Miracle-dz/UniFAR-FTUs huggingface dataset:
Manipulation of natural transformation by AbaR-type islands promotes fixation of antibiotic resistance in Acinetobacter baumannii populations

The opportunistic pathogen Acinetobacter baumannii, a major global public health concern, has developed multiple variants of AbaR-type genomic islands that confer multidrug resistance. The mechanisms facilitating the persistence of these potentially costly islands within A. baumannii populations have remained enigmatic. In this study, we employed a combination of investigative methods to shed light on the factors contributing to their selective advantage and long-term persistence. The dissemination of AbaR islands is intricately linked to their horizontal transfer via natural transformation, a process through which bacteria can import and recombine exogenous DNA, facilitating allelic recombination, genetic acquisition, and deletion. In experimental populations, we first quantified the rate at which natural transformation events occur between individuals. Our findings indicate that the rate of AbaR deletion events is marginally higher than the rate of their acquisition. When this result is integrated into a model of population dynamics not exposed to antibiotic selection pressure, it leads to the swift removal of AbaRs from the population, a pattern that stands in contrast to AbaR prevalence in genomes. Yet, genomic analyses show that nearly all AbaRs-carrying A. baumannii have at least one AbaR disrupting comM, a gene encoding a helicase critical for natural transformation. We discovered that such disruption differentially inhibits the rate of genetic acquisition and deletion. Specifically, they significantly impede the removal of AbaRs while still enabling the host cell to acquire and recombine short sequences, such as allelic variants. Through mathematical evolutionary modeling, we demonstrate that AbaRs inserted into comM gain a selective advantage over AbaRs inserted in sites that do not inhibit or completely inhibit transformation, in line with the genomic observations. The persistence of AbaRs within populations can be ascribed to their targeted integration into a gene, substantially diminishing the likelihood of their removal from the bacterial genome. In contrast, this integration enables the host cell to preserve the ability to acquire and eliminate various short heterologous sequences, enabling the host bacterium - and thus its AbaR - to adapt to the unpredictability of the environment and persist over the long term. This work underscores how AbaRs, and potentially other Mobile Genetic Elements (MGEs), can manipulate natural transformation to ensure their persistence in populations, ultimately leading to the high prevalence of multidrug resistance.
Understanding SARS-CoV-2 Spike glycoprotein clusters and their impact on immunity of the population from Rio Grande do Norte, Brazil

SARS-CoV-2 genome underwent mutations since it started circulating intensively within the human populations. The aim of this study was to understand the fluctuation of the spike clusters concomitant to high rate of population immunity either due to natural infection and/or vaccination in a state of Brazil that had high rate of infection and vaccination coverage. A total of 1715 SARS-CoV-2 sequences from the state of Rio Grande do Norte, Brazil, were retrieved from GISAID and subjected to cluster analysis. Immunoinformatics were used to predict T- and B-cell epitopes, followed by simulation to estimate either pro- or anti-inflammatory responses and correlate with circulating variants. From March 2020 to June 2022, Rio Grande do Norte reported 579,931 COVID-19 cases with a 1.4% fatality rate across three major waves: May-Sept 2020, Feb-Aug 2021, and Jan-Mar 2022. Cluster 0 variants (wild type strain, Zeta) were prevalent in the first wave and Delta in the latter half of 2021, featuring fewer unique epitopes. Cluster 1 (Gamma [P1]) dominated the first half of 2021. Late 2021 had Clusters 2 (Omicron) and 3 (Omicron sublineages) with the most unique epitopes, while Cluster 4 (Delta sublineages) emerged in the second half of 2021 with fewer unique epitopes. Cluster 1 epitopes showed a high pro-inflammatory propensity, while others exhibited a balanced cytokine induction. The clustering method effectively identified Spike groups that may contribute to immune evasion and clinical presentation, and explain in part the clinical outcome. IMPORTANCE Identification of epitopes of emerging or endemic pathogens is of importance to estimate population responses and predict clinical outcomes and contribute to vaccine improvement. In the case of SARS-CoV-2, the virus within 6 months of circulation transitioned from the wild-type to novel variants leading to distinct clinical outcomes. Immunoinformatics analysis of viral epitopes of isolates from the Brazilian state of Rio Grande do Norte was performed using a clustering method. This analysis aimed to clarify how the introduction of novel variants in a population characterized by high infection and/or vaccination rates resulted in immune evasion and distinct clinical disease. Our analysis showed that the epitope profiles of each variant explained the respective potential for cytokine production, including the variants that were more likely to cause cytokine storms. Finally, it serves as a mean to explain the multi-wave patterns observed during SARS-CoV-2 pandemics.
Chimpanzees and bonobos reinstate an interrupted triadic game

When humans engage in joint action, they seem to so with an underlying sense of joint commitment, a feeling of mutual obligation towards their partner and a shared goal. Whether our closest living relatives, bonobos and chimpanzees, experience and understand joint commitment in the same way is subject to debate. Crucial evidence concerns how participants respond to interruptions of joint actions, particularly if they protest or attempt to reengage their reluctant or distracted partners. During dyadic interactions, bonobos and chimpanzees appear to have some sense of joint commitment, according to recent studies. Yet, data are inconsistent for triadic games with objects. We addressed this issue by engaging N=23 apes (5 adult chimpanzees, 5 infant bonobos, 13 adult bonobos) in a “tug-of-war” game with a human experimenter who abruptly stopped playing. Adult apes readily attempted to reengage the experimenter (>60% of subjects on first trial), with no group differences in the way of reengagement. Infant bonobos rarely reengaged and never did so on their first trial. Importantly, when infants reengaged passive partners, they mostly deployed (tactile) signals, yet rarely game-related behaviours (GRBs) as commonly observed in adults. These findings might explain negative results of earlier research. Bonobos and chimpanzees may thus have motivational foundations for joint commitment, although this capacity might develop over lifetime. We discuss this finding in relation to evolutionary and developmental theories on joint commitment.
Intrinsic forebrain arousal dynamics governs sensory stimulus encoding

The neural encoding of sensory stimuli is subject to the brain’s internal circuit dynamics. Recent work has demonstrated that the resting brain exhibits widespread, coordinated activity that plays out over multisecond timescales in the form of quasi-periodic spiking cascades. Here we demonstrate that these intrinsic dynamics persist during the presentation of visual stimuli and markedly influence the efficacy of feature encoding in the visual cortex. During periods of passive viewing, the sensory encoding of visual stimuli was determined by quasi-periodic cascade cycle evolving over several seconds. During this cycle, high efficiency encoding occurred during peak arousal states, alternating in time with hippocampal ripples, which were most frequent in low arousal states. However, during bouts of active locomotion, these arousal dynamics were abolished: the brain remained in a state in which visual coding efficiency remained high and ripples were absent. We hypothesize that the brain’s observed dynamics during awake, passive viewing reflect an adaptive cycle of alternating exteroceptive sensory sampling and internal mnemonic function.
AngoraPy: A Python Toolkit for Modelling Anthropomorphic Goal-Driven Sensorimotor Systems

Goal-driven deep learning is increasingly used to supplement classical modeling approaches in computational neuroscience. The strength of deep neural networks lies in their ability to autonomously learn the connectivity required to solve complex and ecologically valid tasks, obviating the need for hand-engineered or hypothesis-driven connectivity patterns. Consequently, goal-driven models can generate hypotheses about the neurocomputations underlying cortical processing. Whereas goal-driven modeling is becoming increasingly common in perception neuroscience, its application to sensorimotor control is currently hampered by the complexity of the methods required to train models comprising the closed sensation-action loop. To mitigate this hurdle, we introduce AngoraPy, a modeling library that provides researchers with the tools to train complex recurrent convolutional neural networks that model sensorimotor systems.
Deciphering Cancer Genomes with GenomeSpy: A Grammar-Based Visualization Toolkit

Background Visualization is an indispensable facet of genomic data analysis. Despite the abundance of specialized visualization tools, there remains a distinct need for tailored solutions. However, their implementation typically requires extensive programming expertise from bioinformaticians and software developers, especially when building interactive applications. Toolkits based on visualization grammars offer a more accessible, declarative way to author new visualizations. Nevertheless, current grammar-based solutions fall short in adequately supporting the interactive analysis of large data sets with extensive sample collections, a pivotal task often encountered in cancer research. Results We present GenomeSpy, a grammar-based toolkit for authoring tailored, interactive visualizations for genomic data analysis. Users can implement new visualization designs with little effort by using combinatorial building blocks that are put together with a declarative language. These fully customizable visualizations can be embedded in web pages or end-user-oriented applications. The toolkit also includes a fully customizable but user-friendly application for analyzing sample collections, which may comprise genomic and clinical data. Findings can be bookmarked and shared as links that incorporate provenance information. A distinctive element of GenomeSpy’s architecture is its effective use of the graphics processing unit (GPU) in all rendering. GPU usage enables a high frame rate and smoothly animated interactions, such as navigation within a genome. We demonstrate the utility of GenomeSpy by characterizing the genomic landscape of 753 ovarian cancer samples from patients in the DECIDER clinical trial. Our results expand the understanding of the genomic architecture in ovarian cancer, particularly the diversity of chromosomal instability. We also show how GenomeSpy enabled the discovery of clinically actionable genomic aberrations. Conclusions GenomeSpy is a visualization toolkit applicable to a wide range of tasks pertinent to genome analysis. It offers high flexibility and exceptional performance in interactive analysis. The toolkit is open source with an MIT license, implemented in JavaScript, and available at https://genomespy.app/.
Co-transcriptional production of programmable RNA condensates and synthetic organelles

Condensation of RNA and proteins is central to cellular functions, and the ability to program it would be valuable in synthetic biology and synthetic cell science. Here we introduce a modular platform for engineering synthetic RNA condensates from tailor-made, branched RNA nanostructures that fold and assemble co-transcriptionally. Up to three orthogonal condensates can form simultaneously and selectively accumulate guest molecules. The RNA condensates can be expressed within synthetic cells to produce membrane-less organelles with controlled number, size, morphology and compositions, and that display the ability to selectively capture proteins. The in situ expression of programmable RNA condensates could underpin spatial organisation of functionalities in both biological and synthetic cells.
Spatial heterogeneity in tumor adhesion qualifies collective cell migration

Collective cell migration, a canon of most invasive solid tumors, is an emergent property of the interactions between cancer cells and their surrounding extracellular matrix (ECM). However, tumor populations invariably consist of cells expressing variable levels of adhesive proteins that mediate such interactions, disallowing an intuitive understanding of how tumor invasiveness at a multicellular scale is influenced by spatial heterogeneity of cell-cell and cell-ECM adhesion. Here, we have used a Cellular Potts model-based multiscale computational framework that is constructed on the histopathological principles of glandular cancers. In earlier efforts on homogenous cancer cell populations, this framework revealed the relative ranges of interactions, including cell-cell and cell-ECM adhesion that drove collective, dispersed, and mixed multimodal migrations. Here, we constitute a tumor core of two separate cell subsets showing distinct intra-subset cell-cell or cell-ECM adhesion strengths. These two subsets of cells are arranged to varying extents of spatial intermingling, which we call the heterogeneity index (HI). Our simulations show that for a given two intra-subset cell-cell adhesions for two subsets of cells, low and high inter-subset cell adhesion favors migration of high HI and low HI intermingled populations, respectively. In addition, for the most explored values of cell-ECM adhesion strengths, populations with high HI values collectively migrate better than those with lower HI values. We then asked how spatial migration is regulated by progressively intermingled cellular subsets that were epithelial, i.e., showed high cell-cell but poor cell-ECM adhesion, and mesenchymal, i.e., with reversed adhesion strengths to the former. Here too, inter-subset adhesion plays an important role in contextualizing the proportionate relationship between HI and migration. We also observe an exception to this relationship for cases of heterogeneous cell-ECM adhesion where sub-maximal HI patterns with higher outer localization of cells with stronger ECM adhesion collectively migrate better than their relatively higher HI counterparts. Our simulations also reveal how adhesion heterogeneity qualifies migrative dynamics through collective cellular unjamming, when either cell-cell or -ECM adhesion type is varied but incorporates dispersion when both adhesion types are simultaneously altered.
Development of High Protein Tomato Soup Using Milk Protein Concentrate and Pea Protein Isolate

This study aimed to explore the development of a high protein tomato soup to address the nutritional needs of older adults who require higher levels of protein compared to the general population. The specific objective of this study was to explore how the addition of a dairy protein (Milk Protein Concentrate - MPC), a plant-based protein (Pea Protein Isolate - PPI), or their combination affected the techno-functional properties and sensory acceptance of tomato soup. A control soup and three soups containing MPC, PPI and their combination were prepared, and their techno-functional properties were tested. A group of 33 naïve consumers older than 18 years, scored overall liking, liking of appearance, taste, aroma and mouthfeel of the soups using 9-point hedonic scales. A significant increase in pH, apparent viscosity, and L*and b* values and a decrease in a*value for colour were observed with the addition of protein in the tomato soup. The sensory acceptability test of this pilot study showed that the participants liked the taste, aroma, colour, appearance and mouthfeel of the control soups significantly more compared to the soups with added protein. There was a significant negative correlation between changes in colour with overall liking, liking colour and appearance of samples. The age of participants had a significant effect on overall liking and liking of aroma, as participants older than 55 years liked the samples with added protein less compared to the control.
Becoming a Secondary School Science Teacher

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The Economic Impact of a Terrorist Attack on the Twin Ports of Los Angeles-long Beach the Economic Impact of a Terrorist Attack on the Twin Ports of Los Angeles-long Beach Create Report

The Los Angeles metropolitan region is a prime target for a terrorist attack. There are many specific targets: the Los Angeles International Airport (LAX), downtown high-rises, its theme parks, its freeways, and its ports, among many others. We have developed a spatially disaggregated economic impact model that can evaluate all of these and any other plausible attacks. In this paper, we estimate the economic impacts of an attack on the Los Angeles-Long Beach Twin Ports.
Fiscal Rules for Sub-Central Governments: Design and Impact

Against a background of mounting demands for spending on services provided by sub-central governments, this paper examines how fiscal rules can help to ensure that pressure on resources is minimised and available resources are used efficiently. Drawing on questionnaire responses and other sources, this paper gives a detailed picture of fiscal rules for sub-central governments in place among a number of OECD countries. The paper examines the rationales for using fiscal rules, the various impacts fiscal rules can have, the factors making for effective implementation and the interactions between the various types of rule. It then constructs a number of synthetic sub-indicators designed to assess the extent to which sub-central government fiscal frameworks exhibit favourable characteristics for the achievement of fiscal objectives. It concludes with the construction of a composite indicator based on the combined impacts in the different areas of fiscal policy.
Lateral extrusion in the eastern Alps, Part 1: Boundary conditions and experiments scaled for gravity

Lateral extrusion encompasses extensional collapse (gravitational spreading away from a topographic high in an orogenic belt) and tectonic escape (plane strain horizontal motion of wedges driven by forces applied to their boundaries). In the Eastern Alps it resulted from (1) an overall northerly compression (Apulia against Eurasia), (2) a strong foreland (Bohemian massif), (3) lack of constraint along a lateral boundary (Carpathian region), and (4) a previously thickened, gravitationally unstable, thermally weakened crust (Eastern Alpine orogenic belt). Six indentation experiments reproduce lateral extrusion at lithospheric scale. The models have two to four lithospheric layers, with a Mohr/Coulomb rheology for the upper and a viscous rheology for the lower crust. The lithosphere rests upon a low-viscosity asthenosphere. A broad indenter, a narrow deformable area, and a weakly constrained eastern margin fullfill as closely as possible conditions in the Eastern Alps. Indentation produces both thickening in front of the indenter and escape of triangular wedges. Lateral variations in crustal thickness become attenuated by gravitational spreading. The overall fault pattern includes domains of reverse, strike-slip, oblique normal, and pure normal faults. Strike-slip faults in conjugate sets develop serially. The narrow width of the deformable area and the strength of the foreland determine the angles between the sets. Gravitational spreading produces a rhombohedral pattern of oblique and pure normal faults along the unconstrained margin. Opposite the unconstrained margin, the indenter front shows thrusts and folds intersecting with the conjugate strike-slip sets. A triangular indenter favors spreading. High velocity of indentation favors escape. High confinement limits lateral motion, inhibits spreading, and favors thickening. Lateral extrusion in the Eastern Alps is best modeled by (1) a weak lateral confinement, (2) a broad and straight indenter, (3) a narrow width of the deformable area, and (4) a rigid foreland. Crustal thickening, lateral escape, and gravitational spreading all contribute to the overall deformation.
Impact of Brine Chemistry on Oil Recovery

A24 Impact of Brine Chemistry on Oil Recovery A. Lager* (BP) K.J. Webb (BP) & C.J.J. Black (BP) SUMMARY Since its accidental discovery at the beginning of the 20th century waterflooding has become the most successful form of oil rcovery and the vast majority of oil fields without an active aquifer or with a partial water drive are or will be under waterflood. Waterflooding is considered by the majority of reservoir engineers as a technique for pressure maintenance to energise the reservoir and as such the majority of waterflooding research has been conducted on fluid mechanics and the physics behind
Factors, especially sunspot number, causing variations in surface air concentrations and depositions of 7Be in Osaka, Japan

We found that increasing sunspot number caused a significant negative effect on monthly and yearly average air concentration and yearly deposition of 7Be. For more than 15 years monthly average surface air concentration and monthly deposition of 7Be was measured in Osaka, Japan. The maximum monthly average surface air concentration of 7Be was 1.6 times higher than the minimum concentration through the fifteen year measurement span. Increase of several percent in the monthly averaged surface air concentration and monthly deposition of 7Be were observed in the monthly mean for February‐March‐April 1987 period following the 23 February supernova explosion in the Large Magellanic Cloud. The seasonal variation pattern which includes the lowest surface air concentration of 7Be in summer is due to the transport of air masses from low latitudes carrying low 7Be concentrations into the middle latitude region.
Effect of orifice and pressure of counter flow vortex tube

Vortex tube is a non conventional cooling device which will produce cold air and hot air from the source of compressed air without affecting the environment. When a high pressure air is tangentially injected into vortex chamber a strong vortex flow will be created which will be split into two air streams. It can be used for any type of spot cooling or heating application. In this work an attempt is made to design and test a simple counter flow vortex tube. The effect of orifice diameter and inlet pressure is investigated and presented in this paper.