Miracle-dz/UniFAR-FTUs huggingface dataset:
Maternal effects on daily weight gain and ultrasonically recorded backfat in swedish landrace, swedish yorkshire, and swedish hampshire purebred pigs

The aim of this study was to estimate the genetic association between direct and maternal effects for important economic traits measured early and late in the growth period; daily gain (DG) between birth and 12 weeks of age (DG0-12), between 12 weeks of age and ultrasonic test (at approx. 100 kg; DG12-UT), between birth and ultrasonic test (DG0-UT); and backfat at ultrasonic test (BF). Records from Landrace (L; 39,130), Yorkshire (Y; 33,737), and Hampshire (H; 17,832) pigs born between 1997 and 2001 from the Swedish breeding organization Quality Genetics databank were available. Univariate and bivariate analyses were applied. Two statistical models were used. The first model applied for all traits, included the random effect of herd-birth year-birth month combination, the litter environmental effects, and the direct genetic effects. The second model applied only for DG0-UT and BF, and included also the maternal genetic effects. Based on the first single-trait model, estimates of direct heritability (h2) were 0.12, 0.09, and 0.43 for DG0-12; 0.16, 0.22, and 0.41 for DG12-UT; 0.18, 0.24, and 0.28 for DG0-UT; and 0.37, 0.42, and 0.43 for BF in the L, Y, and H breeds respectively. Estimates of litter environmental effects ranged from 0.05 to 0.17. Based on the second single-trait model, the maternal genetic effects were 0.03, 0.05, and 0.09 for DG0-UT, and 0.02, 0.01, and 0.04 for BF. Estimates of direct h2 from the second model were lower and ranged from 0.14 to 0.42 for all traits across breeds. Moderate-low genetic correlation between DG0-12 and DG12-UT (−0.25 to 0.40) and high correlation between DG12-UT and DG0-UT (0.84 to 0.96) were noted in all three breeds together with less maternal influence on traits expressed late in life. This indicates the possibility to treat early growth rate as a maternal trait, and late or overall growth rate as a direct trait in the breeding evaluation.
Regulation of Integrin αvβ3-mediated Endothelial Cell Migration and Angiogenesis by Integrin α5β1 and Protein Kinase A*

Recent studies indicate that angiogenesis depends, in part, on ligation of integrin α5β1 by fibronectin. Evidence is now provided that integrin α5β1 regulates the function of integrin αvβ3 on endothelial cells during their migration in vitro or angiogenesisin vivo. Secretion of fibronectin by endothelial cells leads to the ligation of integrin α5β1, which potentiates αvβ3-mediated migration on vitronectin without influencing αvβ3-mediated cell adhesion. Endothelial cell attachment to vitronectin suppresses protein kinase A (PKA) activity, while addition of soluble anti-α5β1 restores this activity. Moreover, agents that activate intracellular PKA, such as forskolin, dibutyryl cAMP or α5β1 antagonists, suppress endothelial cell migration on vitronectin in vitro or angiogenesis in vivo. In contrast, inhibitors of PKA reverse the anti-migratory or anti-angiogenic effects mediated by α5β1 antagonists. Therefore, αvβ3-mediated endothelial cell migration and angiogenesis can be regulated by PKA activity, which depends on the ligation state of integrin α5β1.
Recursive systems model of fetal birth weight and calving difficulty in beef heifers

The purpose of this study was to use readily available information, including dam pelvic width (PW) and height (PH) and the fetal coronet band (CB) measurement to predict the calving difficulty (CD) score of first-calf heifers under commercial ranch conditions. Data were collected from a cow-calf ranch over a 3-yr period. Using a recursive system of equations, two models were estimated. First, a linear model was used to predict birth weight (BTW) based on the fetal CB measurement. Second, an ordered logit model was used to predict calving difficulty score based on a nonlinear relationship with birth weight, pelvic dimensions of the dam, and interaction terms. The linear model demonstrated that BTW could be predicted using the CB measurement, both the intercept and slope coefficients were significant at P < 0.001. The model R2 was equal to 0.57 and the standard error of the predicted birth weight was 2.77 kg. The ordered logit model correctly predicted 468 of 684 (68.4%) of the CD scores. The results of th.
Bottom culture of the sea cucumber Apostichopus japonicus Selenka (Echinodermata: Holothuroidea) in a fish farm, southern China

The bottom culture of southward-transplanted sea cucumber Apostichopus japonicus in a subtropical fish farm was investigated in a field study at Dapeng Cove, Daya Bay, from January 5-August 5 2011, with the aim of finding the ideal period for culturing A. japonicus in fish farms, and developing an integrated multi-trophic aquaculture (IMTA) in southern China. Results showed that the bottom-cultured sea cucumbers survived well (100%) before summer, survival rates decreased to 65.00 +/- 21.21% in July, and all animals had died at the end of the study. Specific growth rates of the sea cucumbers were high during winter (1.05 +/- 0.03% d(-1)), decreased in early spring (0.44 +/- 0.11% d(-1)) and became negative in the following months. Growth rate was mainly influenced by water temperature, dissolved oxygen and sulphide content; the anoxia caused by water column stratification at the sea-floor in the summer were the main causes of mass mortality. Our results indicate that bottom culture in the temperate season (winter and spring, optimally from late November to early April) is a viable way to rear the deposit feeder A. japonicus underneath a subtropical fish farm.
Validity of Computer Based Administration of Cognitive Assessments compared to Traditional Paper-based Administration

Traditional pen and paper based neuropsychological tests (NPT) for cognition assessment have several challenges limiting their use. They are time consuming, expensive, and require highly trained specialists to administer. This leads to testing being available to only a small portion of the population and often with wait times of several months. In clinical practice, we have found results tend not to be integrated effectively into assessment and plans of the ordering provider. Here we compared several tests using BrainCheck (BC), a computer-based NPT battery, to traditional paper-based NPT, by evaluating individual tests as well as comparing composite scores to scores on traditional screening tools. 26 volunteers took both paper-based tests and BC. We found scores of four assessments (Ravens Matrix, Digit Symbol Modulation, Stroop Color Word Test and Trails Making A&B Test) were highly correlated. The Balance Examination and Immediate/Delayed Hopkins Verbal Learning, however, were not correlated. The BC composite score was correlated to results of the Saint Louis University Mental Status (SLUMS) exam [1], the Mini-Mental State Examination (MMSE) [2], and the Montreal Cognitive Assessment (MoCA). Our results suggest BC may offer a computer-based avenue to address the gap between basic screening and formal neuropsychological testing.
Genetic risk for Alzheimer disease, cognition and Mild Behavioral Impairment in healthy older adults

BACKGROUND: Mild Behavioral Impairment (MBI) is a neuropsychiatric syndrome describing later-life emergent apathy, mood/anxiety symptoms, impulse dyscontrol, social inappropriateness and psychosis that are not attributable to psychiatric diagnoses. MBI is an at-risk state for incident cognitive decline and dementia, and is associated with dementia biomarkers including amyloid beta; and neurofilament light. Thus, MBI may be an early clinical marker of neurodegenerative disease. In this study, we hypothesized that stratification by MBI in a cognitively normal sample would moderate the signal between Alzheimer disease (AD) genetic risk and cognition. METHODS: Genetic, cognitive and MBI data was available for 3,126 PROTECT study participants over 50 without dementia. A general cognitive composite score was constructed based on scores on paired associates learning, digit span, self-ordered search and verbal reasoning. MBI was assessed using the MBI Checklist. Polygenic scores for AD were split by tertile (representing low, medium and high risk) and the sample was stratified by MBI into those with no symptoms and those with any symptoms. RESULTS: AD genetic risk was associated with poorer cognition in the MBI strata only (MBI: F(2,1746)=4.95, p=0.007; no MBI: F(2,1366)=0.72, p=0.49). The mean difference between low and high genetic risk groups was significant (p=0.005) and the standardised effect size in the MBI sample was higher than in the whole sample. CONCLUSIONS: These findings justify MBI screening to enrich samples with at-risk individuals, and underscore the importance of late-life neuropsychiatric symptoms in cognitive ageing.
Single-Cell-Based Models in Biology and Medicine

A Hybrid Multiscale Model of Tumour Invasion: Evolution and the Microenvironment. - Lattice-gas Cellular Automaton Modelling of Developing Cell Systems. - Two-dimensional Multiscale Model of Cell Motion in a Chemotactic Field. - Magnetization to Morphogenesis: A Brief History of the Glazier-Graner-Hogeweg Model. - The Cellular Potts Model and Biophysical Properties of Cells, Tissues and Morphogenesis. - The Cellular Potts Model in Biomedicine. - The Glazier-Graner-Hogeweg Model: Extensions, Future Directions, and Opportunities for Further Study. - Center-based Single-cell Models: An Approach to Multi-cellular Organization Based on a Conceptual Analogy to Colloidal Particles. - Models with Lattice-free Center-based Cells Interacting with Continuum Environment Variables. - Modeling Multicellular Structures Using the Subcellular Element Model. - Cell-based Models of Blood Clotting. - A 3-D Deformable Ellipsoidal Cell Model with Cell Adhesion and Signaling. - Modelling Development of Complex Tissues using Individual Viscoelastic Cells.
Nutritional Investigation of the Metabolism of Glycine and Its Precursors by Chicks Fed a Crystalline Amino Acid Diet

Abstract Wixom et al. (1958) presented data suggesting that both serine and aminoethanol exert a sparing effect on the dietary glycine requirement of growing chicks. Subsequently, it was established that serine could replace dietary glycine on a mole for mole basis (Baker et al., 1968; Akrabawi and Kratzer, 1968) . Work with the rat suggests that several metabolites might conceivably serve as a precursor of glycine through one of the following biosynthetic pathways: choline → betaine → dimethylglycine → sarcosine → glycine; and aminoethanol → glycolic acid → glyoxylic acid → glycine ↔ serine (Meister, 1965). The purpose of the two assays reported here was to evaluate several metabolic intermediates in glycine-choline metabolism to determine if their inclusion in a glycinefree diet would elicit a growth response. …
Reduced purine biosynthesis in humans after their divergence from Neandertals

We analyze the metabolomes of humans, chimpanzees and macaques in muscle, kidney and three different regions of the brain. Whereas several compounds in amino acid metabolism occur at either higher or lower concentrations in humans than in the other primates, metabolites in oxidative phosphorylation and purine biosynthesis are consistently present in lower concentrations in the brains of humans. In particular, metabolites downstream of adenylosuccinate lyase, which catalyzes two reactions in purine synthesis, occur at lower concentrations in humans. This enzyme carries an amino acid substitution that is present in all humans today but absent in Neandertals. By introducing the modern human substitution into the genomes of mice, as well as the ancestral, Neandertal-like substitution into the genomes of human cells, we show that this amino acid substitution is responsible for much or all of the reduction of de novo synthesis of purines in humans.
Neurokinin 1 receptor activation in the rat spinal cord maintains latent sensitization, a model of inflammatory and neuropathic chronic pain

Latent sensitization is a model of chronic pain in which a persistent state of pain hypersensitivity is suppressed by opioid receptors, as evidenced by the ability of opioid antagonists to induce a period of mechanical allodynia. Our objective was to determine if substance P and its neurokinin 1 receptor (NK1R) mediate the maintenance of latent sensitization. Latent sensitization was induced by injecting rats in the hindpaw with complete Freund’s adjuvant (CFA), or by spared nerve injury (SNI). When responses to von Frey filaments returned to baseline (day 28), the rats were injected intrathecally with saline or the NK1R antagonist RP67580, followed 15 min later by intrathecal naltrexone. In both pain models, the saline-injected rats developed allodynia for 2 h after naltrexone, but not the RP67580-injected rats. Saline or RP67580 were injected daily for two more days. Five days later (day 35), naltrexone was injected intrathecally. Again, the saline-injected rats, but not the RP67580-injected rats, developed allodynia in response to naltrexone. To determine if there is sustained activation of NK1Rs during latent sensitization, NK1R internalization was measured in lamina I neurons in rats injected in the paw with saline or CFA, and then injected intrathecally with saline or naltrexone on day 28. The rats injected with CFA had a small amount of NK1R internalization that was significantly higher than in the saline-injected rats. Naltrexone increased NK1R internalization in the CFA-injected rats but nor in the saline-injected rats. Therefore, sustained activation of NK1Rs maintains pain hypersensitivity during latent sensitization.
Dopaminergic neurons establish a distinctive axonal arbor with a majority of non-synaptic terminals

Chemical neurotransmission in the brain typically occurs through synapses, which are structurally and functionally defined as sites of close apposition between an axon terminal and a postsynaptic domain. Ultrastructural examinations of axon terminals established by monoamine neurons in the brain often failed to identify a similar tight pre- and postsynaptic coupling, giving rise to the concept of “diffuse” or “volume” transmission. Whether this results from intrinsic properties of such modulatory neurons remains undefined. Using an efficient co-culture model, we find that dopaminergic neurons establish an axonal arbor that is distinctive compared to glutamatergic or GABAergic neurons in both size and propensity of terminals to avoid direct contact with target neurons. Furthermore, while most dopaminergic varicosities express key proteins involved in exocytosis such as synaptotagmin 1, only ~20% of these are synaptic. The active zone protein bassoon was found to be enriched in a subset of dopaminergic terminals that are in proximity to a target cell. Irrespective of their structure, a majority of dopaminergic terminals were found to be active. Finally, we found that the presynaptic protein Nrxn-1αSS4- and the postsynaptic protein NL-1AB, two major components involved in excitatory synapse formation, play a critical role in the formation of synapses by dopamine neurons. Taken together, our findings support the idea that dopamine neurons in the brain are endowed with a distinctive developmental program that leads them to adopt a fundamentally different mode of connectivity, compared to glutamatergic and GABAergic neurons involved in fast point-to-point signaling. SIGNIFICANCE STATEMENT Midbrain dopamine (DA) neurons regulate circuits controlling movement, motivation, and learning. The axonal connectivity of DA neurons is intriguing due to its hyperdense nature, with a particularly large number of release sites, most of which not adopting a classical synaptic structure. In this study, we provide new evidence highlighting the unique ability of DA neurons to establish a large and heterogeneous axonal arbor with terminals that, in striking contrast with glutamate and GABA neurons, actively avoid contact with the target cells. The majority of synaptic and non-synaptic terminals express proteins for exocytosis and are active. Finally, our finding suggests that, NL-1A+B and Nrxn-1αSS4-, play a critical role in the formation of synapses by DA neurons.
Origin of Novel Coronavirus (COVID-19): A Computational Biology Study using Artificial Intelligence

Origin of the COVID-19 virus has been intensely debated in the scientific community since the first infected cases were detected in December 2019. The disease has caused a global pandemic, leading to deaths of thousands of people across the world and thus finding origin of this novel coronavirus is important in responding and controlling the pandemic. Recent research results suggest that bats or pangolins might be the original hosts for the virus based on comparative studies using its genomic sequences. This paper investigates the COVID-19 virus origin by using artificial intelligence (AI) and raw genomic sequences of the virus. More than 300 genome sequences of COVID-19 infected cases collected from different countries are explored and analysed using unsupervised clustering methods. The results obtained from various AI-enabled experiments using clustering algorithms demonstrate that all examined COVID-19 virus genomes belong to a cluster that also contains bat and pangolin coronavirus genomes. This provides evidences strongly supporting scientific hypotheses that bats and pangolins are probable hosts for the COVID-19 virus. At the whole genome analysis level, our findings also indicate that bats are more likely the hosts for the COVID-19 virus than pangolins.
Results about lysine utilization in growing monogastric animals with special respect to different lysine sources

Object of investigations was to estimate lysine efficiency from different lysine sources (lysinemonohydrochloride and lysinesulfate resp.) for rats, piglets and broiler chickens to reach a higher level of calculation of lysine supply. Lysine limiting diets were based on wheat, soybean meal and wheat gluten, supplemented with different levels of lysine sources under investigation. Balance trials (rat, piglet, chicken) and growth trails with analyses of body composition (chicken) were done to estimate N‐balance resp. N‐deposition. N‐utilization model from Gebhardt (1966) and its further developement for efficiency estimation of feed amino acids were used for data calculation. Results allow conclusion, that there are no differences in utilization of lysine from lysinemonohydrochloride and lysinesulfate. Limitations of efficiency resulting from differences in time course of absorption between protein bound and free lysine were not observed under ad lib. feeding conditions.
The Short Form of the Interferon α/β Receptor Chain 2 Acts as a Dominant Negative for Type I Interferon Action*

We have characterized the functional properties of the short form of the human interferon α/β receptor chain 2 (IFNAR2), denoted IFNAR2.1. IFNAR2.1 contains a shortened cytoplasmic domain when compared with the recently cloned full-length IFNAR2 chain (IFNAR2.2). We show that IFNα8 and IFNβ1b induce antiviral and antiproliferative activity in mouse cell transfectants expressing the human IFNAR1 chain of the receptor and induce the formation of STAT1/STAT2 dimers in IFN-stimulated response element (ISRE)-dependent gel shift assays. In contrast, coexpression of IFNAR2.1 with IFNAR1 reduces the IFN-induced antiviral, antiproliferative and ISRE-dependent gel shift binding activity conferred by IFNAR1 alone. No antiviral or antiproliferative response to IFN, nor IFN-induced ISRE-dependent gel shift binding activity, was observed when IFNAR2.1 was expressed alone in murine cells. Therefore, IFNAR2.1 acts as a dominant negative for these IFN-induced activities. Our results suggest that IFNAR2.1 represents a nonfunctional version of the full-length chain (IFNAR2.2).
Method and effects of incorporating foreign information into United Kingdom production evaluations

Countries, which import a significant amount of semen, embryos and animals, are faced with the problem of how properly to evaluate the animals in the national evaluation system when information on the foreign parents is generally missing. Additional problems arise when the foreign parents obtain an evaluation, usually on the basis of progeny, in the country of import with the result that there are two published evaluations for the animals in question. This paper presents a post-iterative method of incorporating foreign information into home country evaluations. The foreign information is initially converted to the same scale and base as in the home country using procedures recommended by the International Bull Evaluation Service. The method consists essentially of calculating a combined evaluation for animals with home and foreign information as a weighted average of yield deviations, parent averages and progeny contributions from the foreign and home countries. The combined evaluations are used to adjust the evaluations of progeny on the basis of formulae derived from the usual mixed model equations. The same principles were used to combine reliabilities from the respective home and foreign reliabilities. The results from the application of the method to the United Kingdom (UK) Holstein Friesian population are presented. There was re-ranking of both bulls and cows, especially foreign bulls with few UK daughters.
Third International Workshop on Capturing Scientific Knowledge (SciKnow2019): Summary Report

From the early days of Artificial Intelligence, researchers have been interested in capturing scientific knowledge to develop intelligent systems. A variety of formalisms are used today in different areas of science, ranging from ontologies for organizing knowledge - particularly in biology and medicine; process representations to do qualitative reasoning in areas such as physics and chemistry; or probabilistic graphical models used by machine learning scientists. Despite recent advances, scientific knowledge is complex and poses significant challenges for knowledge capture. The Third Workshop for Capturing Scientific Knowledge (Sciknow 2019) 1 provided a forum to discuss, envision and expand existing forms of scientific knowledge representation and dissemination, together with existing systems that use them. SciKnow 2019 took place in Marina del Rey (Los Angeles) on November 19th, 2019; and had roughly 25 attendants during a half full day event. Attendees had mainly a computer science background, but had experience in bioinformatics, humanities and climate sciences. The workshop was the third of a series, which started at K-CAP 2015 with a full day event 2 and continued at K-CAP 2017. 3
Who Is This Explanation for? Human Intelligence and Knowledge Graphs for eXplainable AI

eXplainable AI focuses on generating explanations for the output of an AI algorithm to a user, usually a decision-maker. Such user needs to interpret the AI system in order to decide whether to trust the machine outcome. When addressing this challenge, therefore, proper attention should be given to produce explanations that are interpretable by the target community of users. In this chapter, we claim for the need to better investigate what constitutes a human explanation, i.e. a justification of the machine behaviour that is interpretable and actionable by the human decision makers. In particular, we focus on the contributions that Human Intelligence can bring to eXplainable AI, especially in conjunction with the exploitation of Knowledge Graphs. Indeed, we call for a better interplay between Knowledge Representation and Reasoning, Social Sciences, Human Computation and Human-Machine Cooperation research -- as already explored in other AI branches -- in order to support the goal of eXplainable AI with the adoption of a Human-in-the-Loop approach.