Miracle-dz/UniFAR-FTUs huggingface dataset:
Giving Up on Consciousness as the Ghost in the Machine

Consciousness as used here, refers to the private, subjective experience of being aware of our perceptions, thoughts, feelings, actions, memories (psychological contents) including the intimate experience of a unified self with the capacity to generate and control actions and psychological contents. This compelling, intuitive consciousness-centric account has, and continues to shape folk and scientific accounts of psychology and human behavior. Over the last 30 years, research from the cognitive neurosciences has challenged this intuitive social construct account when providing a neurocognitive architecture for a human psychology. Growing evidence suggests that the executive functions typically attributed to the experience of consciousness are carried out competently, backstage and outside subjective awareness by a myriad of fast, efficient non-conscious brain systems. While it remains unclear how and where the experience of consciousness is generated in the brain, we suggested that the traditional intuitive explanation that consciousness is causally efficacious is wrong-headed when providing a cognitive neuroscientific account of human psychology. Notwithstanding the compelling 1st-person experience (inside view) that convinces us that subjective awareness is the mental curator of our actions and thoughts, we argue that the best framework for building a scientific account is to be consistent with the biophysical causal dependency of prior neural processes. From a 3rd person perspective, (outside view), we propose that subjective awareness lacking causal influence, is (no more) than our experience of being aware, our awareness of our psychological content, knowing that we are aware, and the belief that that such experiences are evidence of an agentive capacity shared by others. While the human mind can be described as comprising both conscious and nonconscious aspects, both ultimately depend on neural process in the brain. In arguing for the counter-intuitive epiphenomenal perspective, we suggest that a scientific approach considers all mental aspects of mind including consciousness in terms of their underlying, preceding (causal) biological changes, in the realization that most brain processes are not accompanied by any discernible change in subjective awareness.
Neurophysiological Synchrony Between Children With Severe Physical Disabilities and Their Parents During Music Therapy

Although physiological synchronization has been associated with the level of empathy in emotionally meaningful relationships, little is known about the interbrain synchrony between non-speaking children with severe disabilities and their familial caregivers. In a repeated measures observational study, we ascertained the degree of interbrain synchrony during music therapy in 10 child-parent dyads, where the children were non-speaking and living with severe motor impairments. Interbrain synchrony was quantified via measurements of spectral coherence and Granger causality between child and parent electroencephalographic (EEG) signals collected during ten 15-min music therapy sessions per dyad, where parents were present as non-participating, covert observers. Using cluster-based permutation tests, we found significant child-parent interbrain synchrony, manifesting most prominently across dyads in frontal brain regions within β and low γ frequencies. Specifically, significant dyadic coherence was observed contra-laterally, between child frontal right and parental frontal left regions at β and lower γ bands in empathy-related brain areas. Furthermore, significant Granger influences were detected bidirectionally (from child to parent and vice versa) in the same frequency bands. In all dyads, significant increases in session-specific coherence and Granger influences were observed over the time course of a music therapy session. The observed interbrain synchrony suggests a cognitive-emotional coupling during music therapy between child and parent that is responsive to change. These findings encourage further study of the socio-empathic capacity and interpersonal relationships formed between caregivers and non-speaking children with severe physical impairments.
Differential Mutation Detection Capability Through Capture-Based Targeted Sequencing in Plasma Samples in Hepatocellular Carcinoma

Circulating tumor DNA (ctDNA) is a promising biomarker for accurate monitoring and less invasive assessment of tumor burden and treatment response. Here, targeted next-generation sequencing (NGS) with a designed gene panel of 176 cancer-relevant genes was used to assess mutations in 90 ctDNA samples from 90 patients with multiple types of liver disease and 10 healthy donor samples for control. Using our ctDNA detection panel, we identified mutations in 98.89% (89/90) of patient plasma biopsy samples, and 19 coding variants located in 10 cancer-related genes [ACVR2A, PCLO, TBCK, adhesion G protein-coupled receptor (ADGRV1), COL1A1, GABBR1, MUC16, MAGEC1, FASLG, and JAK1] were identified in 96.7% of patients (87/90). The 10 top mutated genes were tumor protein p53 (TP53), ACVR2A, ADGRV1, MUC16, TBCK, PCLO, COL11A1, titin (TTN), DNAH9, and GABBR1. TTN and TP53 and TTN and DNAH9 mutations tended to occur together in hepatocellular carcinoma samples. Most importantly, we found that most of those variants were insertions (frameshift insertions) and deletions (frameshift deletions and in-frame deletions), such as insertion variants in ACVR2A, PCLO, and TBCK; such mutations were detected in almost 95% of patients. Our study demonstrated that the targeted NGS-based ctDNA mutation profiling was a useful tool for hepatocellular carcinoma (HCC) monitoring and could potentially be used to guide treatment decisions in HCC.
Periodontitis Is Associated With Risk of Conventional Stent Restenosis: Pilot Case-Control Study

Objectives: Percutaneous coronary angioplasty with stent implantation has been established as the main form of treatment of atherosclerosis. However, 16 to 44% of patients may evolve with stent restenosis. Periodontitis is an inflammatory condition associated with bacterial infection, that may lead to periodontal tissue destruction and tooth loss. This study aimed to evaluate the association between stent restenosis and periodontitis. Materials and Methods: Coronary angiography exams presenting stent imaging with and without restenosis were analyzed. Patients meeting the inclusion and exclusion criteria were selected and allocated in 2 groups: case (restenosis) and control (without restenosis). We evaluated if systemic and periodontal variables were predictors of restenosis (primary outcome) using a multivariable stepwise logistic regression. Additionally, we compared clinical and periodontal conditions between the control and case groups (secondary outcomes) using Chi-square test and ANOVA test. Results: Data from 49 patients (case n = 15; control n = 34) were analyzed. The results showed that stages III and IV periodontitis and lack of physical activity were significant predictors of stent restenosis (OR 5.82 and 5.98, respectively). Comparisons regarding the diagnosis of periodontal conditions between control and case groups did not present significant differences in the incidence of periodontitis and alveolar bone loss. Conclusion: Stages III and IV periodontitis increased the incidence of stent restenosis. These findings suggest that advanced stages of periodontal disease might lead to the occurrence of negative outcomes after coronary angioplasty with stent placement.
A Flow Cytometry-Based Serological Assay to Detect Visceral Leishmaniasis in HIV-Infected Patients

Visceral Leishmaniasis (VL) is a severe parasitic disease that has emerged as an important opportunistic condition in HIV-infected patients and whose control is impaired by inaccurate identification. This is mainly due to the serological tests used for VL having a reduced performance in cases of VL-HIV coinfection due to a low humoral response. In this situation, however, a positive test has even greater diagnostic value when combined with the clinical status. This study aimed to evaluate the application and performance of flow cytometry to detect anti-Leishmania infantum antibodies in HIV-infected patients. Sera from VL/HIV coinfected patients, characterized using “gold standard” techniques, were compared with sera from healthy controls plus sera from HIV-infected individuals. The flow cytometry results were expressed as levels of IgG reactivity, based on the percentage of positive fluorescent parasites (PPFP). A ROC curve analysis of a serum titration indicated a PPFP of 1.26% as being the cutoff point to segregate positive and negative results. At the 1:2,048 dilution, with 89% sensitivity and 83% specificity, flow cytometry showed greater sensitivity in relation to the serological tests evaluated. Futhermore, flow cytometry was the only assay that positively identified all VL-HIV patients with quantified HIV load. Together, these findings suggest that flow cytometry may be used as an alternative serological approach for VL identification and as a tool to characterize the humoral response against Leishmania infantum in HIV-infected patients.
Rotational and translational motions of n-nonadecane in the urea inclusion compound as evidenced by incoherent quasielastic neutron scattering

Incoherent quasielastic neutron scattering (IQNS) experiments have been performed on semi-oriented samples of n-nonadecane/urea-d4. Using two experimental geometries, we were able to show that large amplitude translations of the hydrocarbon chains in the c direction as well as rotations about the main molecular axis are effective in the high temperature disordered phase of the compound. In this paper, we have elaborated a phenomenological model in order to analyze quantitatively and separately the translations and rotations of the n-nonadecane molecules included in the urea channels. Our IQNS results are discussed and compared to literature data.
Habitat Quality Determines Dispersal Decisions and Fitness in a Beetle – Fungus Mutualism

Delayed dispersal of sexually mature offspring is a fundamental component of cooperative breeding. In ambrosia beetles, female offspring temporarily remain in their natal nest and refrain from reproduction, instead investing in alloparental care. Previous work has demonstrated a link between helping behaviour and the increased need for pathogen defence, arising from their close association with fungal cultivars. In the ambrosia beetle Xyleborinus saxesenii, mature female offspring can effectively fight pathogen infections and manage the microbial composition within the nest by adjusting the frequency of different hygienic and nest maintenance behaviours. This suggests a potential to respond flexibly to the ecology of their nest, which calls for a better understanding of the connection between behaviour and the microbial community thriving within their nests. Here, we studied the significance of the mutualistic fungus garden composition for the beetles’ nest ecology and fitness by experimentally varying substrate quality. We found that the vertically transmitted ambrosia fungus garden is composed of at least two fungus mutualist species and a wide variety of other microbes varying in their relative abundance. This is strongly affected by the moisture content of the substrate, which in nature depends on the age and type of wood. We found that the mutualist fungi complement each other in terms of dryness-resistance, allowing the beetles to utilise a broad range of substrates over prolonged time during which the wood gradually desiccates. Under suboptimal humidity conditions, the interaction between host and multiple fungus species has important ramifications for the behaviour of philopatric helpers, including their alloparental investment, sibling cannibalism and the timing of dispersal. Rearing five generations of beetles consecutively in dry substrate resulted in transgenerational effects on philopatry and alloparental care, probably mediated through the dominance of a particular fungus species that was driven by the experimental habitat condition. Interestingly, the nests of these selection lines produced much more offspring after five generations than any first-generation nest, which may have reflected increased egg laying by non-dispersing daughters. Our study highlights the importance of considering the interactions between the microbial community and their insect hosts for understanding social evolution in cooperatively breeding beetles.
Increasing Incidences and Clonal Diversity of Methicillin-Resistant Staphylococcus aureus in the Nordic Countries - Results From the Nordic MRSA Surveillance

Methicillin-resistant Staphylococcus aureus (MRSA) is notifiable in Denmark, Finland, Iceland, Norway and Sweden. The prevalence of MRSA in this region has been low for many years, but all five countries experience increasing numbers of new cases. The aim of the study was to describe the molecular epidemiology in the Nordic countries 2009-2016. Numbers of new cases of MRSA from 1997 to 2016 were compared, and a database containing information on spa-type and place of residence or acquisition, for all new MRSA isolates from 2009 to 2016 was established. A website was developed to visualize the geographic distribution of the spa-types. The incidence of new MRSA cases increased in all Nordic countries with Denmark having 61.8 new cases per 100,000 inhabitants in 2016 as the highest. The number of new cases 2009 to 2016 was 60,984. spa-typing revealed a high genetic diversity, with a total of 2,344 different spa-types identified. The majority of these spa-types (N = 2,017) were found in 1-10 cases. The most common spa-types t127/CC1, t223/CC22, and t304/CC6:8 increased significantly in all Nordic countries during the study period, except for Iceland, while spa-type t002/CC5 decreased in the same four countries. The trends of other common spa-types were different in each of the Nordic countries. The Nordic countries were shown to share similar trends but also to have country-specific characteristics in their MRSA populations. A continued increasing numbers of MRSA will challenge the surveillance economically. A more selected molecular surveillance will probably have to be employed in the future.
In the Wrong Place at the Wrong Time: Identifying Spatiotemporal Co-occurrence of Bycaught Common Dolphins and Fisheries in the Bay of Biscay (NE Atlantic) From 2010 to 2019

The first Unusual Mortality Event (UME) related to fishing activity along the Atlantic coast recorded by the French Stranding Network was in 1989: 697 small delphinids, mostly common dolphins, washed ashore, most of them with evidence of having been bycaught. Since then, UMEs of common dolphins have been observed nearly every year in the Bay of Biscay; unprecedented records were broken every year since 2016. The low and unequally distributed observation efforts aboard fishing vessels in the Bay of Biscay, as well as the lack of data on foreign fisheries necessitated the use of complementary data (such as stranding data) to elucidate the involvement of fisheries in dolphin bycatch. The aim of this work was to identify positive spatial and temporal correlations between the likely origins of bycaught stranded common dolphins (estimated from a mechanistic drift model) and fishing effort statistics inferred from Vessel Monitoring System (VMS) data on vessels >12 m long. Fisheries whose effort correlated positively with dolphin mortality areas after 2016 included French midwater trawlers, French Danish seiners, French gillnetters, French trammel netters, Spanish bottom trawlers, and Spanish gillnetters. For the French fleet only, logbook declarations, sales, and surveys carried out by Ifremer were integrated into fishing effort data. Six fleets were active in common dolphin bycatch areas at least twice between 2016 and 2019: gillnetters fishing hake, trammel netters fishing anglerfish, bottom pair trawlers fishing hake, midwater pair trawlers fishing sea bass and hake, and Danish seiners fishing whiting. Except for changes in hake landings in some fisheries, there were no notable changes in total fishing effort practice (gear or target species) based on the data required by the ICES and Council of the European Union that could explain the large increase in stranded common dolphins recorded along the French Atlantic coast after 2016. Small scale or unrecorded changes could have modified interactions between common dolphins and fisheries, but could not be detected through mandatory data-calls. The recent increase in strandings of bycaught common dolphins could have been caused by changes in their distribution and/or ecology, or changes in fishery practices that were undetectable through available data.
Identification of Hub Genes and Their Correlation With Immune Infiltration Cells in Hepatocellular Carcinoma Based on GEO and TCGA Databases

Hepatocellular carcinoma (HCC) is a primary liver cancer with extremely high mortality in worldwide. HCC is hard to diagnose and has a poor prognosis due to the less understanding of the molecular pathological mechanisms and the regulation mechanism on immune cell infiltration during hepatocarcinogenesis. Herein, by performing multiple bioinformatics analysis methods, including the RobustRankAggreg (RRA) rank analysis, weighted gene co-expression network analysis (WGCNA), and a devolution algorithm (CIBERSORT), we first identified 14 hub genes (NDC80, DLGAP5, BUB1B, KIF20A, KIF2C, KIF11, NCAPG, NUSAP1, PBK, ASPM, FOXM1, TPX2, UBE2C, and PRC1) in HCC, whose expression levels were significantly up-regulated and negatively correlated with overall survival time. Moreover, we found that the expression of these hub genes was significantly positively correlated with immune infiltration cells, including regulatory T cells (Treg), T follicular helper (TFH) cells, macrophages M0, but negatively correlated with immune infiltration cells including monocytes. Among these hub genes, KIF2C and UBE2C showed the most significant correlation and were associated with immune cell infiltration in HCC, which was speculated as the potential prognostic biomarker for guiding immunotherapy.
Model Based Evaluation of Hypersensitivity Adverse Drug Reactions to Antimicrobial Agents in Children

Drug use in children is–in most cases–supported by extrapolation of data generated from clinical trials in adult populations. This puts children at higher risk of developing adverse drug reactions (ADRs) due to “off-label” use of drugs and dosing issues. Major types of ADRs are drug hypersensitivity reactions, an idiosyncratic type of ADRs that are largely unpredictable and can cause high morbidity and mortality in a hard-to-identify specific population of patients. Lack of a complete understanding of the pathophysiology of DHRs and their unpredictive nature make them problematic in clinical practice and in drug development. In addition, ethical and legal obstacles hinder conducting large clinical trials in children, which in turn make children a “therapeutic orphan” where clear clinical guidelines are lacking, and practice is based largely on the personal experience of the clinician, hence making modeling desirable. This brief review summarizes the current knowledge of model-based evaluation of diagnosis and management of drug hypersensitivity reactions (DHRs) to antimicrobial drugs in the pediatric population. Ethical and legal aspects of drug research in children and the effect of different stages of child development and other factors on the risk of DHRs are discussed. The role of animal models, in vitro models and oral provocation test in management of DHRs are examined in the context of the current understanding of the pathophysiology of DHRs. Finally, recent changes in drug development legislations have been put forward to encourage drug developers to conduct trials in children clearly indicate the urgent need for evidence to support drug safety in children and for modeling to guide these clinical trials.
The Carbon-Sulfur Link in the Remineralization of Organic Carbon in Surface Sediments

Here we present the carbon isotopic composition of dissolved inorganic carbon (DIC) and the sulfur isotopic composition of sulfate, along with changes in sulfate concentrations, of the pore fluid collected from a series of sediment cores located along a depth transect on the Iberian Margin. We use these data to explore the coupling of microbial sulfate reduction (MSR) to organic carbon oxidation in the uppermost (up to nine meters) sediment. We argue that the combined use of the carbon and sulfur isotopic composition, of DIC and sulfate respectively, in sedimentary pore fluids, viewed through a δ13CDIC vs. δ34SSO4 cross plot, reveals significant insight into the nature of carbon-sulfur coupling in marine sedimentary pore fluids on continental margins. Our data show systemic changes in the carbon and sulfur isotopic composition of DIC and sulfate (respectively) where, at all sites, the carbon isotopic composition of the DIC decreases before the sulfur isotopic composition of sulfate increases. We compare our results to global data and show that this behavior persists over a range of sediment types, locations and water depths. We use a reactive-transport model to show how changes in the amount of DIC in seawater, the carbon isotopic composition of organic matter, the amount of organic carbon oxidation by early diagenetic reactions, and the presence and source of methane influence the carbon and sulfur isotopic composition of sedimentary pore fluids and the shape of the δ13CDIC vs. δ34SSO4 cross plot. The δ13C of the DIC released during sulfate reduction and sulfate-driven anaerobic oxidation of methane is a major control on the minimum δ13CDIC value in the δ13CDIC vs. δ34SSO4 cross plot, with the δ13C of the organic carbon being important during both MSR and combined sulfate reduction, sulfate-driven AOM and methanogenesis.
Boreal Agriculture Cannot Be Sustainable Without Food Sovereignty

Food sovereignty encompasses the right of humans to have access to, and to produce, healthy and culturally appropriate food. Food sovereignty exists within the “social” pillar of sustainability and sustainable food production. Over time, and as a result of colonialism and neo-liberal food regimes, Indigenous food system patterns in boreal regions have been disrupted. Imports make local food production economically infeasible. The intersection of food sovereignty and international trade is understudied. Food insecurity cycles are likely to perpetuate without deliberate action and government intervention. Policies that facilitate local access, and ownership, of agriculture and food processing facilities may foster food sovereignty. Indigenous community governance, and agricultural practices, are critical to restoring environmental and social sustainability.