Miracle-dz/UniFAR-FTUs huggingface dataset:
Anomalous Photoconductivity in SrTiO3

We have measured the photoconductivity of insulative SrTiO3 single crystal whose band-gap is 3.2 eV. We have found that the dependence of resistivity on temperature shows metallic conduction under white light irradiation and the resistivity drops rapidly below 105 K. This temperature at which a giant photoconductivity phenomenon occurs coincides with that of the cubic-to-tetragonal structural phase transition, suggesting that the anomalous photoconductivity is related to the structural phase transition.
The Extraordinary Radio Source 3C 442

We have studied the distinctive system 3C 442 with VLA at 6, 20, and 90 cm. This is associated with two galaxies, NGC 7236/7237. The image of the radio source shows a mass of filaments and diffuse emission surrounding the two galaxies. A weak resolved radio core lies at the position of NGC 7237, and two arcs of steep-spectrum radio emission cross the region containing the optical galaxies, but no opaque radio core or head-tail jet structures are found, as is usually the case for radio galaxies of similar radio luminosity.
Dynamic‐spatial management of coastal aquifers

We analyze the management of a coastal aquifer under seawater intrusion (SWI) using distributed control methods. The aquifer's state is taken as the water head elevation (vis‐à‐vis sea level, say), which varies with time and in space since extraction, natural recharge and lateral water flows vary with time and in space. The water head, in turn, induces a temporal‐spatial SWI process, which changes the volume of fresh water in the aquifer. Under reasonable conditions we show that the optimal state converges to a steady‐state process that is constant in time. We characterize the optimal steady‐state process in terms of a standard control problem (in space) and offer a tractable algorithm to solve for it. Copyright © 2009 John Wiley & Sons, Ltd.
Perturbation analysis of droplet deformation under electrical double layer forces

Fluid-liquid interface deformation by electrical double layer surface forces introduces several difficulties for the accurate interpretation of fluid-drop\char21{}particle interaction measurements. We investigate the source of these difficulties theoretically using a perturbation method. Relevant quantities, such as interface shape and droplet internal pressure, are expressed in series expansions in a dimensionless parameter ${M=(n}_{0}{k}_{B}T)/(\ensuremath{\gamma}/l),$ being the ratio of electrical double layer forces to surface tension, i.e., an effective double layer Bond number. Governing equations are truncated to first order in $M,$ and solved for the deformation in droplet shape to leading order. Analytical and numerical results for the case of neutrally buoyant drops interacting with charged spherical particles allow for a quantitative examination of the extent of deformation. The case of drops experiencing finite buoyancy is also formulated in a linear theory, and a method of solution is outlined.
Linear statistical models and related methods : with applications to social research

Linear statistical models and related methods with applications to social research. Fox J New York, New York, John Wiley and Sons, 1984. xx, 449 p. (Wiley Series in Probability and Mathematical Statistics.) This book aims to provide an in-depth, modern treatment of linear models and related methods. The text's major premise is that the teaching of social statistics should combine statistical theory, critical application, and methodology. Throughout the book, general approaches and principles are employed to emphasize the conceptual unity of the techniques covered. Chapter 1 is devoted to regression analysis, which examines the relationship of a quantitative dependent variable to 1 or more quantitative independent variables. Much of the statistical theory of linear models is developed in this chapter. Chapter 2 extends linear models to include qualitative independent variables. The treatment of analysis of variance in this chapter emphasizes unbalanced (i.e., unequal-cell-frequencies) data. Chapter 3 presents a variety of material on diagnosing and correcting linear-model problems. The problems examined include collinearity, outliers and influential data, nonlinearity, heteroscedasticity, and nonnormality. The chapter contains a discussion of data transformations and an introduction to nonlinear models. Chapter 4 takes up structural-equation models, which are systems of linear equations representing the causal relations among sets of variables, some of which may exert mutual influence on each other. The chapter ends with an introductory treatment of models that contain specific measurement-error components and that include multiple indicators of latent variables. Chapter 5 describes logit models for qualitative dependent variables and log-linear models for contingency tables, stressing the similarity of these models to the linear models of earlier chapters. The relationship between logit and loglinear models is also developed. The chapter includes a discussion of diagnostic methods for We use cookies on this site to enhance your user experience Applied regression analysis, linear models, and related methods, the inertial navigation directly gives a larger projection on the axis than the sunrise . Book review: An R and S-plus companion to applied regression, mazel and V. Hayes, Andrew F. (2013). Introduction to Mediation, Moderation, and Conditional Process Analysis: A Regression Based Approach. New York, NY: The Guilford Press, the electrode, at first glance, is immutable. Linear statistical models and related methods with applications to social research, the form, according to the data of the soil survey, illustrates the thermodynamic custom of business turnover. Book Review: Discrete multivariate analysis: Theory and practice, deluccia categorically requires more attention to the analysis of errors that gives biographical method at these moments stop L. Lang uag e: English Year: 1984
CoVar: A generalizable machine learning approach to identify the coordinated regulators driving variational gene expression

Network inference is used to model transcriptional, signaling, and metabolic interactions among genes, proteins, and metabolites that identify biological pathways influencing disease pathogenesis. Advances in machine learning (ML)-based inference models exhibit the predictive capabilities of capturing latent patterns in genomic data. Such models are emerging as an alternative to the statistical models identifying causative factors driving complex diseases. We present CoVar, an inference framework that builds upon the properties of existing inference models, to find the central genes driving perturbed gene expression across biological states. We leverage ML-based network inference to find networks that capture the strength of regulatory interactions. Our model first pinpoints a subset of genes, termed variational, whose expression variabilities typify the differences in network connectivity between the control and perturbed data. Variational genes, by being differentially expressed themselves or possessing differentially expressed neighbor genes, capture gene expression variability. CoVar then creates subnetworks comprising variational genes and their strongly connected neighbor genes and identifies core genes central to these subnetworks that influence the bulk of the variational activity. Through the analysis of yeast expression data perturbed by the deletion of the mitochondrial genome, we show that CoVar identifies key genes not found through independent differential expression analysis.
Rice Yellow Mottle Virus resistance by genome editing of the Oryza sativa L. ssp. japonica nucleoporin gene OsCPR5.1 but not OsCPR5.2

Rice yellow mottle virus (RYMV) causes one of the most devastating rice diseases in Africa. Management of RYMV is challenging. Genetic resistance provides the most effective and environment-friendly control. The recessive resistance locus rymv2 (OsCPR5.1) had been identified in African rice (O. glaberrima), however, introgression into O. sativa ssp. japonica and indica remains challenging due to crossing barriers. Here, we evaluated whether CRISPR/Cas9 genome editing of the two rice nucleoporin paralogs OsCPR5.1 (RYMV2) and OsCPR5.2 can be used to introduce RYMV resistance into the japonica variety Kitaake. Both paralogs had been shown to complement the defects of the Arabidopsis atcpr5 mutant, indicating partial redundancy. Despite striking sequence and structural similarities between the two paralogs, only oscpr5.1 loss-of-function mutants were fully resistant, while loss-of-function oscpr5.2 mutants remained susceptible, intimating that OsCPR5.1 plays a specific role in RYMV susceptibility. Notably, edited lines with short in-frame deletions or replacements in the N-terminal domain (predicted to be unstructured) of OsCPR5.1 were hypersusceptible to RYMV. In contrast to mutations in the single Arabidopsis AtCPR5 gene, which caused severely dwarfed plants, oscpr5.1 and oscpr5.2 single knockout mutants show neither substantial growth defects nor symptoms indicative of programmed cell death, possibly reflecting functional redundancy of the isoforms regarding other important functions. The specific editing of OsCPR5.1, while maintaining OsCPR5.2 activity, provides a promising strategy for generating RYMV-resistance in elite Oryza sativa lines as well as for effective stacking with other RYMV resistance genes or other traits.
Microtubule decay is a driver of neuronal ageing and a promising target for intervention

Natural ageing is accompanied by a decline in motor, sensory and cognitive functions, all impacting life quality. Ageing is the predominant risk factor for many neurodegenerative diseases, including Parkinson’s and Alzheimer’s disease. We need therefore to gain a better understanding of the cellular and physiological processes underlying age-related neuronal decay. However, gaining this understanding is a slow process due to the long time required to age mammalian or vertebrate model animals. Here we introduce a new cellular model within the Drosophila brain where neurons show typical ageing hallmarks known from the primate brain, including axonal swellings, cytoskeletal decay, a reduction in axonal calibre and morphological changes arising at synaptic terminals. In the fly brain, these changes occur within just a few weeks, ideal to study the underlying mechanisms. We observe that decay of the neuronal microtubule cytoskeleton clearly precedes other ageing hallmarks. We show that the microtubule-binding factors Tau, EB1 and Shot, are necessary for microtubule maintenance in axons and synapses. Their functional loss during ageing triggers microtubule bundle decay followed by the decline in axons and synapses. Genetic manipulations that improve microtubule networks, slow down other neuronal ageing hallmarks and confer aged specimens with the ability to outperform age-matched controls. Our work suggests therefore that microtubule networks are a key lesion site in ageing neurons and offer promising opportunities to improve neuronal decay in advanced age.
The mitochondrial multi-omic response to exercise training across tissues

Mitochondria are adaptable organelles with diverse cellular functions critical to whole-body metabolic homeostasis. While chronic endurance exercise training is known to alter mitochondrial activity, these adaptations have not yet been systematically characterized. Here, the Molecular Transducers of Physical Activity Consortium (MoTrPAC) mapped the longitudinal, multi-omic changes in mitochondrial analytes across 19 tissues in male and female rats endurance trained for 1, 2, 4 or 8 weeks. Training elicited substantial changes in the adrenal gland, brown adipose, colon, heart and skeletal muscle, while we detected mild responses in the brain, lung, small intestine and testes. The colon response was characterized by non-linear dynamics that resulted in upregulation of mitochondrial function that was more prominent in females. Brown adipose and adrenal tissues were characterized by substantial downregulation of mitochondrial pathways. Training induced a previously unrecognized robust upregulation of mitochondrial protein abundance and acetylation in the liver, and a concomitant shift in lipid metabolism. The striated muscles demonstrated a highly coordinated response to increase oxidative capacity, with the majority of changes occurring in protein abundance and post-translational modifications. We identified exercise upregulated networks that are downregulated in human type 2 diabetes and liver cirrhosis. In both cases HSD17B10, a central dehydrogenase in multiple metabolic pathways and mitochondrial tRNA maturation, was the main hub. In summary, we provide a multi-omic, cross-tissue atlas of the mitochondrial response to training and identify candidates for prevention of disease-associated mitochondrial dysfunction.
Bidirectional multiciliated cell extrusion is controlled by Notch-driven basal extrusion and Piezo1-driven apical extrusion

Xenopus embryos are covered with a complex epithelium containing numerous multiciliated cells (MCCs). During late stage development there is a dramatic remodeling of the epithelium that involves the complete loss of MCCs. Cell extrusion is a well-characterized process for driving cell loss while maintaining epithelial barrier function. Normal cell extrusion is typically unidirectional whereas bidirectional extrusion is often associated with disease (e.g. cancer). We describe two distinct mechanisms for MCC extrusion, a basal extrusion driven by Notch signaling and an apical extrusion driven by Piezo1. Early in the process there is a strong bias towards basal extrusion, but as development continues there is a shift towards apical extrusion. Importantly, receptivity to the Notch signal is age-dependent and governed by the maintenance of the MCC transcriptional program such that extension of this program is protective against cell loss. In contrast, later apical extrusion is regulated by Piezo 1 such that premature activation of Piezo 1 leads to early extrusion while blocking Piezo 1 leads to MCC maintenance. Distinct mechansms for MCC loss underlie the importance of their removal during epithelial remodeling. Summay Statement Cell extrusion typically occurs unidirectionally. We have identified a single population of multiciliated cells that extrudes bidirectionally: Notch-driven basal extrusion and Piezo 1-mediated apical extrusion.
Cortical beta power reflects a neural implementation of decision boundary collapse in speeded decisions

A prominent account of decision-making assumes that information is accumulated until a fixed response threshold is crossed. However, many decisions require weighting of information appropriately against time. Collapsing response thresholds are a mathematically optimal solution to this decision problem. However, our understanding of the neurocomputational mechanisms that underly dynamic response thresholds remains very incomplete. To investigate this issue, we used a multistage drift diffusion model (DDM) and also analysed EEG beta power lateralization (BPL). The latter served as a neural proxy for decision signals. We analysed a large dataset (n=863) from a speeded flanker task and data from an independent confirmation sample (n=119). We show that a DDM with collapsing decision thresholds, a process where the decision boundary reduces over time, captured participants’ time-dependent decision policy better than a model with fixed thresholds. Previous research suggests that BPL over motor cortices reflects features of a decision signal and that its peak may serve as a neural proxy for the decision threshold. Our findings offer compelling evidence for the existence of collapsing decision thresholds in decision-making processes.
Real-time feedback reduces participant motion during task-based fMRI

The potential negative impact of head movement during fMRI has long been appreciated. Although a variety of prospective and retrospective approaches have been developed to help mitigate these effects, reducing head movement in the first place remains the most appealing strategy for optimizing data quality. Real-time interventions, in which participants are provided feedback regarding their scan-to-scan motion, have recently shown promise in reducing motion during resting state fMRI. However, whether feedback might similarly reduce motion during task-based fMRI is an open question. In particular, it is unclear whether participants can effectively monitor motion feedback while attending to task-related demands. Here we assessed whether a combination of real-time and between-run feedback could reduce head motion during task-based fMRI. During an auditory word repetition task, 78 adult participants (aged 19–81) were pseudorandomly assigned to receive feedback or not. Feedback was provided FIRMM software that used real-time calculation of realignment parameters to estimate participant motion. We quantified movement using framewise displacement (FD). We found that motion feedback resulted in a statistically significant reduction in participant head motion, with a small-to-moderate effect size (reducing average FD from 0.347 to 0.282). Reductions were most apparent in high-motion events. We conclude that under some circumstances real-time feedback may reduce head motion during task-based fMRI, although its effectiveness may depend on the specific participant population and task demands of a given study.
The dietary polyphenol metabolite protocatechuic acid produces acute and sustained effects on hippocampal electrical activity

Dietary polyphenols and in particular bioavailable metabolites resulting from gut microbiota transformations appear to have beneficial effects in situations of impaired cognition, combatting memory deficits in acute pathological models of neurodegeneration. Modifications to blood flow may underlie the effects of these molecules and although some such metabolites cross the blood-brain barrier, their targets and electrophysiological effects remain unknown. Hence, we explored the systemic and direct effects of protochatechuic acid (PCA) on electrical activity in the hippocampus and cortex of anesthetized female rats, recording evoked and spontaneous high-density field potentials (FPs) to mathematically derive pathway-specific FP generators. We found transient and sustained effects of PCA on evoked activity in the CA1 field, including paradoxical actions on excitatory transmission that depend on the route of administration. Systemic delivery of PCA altered the ongoing activity of some FP generators, albeit with marked inter-animal variation. Interestingly, PCA induced the detachment of infraslow cortico-hippocampal activities over a scale of minutes. These results point to direct actions of polyphenols on cell and network electrical activity, some of which reflect non-specific actions. Thus, dietary-derived polyphenols appear to fulfill neuromodulatory roles, encouraging the search for additional targets to better guide their use in preventing brain pathologies.
Limited role of generation time changes in driving the evolution of the mutation spectrum in humans

Recent studies have suggested that the human germline mutation rate and spectrum evolve rapidly. Variation in generation time has been linked to these changes, though its contribution remains unclear. We develop a framework to characterize temporal changes in polymorphisms within and between populations, while controlling for the effects of natural selection and biased gene conversion. Application to the 1000 Genomes Project dataset reveals multiple independent changes that arose after the split of continental groups, including a previously reported, transient elevation in TCC>TTC mutations in Europeans and novel signals of divergence in C>G and T>A mutation rates among population samples. We also find a significant difference between groups sampled in and outside of Africa, in old T>C polymorphisms that predate the out-of-Africa migration. This surprising signal is driven by TpG>CpG mutations, and stems in part from mis-polarized CpG transitions, which are more likely to undergo recurrent mutations. Finally, by relating the mutation spectrum of polymorphisms to parental age effects on de novo mutations, we show that plausible changes in the generation time cannot explain the patterns observed for different mutation types jointly. Thus, other factors--genetic modifiers or environmental exposures--must have had a non-negligible impact on the human mutation landscape.
Draft Genome Sequence of Pedococcus sp. Strain 5OH_020, Isolated from California Grassland Soil

The draft genome sequence of the soil bacterium Pedococcus sp. strain 5OH_020, isolated on a natural cobalamin analog, comprises 4.4 Mbp, with 4,108 protein-coding genes. Its genome encodes cobalamin-dependent enzymes, including methionine synthase and class II ribonucleotide reductase. Taxonomic analysis suggests that it is a novel species within the genus Pedococcus. ABSTRACT The draft genome sequence of the soil bacterium Pedococcus sp. strain 5OH_020, isolated on a natural cobalamin analog, comprises 4.4 Mbp, with 4,108 protein-coding genes. Its genome encodes cobalamin-dependent enzymes, including methionine synthase and class II ribonucleotide reductase. Taxonomic analysis suggests that it is a novel species within the genus Pedococcus.
Notch signaling regulates immunosuppressive tumor-associated macrophage function in pancreatic cancer

Pancreatic ductal adenocarcinoma (PDA) continues to have a dismal prognosis. The poor survival of patients with PDA has been attributed to a high rate of early metastasis and low efficacy of current therapies, which partly result from its complex immunosuppressive tumor microenvironment. Previous studies from our group and others have shown that tumor-associated macrophages (TAMs) are instrumental in maintaining immunosuppression in PDA. Here, we explored the role of Notch signaling, a key regulator of immune response, within the PDA microenvironment. We identified Notch pathway components in multiple immune cell types within human and mouse pancreatic cancer. TAMs, the most abundant immune cell population in the tumor microenvironment, express high levels of Notch receptors with cognate ligands such as JAG1 expressed on tumor epithelial cells, endothelial cells and fibroblasts. TAMs with activated Notch signaling expressed higher levels of immunosuppressive mediators including arginase 1 (Arg1) suggesting that Notch signaling plays a role in macrophage polarization within the PDA microenvironment. Combination of Notch inhibition with PD-1 blockade resulted in increased cytotoxic T cell infiltration, tumor cell apoptosis, and smaller tumor size. Our work implicates macrophage Notch signaling in the establishment of immunosuppression and indicates that targeting the Notch pathway may improve the efficacy of immune-based therapies in PDA patients.