Miracle-dz/UniFAR-FTUs huggingface dataset:
Intermediate Phase in Calcium–Silicate–Hydrates: Mechanical, Structural, Rigidity, and Stress Signatures

Topological constraint theory classifies disordered networks as flexible, stressed–rigid, or isostatic based on the balance between the number of topological constraints and degrees of freedom. In contrast with the predictions from a mean-field enumeration of the constraints, the isostatic state—wherein the network is rigid but free of stress—has been suggested to be achieved within a range of compositions, the intermediate phase, rather than at a fixed threshold. However, our understanding of the nature and potential structural signatures of the intermediate phase remains elusive. Here, based on molecular dynamics simulations of calcium–silicate–hydrate systems with varying compositions, we seek for some mechanical and structural signatures of the intermediate phase. We show that this system exhibits a composition-driven rigidity transition. We find that the fracture toughness, fracture energy, mechanical reversibility, and creep compliance exhibit an anomalous behavior within a compositional window at the vicinity of the isostatic threshold. These features are argued to constitute a mechanical signature of an intermediate phase. Notably, we identify a clear structural signature of the intermediate phase in the medium-range order of this system, which is indicative of an optimal space-filling tendency. Based on these simulations, we demonstrate that the intermediate phase observed in this system arises from a bifurcation between the rigidity and stress transitions. These features might reveal to be generic to isostatic disordered networks.
3D and 4D Printing of Polymers for Tissue Engineering Applications

Three-dimensional (3D) and Four-dimensional (4D) printing emerged as the next generation of fabrication techniques, spanning across various research areas, such as engineering, chemistry, biology, computer science, and materials science. Three-dimensional printing enables the fabrication of complex forms with high precision, through a layer-by-layer addition of different materials. Use of intelligent materials which change shape or color, produce an electrical current, become bioactive, or perform an intended function in response to an external stimulus, paves the way for the production of dynamic 3D structures, which is now called 4D printing. 3D and 4D printing techniques have great potential in the production of scaffolds to be applied in tissue engineering, especially in constructing patient specific scaffolds. Furthermore, physical and chemical guidance cues can be printed with these methods to improve the extent and rate of targeted tissue regeneration. This review presents a comprehensive survey of 3D and 4D printing methods, and the advantage of their use in tissue regeneration over other scaffold production approaches.
Atopy Increases Risk of Psychotic Experiences: A Large Population-Based Study

Introduction: Building upon the comorbidity between atopy and schizophrenia, we conducted a large cross-sectional, observational population-based study to examine if such associations also exist between atopic disorders (eczema, allergic rhinitis, and asthma) and nonclinical psychotic experiences. Methods: We examined psychotic experiences in a Dutch population sample through an online survey (≥14 years of age). Participants filled out the Questionnaire for Psychotic Experiences, together with questions screening for atopic disorders (eczema, allergic rhinitis, and asthma). Prevalence rates were calculated; binary logistic regression was used to determine odds ratios (ORs) (age, gender, and years of education as covariates). Results: We included 6,479 participants. Individuals diagnosed with one or more atopic disorders had an increased risk of psychotic experiences as compared with controls (OR = 1.26). Analysis of individual symptoms revealed an OR of 1.27 for hallucinations, whereas delusions only showed a trend. With each additional atopic disorder, the risk of psychotic experiences increased. This was also observed for hallucinations alone but not for delusions alone. Atopy was associated with hallucinations across all modalities (OR ranging from 1.19 to 1.40). These results did not appear to be driven specifically by any one of the atopic disorders. Conclusion: In the largest population sample of adolescents and adults to date, we found that atopic disorders (asthma, eczema, and allergic rhinitis) increase the risk of psychotic experiences, in a dose–response fashion. These results provide further support for the role of immunological components in the predisposition for psychosis and can serve as a base for further research.
A 40 Mb/s soft-output Viterbi decoder

Soft-output decoding has evolved as a key technology for new error correction approaches with unprecedented performance as well as for improvement of well established transmission techniques. In this paper, we present a high-speed VLSI implementation of the soft-output Viterbi algorithm, a low complexity soft-output algorithm, for a 16-state convolutional code. The 43 mm/sup 2/ standard cell chip achieves a simulated throughput of 40 Mb/s, while tested samples achieved a throughput of 50 Mb/s. The chip is roughly twice as big as a 16-state Viterbi decoder without soft outputs. It is thus shown with the design that transmission schemes using soft-output decoding can be considered practical even at very high throughput. Since such decoding systems are more complex to design than hard output systems, special emphasis is placed on the employed design methodology. >
Cover Crop Management Practices Rather Than Composition of Cover Crop Mixtures Affect Bacterial Communities in No-Till Agroecosystems

Cover cropping plays a key role in the maintenance of arable soil health and the enhancement of agroecosystem services. However, our understanding of how cover crop management impacts soil microbial communities and how these interactions might affect soil nutrient cycling is still limited. Here, we studied the impact of four cover crop mixtures varying in species richness and functional diversity, three cover crop termination strategies (i.e., frost, rolling, and glyphosate) and two levels of irrigation at the cover crop sowing on soil nitrogen and carbon dynamics, soil microbial diversity, and structure as well as the abundance of total bacteria, archaea, and N-cycling microbial guilds. We found that total nitrogen and soil organic carbon were higher when cover crops were killed by frost compared to rolling and glyphosate termination treatments, while cover crop biomass was positively correlated to soil carbon and C:N ratio. Modifications of soil properties due to cover crop management rather than the composition of cover crop mixtures were related to changes in the abundance of ammonia oxidizers and denitrifiers, while there was no effect on the total bacterial abundance. Unraveling the underlying processes by which cover crop management shapes soil physico-chemical properties and bacterial communities is of importance to help selecting optimized agricultural practices for sustainable farming systems.
Chalcone Isomerase a Key Enzyme for Anthocyanin Biosynthesis in Ophiorrhiza japonica

Anthocyanins are distributed ubiquitously to terrestrial plants and chalcone isomerase (CHI) catalyzes the stereospecific isomerization of chalcones – a committed step in the anthocyanin biosynthesis pathway. In this study, one gene encoding CHI was isolated from Ophiorrhiza japonica and designated as OjCHI. Multiple sequence alignments and phylogenetic analysis revealed that OjCHI had the conserved CHI active site residues and was classified into type I CHI group. In order to better understand the mechanisms of anthocyanin synthesis in O. japonica, integrative analysis between metabolites and OjCHI expression was conducted. The results showed OjCHI expression matched the accumulation patterns of anthocyanins not only in different tissues but also during the flower developmental stages, suggesting the potential roles of OjCHI in the biosynthesis of anthocyanin. Then biochemical analysis indicated that recombinant OjCHI protein exhibited a typical type I CHI activity which catalyzed the production of naringenin from naringenin chalcone. Moreover, expressing OjCHI in Arabidopsis tt5 mutant restored the anthocyanins and flavonols phenotype of hypocotyl, cotyledon and seed coat, indicating its function as a chalcone isomerase in vivo. In summary, our findings reveal the in vitro as well as in vivo functions of OjCHI and provide a resource to understand the mechanism of anthocyanin biosynthesis in O. japonica.
White Matter Abnormalities in the Corpus Callosum in Acute and Recovered Anorexia Nervosa Patients—A Diffusion Tensor Imaging Study

Objective: Severe malnutrition in patients with anorexia nervosa (AN) as well as possible trait-related aberrations lead to pronounced structural brain changes whose reversibility after recovery is currently unclear. Previous diffusion tensor imaging (DTI) studies investigating white matter (WM) microstructure alterations in AN are inconsistent. Methods: In this so far largest DTI study in adults, we investigated 33 AN patients, 20 recovered (REC), and 33 healthy women. DTI data were processed using the “DTI and Fiber tools,” and the Computational Anatomy Toolbox. WM integrity, both in terms of fractional anisotropy (FA) and mean diffusivity (MD), was assessed. Results: We found a significant FA decrease in the corpus callosum (body) and an MD decrease in the posterior thalamic radiation in the AN group. The REC group displayed FA decrease in the corpus callosum in comparison to HC, whereas there were no MD differences between the REC and HC groups. Conclusion: Despite prolonged restoration of weight in the REC group, no significant regeneration of WM integrity in terms of FA could be observed. Transient changes in MD likely represent a reversible consequence of the acute state of starvation or result from dehydration. Reduction of FA either may be due to WM damage resulting from malnutrition or may be considered a pre-morbid marker.
Emergence and Characterization of Acute Coronary Syndrome in Adults After Confirmed or Missed History of Kawasaki Disease in Japan: A Japanese Nationwide Survey

Background: Acute coronary syndrome (ACS), which is emerging in adults long after confirmed (followed-up or lost-to-follow), or missed Kawasaki disease (KD), is poorly characterized. Methods and Results: A Japanese retrospective nationwide hospital-based questionnaire survey of ACS during 2000–09 was conducted to characterize such patients. Among a total of 67 patients (median age 35, male 76%) recruited, low conventional coronary risks (≤1/6) was noted in 75%, a diagnosis of ST-elevation and myocardial infarction or cardiac arrest in 66%, medication before ACS in 22% (warfarin in 4%), and no prior history of acute myocardial infarction in 94%. One-month mortality was 19%. KD diagnosis was made in 32 during acute illness (Group A), in which 17 were lost to follow, and retrospectively in the other 35 from coronary imaging at ACS (Group B). Group A developed ACS at lower coronary risks (≤2/5 in 87 vs. 65% in group B, p = 0.043) at a younger age (26.5 vs. 40 yo, p < 0.001). In group A, followed-up patients developed ACS under medication before ACS (87 vs. 0% in lost-to-follow patients, p < 0.001) for giant aneurysm in culprit lesions (69 vs. 29%, p = 0.030). One-month mortality was comparable between groups A and B, and between patients followed-up and lost-to-follow in group A. The culprit lesion in group A was characterized by the association of an aneurysm ≥6 mm in acute KD (100%), lack of significant stenosis (61%) or giant aneurysm (50%) in the long-term (median interval 16 y), and the presence of intravascular ultrasound-derived calcification at ACS (86%). Conclusions: The present retrospective nationwide questionnaire survey demonstrated nationwide emergence of initial ACS in young adults at low coronary risks, who are followed-up or lost-to-follow after confirmed KD and initial coronary aneurysms ≥6 mm.
A Large-Scale, Cross-Sectional Investigation Into the Efficacy of Brain Training

Brain training is a large and expanding industry, and yet there is a recurrent and ongoing debate concerning its scientific basis or evidence for efficacy. Much of evidence for the efficacy of brain training within this debate is from small-scale studies that do not assess the type of “brain training,” the specificity of transfer effects, or the length of training required to achieve a generalized effect. To explore these factors, we analyze cross-sectional data from two large Internet-cohort studies (total N = 60,222) to determine whether cognition differs at the population level for individuals who report that they brain train on different devices, and across different timeframes, with programs in common use circa 2010–2013. Examining scores for an assessment of working-memory, reasoning and verbal abilities shows no cognitive advantages for individuals who brain train. This contrasts unfavorably with significant advantages for individuals who regularly undertake other cognitive pursuits such as computer, board and card games. However, finer grained analyses reveal a more complex relationship between brain training and cognitive performance. Specifically, individuals who have just begun to brain train start from a low cognitive baseline compared to individuals who have never engaged in brain training, whereas those who have trained for a year or more have higher working-memory and verbal scores compared to those who have just started, thus suggesting an efficacy for brain training over an extended period of time. The advantages in global function, working memory, and verbal memory after several months of training are plausible and of clinically relevant scale. However, this relationship is not evident for reasoning performance or self-report measures of everyday function (e.g., employment status and problems with attention). These results accord with the view that although brain training programs can produce benefits, these might extend to tasks that are operationally similar to the training regime. Furthermore, the duration of training regime required for effective enhancement of cognitive performance is longer than that applied in most previous studies.
Sleeping Beauty Mouse Models of Cancer: Microenvironmental Influences on Cancer Genetics

The Sleeping Beauty (SB) transposon insertional mutagenesis system offers a streamlined approach to identify genetic drivers of cancer. With a relatively random insertion profile, SB is uniquely positioned for conducting unbiased forward genetic screens. Indeed, SB mouse models of cancer have revealed insights into the genetics of tumorigenesis. In this review, we highlight experiments that have exploited the SB system to interrogate the genetics of cancer in distinct biological contexts. We also propose experimental designs that could further our understanding of the relationship between tumor microenvironment and tumor progression.
Testing the Adaptive Potential of Yellowtail Kingfish to Ocean Warming and Acidification

Estimating the heritability and genotype by environment (GxE) interactions of performance-related traits (e.g., growth, survival, reproduction) under future ocean conditions is necessary for inferring the adaptive potential of marine species to climate change. To date, no studies have used quantitative genetics techniques to test the adaptive potential of large pelagic fishes to the combined effects of elevated water temperature and ocean acidification. We used an experimental approach to test for heritability and GxE interactions in morphological traits of juvenile yellowtail kingfish, Seriola lalandi, under current-day and predicted future ocean conditions. We also tracked the fate of genetic diversity among treatments over the experimental period to test for selection favoring some genotypes over others under elevated temperature and CO2. Specifically, we reared kingfish to 21 days post hatching (dph) in a fully crossed 2 × 2 experimental design comprising current-day average summer temperature (21°C) and seawater pCO2 (500 μatm CO2) and elevated temperature (25°C) and seawater pCO2 (1,000 μatm CO2). We sampled larvae and juveniles at 1, 11, and 21 dph and identified family of origin of each fish (1,942 in total) by DNA parentage analysis. The animal model was used to estimate heritability of morphological traits and test for GxE interactions among the experimental treatments at 21 dph. Elevated temperature, but not elevated CO2 affected all morphological traits. Weight, length and other morphological traits in juvenile yellowtail kingfish exhibited low but significant heritability under current day and elevated temperature. However, there were no measurable GxE interactions in morphological traits between the two temperature treatments at 21 dph. Similarly, there was no detectable change in any of the measures of genetic diversity over the duration of the experiment. Nonetheless, one family exhibited differential survivorship between temperatures, declining in relative abundance between 1 and 21 dph at 21°C, but increasing in relative abundance between 1 and 21 dph at 25°C. This suggests that this family line could perform better under future warming than in current-day conditions. Our results provide the first preliminary evidence of the adaptive potential of a large pelagic fisheries species to future ocean conditions.
A Game-Theoretical Network Formation Model for C. elegans Neural Network

Studying and understanding human brain structures and functions have become one of the most challenging issues in neuroscience today. However, the mammalian nervous system is made up of hundreds of millions of neurons and billions of synapses. This complexity made it impossible to reconstruct such a huge nervous system in the laboratory. So, most researchers focus on C. elegans neural network. The C. elegans neural network is the only biological neural network that is fully mapped. This nervous system is the simplest neural network that exists. However, many fundamental behaviors like movement emerge from this basic network. These features made C. elegans a convenient case to study the nervous systems. Many studies try to propose a network formation model for C. elegans neural network. However, these studies could not meet all characteristics of C. elegans neural network, such as significant factors that play a role in the formation of C. elegans neural network. Thus, new models are needed to be proposed in order to explain all aspects of C. elegans neural network. In this paper, a new model based on game theory is proposed in order to understand the factors affecting the formation of nervous systems, which meet the C. elegans frontal neural network characteristics. In this model, neurons are considered to be agents. The strategy for each neuron includes either making or removing links to other neurons. After choosing the basic network, the utility function is built using structural and functional factors. In order to find the coefficients for each of these factors, linear programming is used. Finally, the output network is compared with C. elegans frontal neural network and previous models. The results implicate that the game-theoretical model proposed in this paper can better predict the influencing factors in the formation of C. elegans neural network compared to previous models.
Theoretical Modeling and Experimental Detection of the Extracellular Phasic Impedance Modulation in Rabbit Hearts

Theoretical cardiac electrophysiology focuses on the dynamics of the membrane and sarcoplasmic reticulum ion currents; however, passive (e.g., membrane capacitance) and quasi-active (response to small signals) properties of the cardiac sarcolemma, which are quantified by impedance, are also important in determining the behavior of cardiac tissue. Theoretically, impedance varies in the different phases of a cardiac cycle. Our goal in this study was to numerically predict and experimentally validate these phasic changes. We calculated the expected impedance signal using analytic methods (for generic ionic models) and numerical computation (for a rabbit ventricular ionic model). Cardiac impedance is dependent on the phase of the action potential, with multiple deflections caused by a sequential activation and inactivation of various membrane channels. The two main channels shaping the impedance signal are the sodium channel causing a sharp and transient drop at the onset of action potential and the inward rectifying potassium channel causing an increase in impedance during the plateau phase. This dip and dome pattern was confirmed in an ex-vivo rabbit heart model using high-frequency sampling through a monophasic action potential electrode. The hearts were immobilized using a myosin-inhibitor to minimize motion artifacts. We observed phasic impedance changes in three out of four hearts with a dome amplitude of 2 − 4Ω. Measurement of phasic impedance modulation using an extracellular electrode is feasible and provides a non-invasive way to gain insight into the state of cardiac cells and membrane ionic channels. The observed impedance recordings are consistent with the dip and dome pattern predicted analytically.
Functional Analysis of Polyprenyl Diphosphate Synthase Genes Involved in Plastoquinone and Ubiquinone Biosynthesis in Salvia miltiorrhiza

Polyprenyl diphosphate synthase (PPS) plays important roles in the biosynthesis of functionally important plastoquinone (PQ) and ubiquinone (UQ). However, only few plant PPS genes have been functionally characterized. Through genome-wide analysis, two PPS genes, termed SmPPS1 and SmPPS2, were identified from Salvia miltiorrhiza, an economically significant Traditional Chinese Medicine material and an emerging model medicinal plant. SmPPS1 and SmPPS2 belonged to different phylogenetic subgroups of plant trans-long-chain prenyltransferases and exhibited differential tissue expression and light-induced expression patterns. Computational prediction and transient expression assays showed that SmPPS1 was localized in the chloroplasts, whereas SmPPS2 was mainly localized in the mitochondria. SmPPS2, but not SmPPS1, could functionally complement the coq1 mutation in yeast cells and catalyzed the production of UQ-9 and UQ-10. Consistently, both UQ-9 and UQ-10 were detected in S. miltiorrhiza plants. Overexpression of SmPPS2 caused significant UQ accumulation in S. miltiorrhiza transgenics, whereas down-regulation resulted in decreased UQ content. Differently, SmPPS1 overexpression significantly elevated PQ-9 content in S. miltiorrhiza. Transgenic lines showing a down-regulation of SmPPS1 expression exhibited decreased PQ-9 level, abnormal chloroplast and trichome development, and varied leaf bleaching phenotypes. These results suggest that SmPPS1 is involved in PQ-9 biosynthesis, whereas SmPPS2 is involved in UQ-9 and UQ-10 biosynthesis.