Miracle-dz/UniFAR-FTUs huggingface dataset:
Prediction of Water Solubility in Glassy Polymers Using Nonequilibrium Thermodynamics

In this study, the sorption of water in poly(methyl methacrylate) (PMMA) was measured at various water vapor activities (0–0.85) at 25, 35, and 45 °C using a quartz spring microbalance. Furthermore, the water sorption isotherms in PMMA were predicted using two nonequilibrium thermodynamic models: the nonequilibrium lattice fluid (NELF) model and nonequilibrium statistical associating fluid theory (NE-SAFT), where excellent agreement between the NE-SAFT prediction and experimental data was observed. In contrast, deviation between the NELF model prediction and water sorption isotherms in PMMA was observed above a water activity of ca. 0.50. In situ time-resolved Fourier transform infrared attenuated total reflectance spectroscopy confirmed the presence of self-associated water (i.e., water clusters) at elevated water activities, providing a rationale for deviation between the NELF model and experimental data, where unlike NE-SAFT, the NELF model does not account for these self-association interactions. The .
Abbreviated title : HISTORY MODULATES DISTRACTORS 1 2 3 4 History modulates early sensory processing of salient distractors 5 6

45 To find important objects, we must focus on our goals, ignore distractions, and take our 46 changing environment into account. This is formalized in models of visual search whereby 47 goal-driven, stimulus-driven and history-driven factors are integrated into a priority map 48 that guides attention. Stimulus history robustly influences where attention is allocated 49 even when the physical stimulus is the same: when a salient distractor is repeated over 50 time, it captures attention less effectively. A key open question is how we come to ignore 51 salient distractors when they are repeated. Goal-driven accounts propose that we use an 52 active, expectation-driven mechanism to attenuate the distractor signal (e.g., predictive 53 coding), whereas stimulus-driven accounts propose that the distractor signal is attenuated 54 due to passive changes to neural activity and inter-item competition (e.g., adaptation). To 55 test these competing accounts, we measured item-specific fMRI responses in human 56 visual cortex during a visual search task where trial history was manipulated (colors 57 unpredictably switched or were repeated). Consistent with a stimulus-driven account of 58 history-based distractor suppression, we found that repeated singleton distractors were 59 suppressed starting in V1, and distractor suppression did not increase in later visual 60 areas. In contrast, we observed signatures of goal-driven target enhancement that were 61 absent in V1, increased across visual areas, and were not modulated by stimulus history. 62 Our data suggest that stimulus history does not alter goal-driven expectations, but rather 63 modulates canonically stimulus-driven sensory responses to contribute to a temporally64 integrated representation of priority. 65 66 67 68 69 70 71 72 73 74 HISTORY MODULATES DISTRACTORS 3 Significance Statement 75 Visual search refers to our ability to find what we are looking for in a cluttered visual world 76 (e.g., finding your keys). To perform visual search, we must integrate information about 77 our goals (e.g., ‘find the red key-chain’), the environment (e.g., salient items capture your 78 attention), and changes to the environment (i.e., stimulus history). Although stimulus 79 history impacts behavior, the neural mechanisms that mediate history-driven effects 80 remain debated. Here, we leveraged fMRI and multivariate analysis techniques to 81 measure history-driven changes to the neural representation of items during visual 82 search. We found that stimulus history influenced the representation of a salient ‘pop-out’ 83 distractor starting in V1, suggesting that stimulus history operates via modulations in early 84 sensory processing rather than goal-driven expectations. 85
An artificial neural network based method for beam position calculation in electron storage ring

Introduction BPM [1] [2] are non-interceptive devices used in electron storage rings for beam position measurement and closed orbit correction. BPM usually consists of four button type electrodes which sense the electric field of electron beam. The button type electrodes used in Indus-2 [3] BPM are not placed on the symmetry axis of vacuum chamber of BPM but are placed on diagonal directions to avoid hitting by synchrotron radiation. Another reason for doing this is due to mechanical constraint of race track geometry adopted for vacuum chamber housing of BPM in Indus-2. This placement of buttons in non-symmetric axis results in non linear response of BPM. The conventional method used to find the position assumes that combinations of the four button signals are proportional to the beam position and is termed as difference over sum method. The difference over sum method [4] for converting BPM signals to beam position works well for beams in the center of the beam pipe, but the linear relationship breaks down at large displacements. In this case a polynomial of suitable degree is used to compute the beam position from four button signals of BPM [5] [6]. The coefficients of the polynomial are computed from bench calibration data of each BPM. The beam position measurement accuracy depends upon the nature of mathematical polynomial used to find the beam position. Moreover it is also important that all the four button electrode signals should be correct and if any BPM is malfunctioning it should be identified. Hence the consistency of these signals should also be checked to avoid any wrong beam position calculation. Finding proper polynomial requires extensive simulation which is tedious and time consuming due to complicated geometry of BPM. In this paper, a new method based on ANN for beam position calculation and for checking consistency of BPM has been described. Artificial neural network architecture ANN can be described as parallel computational models which have tightly interconnected adaptive processing units [7]. Adaptive characteristic of ANN makes them suitable to train them by example. Multi-layered feed-forward backpropagation neural network architecture has been adopted for this system due to its simplicity and speed. Two networks are designed, one for beam position computation and another for detecting malfunctioning of BPM by doing consistency check. The difference between these two networks is in their training data. Both of these networks are made up of one input layer, three hidden layers, and one output layer. Input and output layer each has two neurons (corresponding to two inputs and two outputs) while each hidden layer has 5 neurons. The learning rule is back propagation. The dot-product is used as input function while tansigmoid function that maps the input to the output in the interval (-1, 1) is used as transfer function in each layer. The performance function is mean squared error. LevenbergMarquardt algorithm has been used as back propagation training algorithm.
Towards an increasing regionalization of international politics? An analysis of external competencies of regional international organizations

ABSTRACT Around the world, states cooperate in Regional International Organizations (RIOs). Although most RIOs were created to foster cooperation between their members, most of today’s RIOs are also equipped with external policy competencies, allowing them to become active beyond their borders. This paper sheds light on the evolution of external policy competencies of 76 RIOs over time and between policy areas. It shows that RIO’s external policy competencies increase over time and that some cover a broader range of external policy fields than others. The paper draws on a rational choice framework and develops RIO- and policy-level hypotheses to account for observed variation. A multilevel analysis reveals that RIOs have more external policy competencies when they are more exposed to interdependence in their neighbourhood and when they also have many internal competencies.
Field assessments of heart rate dynamics during spawning migration of wild and hatchery-reared Chinook salmon

During spawning, adult Pacific salmonids (Oncorhynchus spp.) complete challenging upriver migrations during which energy and oxygen delivery must be partitioned into activities such as locomotion, maturation and spawning behaviours under the constraints of an individual's cardiac capacity. To advance our understanding of cardiac function in free-swimming fishes, we implanted migrating adult Chinook salmon (Oncorhynchus tshawytscha) collected near the mouth of the Sydenham River, Ontario, with heart rate (fH) biologgers that recorded fH every 3 min until these semelparous fish expired on spawning grounds several days later. Fundamental aspects of cardiac function were quantified, including resting, routine and maximum fH, as well as scope for fH (maximum−resting fH). Predictors of fH were explored using generalized least-squares regression, including water temperature, discharge, fish size and fish origin (wild versus hatchery). Heart rate was positively correlated with water temperature, which aligned closely with daily and seasonal shifts. Wild fish had slower resting heart rates than hatchery fish, which led to significantly higher scope for fH. Our findings suggest that wild salmon may have better cardiac capacity during migration than hatchery fish, potentially promoting migration success in wild fish. This article is part of the theme issue ‘Measuring physiology in free-living animals (Part I)’.
Combining Computational Thinking and Chibitronics and Makey Makey to Develop a Social Story Teaching Aid System to Improve Social Reciprocity and Emotional Expression Skills for Autistic Children

This study is aimed to teach autistic children to learn social reciprocity and emotional expression through social stories, and build a social story teaching aid system with the aid of sequential computational thinking as learning strategy as well as Chibitronics and Makey Makey. This system can make autistic children to learn situational content from social stories, understand the social stories through computational thinking and arrange corresponding sequential structure. In this study, we recruited three 9 year-old autistic children, carried out teaching experiments four times and observed their behavior for story plot. It showed that technical teaching aid can improve autistic children's learning motivation and interests and provide them with contextual cue of social situation, helping build their social recognition and social reciprocity into social situation and their social reciprocity skills. I believe that autistic children can improve their social reciprocity and emotional expression skills with the help of sequential computational thinking and social teaching aid system designed with Chibitronics and Makey Makey.
Strategy Decision Making in E-commerce: A Case Study of Amazon

Strategy decision making is essential for the development of a firm. However, until now, previous researches about strategy decision making are mostly based on theoretical analysis rather than the prediction of practical effectiveness. This work emphasizes on e-commerce area and sheds light on the discovery of optimal strategy decision making. This article conducts a case study analysis by choosing Amazon as an example and combining with the analysis of Porter's Competitive Theory to illustrate how Amazon made their decisions and became successful accordingly. We indicate that the successful decision making of Amazon is based on the lower cost of marginal physical cost, the variation of products and the technical innovation outcomes.
Performance of elite genotypes of barley, chickpea, lentil, and wheat under conservation agriculture in Mediterranean rainfed conditions

Abstract Conservation agriculture (CA) practices are becoming more important in Mediterranean rainfed areas due to their potential to minimize climatic risk, reduce soil erosion, and improve soil quality and water availability. Due to minimum soil disturbance and crop residue retention, the soil environment for crop growth and development can differ between CA and conventional tillage (CT) practice. However, breeding targets for improving yield performance in CA system remain poorly explored. The objective of this study was to assess the performance of elite genotypes of barley, chickpea, lentil, and wheat grown under CA, a promising alternative agricultural practice in the Mediterranean rainfed conditions. A three-year field study, with contrasting rainfall pattern, was conducted in the International Center for Agriculture Research in the Dry Areas’s research field in Morocco to evaluate the tillage × genotype interaction and its consequence for yield performance of barley, chickpea, lentil, and wheat. Thirteen elite genotypes for each crop were planted under both CA and CT systems. Wheat and chickpea produced significantly higher grain yield (+62% for wheat and +43% for chickpea) under CA than in CT, while lentil and barley performed equally under both systems. Significant effect of tillage × genotype was more frequent for chickpea and wheat than for barley and lentil. Increased yield under CA, mainly in dry year, was associated with higher harvest index (HI). For each crop species yield was mainly influenced by rainfall amount and distribution (75–88% yield variation), and tillage × genotype was of little importance. The overall results suggest that a specific breeding program for CA in lentil, chickpea, wheat, and barley may not be efficient. Few tillage × genotype interaction, especially in dry years, indicated that breeding target on increasing HI, tolerance to drought (high yield in dry years), and potential yield (high yield in wet year) can help to improve yield performance of chickpea, lentil, and wheat genotypes in CA system. Varieties with wider adaptability considering drought tolerance, higher yield with stability, and adoption of CA practices are important in the context of the Mediterranean rainfed environment. Integrating trade-off analysis between yield potential and stability in a rainfall gradient in both CT and CA in the national certification scheme of varieties may be more efficient than developing breeding programs for each type of tillage system.
HOXB8 Counteracts MAPK/ERK Oncogenic Signaling in a Chicken Embryo Model of Neoplasia

HOX transcription factors are members of an evolutionarily conserved family of proteins required for the establishment of the anteroposterior body axis during bilaterian development. Although they are often deregulated in cancers, the molecular mechanisms by which they act as oncogenes or tumor suppressor genes are only partially understood. Since the MAPK/ERK signaling pathway is deregulated in most cancers, we aimed at apprehending if and how Hox proteins interact with ERK oncogenicity. Using an in vivo neoplasia model in the chicken embryo that we have developed, consisting in the overactivation of the ERK1/2 kinases in the trunk neural tube, we analyzed the consequences of HOXB8 gain of function at morphological and transcriptional level in this model. We found that HOXB8 acts as a tumor suppressor, counteracting ERK-induced neoplasia. HOXB8 tumor suppressor function in this model relies on a large reversion of the oncogenic transcriptome induced by ERK. In addition to showing that HOXB8 protein controls the transcriptional responsiveness to ERK oncogenic signaling, our study identified new downstream targets of ERK oncogenic activation in an in vivo context that could provide clues for therapeutic strategies.
Clustering and visualizing the distribution of overlapping reading frames in virus genomes

Gene overlap occurs when two or more genes are encoded by the same nucleotides. This phenomenon is found in all taxonomic domains, but is particularly common in viruses, where it may increase the information content of compact genomes or influence the creation of new genes. Here we report a global comparative study of overlapping reading frames (OvRFs) of 12,609 virus reference genomes in the NCBI database. We retrieved metadata associated with all annotated reading frames in each genome record to calculate the number, length, and frameshift of OvRFs. Our results show that while the number of OvRFs increases with genome length, they tend to be shorter in longer genomes. The majority of overlaps involve +2 frameshifts, predominantly found in ds-DNA viruses. However, the longest overlaps involve no shift in reading frame (+0), increasing the selective burden of the same nucleotide positions within codons, instead of exposing additional sites to purifying selection. Next, we develop a new graph-based representation of the distribution of OvRFs among the reading frames of genomes in a given virus family. In the absence of an unambiguous partition of reading frames by homology at this taxonomic level, we used an alignment-free k-mer based approach to cluster protein coding sequences by similarity. We connect these clusters with two types of directed edges to indicate (1) that constituent reading frames are adjacent in one or more genomes, and (2) that the reading frames overlap. These adjacency graphs not only provide a natural visualization scheme, but also a novel statistical framework for analyzing the effects of gene- and genome-level attributes on the frequencies of overlaps.
Variance reducing and noise correction in protein quantification by measuring fluctuations in fluorescence due to photobleaching

Quantifying the absolute protein number using the ratio between the variance and the mean of the protein Fluorescence intensity is a straightforward method for microscopy imaging. Recently, this method has been expanded to fluorescence decaying processes due to photobleaching with binomial distribution. The article examines the method proposed and shows how it can be adapted to the case of variance in the initial number of proteins between the cells. The article shows that the method can be improved by the implementation of the information processing of each frame independently from other frames. By doing so, the variance in determining the protein number can be reduced. In addition, the article examines the management of unwanted noises in the measurement, offers a solution for the shot noise and background noise, examines the expected error caused by the decay constant inaccuracy, and analyzes the expected difficulties in conducting a practical experiment, which includes a non-exponential decay and variance in the photobleaching rate of the cells. The method can be applied to any superposition of n 0 discrete decaying processes. However, the evaluation of expected errors in quantification is essential for early planning of the experimental conditions and evaluation of the error.
Structural basis for cytoplasmic dynein-1 regulation by Lis1

The lissencephaly 1 gene, LIS1, is mutated in patients with the neurodevelopmental disease lissencephaly. The Lis1 protein is conserved from fungi to mammals and is a key regulator of cytoplasmic dynein-1, the major minus-end-directed microtubule motor in many eukaryotes. Lis1 is the only dynein regulator that binds directly to dynein’s motor domain, and by doing so alters dynein’s mechanochemistry. Lis1 is required for the formation of fully active dynein complexes, which also contain essential cofactors: dynactin and an activating adaptor. Here, we report the first high-resolution structure of the yeast dynein–Lis1 complex. Our 3. 1Å structure reveals, in molecular detail, the major contacts between dynein and Lis1 and between Lis1’s ß-propellers. Structure-guided mutations in Lis1 and dynein show that these contacts are required for Lis1’s ability to form fully active human dynein complexes and to regulate yeast dynein’s mechanochemistry and in vivo function. We present a model for the conserved role of Lis1 in regulating dynein from yeast to humans.
Evolutionary analysis of gene ages across TADs associates chromatin topology with whole genome duplications

Topologically associated domains (TADs) are interaction sub-networks of chromosomal regions in 3D genomes. TAD boundaries frequently coincide with genome breaks while boundary deletion is under negative selection, suggesting that TADs may facilitate genome rearrangements and evolution. We show that genes co-localise by evolutionary age in humans and mice, resulting in TADs having different proportions of younger and older genes. We observe a major transition in the age co-localisation patterns between the genes born during vertebrate whole genome duplications (WGDs) or before, and those born afterwards. We also find that genes recently duplicated in primates and rodents are more frequently essential when they are located in old-enriched TADs and interact with genes that last duplicated during the WGD. Therefore, the evolutionary relevance of recent genes may increase when located in TADs with established regulatory networks. Our data suggests that TADs could play a role in organising ancestral functions and evolutionary novelty. Highlights TADs coincide with clusters of genes that are close in their evolutionary age. Whole genome duplications mark a transition in gene age co-localisation clusters. Gene age co-localisation patterns are associated with TAD insulation. Young essential genes share TADs and interact with old genes.
Essential role of hyperacetylated microtubules in innate immunity escape orchestrated by the EBV-encoded BHRF1 protein

Innate immunity constitutes the first line of defense against viruses, in which mitochondria play an important role in the induction of the interferon (IFN) response. BHRF1, a multifunctional viral protein expressed during Epstein-Barr virus reactivation, modulates mitochondrial dynamics and disrupts the IFN signaling pathway. Mitochondria are mobile organelles that move through the cytoplasm thanks to the cytoskeleton and in particular the microtubule (MT) network. MTs undergo various post-translational modifications, among them tubulin acetylation. In this study, we demonstrated that BHRF1 induces MT hyperacetylation to escape innate immunity. Indeed, expression of BHRF1 induces the aggregation of shortened mitochondria next to the nucleus. This mito-aggresome is organized around the centrosome and its formation is MT-dependent. We also observed that the BHRF1-induced hyperacetylation of MTs involves the α-tubulin acetyltransferase ATAT1. Thanks to a non-acetylatable α-tubulin mutant, we demonstrated that this hyperacetylation is necessary for the mito-aggresome formation. We investigated the mechanism leading to the clustering of mitochondria, and we identified dyneins as motors that are required for the mitochondrial aggregation. Finally, we demonstrated that BHRF1 needs MT hyperacetylation to block the induction of the IFN response. Indeed, in the absence of MT hyperacetylation, BHRF1 is unable to initiate the sequestration of mitochondria into autophagosomes, and mitophagy, which is essential to inhibiting the signaling pathway. Therefore, our results reveal the role of the MT network, and its acetylation level, in the induction of a pro-viral mitophagy.