Miracle-dz/UniFAR-FTUs huggingface dataset:
Using the Comparative Hybrid Approach to Disentangle the Role of Substrate Choice on the Evolution of Cognition

Abstract Understanding the structure and evolution of natural cognition is a topic of broad scientific interest, as is the development of an engineering toolkit to construct artificial cognitive systems. One open question is determining which components and techniques to use in such a toolkit. To investigate this question, we employ agent-based AI, using simple computational substrates (i.e., digital brains) undergoing rapid evolution. Such systems are an ideal choice as they are fast to process, easy to manipulate, and transparent for analysis. Even in this limited domain, however, hundreds of different computational substrates are used. While benchmarks exist to compare the quality of different substrates, little work has been done to build broader theory on how substrate features interact. We propose a technique called the Comparative Hybrid Approach and develop a proof-of-concept by systematically analyzing components from three evolvable substrates: recurrent artificial neural networks, Markov brains, and Cartesian genetic programming. We study the role and interaction of individual elements of these substrates by recombining them in a piecewise manner to form new hybrid substrates that can be empirically tested. Here, we focus on network sparsity, memory discretization, and logic operators of each substrate. We test the original substrates and the hybrids across a suite of distinct environments with different logic and memory requirements. While we observe many trends, we see that discreteness of memory and the Markov brain logic gates correlate with high performance across our test conditions. Our results demonstrate that the Comparative Hybrid Approach can identify structural subcomponents that predict task performance across multiple computational substrates.
Effect of inbreeding and heterosis on piglet survival in a large commercial dataset

INTRODUCTION Breeding companies try to improve production efficiency in terms of lean tissue daily gain, lean tissue feed conversion and sow productivity. In recent years, research on sow productivity has been focused on survival, vitality, and behaviour. This interest stems from increased public awareness for animal rights, from recent major disease outbreaks, and from increased acceptance that improvement of vitality and survival has a clearer genetic background than expected. Piglet survival (±80%) in the Netherlands can be defined as the product of farrowing survival (±93%) and pre-weaning survival (±87%) (Knol, 2001). Farrowing survival is the complement of stillbirth and pre-weaning survival is the complement of pre-weaning mortality. Inbreeding tends to reduce fitness (Falconer, 1960). Inbreeding explains about 0.5% of the variarion of piglet survival (Bereskin et al., 1973). He estimated the effects of piglet survival at –0.10% (10% inbreeding of the dam) and -1.20% (10 % inbreeding of the litter) (Bereskin et al., 1973). Winters et al. (1947) found an effect of -0.20% piglet survival for 10 % inbreeding increase of the litter. The opposite side of inbreeding is heterosis. Quantification of heterosis effects and comparison with inbreeding effects might help to increase understanding. The effect of heterosis on preweaning survival is +5.8% for the litter and +5.0% for the sow (Sellier, 1976 ; Johnson, 1981 ; Gunsett and Robison, 1990). In this paper we want to quantify the influence of inbreeding on piglet survival traits and on other reproduction traits, such as litter size, birth weight, and gestation length. Not only inbreeding of the sow and the litter, but also inbreeding of the service sire will be addressed.
Brain aging, Alzheimer's disease, and the role of stem cells in primate comparative studies

Alzheimer's disease (AD) is a progressive neurodegenerative disease that is ultimately fatal. Currently, millions of Americans are living with AD, and this number is predicted to grow with increases in the aging population. Interestingly, despite the prevalence of AD in human populations, the full AD phenotype has not been observed in any nonhuman primate (NHP) species, and it has been suggested that NHPs are immune to neurodegenerative diseases such as AD.
Melanin‐concentrating hormone regulates the hypercapnic chemoreflex by acting in the lateral hypothalamic area

What is the central question of this study? Melanin‐concentrating hormone (MCH) suppresses the hypercapnic chemoreflex: what is the mechanism by which this effect is produced? What is the main finding and its importance? MCH acting in the lateral hypothalamic area but not in the locus coeruleus in rats, in the light period, attenuates the hypercapnic chemoreflex. The data provide new insight into the role of MCH in the modulation of the hypercapnic ventilatory response.
Afterglow Radiation from Gamma Ray Bursts

Gamma-ray bursts (GRB) are huge fluxes of gamma rays that appear randomly in the sky about once a day. It is now commonly accepted that GRBs are caused by a stellar object shooting off a powerful plasma jet along its rotation axis. After the initial outburst of gamma rays, a lower intensity radiation remains, called the afterglow. Using the data from a hydrodynamical numerical simulation that models the dynamics of the jet, we calculated the expected light curve of the afterglow radiation that would be observed on earth. We calculated the light curve and spectrum and compared them to the light curves and spectra predicted by two analytical models of the expansion of the jet (which are based on the Blandford and McKee solution of a relativistic isotropic expansion; see Sari's model [1] and Granot's model [2]). We found that the light curve did not decay as fast as predicted by Sari; the predictions by Granot were largely corroborated. Some results, however, did not match Granot's predictions, and more research is needed to explain these discrepancies.
Cosmic rays at the knee

We summarize the experimental data on the cosmic radiation in the energy region of the knee (10 1 4 -10 1 6 eV) obtained from the EAS-TOP experiment (Campo Imperatore. 2005 m a.s.l., 820 g/cm 2 ; National Gran Sasso Laboratories, 1989-2000). It is found that the knee is characterized by breaks in the spectra of the lighter components. No break is observed in the heavy primary (iron) spectrum. The connection with the direct measurements performed by means of balloons and satellites, and the generality of the results with respect to the hadron interaction model used for the interpretation are discussed.
An update on nutritional profile, phytochemical compounds, health benefits, and potential applications in the food industry of pulses seed coats: A comprehensive review

Abstract Pulses, as a sustainable source of nutrients, are an important choice for human diets, but vast quantities of seed coats generated in pulses processing are usually discarded or used as low-value ruminant feed. It has been demonstrated that pulses seed coats are excellent sources of dietary nutrients and phytochemicals with potential health benefits. With growing interest in the sustainable use of resources and the circular economy, utilization of pulses seed coats to recover these valuable components is a core objective for their valorization and an important step toward agricultural sustainability. This review comprehensively provides a comprehensive insight on the nutritional and phytochemical profiles presented in pulses seed coats and their health benefits obtained from the findings of in vitro and in vivo studies. Furthermore, in the food industry, pulses seed coats can be acted as potential food ingredients with nutritional, antioxidant and antimicrobial characteristics or as the matrix or active components of films for food packaging and edible coatings. A better understanding of pulses seed coats may provide a reference for increasing the overall added value and realizing the pulses’ sustainable diets.
Proteogenomics reveals sex biased aging genes and coordinated splicing in cardiac aging.

The risks of heart diseases are significantly modulated by age and sex, but how these factors influence baseline cardiac gene expression remains incompletely understood. Here we used RNA sequencing and mass spectrometry to compare gene expression in female and male young adult (4 months) and early aging (20 months) mouse hearts, identifying thousands of age and sex dependent gene expression signatures. Sexually dimorphic cardiac genes are broadly distributed, functioning in mitochondrial metabolism, translation, and other processes. In parallel, we found over 800 genes with differential aging response between male and female, including genes in cAMP and PKA signaling. Analysis of the sex-adjusted aging cardiac transcriptome revealed a widespread remodeling of exon usage patterns that is largely independent from differential gene expression, concomitant with upstream changes in RNA-binding protein and splice factor transcripts. To evaluate the impact of the splicing events on cardiac proteoform composition, we applied an RNA-guided-proteomics computational pipeline to analyze the mass spectrometry data, and detected hundreds of putative splice variant proteins that have the potential to rewire the cardiac proteome. Taken together, the results here suggest that cardiac aging is associated with (1) widespread sex-biased aging genes, and (2) a rewiring of RNA splicing programs, including sex- and age- dependent changes in exon usages and splice patterns that have the potential to influence cardiac protein structure and function. These changes contribute to the emerging evidence for considerable sexual dimorphism in the cardiac aging process that should be considered in the search for disease mechanisms.
Development of a Spine X-Ray-Based Fracture Prediction Model Using a Deep Learning Algorithm

Background Since image-based fracture prediction models using deep learning are lacking, we aimed to develop an X-ray-based fracture prediction model using deep learning with longitudinal data. Methods This study included 1,595 participants aged 50 to 75 years with at least two lumbosacral radiographs without baseline fractures from 2010 to 2015 at Seoul National University Hospital. Positive and negative cases were defined according to whether vertebral fractures developed during follow-up. The cases were divided into training (n=1,416) and test (n=179) sets. A convolutional neural network (CNN)-based prediction algorithm, DeepSurv, was trained with images and baseline clinical information (age, sex, body mass index, glucocorticoid use, and secondary osteoporosis). The concordance index (C-index) was used to compare performance between DeepSurv and the Fracture Risk Assessment Tool (FRAX) and Cox proportional hazard (CoxPH) models. Results Of the total participants, 1,188 (74.4%) were women, and the mean age was 60.5 years. During a mean follow-up period of 40.7 months, vertebral fractures occurred in 7.5% (120/1,595) of participants. In the test set, when DeepSurv learned with images and clinical features, it showed higher performance than FRAX and CoxPH in terms of C-index values (DeepSurv, 0.612; 95% confidence interval [CI], 0.571 to 0.653; FRAX, 0.547; CoxPH, 0.594; 95% CI, 0.552 to 0.555). Notably, the DeepSurv method without clinical features had a higher C-index (0.614; 95% CI, 0.572 to 0.656) than that of FRAX in women. Conclusion DeepSurv, a CNN-based prediction algorithm using baseline image and clinical information, outperformed the FRAX and CoxPH models in predicting osteoporotic fracture from spine radiographs in a longitudinal cohort.
Reliability of Running Economy Measurements: Influence of Shoe Familiarisation

Abstract The purpose was to investigate differences in reliability of running economy measurements between familiar and unfamiliar shoes. Thirty-seven runners were included who all ran in familiar and unfamiliar running shoes while running economy was measured at steady state using a treadmill. Each participant was tested on two different visits (three sessions in total), with two trials in each of the three shoe conditions completed at each visit. Coefficient of variation, standard deviation of differences, and limits of agreement of running economy were used to quantify the repeatability (within-visit variation) and reproducibility (between-visit variation). The coefficient of variation showed a marginal difference in reproducibility across shoe conditions, whereas no differences were seen in coefficient of variation, standard deviation of the differences, or limits of agreement for repeatability across shoes. All three shoe conditions showed greater repeatability than reproducibility for running economy, and enhanced repeatability at visit 3 compared to visit 2. Our results indicate that familiarisation to shoes might not be needed for reliable measurements of running economy. Based on our results, when evaluating benefits in running shoes we suggest that running economy be assessed within the same day. Further, our data suggest a beneficial effect of using multiple familiarisation sessions if small differences between shoe conditions are expected.
β-cell dynamics in type 2 diabetes and in dietary and exercise interventions

ABSTRACT Pancreatic β-cell dysfunction and insulin resistance are two of the major causes of type 2 diabetes (T2D). Recent clinical and experimental studies have suggested that the functional capacity of β-cells, particularly in the first phase of insulin secretion, is a primary contributor to the progression of T2D and its associated complications. Pancreatic β-cells undergo dynamic compensation and decompensation processes during the development of T2D, in which metabolic stresses such as endoplasmic reticulum stress, oxidative stress, and inflammatory signals are key regulators of β-cell dynamics. Dietary and exercise interventions have been shown to be effective approaches for the treatment of obesity and T2D, especially in the early stages. Whilst the targeted tissues and underlying mechanisms of dietary and exercise interventions remain somewhat vague, accumulating evidence has implicated the improvement of β-cell functional capacity. In this review, we summarize recent advances in the understanding of the dynamic adaptations of β-cell function in T2D progression and clarify the effects and mechanisms of dietary and exercise interventions on β-cell dysfunction in T2D. This review provides molecular insights into the therapeutic effects of dietary and exercise interventions on T2D, and more importantly, it paves the way for future research on the related underlying mechanisms for developing precision prevention and treatment of T2D.
Ocular biometric changes following unilateral cataract surgery in children

Purpose To analyze ocular biometric changes following unilateral cataract surgery in children. Methods A total of 57 children aged under 13 years who underwent unilateral cataract surgery were analyzed. Groups were classified according to their age at surgery: group I (age <3), II (3≤ age <6), III (6≤ age <9), and IV (age ≥9). The myopic shift, axial growth, and corneal curvature changes were compared between the pseudophakic eyes and the fellow phakic eyes. Results During 7.81 ± 4.39 years, the overall myopic shift (D) and the rate of myopic shift (D/year) were significantly higher at -3.25 ± 3.21 D and -0.45 ± 0.44 D/year in the pseudophakic eyes than -1.78 ± 2.10 D and -0.22 ± 0.29 D/year in the fellow phakic eyes (P = 0.01, 0.004). Group I (-1.14 ± 0.66 vs -0.02 ± 0.45 D/year) and group II (-0.63 ± 0.37 vs -0.31 ± 0.29 D/year) showed significantly higher rate of myopic shift in the pseudophakic eyes than in the phakic eyes. The rate of myopic shift in the pseudophakic eyes decreased in the older age groups (P = 0.001). There was no significant between-eye difference in the changes in axial length and keratometric values postoperatively. Conclusion Following unilateral cataract surgery, a significant postoperative myopic shift was noticed in the pseudophakic eyes compared to the fellow phakic eyes in groups under 6 years old. Postoperative myopic shift and the resultant anisometropia should be considered when selecting the optimal power of IOL in young children requiring unilateral cataract surgery.
Ultrasonic Guided Waves in Bone: A Decade of Advancement in Review

The use of guided wave ultrasonography as a means to assess cortical bone quality has been a significant practice in bone quantitative ultrasound for more than 20 years. In this article, the key developments within the technology of ultrasonic guided waves (UGW) in long bones during the past decade are documented. The covered topics include data acquisition configurations available for measuring bone guided waveforms, signal processing techniques applied to bone UGW, numerical modeling of ultrasonic wave propagation in cortical long bones, formulation of inverse approaches to extract bone properties from observed ultrasonic signals, and clinical studies to establish the technology’s application and efficacy. The review concludes by highlighting specific challenging problems and future research directions. In general, the primary purpose of this work is to provide a comprehensive overview of bone guided-wave ultrasound, especially for newcomers to this scientific field.
Slouched and Erect Sitting Postures Affect Upper Limb Maximum Voluntary Force Levels and Fatiguability: A Randomized Experimental Study

OCCUPATIONAL APPLICATIONS Modifying the spinal curvature is an empirical approach to treating upper limb musculoskeletal disorders, often attributed to the balance between physical stress and individual functional capacities. We completed an experimental biomechanical study to quantify the effect of seated spinal posture on upper limb functional capacities. Isometric maximum muscle voluntary forces (MVFs) were measured at participants’ shoulder, elbow, and wrist. Fatiguability was also assessed during a repetitive painting task. Participants were asked to assume both slouched and erect spinal postures, in a random order. In the erect posture, participants achieved higher shoulder and elbow isometric MVF levels and took longer to reach a fatigue threshold. Thus, spinal posture tends to remotely influence upper limb functional capacities, especially at the shoulder and elbow. Ergonomists should consider spinal posture even when focusing on musculoskeletal disorders of the upper limb. TECHNICAL ABSTRACT Background Musculoskeletal disorders are a major public health issue, and current treatments often remain unsatisfactory. Treatments based on spinal curvature modifications are empirically used for upper limb musculoskeletal disorders. Purpose To determine whether a slouched or erect sitting posture has an effect on upper limb functional capacities, with tests and outcomes focused on the risk of upper limb musculoskeletal disorders. Methods Randomized experimental study, crossover design. Twenty-two right-handed healthy participants from the local area were assessed in a research laboratory. Participants’ spinal curvatures were increased or decreased, through verbal instructions and light touch, to place them in a slouched or an erect posture that was stable and easily maintained, in a random order. Isometric maximum muscle voluntary forces (MVFs) were measured. Participants also performed a repetitive task that simulated painting, with fatigue level assessed using the CR10 Borg scale. Upper limb positioning, task setting, and instructions to participants were standardized, and the investigator was blind to the results of MVF measurements. The main outcomes were normalized differences in MVF values and time-to-reach “7” on the CR10 scale. Results There were significantly higher MVF values in the erect posture for the shoulder and elbow, with respective mean (SD) normalized differences of 11.4 (18.2)% and 11.8 (19.2)%; differences approached significance at the wrist [7.7 (18.5)%]. The normalized difference in time-to-reach “7” on the CR10 scale was significantly higher in the erect posture (by 11.4%). Conclusions Spinal posture modified individual upper limb functional capacities and could thus influence the risk of upper limb musculoskeletal disorders.
Dynamics of Temporal Integration in the Lateral Geniculate Nucleus

Abstract Before visual information from the retina reaches primary visual cortex (V1), it is dynamically filtered by the lateral geniculate nucleus (LGN) of the thalamus, the first location within the visual hierarchy at which nonretinal structures can significantly influence visual processing. To explore the form and dynamics of geniculate filtering we used data from monosynpatically connected pairs of retinal ganglion cells (RGCs) and LGN relay cells in the cat that, under anesthetized conditions, were stimulated with binary white noise and/or drifting sine-wave gratings to train models of increasing complexity to predict which RGC spikes were relayed to cortex, what we call “relay status. ” In addition, we analyze and compare a smaller dataset recorded in the awake state to assess how anesthesia might influence our results. Consistent with previous work, we find that the preceding retinal interspike interval (ISI) is the primary determinate of relay status with only modest contributions from longer patterns of retinal spikes. Including the prior activity of the LGN cell further improved model predictions, primarily by indicating epochs of geniculate burst activity in recordings made under anesthesia, and by allowing the model to capture gain control-like behavior within the awake LGN. Using the same modeling framework, we further demonstrate that the form of geniculate filtering changes according to the level of activity within the early visual circuit under certain stimulus conditions. This finding suggests a candidate mechanism by which a stimulus specific form of gain control may operate within the LGN.
Ezrin deficiency triggers glial fibrillary acidic protein upregulation and a distinct reactive astrocyte phenotype

Astrocytes are increasingly being recognized as contributors to physiological brain function and behavior. Astrocytes engage in glia‐synaptic interactions through peripheral astrocyte processes, thus modulating synaptic signaling, for example, by handling glutamate removal from the synaptic cleft and (re)provision to axonal terminals. Peripheral astrocyte processes are ultrafine membrane protrusions rich in the membrane‐to‐actin cytoskeleton linker Ezrin, an essential component of in vitro filopodia formation and in vivo peripheral astrocyte process motility. Consequently, it has been postulated that Ezrin significantly contributes to neurodevelopment as well as astrocyte functions within the adult brain. However, while Ezrin has been studied in vitro within cultured primary astrocytes, in vivo studies on the role of Ezrin in astrocytes remain to be conducted and consequences of its depletion to be studied. Here, we investigated consequences of Ezrin deletion in the mouse brain starting from early neuronal specification. While Ezrin knockout did not impact prenatal cerebral cortex development, behavioral phenotyping depicted reduced exploratory behavior. Starting with postnatal appearance of glia cells, Ezrin was verified to remain predominantly expressed in astrocytes. Proteome analysis of Ezrin deficient astrocytes revealed alterations in glutamate and ion homeostasis, metabolism and cell morphology – important processes for synaptic signal transmission. Notably, Ezrin deletion in astrocytes provoked (GFAP) glial fibrillary acidic protein upregulation – a marker of astrocyte activation and reactive astrogliosis. However, this spontaneous, reactive astrogliosis exhibited proteome changes distinct from ischemic‐induced reactive astrogliosis. Moreover, in experimental ischemic stroke, Ezrin knockout mice displayed reduced infarct volume, indicating a protective effect of the Ezrin deletion‐induced changes and astrogliosis.