Miracle-dz/UniFAR-FTUs huggingface dataset:
VICTOR: An Implicit Approach to Mitigate Misinformation via Continuous Verification Reading

We design and evaluate VICTOR, an easy-to-apply module on top of a recommender system to mitigate misinformation. VICTOR takes an elegant, implicit approach to deliver fake-news verifications, such that readers of fake news can continuously access more verified news articles about fake-news events without explicit correction. We frame fake-news intervention within VICTOR as a graph-based question-answering (QA) task, with Q as a fake-news article and A as the corresponding verified articles. Specifically, VICTOR adopts reinforcement learning: it first considers fake-news readers’ preferences supported by underlying news recommender systems and then directs their reading sequence towards the verified news articles. To verify the performance of VICTOR, we collect and organize VERI, a new dataset consisting of real-news articles, user browsing logs, and fake-real news pairs for a large number of misinformation events. We evaluate zero-shot and few-shot VICTOR on VERI to simulate the never-exposed-ever and seen-before conditions of users while reading a piece of fake news. Results demonstrate that compared to baselines, VICTOR proactively delivers 6% more verified articles with a diversity increase of 7.5% to over 68% of at-risk users who have been exposed to fake news. Moreover, we conduct a field user study in which 165 participants evaluated fake news articles. Participants in the VICTOR condition show better exposure rates, proposal rates, and click rates on verified news articles than those in the other two conditions. Altogether, our work demonstrates the potentials of VICTOR, i.e., combat fake news by delivering verified information implicitly.
Mesostats—A multiplexed, low-cost, do-it-yourself continuous culturing system for experimental evolution of mesocosms

Microbial experimental evolution allows studying evolutionary dynamics in action and testing theory predictions in the lab. Experimental evolution in chemostats (i.e. continuous flow through cultures) has recently gained increased interest as it allows tighter control of selective pressures compared to static batch cultures, with a growing number of efforts to develop systems that are easier and cheaper to construct. This protocol describes the design and construction of a multiplexed chemostat array (dubbed “mesostats”) designed for cultivation of algae in 16 concurrent populations, specifically intended for studying adaptation to herbicides. We also present control data from several experiments run on the system to show replicability, data illustrating the effects of common issues like leaks, contamination and clumps, and outline possible modifications and adaptations of the system for future research.
Synapses learn to utilize pre-synaptic noise for the prediction of postsynaptic dynamics

Synapses in the brain are highly noisy, which leads to a large trial-by-trial variability. Given how costly synapses are in terms of energy consumption these high levels of noise are surprising. Here we propose that synapses use their noise to represent uncertainties about the activity of the post-synaptic neuron. To show this we utilize the free-energy principle (FEP), a well-established theoretical framework to describe the ability of organisms to self-organize and survive in uncertain environments. This principle provides insights on multiple scales, from high-level behavioral functions such as attention or foraging, to the dynamics of single microcircuits in the brain, suggesting that the FEP can be used to describe all levels of brain function. The synapse-centric account of the FEP that is pursued here, suggests that synapses form an internal model of the somatic membrane dynamics, being updated by a synaptic learning rule that resembles experimentally well-established LTP/LTD mechanisms. This approach entails that a synapse utilizes noisy processes like stochastic synaptic release to also encode its uncertainty about the state of the somatic potential. Although each synapse strives for predicting the somatic dynamics of its neuron, we show that the emergent dynamics of many synapses in a neuronal network resolve different learning problems such as pattern classification or closed-loop control in a dynamic environment. Hereby, synapses coordinate their noise processes to represent and utilize uncertainties on the network level in behaviorally ambiguous situations.
Gene Transfer-based Phylogenetics: Analytical Expressions and Additivity via Birth–Death Theory

The genomic era has opened up vast opportunities in molecular systematics, one of which is deciphering the evolutionary history in fine detail. Under this mass of data, analysing the point mutations of standard markers is too crude and slow for fine-scale phylogenetics. Nevertheless, genome dynamics events provide far richer information. The synteny index (SI) between a pair of genomes combines gene order and gene content information, allowing the comparison of genomes of unequal gene content, together with order considerations of their common genes. Recently, genome dynamics has been modelled as a continuous-time Markov process, and gene distance in the genome as a birth–death–immigration process. Nevertheless, due to complexities arising in this setting such as overlapping neighbourhoods and other confounding factors, no precise and provably consistent estimators could be derived. Here, we extend this modelling approach by using techniques from birth–death theory to derive explicit expressions of the system’s probabilistic dynamics in the form of rational functions of the model parameters. This, in turn, allows us to infer analytically the expected distances between organisms based on a transformation of their SI. Despite the complexity of the expressions obtained, we establish additivity of this estimated evolutionary distance (a desirable property yielding phylogenetic consistency). Applying the new measure in simulation studies shows that it attains very accurate results in realistic settings and even under model extensions. In the real-data realm, we applied the new formulation to unique data structure that we constructed - the ordered orthology DB - based on a new version of the EggNOG database, to construct a tree with more than 4.5K taxa. The resulted tree was compared it with a NCBI taxonomy for these organisms. To the best of our knowledge, this is the largest gene-order-based tree constructed and it overcomes flaws found in previous approaches.
Multisite imaging of neural activity using a genetically encoded calcium sensor in the honey bee

Understanding of the neural bases for complex behaviors in Hymenoptera insect species has been limited by a lack of tools that allow measuring neuronal activity simultaneously in different brain regions. Here, we developed the first pan-neuronal genetic driver in a Hymenopteran model organism, the honey bee, and expressed the calcium indicator GCaMP6f under the control of the honey bee synapsin promoter. We show that GCaMP6f is widely expressed in the honey bee brain, allowing to record neural activity from multiple brain regions. To assess the power of this tool, we focused on the olfactory system, recording simultaneous responses from the antennal lobe, and from the more poorly investigated lateral horn and mushroom body calyces. Neural responses to 16 distinct odorants demonstrate that odorant quality (chemical structure) and quantity are faithfully encoded in the honey bee antennal lobe. In contrast, odor coding in the lateral horn departs from this simple physico-chemical coding, supporting the role of this structure in coding the biological value of odorants. We further demonstrate robust neural responses to several bee pheromone odorants, key drivers of social behavior, in the lateral horn. Combined, these brain recordings represent the first use of a neurogenetic tool for recording large-scale neural activity in a eusocial insect, and will be of utility in assessing the neural underpinnings of olfactory and other sensory modalities and of social behaviors and cognitive abilities.
Statistical learning of distractor co-occurrences facilitates visual search

Visual search is facilitated by knowledge of the relationship between the target and the distractors, including both where the target is likely to be amongst the distractors and how it differs from the distractors. Whether the statistical structure amongst distractors themselves, unrelated to target properties, facilitates search is less well understood. Here, we assessed the benefit of distractor structure using novel shapes whose relationship to each other was learned implicitly during visual search. Participants searched for target items in arrays of shapes that comprised either four pairs of co-occurring distractor shapes (structured scenes) or eight distractor shapes randomly partitioned into four pairs on each trial (unstructured scenes). Across five online experiments (N=1140), we found that after a period of search training, participants were more efficient when searching for targets in structured than unstructured scenes. This structure-benefit emerged independently of whether the position of the shapes within each pair was fixed or variable, and despite participants having no explicit knowledge of the structured pairs they had seen. These results show that implicitly learned co-occurrence statistics between distractor shapes increases search efficiency. Increased efficiency in the rejection of regularly co-occurring distractors may contribute to the efficiency of visual search in natural scenes, where such regularities are abundant.
Evolutionary conservation and divergence of the transcriptional regulation of bivalve shell secretion across life-history stages

Adult molluscs produce shells with diverse morphologies and ornamentations, different colour patterns and microstructures. The larval shell however, is a phenotypically more conserved structure. How do developmental and evolutionary processes generate varying diversity at different life history stages? Using live-imaging, histology, scanning electron microscopy and transcriptomic profiling, we have described shell development in a heteroconchian bivalve the Antarctic clam, Laternula elliptica and compared it to adult shell secretion processes in the same species. Adult downstream shell genes, such as those encoding extracellular matrix proteins and biomineralisation enzymes, were largely not expressed during shell development, and instead, a development-specific downstream gene repertoire was expressed. Upstream regulatory genes such as transcription factors and signalling molecules were conserved between developmental and adult shell secretion. Comparing heteroconchian transcriptomic data with recently reported pteriomorphian larval shell proteome data suggests that, despite being phenotypically more conserved, the downstream effectors constituting the larval shell “tool-kit” may be as diverse as that of adults. Overall, our new data suggests that a larval shell formed using development-specific downstream effector genes is a conserved and ancestral feature of the bivalve lineage, and possibly more broadly across the molluscs.
The effect of sleep continuity disruption on multimodal emotion processing and regulation: a laboratory‐based, randomised, controlled experiment in good sleepers

Previous research shows that experimental sleep deprivation alters emotion processing, suggesting a potential mechanism linking sleep disruption to mental ill‐health. Extending previous work, we experimentally disrupted sleep continuity in good sleepers and assessed next‐day emotion processing and regulation using tasks with established sensitivity to depression. In a laboratory‐based study, 51 good sleepers (37 female; mean [SD] age 24 [3.63] years), were randomised to 1 night of uninterrupted sleep (n = 24) or sleep continuity disruption (n = 27). We assessed emotion perception, attention, and memory the following day. Participants also completed an emotion regulation task and measures of self‐reported affect, anxiety, sleepiness, overnight declarative memory consolidation, and psychomotor vigilance. Confirming the effects of the manipulation, sleep continuity disruption led to a marked decrease in polysomnography‐defined total sleep time (229.98 versus 434.57 min), increased wake‐time after sleep onset (260.66 versus 23.84 min), and increased sleepiness (d = 0.81). Sleep continuity disruption led to increased anxiety (d = 0.68), decreased positive affect (d = −0.62), reduced overnight declarative memory consolidation (d = −1.08), and reduced psychomotor vigilance (longer reaction times [d = 0.64] and more lapses [d = 0.74]), relative to control. However, contrary to our hypotheses, experimental sleep disruption had no effect on perception of, or bias for, emotional facial expressions, emotional memory for words, or emotion regulation following worry induction. In conclusion, 1 night of sleep continuity disruption had no appreciable effect on objective measures of emotion processing or emotion regulation in response to worry induction, despite clear effects on memory consolidation, vigilance, and self‐reported affect and anxiety.
Omics of an enigmatic marine amoeba uncovers unprecedented giant viruses gene trafficking and provides insights into its complex life cycle

Amoebozoa include lineages of diverse ecology, behavior and morphology. They are assumed to encompass members with the largest genome sizes of all living things, yet genomic studies in the group are limited. Trichosphaerium, a polymorphic, multinucleate, marine amoeba with a complicated life cycle has puzzled experts in the field for over a century. In an effort to explore the genomic diversity, and investigate extraordinary behavior observed among the Amoebozoa, we used integrated omics approaches to study this enigmatic marine amoeba. Omics data, including single-cell transcriptomics and cytological data, demonstrate that Trichosphaerium sp. possesses the complete meiosis toolkit genes. These genes are expressed in life stages of the amoeba including medium and large cells. The life cycle of Trichosphaerium sp. involves asexual processes via binary fission and multiple fragmentation of giant cells, and sexual-like processes involving genes implicated in sexual reproduction and polyploidization. These findings are in stark contrast to a life cycle previously reported for this amoeba. Despite the extreme morphological plasticity observed in Trichosphaerium, our genomic data showed populations maintain a species-level intragenomic variation. A draft genome of Trichosphaerium indicates elevated lateral gene transfer (LGT) from bacteria and giant viruses. Gene trafficking in Trichosphaerium is the highest within Amoebozoa, and among the highest in microbial eukaryotes. Significance statement Amoebozoa include various genome complexities and life cycles, however, the genomes of the vast diversity of amoebozoans remains unexplored. In this study an integrated omics approach is used to investigate the genome and life cycle of Trichophaerium, an enigmatic polymorphic marine amoeba. We uncovered elevated gene trafficking from giant viruses and presence of the complete meiosis gene toolkit. Despite the observed large morphological plasticity, the population of Trichophaerium maintains intragenomic variation of a species level.
FGF signaling promotes precursor spreading for adult adipogenesis in Drosophila

Knowledge of adipogenetic mechanisms is essential to understand and treat conditions affecting organismal metabolism and adipose tissue health. In Drosophila, mature adipose tissue (fat body) exists in larvae and adults. In contrast to the well-known development of the larval fat body from the embryonic mesoderm, adult adipogenesis has remained mysterious. Furthermore, conclusive proof of its physiological significance is lacking. Here, we show that the adult fat body originates from a pool of undifferentiated mesodermal precursors that migrate from the thorax into the abdomen during metamorphosis. Through in vivo imaging, we found that these precursors spread from the ventral midline and cover the inner surface of the abdomen in a process strikingly reminiscent of embryonic mesoderm migration, requiring FGF signaling as well. FGF signaling guides migration dorsally and regulates adhesion to the substrate. After spreading is complete, precursor differentiation involves fat accumulation and cell fusion that produces mature binucleate and tetranucleate adipocytes. Finally, we show that flies where adult adipogenesis is impaired by knock down of FGF receptor Heartless or transcription factor Serpent display ectopic fat accumulation in oenocytes and decreased resistance to starvation. Our results reveal that adult adipogenesis occurs de novo during metamorphosis and demonstrate its crucial physiological role.
CASK and FARP coordinately control pre- and post-synaptic function

Synaptic proteins are immobilized at synapses via interactions with scaffolding proteins. Scaffolding proteins for glutamatergic and GABAergic synapses have been extensively studied; however, far less is known about how scaffolds shape the function of cholinergic synapses. Here we analyze the role of two C. elegans post-synaptic scaffolding proteins (LIN-2/CASK and FRM-3/FARP) at cholinergic neuromuscular junctions. Constitutive knockouts or muscle specific inactivation of lin-2 and frm-3 dramatically reduced spontaneous and evoked post-synaptic currents. These synaptic defects resulted from decreased abundance of post-synaptic ionotropic acetylcholine receptors (AChRs) and decreased presynaptic ACh release. Thus, our findings show that post-synaptic LIN-2/FRM-3 complexes coordinately control pre- and post-synaptic function, thereby promoting cholinergic synaptic transmission.
The nanoCUT&RUN technique visualizes telomeric chromatin in Drosophila

Advances in genomic technology led to a more focused pattern for the distribution of chromosomal proteins and a better understanding of their functions. The recent development of the CUT&RUN technique marks one of the important such advances. Here we develop a modified CUT&RUN technique that we termed nanoCUT&RUN, in which a high affinity nanobody to GFP is used to bring micrococcal nuclease to the binding sites of GFP-tagged chromatin proteins. Subsequent activation of the nuclease cleaves the chromatin, and sequencing of released DNA identifies binding sites. We show that nanoCUT&RUN efficiently produces high quality data for the TRL transcription factor in Drosophila embryos, and distinguishes binding sites specific between two TRL isoforms. We further show that nanoCUT&RUN dissects the distributions of the HipHop and HOAP telomere capping proteins, and uncovers unexpected binding of telomeric proteins at centromeres. nanoCUT&RUN can be readily applied to any system in which a chromatin protein of interest, or its isoforms, carries the GFP tag.
Reciprocal feature encoding by cortical excitatory and inhibitory neurons

In the cortex, the interplay between excitation and inhibition determines the fidelity of neuronal representations. However, while the receptive fields of excitatory neurons are often fine-tuned to the encoded features, the principles governing the tuning of inhibitory neurons are still elusive. We addressed this problem by recording populations of neurons in the postsubiculum (PoSub), a cortical area where the receptive fields of most excitatory neurons correspond to a specific head-direction (HD). In contrast to PoSub-HD cells, the tuning of fast-spiking (FS) cells, the largest class of cortical inhibitory neurons, was broad and heterogeneous. However, we found that PoSub-FS cell tuning curves were often fine-tuned in the spatial frequency domain, which resulted in various radial symmetries in their HD tuning. In addition, recordings and specific optogenetic manipulations of the upstream thalamic populations as well as computational models suggest that this population co-tuning in the frequency domain has a local origin. Together, these findings provide evidence that the resolution of neuronal tuning is an intrinsic property of local cortical networks, shared by both excitatory and inhibitory cell populations.
Aspects Based Opinion Mining for Teacher and Course Evaluation

: Teacher and course evaluation by students at the end of each term is an important task in almost every academic institution worldwide. It helps in assessing faculty performance and suitability of the course in any academic program. The data collected from evaluation comprises of two parts, Likert Scale and open-ended feedback. Computationally, the Likert Scale form can be handled easily as it is numerical in nature but to handle open-ended feedback is a challenging task. Presently, in most of the organizations it is processed manually, which contains many problems like it is error-prone, tedious and full of human biases. The objective of this study is to solve these problems, using two-step rule-based strategy from Machine Learning and Natural Language Processing (NLP) techniques. The first step is to extract overall topic of the feedback text using supervised machine learning followed by exploitation of NLP rules to find out specific aspect and related opinion word about which the feedback is given along with orientation of the opinion either positive, negative or neutral. Using, this two-step strategy combining with NLP, machine learning techniques and data from past seven years of real feedback at a public sector university in Pakistan, we are able to achieve a recall and precision of 83.89% and 84% on topic identification i.e. to classify a feedback in teacher and course category. The system is able to extract different aspects of teacher and course with a precision of 83% and recall of 80%, whereas overall sentiment classification accuracy is 90%. To the best of our knowledge, this is the first rule-based approach for such problem with quite satisfactory results.
BUSINESS AND MILITARY ESP TEACHING ACTIVITIES, WITHIN THE FOREIGN LANGUAGE CURRICULUM

The world of teaching has always reminded listeners that "the most important language in the world is the one spoken by the client". As this message has not always been heard, let alone promoted the survival and growth of many teaching activities is beginning to hinge on the ability to compete on a worldwide basis. Leaders in teaching have stressed the importance of foreign language study for the entire community of business professionals. Teachers of foreign languages shall have to make use of methods to develop an interest in and an understanding of the world outside our own, that do not necessarily rel y on direct experience. A major charge will fall on the educational system, both formally in undergraduate and graduat e courses, and informally through a variety of continuing education programs. The study looks at the best ways that can make our students get basic communicative ability, cross-cultural compr ehension, an introduction to basic business, military and technical vocabulary.
Artefacts Removal from Optical Coherence Tomography Angiography

This paper presents a new approach for artefacts removal from opti- cal coherence tomography angiography (OCTA). The artefacts mainly arise as a result of distortion due to eye movements during OCT scanning process. These distortions manifest themselves as visible motion artefacts when doctors review the enface image of OCTA data. To remove these artefacts, firstly we perform motion registration for the captured OCT volume data and subsequent- ly perform motion correction to obtain the registered OCT data. Next, we com- pute the OCTA from the registered OCT data using an enhanced correlation mapping technique. Thereafter, we compute the enface image from the OCTA data. In the next step, we attempt to locate regions where there is misalignment in the OCT frames of the various B-scans. Finally, we attempt to restore the re- gions where correct data is postulated to be absent. Our experimental results demonstrate the effectiveness of our proposed approach.