Manipulation of broiler breeder (BB) nutrition and management can influence chick quality, robustness, and resilience to stressors in the production environment. The present review examines the role of feeding BB functional polyunsaturated omega-3 fatty acids (n-3 PUFA) and subsequent impact on the indices of immunocompetence, skeletal, and gastrointestinal (GIT) development in broiler chickens. Research in mammalian and avian models led evidence that perinatal feeding of long chain n-3 PUFA such as eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) engender transgenerational effects through regulation of a variety of biological processes including development of vital organs such as skeleton, brain and GIT. It is shown that feeding poultry breeders n-3 PUFA decreases inflammatory states and enriches hatching eggs with n-3 PUFA and immunoglobulins. Further evidence also shows that after 15 days of incubation, chicken embryos preferentially utilize long chain n-3 PUFA-critical for optimal cell, tissues, and organ development. Enrichment of n-3 PUFA in newly hatchling tissues reduce proinflammatory eicosanoids with consequences of enhanced bone mineralization. Dietary n-3 PUFA also modulates breeder GIT microbiota with consequences of microbial colonization and succession in chicks. As well, research shows that feeding poultry breeders n-3 PUFA bolsters progeny immunocompetence through enhanced passive immunity and antibody titres against routine vaccination. In conclusion, it appears that chicks may benefit from the incorporation of n-3 PUFA in the breeder diets; however, little attention is paid to fatty acids composition in breeder nutrition. We also highlight gaps in knowledge and future research perspectives.