Miracle-dz/UniFAR-FTUs huggingface dataset:
Spot the Difference: A Cooperative Object-Referring Game in Non-Perfectly Co-Observable Scene

Visual dialog has witnessed great progress after introducing various vision-oriented goals into the conversation, especially such as GuessWhich and GuessWhat, where the only image is visible by either and both of the questioner and the answerer, respectively. Researchers explore more on visual dialog tasks in such kind of single- or perfectly co-observable visual scene, while somewhat neglect the exploration on tasks of non perfectly co-observable visual scene, where the images accessed by two agents may not be exactly the same, often occurred in practice. Although building common ground in non-perfectly co-observable visual scene through conversation is significant for advanced dialog agents, the lack of such dialog task and corresponding large-scale dataset makes it impossible to carry out in-depth research. To break this limitation, we propose an object-referring game in non-perfectly co-observable visual scene, where the goal is to spot the difference between the similar visual scenes through conversing in natural language. The task addresses challenges of the dialog strategy in non-perfectly co-observable visual scene and the ability of categorizing objects. Correspondingly, we construct a large-scale multimodal dataset, named SpotDiff, which contains 87k Virtual Reality images and 97k dialogs generated by self-play. Finally, we give benchmark models for this task, and conduct extensive experiments to evaluate its performance as well as analyze its main challenges.
Fiber-optic diagnostic system for future accelerator magnets

The next generation high energy physics accelerators will require magnetic fields at ~20 T. HTS coils will be an essential component of future accelerator magnets and several efforts are currently dedicated on designing 20 T HTS- LTS hybrid magnets. Among the existing challenges, there is the lack of a robust quench detection system for hybrid magnet technology. Another big challenge is represented by the high number of training quenches required by Nb3Sn magnets to reach performance level. In this framework it is important to find a tool that allow local real-time monitoring of magnet strain and temperature. In this paper, we propose the use of fiber optics sensors for diagnostic and quench detection in future accelerator superconducting magnets. Discrete and distributed fiber optic sensors have demonstrated to be a promising tool. The goal is to instrument hundreds of accelerator superconducting magnets and to move beyond the proof-of-concept level. Significant developments are still needed. Here, we are going to present the most recent results and discuss the most urgent technical developments in order to make those sensors a robust and reliable diagnostic tool for accelerator superconducting magnets over the next 10 year. We foresee that discrete fiber sensors will be a stable diagnostic probe for superconducting magnets over the next 3 to 5 years. More R&D work will be necessary for distributed fibers. The most urgent needs are the increase of sample rate and sensitivity. Close collaboration with vendors will be necessary to improve mechanical properties and fabrication processes in order to produce hundreds of meters of fiber and instrument a large number of accelerator superconducting magnets. Those R&D efforts will last up to 10 years with a founding level that spans between 5-10 M$.
Data, geometry and homology

Homology-based invariants can be used to characterize the geometry of datasets and thereby gain some understanding of the processes generating those datasets. In this work we investigate how the geometry of a dataset changes when it is subsampled in various ways. In our framework the dataset serves as a reference object; we then consider different points in the ambient space and endow them with a geometry defined in relation to the reference object, for instance by subsampling the dataset proportionally to the distance between its elements and the point under consideration. We illustrate how this process can be used to extract rich geometrical information, allowing for example to classify points coming from different data distributions.
Morphological Reinflection with Multiple Arguments: An Extended Annotation schema and a Georgian Case Study

In recent years, a flurry of morphological datasets had emerged, most notably UniMorph, aa multi-lingual repository of inflection tables. However, the flat structure of the current morphological annotation makes the treatment of some languages quirky, if not impossible, specifically in cases of polypersonal agreement. In this paper we propose a general solution for such cases and expand the UniMorph annotation schema to naturally address this phenomenon, in which verbs agree with multiple arguments using true affixes. We apply this extended schema to one such language, Georgian, and provide a human-verified, accurate and balanced morphological dataset for Georgian verbs. The dataset has 4 times more tables and 6 times more verb forms compared to the existing UniMorph dataset, covering all possible variants of argument marking, demonstrating the adequacy of our proposed scheme. Experiments on a reinflection task show that generalization is easy when the data is split at the form level, but extremely hard when splitting along lemma lines. Expanding the other languages in UniMorph according to this schema is expected to improve both the coverage, consistency and interpretability of this benchmark.
CUE Vectors: Modular Training of Language Models Conditioned on Diverse Contextual Signals

We propose a framework to modularize the training of neural language models that use diverse forms of context by eliminating the need to jointly train context and within-sentence encoders. Our approach, contextual universal embeddings (CUE), trains LMs on one type of contextual data and adapts to novel context types. The model consists of a pretrained neural sentence LM, a BERT-based contextual encoder, and a masked transfomer decoder that estimates LM probabilities using sentence-internal and contextual evidence.When contextually annotated data is unavailable, our model learns to combine contextual and sentence-internal information using noisy oracle unigram embeddings as a proxy. Real context data can be introduced later and used to adapt a small number of parameters that map contextual data into the decoder’s embedding space. We validate the CUE framework on a NYTimes text corpus with multiple metadata types, for which the LM perplexity can be lowered from 36.6 to 27.4 by conditioning on context. Bootstrapping a contextual LM with only a subset of the metadata during training retains 85% of the achievable gain. Training the model initially with proxy context retains 67% of the perplexity gain after adapting to real context. Furthermore, we can swap one type of pretrained sentence LM for another without retraining the context encoders, by only adapting the decoder model. Overall, we obtain a modular framework that allows incremental, scalable training of context-enhanced LMs.
Spintronic THz emitters based on transition metals and semi-metals/Pt multilayers

Spintronic terahertz (THz) emitters based on the inverse spin Hall effect in ferromagnetic/heavy metal (FM/HM) heterostructures have become important sources for THz pulse generation. The design, materials, and control of these interfaces at the nanometer level have become vital to engineer their THz emission properties. In this work, we present studies of the optimization of such structures through a multi-pronged approach, taking advantage of material and interface engineering to enhance THz spintronic emission. This includes the application of multi-stacks of HM/FM junctions and their application to trilayer structures, the use of spin-sinks to simultaneously enhance the THz emitted fields and reduce the use of thick Pt layers to reduce optical absorption, and the use of semi-metals to increase the spin polarization and, thus, THz emission. Through these approaches, significant enhancements of the THz field can be achieved. Importantly, taking into account the optical absorption permits to elucidate novel phenomena such as the relation between the spin diffusion length and the spin-sink using THz spectroscopy, as well as possibly distinguishing between self- and interface-spin-to-charge conversion in semi-metals.
GOMP-ST: Grasp Optimized Motion Planning for Suction Transport

Suction cup grasping is very common in industry, but moving too quickly can cause suction cups to detach, causing drops or damage. Maintaining a suction grasp throughout a high-speed motion requires balancing suction forces against inertial forces while the suction cups deform under strain. In this paper, we consider Grasp Optimized Motion Planning for Suction Transport (GOMP-ST), an algorithm that combines deep learning with optimization to decrease transport time while avoiding suction cup failure. GOMP-ST first repeatedly moves a physical robot, vacuum gripper, and a sample object, while measur-ing pressure with a solid-state sensor to learn critical failure conditions. Then, these are integrated as constraints on the accelerations at the end-effector into a time-optimizing motion planner. The resulting plans incorporate real-world ef-fects such as suction cup deformation that are difficult to model analytically. In GOMP-ST, the learned constraint, modeled with a neural network, is linearized using Autograd and integrated into a sequential quadratic program optimization. In 420 experiments with a physical UR5 transporting objects rang-ing from 1.3 to 1.7kg, we compare GOMP-ST to baseline optimizing motion planners. Results suggest that GOMP-ST can avoid suction cup failure while de-creasing transport times from 16% to 58%. For code, video, and datasets, see https://sites.google. com/view/gomp-st
Thermodynamic Equation of State and Joule-Thomson Expansion for a FRW Universe

We investigate the thermodynamics for a FRW (Friedmann-Robertson-Walker) universe in the extended phase space. From the uniﬁed ﬁrst law for a FRW universe, we derive the ﬁrst law of thermodynamics, and discover that the proper thermodynamic pressure for a FRW universe with the cosmological constant should be deﬁned by the combination of the work density of the matter ﬁeld and the cosmological constant. With such deﬁnition, we obtain the thermodynamic equation of state for a FRW universe, i.e. P = P ( R A , T ). Furthermore, we study the Joule-Thomson expansion as an application of the thermodynamic equation of state to ﬁnd the cooling-heating property of the FRW universe. We demonstrate that there is an inversion temperature for a FRW universe if its enthalpy H is negative. These investigations shed insights on the evolution of our universe in view of thermodynamics.
How quantum nonlocality without entanglement witnesses classical processes without causal order

We show a correspondence between quantum nonlocality without entanglement and logically consistent classical processes without causal order. Three parties with access to a noncausal classical process—the AF/BW process—can perfectly discriminate the states in an ensemble—the SHIFT ensemble—exhibiting quantum nonlocality without entanglement, something impossible with local operations and classical communication (LOCC): The LOCC restriction implicitly assumes causal classical communication. This provides an operational interpretation of the AF/BW process as a noncausal information-theoretic resource. From a foundational perspective, this means that the ability to perfectly discriminate quantum states in the SHIFT ensemble via local operations and classical communication would serve as an operational witness of noncausality. We then generalize our result to show how any Boolean classical process without global past can be transformed to an ensemble of states that exhibits quantum nonlocality without entanglement. Since multipartite generalizations of the AF/BW process are known, this yields novel multiqubit ensembles of quantum nonlocality without entanglement, which is of independent interest.
Elevated human impact on islands increases the introduction and extinction status of native insular reptiles

Species ranges are changing in the Anthropocene, the ranges of introduced species are expanding, while extinction-prone species are contracting. Introductions and extinctions are both caused by how species respond to human impacts, but it is unknown why the ranges of some species expand and some contract. Here, we test that this opposite response of human impact is due to introduced and extinction-prone species falling at opposite ends of geographic, evolutionary, or ecological trait continua. We constructed a database of native range maps, traits, phylogenetic relationships, and the introduction and extinction-prone status of squamate reptiles with ranges native to the Western Hemisphere. Across >3,000 snake and lizard species (88% of known native squamates), 142 had been introduced elsewhere and 483 were extinction-prone (i.e., extinct, vulnerable, threatened). To explain variation in status, we first tested if the same human-impacted regions in the Americas contained the native ranges of species of either status. Second, we tested for phylogenetic signal in species status. Finally, we tested the explanatory power of multiple trait continua. The native ranges of introduced and extinction-prone reptiles were clustered in island regions with high human impact vs. mainland regions with lower human impact. Phylogenetic signal was weak for status, but introduced and extinction-prone species were clustered in different clades. All geographic and ecological traits that explained both statuses supported the opposite ends hypothesis. Introduced species had larger, edgier ranges, while extinction-prone species had smaller, simpler ranges. Introduced species were mostly herbivorous/omnivorous, while extinction-prone species were mostly carnivorous. Introduced species produced larger clutches, while extinction-prone species were smaller in body size. In the Anthropocene, the naive ranges of introduced and extinction-prone species are in the same human-impacted regions where trait continua, having opposite effects, determine whether species ranges expand or contract in the continuing face of global change.
Impairments in Fear Extinction Memory and Basolateral Amygdala Plasticity in the TgF344-AD Rat Model of Alzheimer’s Disease Are Distinct from Nonpathological Aging

Abstract Fear-based disorders such as post-traumatic stress disorder (PTSD) steepen age-related cognitive decline and double the risk for developing Alzheimer’s disease (AD). Because of the seemingly hyperactive properties of fear memories, PTSD symptoms can worsen with age. Perturbations in the synaptic circuitry supporting fear memory extinction are key neural substrates of PTSD. The basolateral amygdala (BLA) is a medial temporal lobe structure that is critical in the encoding, consolidation, and retrieval of fear memories. As little is known about fear extinction memory and BLA synaptic dysfunction within the context of aging and AD, the goal of this study was to investigate how fear extinction memory deficits and basal amygdaloid nucleus (BA) synaptic dysfunction differentially associate in nonpathologic aging and AD in the TgF344AD (TgAD) rat model of AD. Young, middle-aged, and older-aged WT and TgAD rats were trained on a delay fear conditioning and extinction procedure before ex vivo extracellular field potential recording experiments in the BA. Relative to young WT rats, long-term extinction memory was impaired, and in general, was associated with a hyperexcitable BA and impaired LTP in TgAD rats at all ages. In contrast, long-term extinction memory was impaired in aged WT rats and was associated with impaired LTP but not BA hyperexcitability. Interestingly, the middle-aged TgAD rats showed intact short-term extinction and BA LTP, which is suggestive of a compensatory mechanism, whereas differential neural recruitment in older-aged WT rats may have facilitated short-term extinction. As such, associations between fear extinction memory and amygdala deficits in nonpathologic aging and AD are dissociable.
Contribution of the Golgi apparatus in morphogenesis of a virus-induced cytopathic vacuolar system

Electron tomography reveals four classes of cytopathic vesicles-II (CPV-II) stemming from the host Golgi apparatus after Venezuelan equine encephalitis virus infection. The Golgi apparatus (GA) in mammalian cells is pericentrosomally anchored and exhibits a stacked architecture. During infections by members of the alphavirus genus, the host cell GA is thought to give rise to distinct mobile pleomorphic vacuoles known as CPV-II (cytopathic vesicle-II) via unknown morphological steps. To dissect this, we adopted a phased electron tomography approach to image multiple overlapping volumes of a cell infected with Venezuelan equine encephalitis virus (VEEV) and complemented it with localization of a peroxidase-tagged Golgi marker. Analysis of the tomograms revealed a pattern of progressive cisternal bending into double-lamellar vesicles as a central process underpinning the biogenesis and the morphological complexity of this vacuolar system. Here, we propose a model for the conversion of the GA to CPV-II that reveals a unique pathway of intracellular virus envelopment. Our results have implications for alphavirus-induced displacement of Golgi cisternae to the plasma membrane to aid viral egress operating late in the infection cycle.
Improved basic cytogenetics challenges holocentricity of butterfly chromosomes

Mitotic chromosomes of butterflies, which look like dots or short filaments in most published data, are generally considered to lack localised centromeres and thus to be holokinetic. This particularity, observed in a number of other invertebrates, is associated with meiotic particularities known as “inverted meiosis”, in which the first division is equational, i.e., centromere splitting-up and segregation of sister chromatids instead of that of homologous chromosomes. However, the accurate analysis of butterfly chromosomes is difficult. 1) Their size is very small, equivalent to a single band of a mammalian metaphase chromosome. 2) They lack satellite DNA/heterochromatin in putative centromere regions and therefore marked primary constrictions. Our improved conditions for chromosome preparations in six butterfly species belonging to the Nymphalidae and Pieridae families challenges the holocentricity of their chromosomes: in spite of the absence of primary constriction, sister chromatids are recurrently held together at definite positions during mitotic metaphase, which makes possible to establish karyotypes composed of acrocentric and sub-metacentric chromosomes. The total number of chromosomes per karyotype is roughly inversely proportional to that of non-acrocentric chromosomes, which suggests the occurrence of frequent Robertsonian-like fusions or fissions during evolution. Furthermore, the behaviour and morphological changes of chromosomes along the various phases of meiosis do not differ much from those of canonical meiosis. In particular at metaphase II, chromosomes clearly have two sister chromatids, which refutes that anaphase I was equational. Thus, we propose an alternative mechanism to holocentricity for explaining the large variations in chromosome numbers in butterflies: 1) in the ancestral karyotype, composed of about 60-62 acrocentric chromosomes, the centromeres, devoid of centromeric heterochromatin/satellite DNA, were located at contact with telomeric heterochromatin; 2) the instability of telomeric heterochromatin largely contributed to drive the multiple chromosome rearrangements, which occurred during butterfly evolution.
Oxidative phosphorylation pathway disruption is an alternative pathological mechanism leading to Diamond-Blackfan anemia

Diamond-Blackfan anemia (DBA) is a rare congenital disorder characterized by the failure of erythroid progenitor differentiation; however, the molecular mechanisms leading to erythroid defects remain unclear. By analyzing the transcriptomic profiles of bone marrow from patients with DBA (n = 10), we identified the dysfunction of the oxidative phosphorylation (OXPHOS) pathway as a possible cause of DBA. We established a DBA cell model using differentiating hematopoietic stem progenitor cells in which the OXPHOS pathway was suppressed to completely recapitulate the defects in erythroid progenitor differentiation, ribosome biogenesis, and heme biosynthesis, which are representative characteristics of patients with DBA. Disruption of the OXPHOS pathway led to ribosomal defects and associated erythroid defects via abolishment of the Ran GTPase activating protein RanGAP1, which is pivotal in the RNA transport pathway. The composition of the ribosomal proteins in the established DBA cells was unchanged, but an overall reduction in ribosomal protein levels was observed, leading to an alteration in the translation of a subset of transcripts specific to erythropoiesis. We revealed that the OXPHOS pathway participates in erythropoiesis, particularly at an early stage, and reinforced the relationship between the OXPHOS pathway and erythropoiesis. Coenzyme Q10, an activator of OXPHOS, largely rescued the erythroid defects in DBA cells. Our results reveal that OXPHOS repression is an alternative pathological mechanism leading to DBA, demonstrating its potential as a therapeutic pathway. Key Points Oxidative phosphorylation (OXPHOS) pathway disruption is an alternative pathological mechanism underlying Diamond-Blackfan anemia (DBA). Suppression of OXPHOS leads to defects in erythropoiesis and ribosomal biogenesis via the RanGAP1 protein.
A new insight into RecA filament regulation by RecX from the analysis of conformation-specific interactions

RecA protein mediates homologous recombination repair in bacteria through assembly of long helical filaments on single-stranded DNA (ssDNA) in an ATP dependent manner. RecX, an important negative regulator of RecA, is known to inhibit RecA activity by stimulating the disassembly of RecA nucleoprotein filaments. Here we use a single-molecule approach to address the regulation of (E. coli) RecA-ssDNA filaments by RecX (E. coli) within the framework of distinct conformational states of RecA-ssDNA filament. Our findings revealed that RecX effectively binds the inactive conformation of RecA-ssDNA filaments and slows down the transition to the active state. Results of this work provide new mechanistic insights into the RecX-RecA interactions and highlight the importance of conformational transitions of RecA filaments as an additional level of regulation of its biological activity.
Sulfur-mediated chalcogen versus hydrogen bonds in proteins: a see-saw effect in the conformational space

Divalent sulfur (S) form chalcogen bond (Ch-bond) via its σ–holes and hydrogen bond (H-bond) via its lone-pairs. Relevance of these interactions and their interplay for protein structure and function is unclear. Based on the analyses of the crystal structures of small organic/organometallic molecules and proteins, and their Molecular Electrostatic Surface Potential, we show that the reciprocity of the substituent-dependent strength of the σ–holes and lone-pairs correlate with the formation of either Ch-bond or H-bond. In proteins, disulfide-bonded cystine preferentially forms Ch-bond, metal-chelated cysteine forms H-bond, while methionine forms either of them with comparable frequencies. This has implications to the positioning of these residues and their role in protein structure and function. Computational analyses reveal that the S-mediated interactions stabilize protein secondary structures by mechanisms such as helix capping, protecting free β-sheet edges by negative-design, and augmenting the stability of β-turns. We find that Ch-bond can be as strong as H-bond. The study highlights the importance of S-mediated Ch-bond and H-bond for understanding protein folding and function, development of improved strategies for protein/peptide structure prediction and design, and structure-based drug discovery.