Miracle-dz/UniFAR-FTUs huggingface dataset:
Self-Organization and Information Processing: From Basic Enzymatic Activities to Complex Adaptive Cellular Behavior

One of the main aims of current biology is to understand the origin of the molecular organization that underlies the complex dynamic architecture of cellular life. Here, we present an overview of the main sources of biomolecular order and complexity spanning from the most elementary levels of molecular activity to the emergence of cellular systemic behaviors. First, we have addressed the dissipative self-organization, the principal source of molecular order in the cell. Intensive studies over the last four decades have demonstrated that self-organization is central to understand enzyme activity under cellular conditions, functional coordination between enzymatic reactions, the emergence of dissipative metabolic networks (DMN), and molecular rhythms. The second fundamental source of order is molecular information processing. Studies on effective connectivity based on transfer entropy (TE) have made possible the quantification in bits of biomolecular information flows in DMN. This information processing enables efficient self-regulatory control of metabolism. As a consequence of both main sources of order, systemic functional structures emerge in the cell; in fact, quantitative analyses with DMN have revealed that the basic units of life display a global enzymatic structure that seems to be an essential characteristic of the systemic functional metabolism. This global metabolic structure has been verified experimentally in both prokaryotic and eukaryotic cells. Here, we also discuss how the study of systemic DMN, using Artificial Intelligence and advanced tools of Statistic Mechanics, has shown the emergence of Hopfield-like dynamics characterized by exhibiting associative memory. We have recently confirmed this thesis by testing associative conditioning behavior in individual amoeba cells. In these Pavlovian-like experiments, several hundreds of cells could learn new systemic migratory behaviors and remember them over long periods relative to their cell cycle, forgetting them later. Such associative process seems to correspond to an epigenetic memory. The cellular capacity of learning new adaptive systemic behaviors represents a fundamental evolutionary mechanism for cell adaptation.
The Impact of SARS-COVID-19 Outbreak on European Cities Urban Mobility

The global outbreak of the SARS-COVID-19 pandemic has changed our lives, driving an unprecedented transformation of our habits. In response, the authorities have enforced several measures, including social distancing and travel restrictions that lead to the temporary closure of activities centered around schools, companies, local businesses to those pertaining to the recreation category. As such, with a mobility reduction, the life of our cities during the outbreak changed significantly. In this paper, we aim at drawing attention to this problem and perform an analysis for multiple cities through crowdsensed information available from datasets such as Apple Maps, to shed light on the changes undergone during both the outbreak and the recovery. Specifically, we exploit data characterizing many mobility modes like driving, walking, and transit. With the use of Gaussian Processes and clustering techniques, we uncover patterns of similarity between the major European cities. Further, we perform a prediction analysis that permits forecasting the trend of the recovery process and exposes the deviation of each city from the trend of the cluster. Our results unveil that clusters are not typically formed by cities with geographical ties, but rather on the spread of the infection, lockdown measures, and citizens’ reactions.
Breath-Hold Diving – The Physiology of Diving Deep and Returning

Breath-hold diving involves highly integrative physiology and extreme responses to both exercise and asphyxia during progressive elevations in hydrostatic pressure. With astonishing depth records exceeding 100 m, and up to 214 m on a single breath, the human capacity for deep breath-hold diving continues to refute expectations. The physiological challenges and responses occurring during a deep dive highlight the coordinated interplay of oxygen conservation, exercise economy, and hyperbaric management. In this review, the physiology of deep diving is portrayed as it occurs across the phases of a dive: the first 20 m; passive descent; maximal depth; ascent; last 10 m, and surfacing. The acute risks of diving (i.e., pulmonary barotrauma, nitrogen narcosis, and decompression sickness) and the potential long-term medical consequences to breath-hold diving are summarized, and an emphasis on future areas of research of this unique field of physiological adaptation are provided.
Microbial Community Interactions Are Sensitive to Small Changes in Temperature

Microbial communities are essential for human and environmental health, often forming complex interaction networks responsible for driving ecosystem processes affecting their local environment and their hosts. Disturbances of these communities can lead to loss of interactions and thereby important ecosystem functionality. The research on what drives interactions in microbial communities is still in its infancy, and much information has been gained from the study of model communities. One purpose of using these model microbial communities is that they can be cultured under controlled conditions. Yet, it is not well known how fluctuations of abiotic factors such as temperature affect their interaction networks. In this work, we have studied the effect of temperature on interactions between the members of the model community THOR, which consists of three bacterial species: Pseudomonas koreensis, Flavobacterium johnsoniae, and Bacillus cereus. Our results show that the community-intrinsic properties resulting from their interspecies interactions are highly dependent on incubation temperature. We also found that THOR biofilms had remarkably different abundances of their members when grown at 11, 18, and 25°C. The results suggest that the sensitivity of community interactions to changes in temperature is influenced, but not completely dictated, by different growth rates of the individual members at different temperatures. Our findings likely extend to other microbial communities and environmental parameters. Thus, temperature could affect community stability and may influence diverse processes including soil productivity, bioprocessing, and disease suppression. Moreover, to establish reproducibility between laboratories working with microbial model communities, it is crucial to ensure experimental stability, including carefully managed temperature conditions.
Accurate Prediction of Prognosis by Integrating Clinical and Molecular Characteristics in Colon Cancer

Various factors affect the prognosis of patients with colon cancer. Complicated factors are found to be conducive to accurate assessment of prognosis. In this study, we developed a series of prognostic prediction models for survival time of colon cancer patients after surgery. Analysis of nine clinical characteristics showed that the most important factor was the positive lymph node ratio (LNR). High LNR was the most important clinical factor affecting 1- and 3-year survival; M0&age < 70 was the most important feature for 5 years. The performance of the model was improved through the integration of clinical characteristics and four types of molecule features (mRNA, lncRNA, miRNA, DNA methylation). The model provides guidance for clinical practice. According to the high-risk molecular features combined with age ≥ 70&T3, poorly differentiated or undifferentiated, M0&well differentiated, M0&T2, LNR high, T4&poorly differentiated, or undifferentiated, the survival time may be less than 1 year; for patients with high risk of molecular features combined with M0&T2, M0&T4, LNR 0& M0, LNR median &T3, and LNR high, the survival is predicted less than 3 years; and the survival of patients with M1&T3, M0 and high risk molecular features is less than 5 years. Using multidimensional and complex patient information, this study establishes potential criteria for clinicians to evaluate the survival of patients for colon cancer.
Retinal Ganglion Cells—Diversity of Cell Types and Clinical Relevance

Retinal ganglion cells (RGCs) are the bridging neurons that connect the retinal input to the visual processing centres within the central nervous system. There is a remarkable diversity of RGCs and the various subtypes have unique morphological features, distinct functions, and characteristic pathways linking the inner retina to the relevant brain areas. A number of psychophysical and electrophysiological tests have been refined to investigate this large and varied population of RGCs. Technological advances, such as high-resolution optical coherence tomography imaging, have provided additional tools to define the pattern of RGC involvement and the chronological sequence of events in both inherited and acquired optic neuropathies. The mechanistic insights gained from these studies, in particular the selective vulnerability and relative resilience of particular RGC subtypes, are of fundamental importance as they are directly relevant to the development of targeted therapies for these invariably progressive blinding diseases. This review provides a comprehensive description of the various types of RGCs, the developments in proposed methods of classification, and the current gaps in our knowledge of how these RGCs are differentially affected depending on the underlying aetiology. The synthesis of the current body of knowledge on the diversity of RGCs and the pathways that are potentially amenable to therapeutic modulation will hopefully lead to much needed effective treatments for patients with optic neuropathies.
Value Associations Modulate Visual Attention and Response Selection

Every day, we are confronted with a vast amount of information that all competes for our attention. Some of this information might be associated with rewards (e.g., gambling) or losses (e.g., insurances). To what extent such information, even if irrelevant for our current task, not only attracts attention but also affects our actions is still a topic under examination. To address this issue, we applied a new experimental paradigm that combines visual search and a spatial compatibility task. Although colored stimuli did not modulate the spatial compatibility effect more than gray stimuli, we found clear evidence that reward and loss associations attenuated this effect, presumably by affecting attention and response selection. Moreover, there are hints that differences in these associations are also reflected in a modulation of the spatial compatibility effect. We discuss theoretical implications of our results with respect to the influences of color, reward, and loss association on selective attention and response selection.
The Psychometric Properties of the Resilience Scale (RS-14) in Lithuanian Adolescents

In the current study, we provided the evidence of satisfactory validity of the RS-14 scale in the Lithuanian adolescents’ sample (N = 1299; Mage = 14.24; SDage = 1.26), based on its internal structure, and relations to other variables. The results of the study indicated an acceptable model fit for a single-factor structure of the scale with a high internal consistency (McDonald’s omega = 0.89). We also confirmed the scalar measurement invariance across groups of adolescents in terms of their age (i.e., early and middle adolescence) and mental health profile as well as partial scalar gender invariance. Adolescents characterized by high levels of socio-emotional problems reported lower levels of resilience, in comparison to adolescents that reported low levels of socio-emotional problems. However, the data indicated that adolescents from emotional problems and behavioral problems groups cannot be differentiated with the RS-14 scale.
Global Advances in Tomato Virome Research: Current Status and the Impact of High-Throughput Sequencing

Viruses cause a big fraction of economically important diseases in major crops, including tomato. In the past decade (2011–2020), many emerging or re-emerging tomato-infecting viruses were reported worldwide. In this period, 45 novel viral species were identified in tomato, 14 of which were discovered using high-throughput sequencing (HTS). In this review, we first discuss the role of HTS in these discoveries and its general impact on tomato virome research. We observed that the rate of tomato virus discovery is accelerating in the past few years due to the use of HTS. However, the extent of the post-discovery characterization of viruses is lagging behind and is greater for economically devastating viruses, such as the recently emerged tomato brown rugose fruit virus. Moreover, many known viruses still cause significant economic damages to tomato production. The review of databases and literature revealed at least 312 virus, satellite virus, or viroid species (in 22 families and 39 genera) associated with tomato, which is likely the highest number recorded for any plant. Among those, here, we summarize the current knowledge on the biology, global distribution, and epidemiology of the most important species. Increasing knowledge on tomato virome and employment of HTS to also study viromes of surrounding wild plants and environmental samples are bringing new insights into the understanding of epidemiology and ecology of tomato-infecting viruses and can, in the future, facilitate virus disease forecasting and prevention of virus disease outbreaks in tomato.
The Abnormal Functional Connectivity in the Locus Coeruleus-Norepinephrine System Associated With Anxiety Symptom in Chronic Insomnia Disorder

Background Mental syndromes such as anxiety and depression are common comorbidities in patients with chronic insomnia disorder (CID). The locus coeruleus noradrenergic (LC-NE) system is considered to be crucial for modulation of emotion and sleep/wake cycle. LC-NE system is also a critical mediator of the stress-induced anxiety. However, whether the LC-NE system contributes to the underlying mechanism linking insomnia and these comorbidities remain unclear. This study aimed to investigate the LC-NE system alterations in patients with insomnia and its relationship with depression and anxiety symptoms. Materials and Methods Seventy patients with CID and 63 matched good sleep control (GSC) subjects were recruited and underwent resting-state functional MRI scan. LC-NE functional network was constructed by using seed-based functional connectivity (FC) analysis. The alterations in LC-NE FC network in patients with CID and their clinical significance was explored. Results Compared with GSC group, the CID group showed decreased left LC-NE FC in the left inferior frontal gyrus, while they had increased LC-NE FC in the left supramarginal gyrus and the left middle occipital gyrus (MOG). For the right LC-NE FC network, decreased FC was found in left dorsal anterior cingulate cortex (dACC). Interesting, the increased LC-NE FC was located in sensory cortex, while decreased LC-NE FC was located in frontal control cortex. In addition, the FC between the left LC and left MOG was associated with the duration of the disease, while abnormal FC between right LC and left dACC was associated with the anxiety scores in patients with CID. Conclusion The present study found abnormal LC-NE functional network in patients with CID, and the altered LC-NE function in dACC was associated with anxiety symptoms in CID. The present study substantially extended our understanding of the neuropathological basis of CID and provided the potential treatment target for CID patients who also had anxiety.
Monitoring Gait Complexity as an Indicator for Running-Related Injury Risk in Collegiate Cross-Country Runners: A Proof-of-Concept Study

Dynamical systems theory suggests that studying the complexity of biological signals could lead to a single gait metric that reliably predicts risk of running-related injury (RRI). The purposes of this pilot study were to examine center of mass (COM) acceleration complexity at baseline, prior to RRI, and the change between timepoints between collegiate runners who developed RRI during a competitive season and those who remained uninjured, and to determine if complexity at these timepoints was associated with increased odds of RRI. Twenty-two collegiate runners from the same cross-country team wore a waist-mounted triaxial accelerometer (100 Hz) during easy-intensity runs throughout the competitive season. RRIs requiring medical attention were reported via an online survey. Control entropy was used to estimate the complexity of the resultant COM acceleration recorded during each run. Associations between complexity and RRI were assessed using a frequency-matching strategy where uninjured participants were paired with injured participants using complexity from the most time-proximal run prior to RRI. Seven runners sustained an RRI. No significant differences were observed between injured and uninjured groups for baseline complexity (p = 0.364, d = 0.405), pre-injury complexity (p = 0.258, d = 0.581), or change from baseline to pre-injury (p = 0.101, d = 0.963). There were no statistically significant associations found between complexity and RRI risk. Although no significant associations were found, the median effect from the models indicated that an increase in baseline complexity, pre-injury complexity, and change in complexity from baseline each corresponded to an increased odds of sustaining an RRI [baseline: odds ratio (OR) = 1.560, 95% CI = 0.587–4.143, p = 0.372; pre-injury: OR = 1.926, 95% CI: 0.689–5.382, p = 0.211; change from baseline: OR = 1.119; 95% CI: 0.839–1.491, p = 0.445). Despite non-significance and wide confidence intervals that included both positive and negative associations, the point estimates for >98% of the 10,000 frequency-case–control-matched model fits indicated that matching strategy did not influence the directionality of the association estimates between complexity and RRI risk (i.e., odds ratio >1.0). This pilot study demonstrates initial feasibility that additional research may support COM acceleration complexity as a useful single-metric monitoring system for RRI risk during real-world training. Follow-up work should assess longitudinal associations between gait complexity and running-related injury in larger cohorts.
GABAA Alpha 2,3 Modulation Improves Select Phenotypes in a Mouse Model of Fragile X Syndrome

Fragile X syndrome (FXS) is the most common cause of inherited intellectual disability. FXS is caused by functional loss of the Fragile X Protein (FXP), also known as Fragile X Mental Retardation Protein (FMRP). In humans and animal models, loss of FXP leads to sensory hypersensitivity, increased susceptibility to seizures and cortical hyperactivity. Several components of the GABAergic system, the major inhibitory system in the brain, are dysregulated in FXS, and thus modulation of GABAergic transmission was suggested and tested as a treatment strategy. However, so far, clinical trials using broad spectrum GABAA or GABAB receptor-specific agonists have not yielded broad improvement of FXS phenotypes in humans. Here, we tested a more selective strategy in Fmr1 knockout (KO) mice using the experimental drug BAER-101, which is a selective GABAA α2/α3 agonist. Our results suggest that BAER-101 reduces hyperexcitability of cortical circuits, partially corrects increased frequency-specific baseline cortical EEG power, reduces susceptibility to audiogenic seizures and improves novel object memory. Other Fmr1 KO-specific phenotypes were not improved by the drug, such as increased hippocampal dendritic spine density, open field activity and marble burying. Overall, this work shows that BAER-101 improves select phenotypes in Fmr1 KO mice and encourages further studies into the efficacy of GABAA-receptor subunit-selective agonists for the treatment of FXS.
Attention Enhancement for Exoskeleton-Assisted Hand Rehabilitation Using Fingertip Haptic Stimulation

Active enrollment in rehabilitation training yields better treatment outcomes. This paper introduces an exoskeleton-assisted hand rehabilitation system. It is the first attempt to combine fingertip cutaneous haptic stimulation with exoskeleton-assisted hand rehabilitation for training participation enhancement. For the first time, soft material 3D printing techniques are adopted to make soft pneumatic fingertip haptic feedback actuators to achieve cheaper and faster iterations of prototype designs with consistent quality. The fingertip haptic stimulation is synchronized with the motion of our hand exoskeleton. The contact force of the fingertips resulted from a virtual interaction with a glass of water was based on data collected from normal hand motions to grasp a glass of water. System characterization experiments were conducted and exoskeleton-assisted hand motion with and without the fingertip cutaneous haptic stimulation were compared in an experiment involving healthy human subjects. Users’ attention levels were monitored in the motion control process using a Brainlink EEG-recording device and software. The results of characterization experiments show that our created haptic actuators are lightweight (6.8 ± 0.23 g each with a PLA fixture and Velcro) and their performance is consistent and stable with small hysteresis. The user study experimental results show that participants had significantly higher attention levels with additional haptic stimulations compared to when only the exoskeleton was deployed; heavier stimulated grasping weight (a 300 g glass) was associated with significantly higher attention levels of the participants compared to when lighter stimulated grasping weight (a 150 g glass) was applied. We conclude that haptic stimulations increase the involvement level of human subjects during exoskeleton-assisted hand exercises. Potentially, the proposed exoskeleton-assisted hand rehabilitation with fingertip stimulation may better attract user’s attention during treatment.