Miracle-dz/UniFAR-FTUs huggingface dataset:
Experimental demonstration of quantum illumination using polarization-entangled photon pairs and CHSH value as measure

Entangled light sources for illuminating objects offers advantages over conventional illumination methods by enhancing the detection sensitivity of a reflecting object. The crux of the quantum advantage lies in way we can practically leverage quantum correlations to isolate the background noise and detect the low reflectivity object. In this work we experimentally demonstrated the advantages of using polarization-entangled photon pairs for quantum illumination and show that the quantum correlation measure using CHSH value is robust against background noise and losses. We also show that the residual of quantum correlations help in identifying the object of reflectivity, $\eta$ as low as 0.05 and when signal-to-noise ratio is as low as 0.003 for $\eta=0.7$, surpassing the earlier demonstrated results. Robustness of correlation measure with photon attenuation in atmospheric condition is analysed to show the practical feasibility of the real time application.
Phase Transition to RS: Cool, not Supercool

Motivated by the warped conifold compactification, we model the infrared (IR) dynamics of confining gauge theories in a Randall-Sundrum (RS)-like setup by modifying the stabilizing Goldberger-Wise (GW) potential so that it becomes large (in magnitude) in the IR and back-reacts on the geometry. We study the high-temperature phase by considering a black brane background in which we calculate the entropy and free energy of the strongly back-reacted solution. As with Buchel's result for the conifold (arXiv:2103.15188), we find a minimum temperature beyond which the black brane phase is thermodynamically unstable. In the context of a phase transition to the confining background, our results suggest that the amount of supercooling that the metastable black brane phase undergoes can be limited. It also suggests the first-order phase transition (and the associated gravitational waves from bubble collision) is not universal. Our results therefore have important phenomenological implications for early universe model building in these scenarios.
Antonym vs Synonym Distinction using InterlaCed Encoder NETworks (ICE-NET)

Antonyms vs synonyms distinction is a core challenge in lexico-semantic analysis and automated lexical resource construction. These pairs share a similar distributional context which makes it harder to distinguish them. Leading research in this regard attempts to capture the properties of the relation pairs, i.e., symmetry, transitivity, and trans-transitivity. However, the inability of existing research to appropriately model the relation-specific properties limits their end performance. In this paper, we propose InterlaCed Encoder NETworks (i.e., ICE-NET) for antonym vs synonym distinction, that aim to capture and model the relation-specific properties of the antonyms and synonyms pairs in order to perform the classification task in a performance-enhanced manner. Experimental evaluation using the benchmark datasets shows that ICE-NET outperforms the existing research by a relative score of upto 1.8% in F1-measure.
Image Translation as Diffusion Visual Programmers

We introduce the novel Diffusion Visual Programmer (DVP), a neuro-symbolic image translation framework. Our proposed DVP seamlessly embeds a condition-flexible diffusion model within the GPT architecture, orchestrating a coherent sequence of visual programs (i.e., computer vision models) for various pro-symbolic steps, which span RoI identification, style transfer, and position manipulation, facilitating transparent and controllable image translation processes. Extensive experiments demonstrate DVP's remarkable performance, surpassing concurrent arts. This success can be attributed to several key features of DVP: First, DVP achieves condition-flexible translation via instance normalization, enabling the model to eliminate sensitivity caused by the manual guidance and optimally focus on textual descriptions for high-quality content generation. Second, the framework enhances in-context reasoning by deciphering intricate high-dimensional concepts in feature spaces into more accessible low-dimensional symbols (e.g., [Prompt], [RoI object]), allowing for localized, context-free editing while maintaining overall coherence. Last but not least, DVP improves systemic controllability and explainability by offering explicit symbolic representations at each programming stage, empowering users to intuitively interpret and modify results. Our research marks a substantial step towards harmonizing artificial image translation processes with cognitive intelligence, promising broader applications.
Hydraulic Performance of Ski-Jump-Step Energy Dissipater

AbstractConsidering the limitations of unit discharge for stepped chutes, a ski-jump-step energy dissipater, which is a new type of energy dissipater, is first proposed for increasing the maximum available unit discharges. In this system, preaerations are achieved through jets generated by ski-jumps and further aerations are achieved via aeration basins. It provides fully aerated flows for the stepped chutes with large unit discharges, and the problems caused by high-speed flows like energy dissipation, cavitation, and atomization are well solved. Experimental investigations about hydraulic characteristics of the ski-jump-step energy dissipater were conducted, including the flow regimes, the principle and effectiveness of energy dissipation and the characteristics of the air entrainment and the pressure distribution. Even under conditions of large unit discharges (q=118.00 m2/s on the prototype), results obtained demonstrate energy dissipation as high as 75.8% and air concentrations of at least 3.6% alon.
Astrocytic CREB in nucleus accumbens promotes susceptibility to chronic stress

Background Increasing evidence implicates astrocytes in stress and depression in both rodent models and human Major Depressive Disorder (MDD). Despite this, little is known about the transcriptional responses to stress of astrocytes within the nucleus accumbens (NAc), a key brain reward region, and their influence on behavioral outcomes. Methods We used whole cell sorting, RNA-sequencing, and bioinformatic analyses to investigate the NAc astrocyte transcriptome in male mice in response to chronic social defeat stress (CSDS). Immunohistochemistry was used to determine stress-induced changes in astrocytic CREB within the NAc. Finally, astrocytic regulation of depression-like behavior was investigated using viral-mediated manipulation of CREB in combination with CSDS. Results We found a robust transcriptional response in NAc astrocytes to CSDS in stressed mice, with changes seen in both stress-susceptible and stress-resilient animals. Bioinformatic analysis revealed CREB, a transcription factor widely studied in neurons, as one of the top-predicted upstream regulators of the NAc astrocyte transcriptome, with opposite activation states seen in resilient versus susceptible mice. This bioinformatic result was confirmed at the protein level with immunohistochemistry. Viral overexpression of CREB selectively in NAc astrocytes promoted susceptibility to chronic stress. Conclusions Together, our data demonstrate that the astrocyte transcriptome responds robustly to CSDS and, for the first time, that transcriptional regulation in astrocytes contributes to depressive-like behaviors. A better understanding of transcriptional regulation in astrocytes may reveal unknown molecular mechanisms underlying neuropsychiatric disorders.
The probability of a unique gene occurrence at the tips of a phylogenetic tree in the absence of horizontal gene transfer (the last-one-out)

Gene loss is an important process in gene and genome evolution. If a gene is present at the root of a rooted binary phylogenetic tree and can be lost in one descendant lineage, it can be lost in other descendant lineages as well, and potentially can be lost in all of them, leading to extinction of the gene on the tree. In that case, just before the gene goes extinct in the rooted phylogeny, there will be one lineage that still retains the gene for some period of time, representing a ‘last-one-out’ distribution. If there are many (hundreds) of leaves in one clade of a phylogenetic tree, yet only one leaf possesses the gene, it will look like the result of a recent gene acquisition, even though the distribution at the tips was generated by loss. Here we derive the probability of observing last-one-out distributions under a Markovian loss model and a given gene loss rate µ. We find that the probability of observing such cases can be calculated mathematically, and can be surprisingly high, depending upon the tree and the rate of gene loss. Examples from real data show that gene loss can readily account for the observed frequency of last-one-out gene distribution patterns that might otherwise be attributed to lateral gene transfer.
Variation in the response to antibiotics and life-history across the major Pseudomonas aeruginosa clone type (mPact) panel

Pseudomonas aeruginosa is a ubiquitous, opportunistic human pathogen. Since it often expresses multidrug resistance, it is ranked by the World Health Organization among the top 3 high priority pathogens, for which new treatment options are urgently required. An evaluation of new treatments is usually performed experimentally with one of the canonical laboratory strains (e.g., PAO1 or PA14). However, these two strains are unlikely representative of the strains infecting patients, because they have adapted to laboratory conditions and do not capture the enormous genomic diversity of the species. Here, we characterized the major P. aeruginosa clone type (mPact) panel. This panel consists of 20 strains, which reflect the genomic diversity of the species, cover all major clone types, and have both patient and environmental origins. We found significant strain variation in distinct responses towards antibiotics and general growth characteristics. Only few of the measured traits are related, and if so, only for specific antibiotics. Moreover, high levels of resistance were only identified for clinical mPact isolates and could be linked to known AMR (antimicrobial resistance) genes in the sequenced genomes. One strain also produced highly unstable AMR, indicating an evolutionary cost to resistance expression. By linking isolation source, growth, and virulence to life history traits, we further identified specific adaptive strategies for individual mPact strains towards either host processes or degradation pathways. Overall, the mPact panel provides a reasonably sized set of distinct strains, enabling in-depth analysis of new treatment designs or evolutionary dynamics in consideration of the species’ genomic diversity. Importance New treatment strategies are urgently needed for high risk pathogens such as the opportunistic and often multidrug resistant pathogen Pseudomonas aeruginosa. Here, we characterize the major P. aeruginosa clone type (mPact) panel. It consists of 20 strains with different origins that cover the major clone types of the species as well as its genomic diversity. This mPact panel shows significant variation in (i) resistance against distinct antibiotics, including several last resort antibiotics, (ii) related traits associated with the response to antibiotics, and (iii) general growth characteristics. We further developed a novel approach that integrates information on resistance, growth, virulence, and life-history characteristics, allowing us to demonstrate the presence of distinct adaptive strategies of the strains that focus either on host interaction or resource processing. In conclusion, the mPact panel provides a manageable number of representative strains for this important pathogen for further in-depth analyses of treatment options and evolutionary dynamics.
General mechanisms of task engagement in the primate frontal cortex

Staying engaged with a task is necessary to maintain goal-directed behaviors. Although engagement varies with the specific task at hand it also exhibits continuous, intrinsic fluctuations widely. This intrinsic component of engagement is difficult to isolate behaviorally or neurally in controlled experiments with humans. By contrast, animals spontaneously move between periods of complete task engagement and disengagement, even in experimental settings. We, therefore, looked at behavior in macaques in a series of four tasks while recording fMRI signals. We identified consistent autocorrelation in task disengagement. This made it possible to build models capturing task-independent engagement and to link it to neural activity. Across all tasks, we identified common patterns of neural activity linked to impending task disengagement in mid-cingulate gyrus. By contrast, activity centered in perigenual anterior cingulate cortex (pgACC) was associated with maintenance of task performance. Importantly, we were able to carefully control for task-specific factors such as the reward history, choice value, and other motivational effects, such as response vigor, as indexed by response time, when identifying neural activity associated with task engagement. Moreover, we showed pgACC activity had a causal link to task engagement; in one of our tasks, transcranial ultrasound stimulation of pgACC, but not of control regions, changed task engagement/disengagement patterns.
Long-horizon associative learning explains human sensitivity to statistical and network structures in auditory sequences

Networks are a useful mathematical tool for capturing the complexity of the world. In a previous behavioral study, we showed that human adults were sensitive to the high-level network structure underlying auditory sequences, even when presented with incomplete information. Their performance was best explained by a mathematical model compatible with associative learning principles, based on the integration of the transition probabilities between adjacent and non-adjacent elements with a memory decay. In the present study, we explored the neural correlates of this hypothesis via magnetoencephalography (MEG). Participants passively listened to sequences of tones organized in a sparse community network structure comprising two communities. An early difference (~150 ms) was observed in the brain responses to tone transitions with similar transition probability but occurring either within or between communities. This result implies a rapid and automatic encoding of the sequence structure. Using time-resolved decoding, we estimated the duration and overlap of the representation of each tone. The decoding performance exhibited exponential decay, resulting in a significant overlap between the representations of successive tones. Based on this extended decay profile, we estimated a long-horizon associative learning novelty index for each transition and found a correlation of this measure with the MEG signal. Overall, our study sheds light on the neural mechanisms underlying human sensitivity to network structures and highlights the potential role of Hebbian-like mechanisms in supporting learning at various temporal scales.
A novel human pluripotent stem cell-based gene activation system identifies IGFBP2 as a mediator in the production of hematopoietic progenitors in vitro

A major challenge in the stem cell biology field is the ability to produce fully functional cells from induced pluripotent stem cells (iPSCs) that are a valuable resource for cell therapy, drug screening and disease modelling. Here we developed a novel inducible CRISPR-mediated activation strategy (iCRISPRa) to drive the expression of multiple endogenous transcription factors important for in vitro cell fate and differentiation of iPSCs to haematopoietic progenitor cells and used this to identify a key paracrine role for IGFBP2 in the development of hematopoietic progenitors. We first identified nine candidate transcription factors that we predicted to be involved in blood cell emergence during development, then generated novel gRNAs directed to the transcriptional start site of these transcription factors that could also be detected during scRNAseq. iCRISPRa activation of these endogenous transcription factors resulted in a significant expansion of arterial-fated endothelial cells expressing high levels of IGFBP2 and showed that IGFBP2 remodels the metabolic activity during in vitro endothelial to hematopoietic transition. As well as providing fundamental new insights into the mechanisms of haematopoietic cell fate and differentiation, the broader applicability of iCRISPRa provides a valuable tool for studying dynamic processes controlling developmental events as well as for recapitulating abnormal phenotypes characterised by ectopic activation of specific endogenous gene expression in a wide range of systems.
Prediction error determines how memories are organized in the brain: a study of Pavlovian fear extinction in rats

How is new information organized in memory? According to latent state theories, this is determined by the level of surprise, or prediction error, generated by the new information: small prediction error = updating of existing memory, large prediction error = encoding of new memory. We tested this idea using a protocol in which rats were first conditioned to fear a stimulus paired with shock. The stimulus was then gradually extinguished by progressively reducing the shock intensity until the stimulus was presented alone. Consistent with latent state theories, this gradual extinction protocol (small prediction errors) was better than standard extinction (large prediction errors) in producing long-term suppression of fear responses; and the benefit of gradual extinction was due to updating of the conditioning memory with information about extinction. Thus, prediction error determines how new information is organized in memory, and latent state theories adequately describe the ways in which this occurs.
Spatiotemporal visualization of DNA replication by click chemistry reveals bubbling of viral DNA in virion formation

The organisation of human chromosomes reversibly changes in cell division, and irreversibly in apoptosis or erythropoiesis by DNA condensation and fragmentation processes. Yet, how viral replication in the nucleus affects host and viral chromatin organisation remains poorly understood. Here we used dual-color click chemistry to image human adenovirus DNA replication, demonstrating host chromatin compaction during active expansion of the viral replication compartment (VRC). Early-replicated viral DNA (vDNA) segregated from VRC and lost phospho-serine5-RNA Pol-II and viral DNA-binding protein (DBP), while late-replicated vDNA retained active RNA Pol-II, besides viral RNA-splicing and DNA-packaging proteins. Depending on replication and the assembly protein 52K, the late-stage VRCs gave rise to progeny by droplet formation of vDNA with GFP-tagged virion protein V into 52K biomolecular condensates. The study reveals distinct functions of early and late-replicated vDNA and provides insight into active and passive liquid phase separated zones conducive to selective genome packaging of nascent virions.
SAM-DNMT3A, a strategy for induction of genome-wide DNA methylation, identifies DNA methylation as a vulnerability in ER-positive breast cancers

DNA methylation is an epigenetic mark that plays a critical role in regulation of gene expression. DNA methylase (DNMT) inhibitors, inhibit global DNA methylation, and have been a key tool in studies of DNA methylation in healthy or disease conditions. A major bottleneck is the lack of tools to induce global DNA methylation. Here, we engineered a CRISPR based approach, that was initially designed, to enable site specific DNA methylation. Using the synergistic activation mediator (SAM) system, we unexpectedly found that regardless of the targeted sequence any sgRNA induced global genome-wide DNA methylation. We termed this new method SAM-DNMT3A and show that induction of global DNA methylation is a unique vulnerability in ER-positive breast cancer suggesting a therapeutic approach. Our findings highlight the need of caution when using CRISPR based approaches for inducing DNA methylation and demonstrate a new method for global induction of DNA methylation.
Submarine drumlins on the continental shelf offshore of NW Ireland

Drumlins are streamlined subglacial landforms, usually formed of sediment, that record the former direction of ice-sheet flow across a landscape (Clark et al. 2009). They have been widely observed in a range of glacial environments, both terrestrial and marine. On the continental shelf offshore of NW Ireland multibeam-bathymetric data show elongate landforms with a morphology consistent with published observations of drumlins (Fig. 1). These landforms record the former flow of a terrestrially sourced, grounded Irish Ice Sheet across the continental shelf during the last glaciation (O Cofaigh et al. 2012). Fig. 1. Drumlins on the continental shelf offshore of NW Ireland. Acquisition systems Simrad EM1002S and EM3002 on the Celtic Voyager and EM1002 on the Celtic Explorer . Grid-cell size 20 m. ( a ) Oblique view of the seabed 5 km NW of Tory Island showing a swarm of closely spaced drumlins indicating NW ice-flow. VE×5. ( b ) Close-up of drumlins showing …
Hope Rising Out of Despair: The Spiritual Journey of Patients Admitted to a Hospice

SUMMARY It is noted that the suddenness of grief and loss awakens individuals to their own spiritual journey. Studies have shown that spirituality increases when death is faced (Derrickson 1996; Millison & Dudley 1992) with others indicating the need for those living with dying patients, to be in touch with their own spirituality (English 1998; Irion 1988). This paper, part of a larger PhD study, reports conversations with patients as to their spiritual ‘journey. ’ Their responses were categorised using a three step framework generated by Chandler (1999) which incorporates elements of grief from Perlman, and Takaacs (1990). Their responses give some indication as to their level of ‘despair’ and ‘hope’ whilst on their spiritual journey and gives health care providers guidance as to how to assist patients with their spiritual needs.
25 years of VAT! And tomorrow: A Green VAT? The use of VAT as a climate tool 1

This article examines the extent to which VAT could be used as a tax incentive in the context of the fight against global warming. Since VAT is a general consumption tax that is already applied by a well-equipped and efficient administration, giving it the character of an incentive ecological tax makes it possible to easily reach all economic sectors that need to be reached without requiring new administrative resources. However, the contribution shows that using VAT in its current functioning, in particular by introducing rate differentiation to favor green products or penalize polluting products, is an approach which is moderately effective. In particular because of the way VAT operates, notably the right to deduct input tax, the incentive nature of VAT would be essentially limited to final consumers and would have no effect on a very large part of the economy. The article therefore proposes an alternative approach that would take advantage of the existence of VAT as a general consumption tax and the tax administration that applies it. The idea is to use VAT as a vector to levy a surcharge with an essentially ecological purpose. This "General Green Tax" would be levied in parallel to the VAT. It would consist of an additional rate levied on revenues subject to this tax, but which could not be deducted as input tax by companies subject to VAT. The GGT surcharge rates would obviously be different depending on the goods or services covered by the measure. The introduction of such a VAT-based ecological tax would require a new constitutional basis. But it would have many advantages that are outlined in the article, including the possibility of a phased implementation and the ability to reach all economic sectors with a simple mechanism that would build on an already existing administration.