Institute for Globally Distributed Open Research and Education (IGDORE)

The relationship between Schistosoma mansoni (Sm) and hepatocellular carcinoma (HCC) has been evaluated by many studies that point towards a co-relation between schistosomal infection and HCC. While many such studies demonstrated that Sm infection in the presence of another carcinogenic factors leads to HCC, none of these studies could conclusively prove the cancer-inducing ability of Sm in humans, independent of other carcinogenic factors. The aim of this work is to present the current understanding on the association of Sm with HCC. Many epidemiological, pathological, and clinical studies have shown the role of multiple events like chronic inflammation and fibrosis as well as hepato-toxic agents like soluble egg antigens (SEAs), which help in creating a micro-environment which is suitable for HCC development. The role of Sm infection and deposited eggs in causing persistent inflammation, advanced fibrosis, and the role of SEAs, especially IPSE/alpha-1, is emphasised. This work concludes that Sm infection has the potential to induce cancer independently but the same has not been reported in humans to date. Extensive research is required to establish a causal relationship between Sm infection and HCC induction, or a complete lack thereof. However, Sm infection definitely acts along with other carcinogenic factors to induce HCC at a much faster pace and also leads to an aggressive form of liver cancer, which the other carcinogenic factor could not have achieved alone.

Plain Language Summary The so called reciprocal effects model of academic self-concept and achievement might be wrong In a recent aggregation of findings from several studies, a so called meta-analysis, researchers claimed to have found evidence that academic self-concept (that is, self-perceived academic competence) had an increasing effect on future academic achievement and that academic achievement, likewise, had an increasing effect on future academic self-concept. However, the used method of statistical analysis is known to often deliver defective results. In the present study, we analyzed the same data and found that the data can be claimed to show both an increasing and a decreasing effect of academic self-concept on future academic achievement. Due to these incongruent results, we believe that the claims in the previous meta-analysis lack solid support and can be challenged. There may still exist a correlation between academic self-concept and achievement, but correlations do not prove causal effects. We also carried out simulations, and these showed that results as in the challenged meta-analysis can be observed even without any true increasing effects between academic self-concept and achievement. In the present article, we also present something we call the extended skill development model (ESDM).

We aimed to replicate previous effects of functional magnetic resonance imaging neurofeedback (fMRI-NF) in right inferior frontal cortex (rIFC) on IFC activation during a Stop Task in a larger group of boys with attention-deficit/hyperactivity disorder (ADHD). The present double-blind, randomized controlled trial tested the effects of 15 runs of active versus sham fMRI-NF of rIFC on performance and activation associated with successful and failed inhibition versus Go trials during a tracking Stop task in 88 boys with ADHD (44 active; 44 sham), controlling for age and medication status. No significant group-by-time interaction effects were observed for performance or brain activation during the successful stop trials, and post hoc analysis showed very low numbers of active fMRI-NF learners. Nevertheless, during error monitoring, there was a significant group-by-time interaction effect on post-error reaction time slowing and in left IFC activation, which were both increased after active compared to sham fMRI-NF. The findings are in line with our previous observation of left IFC upregulation after fMRI-NF of rIFC relative to active fMRI-NF of parahippocampal gyrus. This highlights the potentially wider regional effects that fMRI-NF of a particular self-control target region has on other self-regulatory regions in ADHD. This article is part of the theme issue ‘Neurofeedback: new territories and neurocognitive mechanisms of endogenous neuromodulation’.

In this study, we analysed biological pathway diversity among Europeans and Northern Americans of European origin, the groups of people that share a common genetic ancestry but live in different geographic regions. We used a novel complex approach for analysing genomic data: we studied the total effects of multiple weak selection signals, accumulated from independent SNPs within a pathway. We found significant differences between immunity-related biological pathways from the two groups. All identified pathways included genes belonging to the major histocompatibility complex (MHC) system, which plays an important role in adaptive immune responses. We suggest that the ways of evolution were different for the MHC-I and MHC-II gene groups at least in Europeans and Americans of European origin. We hypothesise that the observed variability between the two populations was triggered by selection pressures due to the different pathogen landscapes and pathogen loads on the two continents. Our findings can be important for epidemic prevention and control, as well as for analysing processes related to allergies, organ transplantation, and autoimmune diseases.

An abundance of degrees of freedom (DOF) exist when executing a countermovement jump (CMJ). This research aims to simplify the understanding of this complex system by comparing jump performance and independent functional DOF (fDOF) present in CMJs without (CMJNoArms) and with (CMJArms) an arm swing. Principal component analysis was used on 39 muscle forces and 15 3-dimensional joint contact forces obtained from kinematic and kinetic data, analyzed in FreeBody (a segment-based musculoskeletal model). Jump performance was greater in CMJArms with the increased ground contact time resulting in higher external (p = 0.012), hip (p < 0.001) and ankle (p = 0.009) vertical impulses, and slower hip extension enhancing the proximal-to-distal joint extension strategy. This allowed the hip muscles to generate higher forces and greater time-normalized hip vertical impulse (p = 0.006). Three fDOF were found for the muscle forces and 3-dimensional joint contact forces during CMJNoArms, while four fDOF were present for CMJArms. This suggests that the underlying anatomy provides mechanical constraints during a CMJ, reducing the demand on the control system. The additional fDOF present in CMJArms suggests that the arms are not mechanically coupled with the lower extremity, resulting in additional variation within individual motor strategies.

Background The conceptualisation of autism as a disorder where Theory of Mind (ToM) and pragmatics are fundamentally impaired has prompted a wealth of research on autistic deficits, most of which is characterised by two main assumptions: first, that autistic people would display said deficits, if present, with any conversation partner and in any situation; second, that neurotypical people do not present these deficits, regardless of the conversation partner. However, this is not necessarily reflected in autistic accounts of the way they experience social cognition and pragmatics. Aims The present paper aims to investigate the autistic experience of communication with both autistic and neurotypical people, with a particular focus on their perception of the ability of autistic and neurotypical people to understand their communicative intentions. Methods & Procedures Participants, 23 adult Italian autistic people without intellectual disability or language disorders, were recruited online. Two virtual focus groups of 2 hours each were conducted, transcribed and analysed through thematic analysis with a descriptive phenomenological approach by two independent researchers. Outcomes & Results Six themes were developed from the analysis, the most relevant being Autistic–Autistic communication and Autistic ToM. The results, in line with the Double Empathy theory, suggest there seem to be important differences between neurotypical and autistic people's ToM. These appear to make it easier for autistic people to communicate with one another, as well as to create difficulties for neurotypical people to understand autistic people, not just the other way around. Conclusions & Implications These results seem to confirm that challenges in cross‐neurotype communication are better interpreted as mutual miscomprehension and reciprocal differences in ToM rather than deficits on the autistic part. This calls for a reframing of ToM and/or the need for autistic ToM as a construct, of which neurotypical people seem to be lacking. Moreover, these insights should be taken into account for speech and language therapy and clinical practice in general, advocating for a neurodiversity‐informed view of co‐constructed communication as well as for a broader societal change in which therapists can play a crucial role, through participatory approaches or raising awareness in their daily practice. WHAT THIS PAPER ADDS What is already known on the subject Autism is conceived as characterised by social cognition and communication difficulties, often linked to Theory of Mind (ToM) deficits. However, recent research suggested variations in ToM abilities within the autistic population and proposed alternative theories like the Double Empathy theory. Nevertheless, only a few studies examined how autistic individuals perceive communication across neurotypes. What this study adds Autistic individuals seem to find it easier to communicate with other autistic people, and they identify specific characteristics of neurotypical communication that hinder successful communication. Moreover, neurotypical people are perceived as having difficulties in autistic ToM, which seems to emerge as a relevant and needed construct in light of the Double Empathy problem. What are the clinical implications of this work? These findings can inform speech and language therapy and clinical practice about the potential gains of raising awareness on the Double Empathy problem and the higher communication ease inside the autistic community, alongside individualised support. Participatory approaches and closer collaboration with the autistic community also seem to be crucial for therapists to help improve communication experiences for autistic individuals.

There is such a vast proliferation of scientific theories of consciousness that it is worrying some scholars. There are even competitions to test different theories, and the results are inconclusive. Consciousness research, far from converging toward a unifying framework, is becoming more discordant than ever, especially with respect to theoretical elements that do not have a clear neurobiological basis. Rather than dueling theories, an integration across theories is needed to facilitate a comprehensive view on consciousness and on how normal nervous system dynamics can develop into pathological states. In dealing with what is considered an extremely complex matter, we try to adopt a perspective from which the subject appears in relative simplicity. Grounded in experimental and theoretical observations, we advance an encompassing biophysical theory, MaxCon, which incorporates aspects of several of the main existing neuroscientific consciousness theories, finding convergence points in an attempt to simplify and to understand how cellular collective activity is organized to fulfill the dynamic requirements of the diverse theories our proposal comprises. Moreover, a computable index indicating consciousness level is presented. Derived from the level of description of the interactions among cell networks, our proposal highlights the association of consciousness with maximization of the number of configurations of neural network connections-constrained by neuroanatomy, biophysics and the environment-that is common to all consciousness theories.

Test‐retest reliability—establishing that measurements remain consistent across multiple testing sessions—is critical to measuring, understanding, and predicting individual differences in infant language development. However, previous attempts to establish measurement reliability in infant speech perception tasks are limited, and reliability of frequently used infant measures is largely unknown. The current study investigated the test‐retest reliability of infants’ preference for infant‐directed speech over adult‐directed speech in a large sample ( N = 158) in the context of the ManyBabies1 collaborative research project. Labs were asked to bring in participating infants for a second appointment retesting infants on their preference for infant‐directed speech. This approach allowed us to estimate test‐retest reliability across three different methods used to investigate preferential listening in infancy: the head‐turn preference procedure, central fixation, and eye‐tracking. Overall, we found no consistent evidence of test‐retest reliability in measures of infants’ speech preference (overall r = 0.09, 95% CI [−0.06,0.25]). While increasing the number of trials that infants needed to contribute for inclusion in the analysis revealed a numeric growth in test‐retest reliability, it also considerably reduced the study's effective sample size. Therefore, future research on infant development should take into account that not all experimental measures may be appropriate for assessing individual differences between infants. Research Highlights We assessed test‐retest reliability of infants’ preference for infant‐directed over adult‐directed speech in a large pre‐registered sample ( N = 158). There was no consistent evidence of test‐retest reliability in measures of infants’ speech preference. Applying stricter criteria for the inclusion of participants may lead to higher test‐retest reliability, but at the cost of substantial decreases in sample size. Developmental research relying on stable individual differences should consider the underlying reliability of its measures.

Fault-tolerant operations based on stabilizer codes are the state of the art in suppressing error rates in quantum computations. Most such codes do not permit a straightforward implementation of non-Clifford logical operations, which are necessary to define a universal gate set. As a result, implementations of these operations must use either error-correcting codes with more complicated error correction procedures or gate teleportation and magic states, which are prepared at the logical level, increasing overhead to a degree that precludes near-term implementation. Here, we implement a small quantum algorithm, one-qubit addition, fault-tolerantly on a trapped-ion quantum computer, using the [[ 8 , 3 , 2 ]] color code. By removing unnecessary error correction circuits and using low-overhead techniques for fault-tolerant preparation and measurement, we reduce the number of error-prone two-qubit gates and measurements to 36. We observe arithmetic errors with a rate of ∼1.1 × 10 ⁻³ for the fault-tolerant circuit and ∼9.5 × 10 ⁻³ for the unencoded circuit.

Natural sciences paradigms guide this essay's perspectives. Given the complex-adaptive dynamics of the Earth System, cultures are drivers and prompts of human and natural (sub)systems, respectively. The essay combines geo-philosophical thought and Semiotic Cultural Psychological Theory to depict an ideal-typic narrative of people's sensemaking culture as an intrinsic part of the Earth System. Generic characteristics of marine operations (e.g., mining at the seabed) illustrate the description. The essay claims that human culture is an attribute of the Earth System, i.e., the nexus that ties human socio-cultural domains and planetary technosphere, biosphere and geosphere, and that more-than-humanness is one of the nexus' attributes.

Global warming is leading understory and canopy plant communities of temperate deciduous forests to grow leaves earlier in spring and drop them later in autumn. If understory species extend their leafy seasons less than canopy trees, they will intercept less light. We look for mismatched phenological shifts between canopy and understory in 28 years (1995–2022) of weekly data from Trelease Woods, Urbana, IL, USA. The observations cover 31 herb species of contrasting seasonality (for 1995–2017), three sapling species, and the 15 most dominant canopy tree species for all years, combined with solar radiation, temperature and canopy light transmittance data. We estimate how understory phenology, cold temperatures, canopy phenology, and solar radiation have individually limited understory plants’ potential light interception over >2 decades. Understory and canopy phenology were the two factors most limiting to understory light availability, but which was more limiting varied greatly among species and among/within seasonality groups; solar radiation ranked third and cold fourth. Understory and canopy phenology shifts usually occurred in the same direction; either both strata were early or both were late, offsetting each other’s effects. The four light-limiting factors combined showed significant temporal trends for six understory species, five toward less light interception. Warmer springs were significantly associated with shifts toward more light interception in three sapling species and 19 herb species. Canopy phenology became more limiting in warmer years for all three saplings species and 31 herb species. However, in aggregate, these variables mostly offset one another; only one sapling and seven herb species showed overall significant (and negative) relationships between light interception and spring temperature. The few understory species mismatched with canopy phenology due to changing climate are likely to intercept less light in future warmer years. The few species with data for carbon assimilation show broadly similar patterns to light interception.

High Frequency Impulse for Microgravity (HIFIm) is an exercise countermeasure that is designed to minimize force and vibration transmission to the spacecraft during exercise without the need for an additional VIS. The purpose of this study was to evaluate the effectiveness of HIFIm in mitigating force transmission in microgravity during parabolic flight. Force between HIFIm and the aircraft was measured using a custom-made arrangement of load cells during repeated jumping by two participants. Mean peak force transmission to the aircraft was 4.79 ± 0.68 N.kg− 1. In addition, the frequency spectra for the upper and lower fixations to the aircraft were within the envelope of what is permissible for an exercise countermeasure on Gateway. These data support the design concept of HIFIm and suggest that HIFIm could be installed in a space habitat with no, or minimal, additional VIS. Measuring the force and vibration transmission of exercise countermeasures in microgravity during parabolic flight is highly challenging due to the safety constraints of the experimental platform and the extreme changes in acceleration (from 0 to 1.8 g). The fact that this performance can be directly measured for HIFIm is a key advantage. The results presented here add to the mounting evidence that HIFIm is the future of exercise countermeasures.

In a sample of Italian adolescents (N = 754) and their parents (N = 469), we examined the levels of essentialist beliefs about nationality, the extent to which adolescents’ beliefs were shaped by parental beliefs and classroom ethnic diversity, and the implications of essentialist beliefs for attitudes and behaviors toward national outgroups as well as for intergenerational transmission of prejudice. Results of path analyses showed that adolescents who had parents higher in essentialism and who attended less diverse classrooms expressed higher levels of essentialism. Adolescents and parents with higher levels of essentialism expressed higher levels of anti-immigrant prejudice and fewer friendships with immigrants. In addition, parent-adolescent concordance in essentialism partly explained intergenerational similarity in prejudice. These findings offer preliminary support for working with youth’s essentialist beliefs as a means to counteract the development of prejudice.

Suicide-related media content has preventive or harmful effects depending on the specific content. Proactive media screening for suicide prevention is hampered by the scarcity of machine learning approaches to detect specific characteristics in news reports. This study applied machine learning to label large quantities of broadcast (TV and radio) media data according to media recommendations reporting suicide. We manually labeled 2519 English transcripts from 44 broadcast sources in Oregon and Washington, USA, published between April 2019 and March 2020. We conducted a content analysis of media reports regarding content characteristics. We trained a benchmark of machine learning models including a majority classifier, approaches based on word frequency (TF-IDF with a linear SVM) and a deep learning model (BERT). We applied these models to a selection of more simple (e.g., focus on a suicide death), and subsequently to putatively more complex tasks (e.g., determining the main focus of a text from 14 categories). Tf-idf with SVM and BERT were clearly better than the naive majority classifier for all characteristics. In a test dataset not used during model training, F1-scores (i.e., the harmonic mean of precision and recall) ranged from 0.90 for celebrity suicide down to 0.58 for the identification of the main focus of the media item. Model performance depended strongly on the number of training samples available, and much less on assumed difficulty of the classification task. This study demonstrates that machine learning models can achieve very satisfactory results for classifying suicide-related broadcast media content, including multi-class characteristics, as long as enough training samples are available. The developed models enable future large-scale screening and investigations of broadcast media.

Repeated jumping has been demonstrated as a feasible exercise countermeasure in microgravity and has been shown to reduce deconditioning in head down bed rest studies. However, varying landing stiffness may provide greater contribution of both axial and medio-lateral bone strain and muscle loading at greater muscle lengths, which may help minimize bone and muscle deconditioning. Therefore, this study investigated the effect of different landing styles on the force profile and ground contact time during repeated jumping using HIFIm in microgravity. Two participants performed repeated jumping on the HIFIm jump sled in microgravity during a parabolic flight campaign. ‘Ground’ forces and ground contact time were compared between landing styles where increased landing stiffness was instructed to the jumper, and increased spring resistance. The results show that the forces experienced when performing repeated jumps in microgravity are sensitive to the landing style employed. As greater stiffness was instructed, peak forces increased, and ground contact time decreased significantly. Peak forces and ground contact time also significantly increased when spring resistance increased. These results highlight that landing instructions and spring configurations could be used as training variables when developing an astronaut training program, which can use different jump styles to minimize bone and muscle deconditioning. Further research using bed rest analogs and repeated jumping using HIFIm is needed to demonstrate varied repeated jumping interventions as an effective exercise method for minimizing deconditioning in astronauts.

With growing recognition and acknowledgement of the genuine complexity of proteomes, we are finally entering the post-proteogenomic era. Routine assessment of proteomes as inferred correlates of gene sequences (i.e., canonical ‘proteins’) cannot provide the necessary critical analysis of systems-level biology that is needed to understand underlying molecular mechanisms and pathways or identify the most selective biomarkers and therapeutic targets. These critical requirements demand the analysis of proteomes at the level of proteoforms/protein species, the actual active molecular players. Currently, only highly refined integrated or integrative top-down proteomics (iTDP) enables the analytical depth necessary to provide routine, comprehensive, and quantitative proteome assessments across the widest range of proteoforms inherent to native systems. Here we provide a broad perspective of the field, taking in historical and current realities, to establish a more balanced understanding of where the field has come from (in particular during the ten years since Proteomes was launched), current issues, and how things likely need to proceed if necessary deep proteome analyses are to succeed. We base this in our firm belief that the best proteomic analyses reflect, as closely as possible, the native sample at the moment of sampling. We also seek to emphasise that this and future analytical approaches are likely best based on the broad recognition and exploitation of the complementarity of currently successful approaches. This also emphasises the need to continuously evaluate and further optimize established approaches, to avoid complacency in thinking and expectations but also to promote the critical and careful development and introduction of new approaches, most notably those that address proteoforms. Above all, we wish to emphasise that a rigorous focus on analytical quality must override current thinking that largely values analytical speed; the latter would certainly be nice, if only proteoforms could thus be effectively, routinely, and quantitatively assessed. Alas, proteomes are composed of proteoforms, not molecular species that can be amplified or that directly mirror genes (i.e., ‘canonical’). The problem is hard, and we must accept and address it as such, but the payoff in playing this longer game of rigorous deep proteome analyses is the promise of far more selective biomarkers, drug targets, and truly personalised or even individualised medicine.

Python for Population Genomics (PyPop) is a software package that processes genotype and allele data and performs large-scale population genetic analyses on highly polymorphic multi-locus genotype data. In particular, PyPop tests data conformity to Hardy-Weinberg equilibrium expectations, performs Ewens-Watterson tests for selection, estimates haplotype frequencies, measures linkage disequilibrium, and tests significance. Standardized means of performing these tests is key for contemporary studies of evolutionary biology and population genetics, and these tests are central to genetic studies of disease association as well. Here, we present PyPop 1.0.0, a new major release of the package, which implements new features using the more robust infrastructure of GitHub, and is distributed via the industry-standard Python Package Index. New features include implementation of the asymmetric linkage disequilibrium measures and, of particular interest to the immunogenetics research communities, support for modern nomenclature, including colon-delimited allele names, and improvements to meta-analysis features for aggregating outputs for multiple populations. Code available at: https://zenodo.org/records/10080668 and https://github.com/alexlancaster/pypop