Miracle-dz/UniFAR-FTUs huggingface dataset:
A comprehensive motifs-based interactome of the C/EBPα transcription factor

The pioneering transcription factor C/EBPα coordinates cell fate and cell differentiation. C/EBPα represents an intrinsically disordered protein with multiple short linear motifs and extensive post-translational side chain modifications (PTM), reflecting its modularity and functional plasticity. Here, we combined arrayed peptide matrix screening (PRISMA) with biotin ligase proximity labeling proteomics (BioID) to generate a linear, isoform specific and PTM-dependent protein interaction map of C/EBPα in myeloid cells. The C/EBPα interactome comprises promiscuous and PTM-regulated interactions with protein machineries involved in gene expression, epigenetics, genome organization, DNA replication, RNA processing, and nuclear transport as the basis of functional C/EBPα plasticity. Protein interaction hotspots were identified that coincide with homologous conserved regions of the C/EBP family and revealed interaction motifs that score as molecular recognition features (MoRF). PTMs alter the interaction spectrum of multi-valent C/EBP-motifs to configure a multimodal transcription factor hub that allows interaction with multiple co-regulatory components, including BAF/SWI-SNF or Mediator complexes. Combining PRISMA and BioID acts as a powerful strategy to systematically explore the interactomes of intrinsically disordered proteins and their PTM-regulated, multimodal capacity. Key points Integration of proximity labeling and arrayed peptide screen proteomics refines the interactome of C/EBPα isoforms Hotspots of protein interactions in C/EBPα mostly occur in conserved short linear motifs Interactions of the BAF/SWI-SNF complex with C/EBPα are modulated by arginine methylation and isoform status The integrated experimental strategy suits systematic interactome studies of intrinsically disordered proteins
A Non-spiking Neuron Model With Dynamic Leak to Avoid Instability in Recurrent Networks

Recurrent circuitry components are distributed widely within the brain, including both excitatory and inhibitory synaptic connections. Recurrent neuronal networks have potential stability problems, perhaps a predisposition to epilepsy. More generally, instability risks making internal representations of information unreliable. To assess the inherent stability properties of such recurrent networks, we tested a linear summation, non-spiking neuron model with and without a “dynamic leak”, corresponding to the low-pass filtering of synaptic input current by the RC circuit of the biological membrane. We first show that the output of this neuron model, in either of its two forms, follows its input at a higher fidelity than a wide range of spiking neuron models across a range of input frequencies. Then we constructed fully connected recurrent networks with equal numbers of excitatory and inhibitory neurons and randomly distributed weights across all synapses. When the networks were driven by pseudorandom sensory inputs with varying frequency, the recurrent network activity tended to induce high frequency self-amplifying components, sometimes evident as distinct transients, which were not present in the input data. The addition of a dynamic leak based on known membrane properties consistently removed such spurious high frequency noise across all networks. Furthermore, we found that the neuron model with dynamic leak imparts a network stability that seamlessly scales with the size of the network, conduction delays, the input density of the sensory signal and a wide range of synaptic weight distributions. Our findings suggest that neuronal dynamic leak serves the beneficial function of protecting recurrent neuronal circuitry from the self-induction of spurious high frequency signals, thereby permitting the brain to utilize this architectural circuitry component regardless of network size or recurrency.
Adducin Regulates Sarcomere Disassembly During Cardiomyocyte Mitosis

Recent interest in understanding cardiomyocyte cell-cycle has been driven by potential therapeutic applications in cardiomyopathy. However, despite recent advances, cardiomyocyte mitosis remains a poorly understood process. For example, it is unclear how sarcomeres are disassembled during mitosis to allow abscission of daughter cardiomyocytes. Here we identify adducin as a regulator of sarcomere disassembly during mammalian cardiomyocyte mitosis. α/γ-adducins are selectively expressed in neonatal mitotic cardiomyocytes, and their levels decline precipitously thereafter. Cardiomyocyte-specific overexpression of various splice isoforms and phosphoforms of α-adducin in-vitro and in-vivo identified Thr445/Thr480 phosphorylation of a short isoform of α adducin as a potent inducer of neonatal cardiomyocyte sarcomere disassembly. Concomitant overexpression of this α-adducin variant along with γ-adducin resulted in stabilization of the adducin complex and persistent sarcomere disassembly in adult mice, which is mediated by interaction with α-actinin. These results highlight an important mechanism for coordination of cytoskeletal morphological changes during cardiomyocyte mitosis.
The mechanism underlying transient weakness in myotonia congenita

In addition to the hallmark muscle stiffness, patients with recessive myotonia congenita (Becker disease) experience debilitating bouts of transient weakness that remain poorly understood despite years of study. We made intracellular recordings from muscle of both genetic and pharmacologic mouse models of Becker disease to identify the mechanism underlying transient weakness. Our recordings reveal transient depolarizations (plateau potentials) of the membrane potential to −25 to −35 mV in the genetic and pharmacologic models of Becker disease. Both Na+ and Ca2+ currents contribute to plateau potentials. Na+ persistent inward current (NaPIC) through Naγ1. 4 channels is the key trigger of plateau potentials and current through Cav1.1 Ca2+ channels contributes to the duration of the plateau. Inhibiting NaPIC with ranolazine prevents the development of plateau potentials and eliminates transient weakness in vivo. These data suggest that targeting NaPIC may be an effective treatment to prevent transient weakness in myotonia congenita. Impact Statement Transient weakness in myotonia congenita is caused by depolarization secondary to activation of persistent Na+ current in skeletal muscle.
The hidden state-dependency of transcranial alternating current stimulation (tACS)

Non-invasive techniques to electrically stimulate the brain such as transcranial direct and alternating current stimulation (tDCS/tACS) are increasingly used in human neuroscience and offer potential new avenues to treat brain disorders. However, their often weak and variable effects have also raised concerns in the scientific community. A possible factor influencing the efficacy of these methods is the dependence on brain-states. Here, we utilized Hidden Markov Models (HMM) to decompose concurrent tACS-magnetoencephalography data into transient brain-states with distinct spatial, spectral and connectivity profiles. We found that out of four spontaneous brain-states only one was susceptible to tACS. No or only marginal effects were found in the remaining states. TACS did not influence the time spent in each state. Our results suggest, that tACS effects may be mediated by a hidden, spontaneous state-dependency and provide novel insights to the changes in oscillatory activity underlying aftereffects of tACS.
Persistence of emotion in the process of inoculation: experiencing post-attack threat, fear, anger, happiness, sadness, and surprise

ABSTRACT This investigation assessed the mechanisms that contribute to post-attack attitudinal persistence. A three-phase experiment was designed to uncover why inoculation works even after it has been challenged by a counterattitudinal attack. The results of this study show that threat, both motivational and apprehensive, not only persists after the attack, but it may be heightened by an increase in post-attack fear and sadness. Greater anger and less happiness were also expressed by inoculated individuals in response to the attack. An increase, rather than decrease, in surprise was a surprising outcome. Taken together, the findings from this study suggest that the effects of inoculation continue to persist beyond the attack as threat and multiple other emotions interact to form and inspire a formidable attitudinal barrier that endures over time.
Deciphering colchicine like actions of clerodin in terms of microtubule destabilization based mitotic abnormalities, G2/M-phase arrest, and plant polyploidy

Clerodin (C24H34O7), a clerodane diterpenoid, is a bitter principle of Clerodendrum viscosum. The present study aimed to decipher colchicine-like actions of clerodin in terms of microtubule destabilization based mitotic abnormalities, G2-M arrest, and plant polyploidy. Purified clerodin showed increased metaphase frequency in Human Peripheral Blood Lymphocytes (HPBLs), Human Embryonic Kidney cells (HEK-293), and Allium cepa root apical meristem cells. Both squashed slide of the onion root tip and flow cytometric analysis of radish protoplast revealed a significantly increased frequency of polyploid cells. Flow cytometric analysis showed an increase in frequencies of G2-M in MCF-7 cells from 6.10 to 16.25% after clerodin (200μg/mL) treatment for 24 h. Confocal microscopy imaging of tubulin in clerodin-treated MCF-7 cells revealed microtubule destabilization. Molecular docking and LIGPLOT analysis indicate that clerodin interact in the colchicine binding site, including, single hydrogen bond with Asn 101 of α-tubulin. In summary, our experimental data revealed that clerodin has metaphase arresting, microtubule destabilization, and polyploidy inducing ability similar to colchicine. Molecular docking analysis revealed for the first time that clerodin and colchicine interact at the common site of tubulin residue indicating a common mechanism of action. The results also indicate similar cytotoxic potentialities of both clerodin and colchicine even though they belong to different chemical groups. Thus, clerodin may be used in place of colchicine as a plant polyploidy inducing agent in plant breeding programs in Agriculture.
Celebrating the contributions of Govindjee after his retirement: 1999–2020

ABSTRACT Govindjee, Professor Emeritus of Biochemistry, Biophysics and Plant Biology at the University of Illinois at Urbana-Champaign since 1999, is renowned for his pioneering work in the light reactions of photosynthesis and important accomplishments as educator, editor, historian and advocate of photosynthesis. In his honour, we review his contributions over the last twenty years, which were often achieved in collaboration with scientists working in laboratories around the world. We start with a short presentation about Govindjee’s career and continue with a section highlighting his passion and dedication to teach the younger generations of students and researchers about photosynthesis. His research work is grouped under different areas, including primary photochemistry; the relationship of chlorophyll a fluorescence to photosynthesis; short time-scale regulation processes of photosynthesis; studies toward improving photosynthesis and biomass yields; and, mathematical modelling of photosynthesis and artificial photosynthesis. He is best known for the discovery of the key role of bicarbonate on the electron acceptor side of Photosystem II. We also present his active involvement in the recognition of scientists at conferences and beyond, as well as of those who are no longer with us. He is committed to keeping alive the pioneers and discoverers in the field of photosynthesis in the collective memory of those in the field.
Complex Patterns in a Periodically Forced Surface Reaction

Effects of time-periodic, spatially uniform forcing on oscillatory chemical turbulence are studied in experiments with catalytic CO oxidation on a platinum(110) single-crystal surface. A variety of complex spatiotemporal reaction-diffusion patterns is investigated under variation of the forcing amplitude and frequency. Near harmonic resonance with the forcing, intermittent turbulence characterized by the presence of localized turbulent bubbles on a homogeneously oscillating background and disordered cellular structures are observed. In the parameter region where the system exhibits 2:1 subharmonic resonance, irregular oscillatory stripes and cluster patterns are found. For such resonant patterns, a frequency demodulation technique is used to reconstruct phase and amplitude variables from the experimental data.
Integrated Design and Structure Analysis of Robust Iterative Learning Control System Based on a Two-Dimensional Model

In this paper, an iterative learning control (ILC) system is modeled as a two-dimensional (2D) Roesser system and the design of a robust ILC for a repetitive process with uncertain parameter perturbations and uncertain initial conditions is transformed to a robust stabilization problem of a 2D system. Based on the 2D robust control theory [Shi et al., J. Process Control 2005, 15, 907−924], a general design framework of robust ILC is formulated, which results in an ILC scheme consisting of two types of controls: a robust feedback control for ensuring the performances over time, and a P-type ILC for improving the tracking performance from cycle to cycle. The proposed design algorithms allow these two types of controls to be optimized, extended, and designed in an integrated fashion. To avoid the requirement of state feedback, an input−output-based ILC scheme is also developed.
Use of encapsulated Bacillus subtilis and essential oils to improve antioxidant and immune status of blood and production and hatching performance of laying hens

Abstract The study was conducted to evaluate the effects of increasing inclusion levels of the mixture of Bacillus subtilis and essential oils (BSEO) on production, hatching performance, egg quality, serum antioxidant capacity, immune response, and hormone levels of laying hens. A total of 768 24-wk-old layers were randomly allotted into 4 treatments with 6 replicates of 32 birds each replicate. The experiment lasted for 84 d, and the birds were fed a basal diet (CON) or diets with BSEO at 300 (BSEO-1), 600 (BSEO-2), and 900 mg/kg (BSEO-3) in the other 3 groups, respectively. As the BSEO level increased, egg production (linear, p < .05), yolk index (linear, p < .01), glutathione peroxidase activity (linear, p < .01), total antioxidant capacity (linear, p < .01), oestradiol level (linear, p < .01), the value luteinizing hormone/follicle-stimulating hormone (linear, p < .05) increased in a linear manner. Hatchability (linear and quadratic, p < .01), hatchability of fertile of eggs (linear and quadratic, p < .05), avian influenza virus antibody level (linear, p < .01; quadratic, p < .05), parathyroid hormone level (linear and quadratic, p < .01) in the serum increased linearly and quadratically. Taken together, dietary with BSEO in laying hens could significantly improve egg production, hatchability, and hatchability of fertile eggs, which were associated with an enhancement of antioxidant capacity and the level of AIV-Ab in the serum. This study provided evidence of using BSEO as a potential feed additive for laying hens. Highlights Dietary supplementation of BSEO decreased the feed conversion ratio and eggshell thickness of laying hens. Dietary supplementation of BSEO improved the egg weight, fertility, hatchability, hatchability of fertile eggs, and yolk index of laying hens. Dietary supplementation of BSEO enhanced the antioxidant capacity and the level of AIV-Ab in the serum.
How a business model’s sustainability and scalability interact

ABSTRACT Changes in current business create modern mechanisms for businesses to determine what they aim for and the achievement of their high performance. The ability to maintain high performance becomes a guide for business continuity. The mechanism that can adopt such assumption is a business model that has the ability to generate outcomes in every market situation. Business ventures are continuously aiming at developing feasible business models for solving challenges in the society. The significance of a business model in determining the sustainability and scalability of business performance has been widely acknowledged in the literature. A characteristic that explains the adaptability of a business model is its sustainability and scalability. As factors that ensure efficiency of work, sustainability and scalability can be applied to the concept of a business model as the ability of businesses to maintain higher performance through their operations. The study aims at determining how business model sustainability and scalability interact in different conditions. The study presents the concept of sustainability and scalability with explanations to determine the performance of business. Dwelling on literature on business models and innovation adoption, the study developed a business model built on the triangle of optimization of economic, social, and environmental value. The study applied the business model to Bcomp, a clean-tech venture with the mission of producing of linen-based composite material. The study tested the sustainability and scalability of the business performance and found an interaction between business model sustainability and scalability.
Agroindustrial by-products from tomato, grape and myrtle given at low dosage to lactating dairy ewes: effects on rumen parameters and microbiota

Abstract The inclusion of by-products in composite pellet feeds could be a strategy to recycle nutritional components and a commercial opportunity for feeds industries. Aim of this study was to evaluate if the use of small amount of dried by-products containing polyphenols could alter rumen fermentation parameters and microbiota in dairy ewes. Thirty-six ewes (9 animals per group) were fed control diet (CON), and diets supplemented with 100 g/d per animal of tomato pomace (TP), 100 g/d per animal of grape marc (GM), and 75 g/d per animal of exhausted myrtle berries (EMB). Treatment showed significant effects only on pH, whereas sampling time affected almost all rumen fermentation parameters. No differences in the proportion of any phylum were detected in GM group compared to CON group. TP, compared to CON, evidenced higher abundance of Proteobacteria phylum (counts of 4.86; log fold chain of 5.61) which was dominated by Acetobacteraceae family with Acetobacter genus. The supplementation of EMB resulted in higher abundance of Succinivibrionaceae and lower abundance of Veillonellaceae family. Furthermore, in EMB group the Paraprevotellaceae and Prevotellaceae families dominated the phylum of Bacteroidetes. This phylum was significantly different between EMB and CON diet (counts of 57.06; log fold change of 1.10). The estimated production of methane and rumen fermentation parameters were not affected by the diets. The supplementation in small doses of GM, TP and EMB in the diets of sheep did not evidence a clear variation in rumen fermentation parameters nor changes in the general structure of rumen microbiota. HIGHLIGHTS The agroindustrial by-products did not affect the rumen biochemical parameters. The structure of bacteria community was influenced by EMB diet. GM and TP diets did not increase rumen ammonia.
Semi-supervised Classification of Paddy Fields from Dual Polarized Synthetic Aperture Radar (SAR) images using Deep Learning

ABSTRACT Rice is the major food grain for many countries in this world, in particular South Asian countries such as Pakistan, India, Bangladesh, Sri Lanka, Myanmar, Thailand, etc. India is one of the leading producers of rice, with agriculture contributing 14% to 15% to the Gross domestic product (GDP). Detection of paddy field requires constant monitoring of a region throughout the year. Hence, we use dual-polarized Sentinel-1 Synthetic Aperture Radar (SAR) data with 20 m resolutions for our study. In this paper, we propose a semi-supervised algorithm that detects paddy fields in various seasons. The technique is divided into two parts, unsupervised and supervised. Feature extraction layers of the Visual Geometry Group (VGG16) model are used to segregate patches into five clusters using an entropy-based loss function. Depending on the availability of the ground truth, data is sampled (stratified sampling), and only a certain amount of data is further used for the supervised section. Clusters showing higher similarity (Jaccard/Tanimoto test) with the paddy or nonpaddy classes are connected to a three-layer neural network used for the supervised method. This has been tested on two study sites using 10 data sets, five from 2018 to 2019, each. The highest accuracy reported for 2018 and 2019 is 85.61% and 84.92%, respectively. The two sites are selected from different districts of West Bengal, India. Our model has also shown higher generalization capability against the conventional-supervised models.
The Improvement of Productive Performances of Clementine Trees (Citrus Clementina Hort. Ex Tan.) Sprayed with Reflective Material

ABSTRACT Decrease in photosynthesis results from high leaf temperature, photosynthetic photon flux density, and UV-B. Here, we investigated whether a reflective material (kaolin) could improve photosynthetic performance and yield of clementine (Citrus clementina Hort. ex Tan., “Comune” cultivar) in southern Italy. Kaolin was sprayed on tree canopies every month during two summers; gas exchange, fluorimetry, and qualitative and productive parameters were measured. Kaolin increased the total average yield per tree and improved fruit color. PCA indicated that the best performances were obtained with kaolin in the last harvest. Kaolin affected the final fruit price by 3%, justifying its use.
Live performance, digestive tract features, and ileal nutrient digestibility in broilers fed diets containing soy hulls

Abstract This study aimed at determining the impact of dietary soy hulls (SH) addition on growth performance, digestive tract attributes, and apparent ileal digestibility of dry matter (DM), nitrogen, and phosphorus (P) in broiler chickens. Male broilers (Ross 308, n = 224) were assigned to one of four diets, including 0, 20, 40, or 60 g/kg SH, with eight replications per treatment from 0 to 21 d of age in a completely randomised design. Dietary chromic oxide was the indigestible marker for determining the apparent ileal digestibility. Data were subjected to orthogonal polynomial contrasts using the Proc GLM of SAS. Growth performance and small intestine weight and length, and gizzard content pH were not influenced (p > .05) by increasing levels of dietary SH. Increasing the dietary SH level resulted in a linear increase (p < .01) in absolute empty gizzard weight. Relative gizzard weight was greater (p < .05) in birds fed on 60 g/kg SH diet compared to birds fed on 40 g/kg SH diet. Apparent ileal digestibility of nitrogen was not affected (p > .05) by dietary SH inclusion. However, apparent ileal digestibility of DM and P increased linearly (p < .01) with increasing dietary SH levels. In conclusion, the addition of SH up to 60 g/kg improved the ileal digestibility of DM and P and increased gizzard weight without affecting the proportionate small intestine morphology and live performance of broiler chickens at 21 d of age. HIGHLIGHTS Soy hulls did not have any effect on growth Soy hulls increased the digestibility of P Soy hulls increased gizzard weight