Miracle-dz/UniFAR-FTUs huggingface dataset:
Beta- and gamma-band oscillatory connectivity support naturalistic reading of continuous text

Large-scale integration of information across cortical structures, building on neural connectivity, has been proposed to be a key element in supporting human cognitive processing. In electrophysiological neuroimaging studies of reading, quantification of neural interactions has been limited to the level of isolated words or sentences due to artefacts induced by eye movements. Here, we combined magnetoencephalography recording with advanced artefact rejection tools to investigate both cortico-cortical coherence and directed neural interactions during naturalistic reading of full-page texts. Our results show that reading vs. visual scanning of text was associated with wide-spread increases of cortico-cortical coherence in the beta- and gamma-bands. We further show that the reading task was linked with increased directed neural interactions compared to the scanning task across a sparse set of connections within a wide range of frequencies. Together, the results demonstrate that neural connectivity flexibly builds on different frequency bands to support continuous natural reading.
Spatial patterns in the diet of Gyps vultures in India and their implications for conservation

Dietary analyses are particularly useful for developing conservation programmes for species threatened by resource depletion, poisoning and environmental pollution. Gyps vultures in South Asia represent one such case, having undergone a population collapse caused by feeding on carcasses of cattle treated with the non-steroidal anti-inflammatory drug diclofenac. Following a ban on the veterinary use of diclofenac, populations of vultures remain low and mostly concentrated near protected areas. Understanding the role of protected areas in the recovery of these critically endangered species requires analyses of spatial variation in their diet. We used faecal metabarcoding to investigate the spatial variation in the diet of Gyps vultures across four landscapes from sites located inside and outside protected areas. We collected faecal 642 samples, of which 419 yielded adequate molecular data to identify the vulture species and 30 molecular operational taxonomic units corresponding to at least 28 diet species. The diet was dominated by large ungulates and varied across landscapes, protection status and vulture species, with the observed variation largely explained by differential intake of wild and domestic species. Domestic livestock was present in >95% of the samples from central, west and north India, but 77% of the samples had only wild species in south India. This variation was explained by livestock density within 100 km radius of the sampling site. Our results imply that protected areas may not offer a respite from possibility of diclofenac-poisoning across most parts of the country and efforts should continue unabated to remove nephrotoxic drugs from veterinary use.
Index Tuning with Machine Learning on Quantum Computers for Large-Scale Database Applications

Selecting appropriate index configurations that can minimize query processing costs is essential to database applications. This problem becomes more complicated when the database is replicated on multiple nodes. There have been divergent design index tuning algorithms utilizing either heuristic or optimization methods to solve this NP-Hard problem. However, this index selection problem becomes much more complex for large-scale replicated database applications and efficient algorithms are needed. While quantum computing has been investigated with promising results in several areas of database management, such as query optimization and transaction scheduling, no work exists that studies the divergent design index tuning problem for replicated databases. To fill this gap, in this paper, we provide our vision of a machine learning-based quantum divergent design index tuning algorithm for replicated databases. We first discuss the issues that should be handled when designing such an algorithm. We then describe an algorithm for classical computers that has been shown to perform better than other existing algorithms and present our vision of how to transform the algorithm to its quantum version.
A suppressor screen in C. elegans identifies a multi-protein interaction interface that stabilizes the synaptonemal complex

Successful chromosome segregation into gametes depends on tightly-regulated interactions between the parental chromosomes. During meiosis, chromosomes are aligned end-to-end by an interface called the synaptonemal complex, which also regulates exchanges between them. However, despite the functional and ultrastructural conservation of this essential interface, how protein-protein interactions within the synaptonemal complex regulate chromosomal interactions remains poorly understood. Here we describe a novel interaction interface in the C. elegans synaptonemal complex, comprised of short segments of three proteins, SYP-1, SYP-3 and SYP-4. We identified the interface through a saturated suppressor screen of a mutant that destabilizes the synaptonemal complex. The specificity and tight distribution of suppressors point to a charge-based interface that promotes interactions between synaptonemal complex subunits and, in turn, allows intimate interactions between chromosomes. Our work highlights the power of genetic studies to illuminate the mechanisms that underly meiotic chromosome interactions. Significance Statement Gamete production requires tightly regulated interactions between the parental chromosomes, which co-align and exchange information. These events are mediated by the synaptonemal complex – a thread-like structure that assembles between the parental chromosomes. The molecular interactions that underly synaptonemal complex assembly remain poorly understood due to rapid sequence divergence and challenges in biochemical reconstitution. Here we identify a novel three-component interface in the nematode synaptonemal complex. Destabilization and subsequent restoration of this interface link the integrity of the synaptonemal complex with chromosome alignment and regulation of exchanges. Beyond mechanistic understanding of chromosomal interactions, our work provides a blueprint for genetic probing of large cellular assemblies that are refractory to structural analysis and sheds light on the forces that shape their evolution.
Hypothetical gene Rv0495c regulates redox homeostasis in Mycobacterium tuberculosis

Mycobacterium tuberculosis (Mtb) has evolved sophisticated surveillance mechanisms to regulate and neutralize redox imbalances and associated lethal consequences. Failing this, the accumulated ROS induces toxicity by oxidizing a variety of biological molecules including proteins, nucleic acids and lipids. In the present study we identified Mtb’s Rv0495c gene as an important regulator of oxidized cytosolic environment. Compared to wild type Mtb strain lacking the Rv0495c gene, ΔRv0495c, had increased ROS and NAD+/NADH ratio creating a highly oxidized intracellular environment. ΔRv0495c strain demonstrated slow growth phenotype under in vitro and ex-vivo growth conditions and demonstrated enhanced susceptibility to drugs, oxidative, nitrosative and hypoxic growth conditions. In addition, the increase in the superoxide radicals triggered a Fenton-like reaction rendering the ΔRv0495c susceptible to free iron. The increase in the intracellular ROS levels of the ΔRv0495c was further corroborated by an increase in the expression of proteins involved in antioxidant defense and enhanced ROS-mediated oxidation and degradation of mycobacterial lipids. This superoxide-induced lipid degradation resulted in altered colony morphology and loss of membrane integrity in the ΔRv0495c. Surprisingly, despite showing a growth defect phenotype in an ex-vivo macrophage infection model, the absence of the Rv0495c gene in Mtb enhanced the pathogenicity and augmented the ability of the Mtb to grow inside the host. Gene expression analysis revealed a Rv0495c mediated immunomodulation of the host controls inflammation and helps creates a favorable niche for long-term survival of Mtb inside the host. In summary, the current study underscores the fact that the truce in the war between the host and the pathogen favors long-term disease persistence in tuberculosis. We believe targeting Rv0495c could potentially be explored as a strategy to potentiate the current anti-TB regimen.
Unraveling Vulnerabilities in Endocrine Therapy-Resistant HER2+/ER+ Breast Cancer

Background Breast tumors overexpressing human epidermal growth factor receptor (HER2) confer intrinsic resistance to endocrine therapy (ET), and patients with HER2/ estrogen receptor-positive (HER2+/HR+) breast cancer (BCa) are less responsive to ET than HER2−/ER+. However, real-world evidence reveals that a large subset of HER2+/ER+ patients receive ET as monotherapy, positioning this treatment pattern as a clinical challenge. In the present study, we developed and characterized two distinct in vitro models of ET-resistant (ETR) HER2+/ER+ BCa to identify possible therapeutic vulnerabilities. Methods To mimic ETR to aromatase inhibitors (AI), we developed two long-term estrogen-deprived (LTED) cell lines from BT-474 (BT474) and MDA-MB-361 (MM361). Growth assays, PAM50 molecular subtyping, genomic and transcriptomic analyses, followed by validation and functional studies, were used to identify targetable differences between ET-responsive parental and ETR-LTED HER2+/ER+ cells. Results Compared to their parental cells, MM361 LTEDs grew faster, lost ER, and increased HER2 expression, whereas BT474 LTEDs grew slower and maintained ER and HER2 expression. Both LTED variants had reduced responsiveness to fulvestrant. Whole-genome sequencing of the more aggressive MM361 LTED model system identified exonic mutations in genes encoding transcription factors and chromatin modifiers. Single-cell RNA sequencing demonstrated a shift towards non-luminal phenotypes, and revealed metabolic remodeling of MM361 LTEDs, with upregulated lipid metabolism and antioxidant genes associated with ferroptosis, including GPX4. Combining the GPX4 inhibitor RSL3 with anti-HER2 agents induced significant cell death in both the MM361 and BT474 LTEDs. Conclusions The BT474 and MM361 AI-resistant models capture distinct phenotypes of HER2+/ER+ BCa and identify altered lipid metabolism and ferroptosis remodeling as vulnerabilities of this type of ETR BCa.
Factorial state-space modelling for kinetic clustering and lineage inference

Single-cell RNA sequencing (scRNAseq) protocols measure the abundance of expressed transcripts for single cells. Gene expression profiles of cells (cell-states) represent the functional properties of the cell and are used to cluster cell-states that have a common functional identity (cell-type). Standard clustering methods for scRNAseq data perform hard clustering based on KNN graphs. This approach implicitly assumes that variation among cell-states within a cluster does not correspond to changes in functional properties. Differentiation is a directed process of transitions between cell-types via gradual changes in cell-states over the course of the process. We propose a latent state-space Markov model that utilises cell-state transitions derived from RNA velocity to model differentiation as a sequence of latent state transitions and to perform soft kinetic clustering of cell-states that accommodates the transitional nature of cells in a differentiation process. We applied this model to the differentiation of Radial-glia cells into mature neurons and demonstrate the utility of our method in discriminating between functional and transitional cell-states.
Frontal hip exoskeleton assistance does not appear promising for reducing the metabolic cost of walking: A preliminary experimental study

Background During walking, humans exert a substantial hip abduction moment to maintain balance and prevent pelvic drop. This significant torque requirement suggests that assisting the frontal hip muscles could be a promising strategy to reduce the energy expenditure associated with walking. A previous musculoskeletal simulation study also predicted that providing hip abduction assistance through an exoskeleton could potentially result in a large reduction in whole-body metabolic rate. However, to date, no study has experimentally assessed the metabolic cost of walking with frontal hip assistance. Methods In this case study involving a single subject (N = 1), a tethered hip exoskeleton emulator was used to assess the feasibility of reducing metabolic expenditure through frontal-plane hip assistance. Human-in-the-loop optimization was conducted separately under torque and position control to determine energetically optimal assistance parameters for each control scheme. Results The optimized profiles in both control schemes did not reduce metabolic rate compared to walking with assistance turned off. The optimal peak torque magnitude was found to be close to zero, suggesting that any hip abduction torque would increase metabolic rate. Both bio-inspired and simulation-inspired profiles substantially increased metabolic cost. Conclusion Frontal hip assistance does not appear to be promising in reducing the metabolic rate of walking. This could be attributed to the need for maintaining balance, as humans may refrain from relaxing certain muscles as a precaution against unexpected disturbances during walking. An investigation of different control architectures is needed to determine if frontal-plane hip assistance can yield successful results.
STAN: Spatio-Temporal Attention Network for Pandemic Prediction Using Real World Evidence

OBJECTIVE The COVID-19 pandemic has created many challenges that need immediate attention. Various epidemiological and deep learning models have been developed to predict the COVID-19 outbreak, but all have limitations that affect the accuracy and robustness of the predictions. Our method aims at addressing these limitations and making earlier and more accurate pandemic outbreak predictions by (1) using patients' EHR data from different counties and states that encode local disease status and medical resource utilization condition; (2) considering demographic similarity and geographical proximity between locations; and (3) integrating pandemic transmission dynamics into deep learning models. MATERIALS AND METHODS We proposed a spatio-temporal attention network (STAN) for pandemic prediction. It uses an attention-based graph convolutional network to capture geographical and temporal trends and predict the number of cases for a fixed number of days into the future. We also designed a physical law-based loss term for enhancing long-term prediction. STAN was tested using both massive real-world patient data and open source COVID-19 statistics provided by Johns Hopkins university across all U.S. counties. RESULTS STAN outperforms epidemiological modeling methods such as SIR and SEIR and deep learning models on both long-term and short-term predictions, achieving up to 87% lower mean squared error compared to the best baseline prediction model. CONCLUSIONS By using information from real-world patient data and geographical data, STAN can better capture the disease status and medical resource utilization information and thus provides more accurate pandemic modeling. With pandemic transmission law based regularization, STAN also achieves good long-term prediction performance.
Towards Adaptive Fault-Tolerant Sharded Databases

Data fragmentation and replication schemes play an important role in making parallel and transactional databases scalable and reliable. Existing data schemes generally assume a trusted environment where a node may fail, but no node will act adversarially. Here, we present our vision for RLShard, a reinforcement learning-powered fragmentation and replication schemefortransactionaldatabasesinByzantineenvironmentscapableofadaptingtodynamicworkloads. Wefirstdescribethe implications of Byzantine environments on data fragmentation schemes. Then, we explore two different system architectures for RLShard: a centralized architecture that relies on a trusted administrative domain and a fully decentralized architecture that uses collaborative reinforcement learning. Based on our first-cut design, we outline open research challenges towards our vision of adaptive fault-tolerant sharded databases.
Empirical Evaluation of A Quantum Accelerated Approach for The Central Path Method in Linear Programming

The central path method is a crucial technique for solving a wide range of optimization problems. The method relies on an equation solving step, which hits its limit for very large instances in practise. This paper proposes to explore the use of quantum approaches to enhance the central path method’s performance when solving very large linear programs. We will go through the potential benefits and limitations of replacing the iterative equation-solving step with the HHL quantum algorithm. We experiment with several instance types using each proposed algorithm and evaluate their effectiveness through numerical simulations to find a promising approach for the central path method.
In/Out Judgement by Ball Tracking in Table Tennis

In this study, we focus on the edge ball, and propose a vision-based method for determining whether a table tennis ball bounces on the table including edge balls, or goes out of bounds. For the judgement, we calculate the trajectory based on the ball detection by deep learning, and examine two methods based on the information from them. The first is to express the trajectory by two linear functions and judge from the angle formed by them. The second is to express the trajectory by one quadratic function in addition to the two linear functions and judge from the mean square error calculated by the detection point of the ball and the trajectory. As a result of evaluation, the former sometimes misjudged the edge ball. On the other hand, the latter judged correctly the edge ball which misjudged the former. Therefore, in the proposal, it is better to use the error of the detection point and trajectory of the ball to determine whether batted balls bounce on the table including edge balls, or go out of bounds. In addition, the position of the camera that takes videos must set so as not to disturb the match. Therefore, we change the distance between the camera and the table tennis table to 1.0m, 1.5m, and 1.0m for taking videos and judging. As a result of experiments, the judgement was sometimes incorrect due to an increase in error. However, the accuracy of the judgement was increased by limiting the range of ball detection.
Impact of post-quantum signatures on blockchain and DLT system

Blockchain and Distributed Ledger Technologies (DLT) are accelerating in deployment and increasingly being used to securely store digital assets. As the world digitises, there will be an acceleration of asset tokenisation with new marketplaces created for fractionalised tokenised digital assets. Blockchain and DLT systems using ECDSA signatures are vulnerable to a quantum adversary. The NIST post-quantum cryptography competition and the NIST stateful hash-based signature recommendations were used to determine the impact of using any of the proposed NIST finalist quantum-safe digital signature schemes. We examined the impact on both block sizes and block interval times that would be required if today’s ECDSA signatures were replaced by a NIST post-quantum signature scheme. We observed that the increased cost of adopting a cryptographic scheme has a significant negative impact on blockchain storage and communications costs. This research illustrates the need for smaller, more efficient cryptographic signature schemes that are closer to the size of the currently deployed ECDSA signatures and supports the adoption of layer-2 blockchain and layer-2 rollup protocols to mitigate the cost and increase the transaction throughput of the post-quantum blockchain or DLT system.
Online Processing Redux.

The term \online" has become an all-too-common addendum to database system names of the day. In this article we reexamine the notion of processing queries online. We distinguish between online processing and preprocessing, and argue that online processing for large queries requires redesigning major portions of a database system. We highlight pressing applications for truly online processing, and sketch ongoing research in these applications at Berkeley. We also outline basic techniques for running long queries online. We close by reevaluating the typical measurements of cost/performance for online systems, and propose a mass-market approach for designing and measuring data-intensive processing.
Evolution tectonique du Tianshan au Cénozoïque liée à la collision Inde-Asie Apports de la magnétostratigraphie et de la géochronologie isotopique U-Th/He.

Le Tianshan est une des chaines majeures d'Asie qui s'etend sur pres de 2500 km de longitude avec des reliefs superieurs a 7000 m. Il s'agit de l'orogene intracontinental le plus actif au monde issu d'une accretion initiale au Paleozoique suivie d'une reactivation majeure au Cenozoique en reponse a la collision Inde-Asie. Mais l'âge exact d'initiation de la deformation cenozoique reste mal contraint, ce qui est un obstacle important a la comprehension et a la determination de l'evolution de la deformation en Asie. Les piemonts Nord et Sud du Tianshan sont constitues par deux remarquables prismes d'avant chaine ou les sediments permiens au quaternaires des bassins flexuraux adjacents de Kuche et de la Junggarie sont tres bien exposes. L'histoire de la construction du Tianshan peut etre determinee grâce a une etude de l'enregistrement sedimentaire facilement accessible au niveau des piemonts. Ainsi, nous avons realise trois etudes magnetostratigraphiques le long des coupes de la Kuitun et de la Jingou He au Nord et le long de celle de Yaha au sud pour lesquelles nous avons identifie respectivement 16, 22 et 18 chrons magnetiques que nous avons correles a l'echelle de reference donnant des âges compris entre, 3.1 et 10.5 Ma, 8.5 Ma et 22 Ma et 5.2 et 12.6 Ma respectivement. Les vitesses de sedimentations deduites de ces correlations montrent une acceleration a ~11 Ma sur la coupe de Yaha et celle de la Jingou He qui presente egalement une acceleration anterieure a ~15 Ma alors que les vitesses restent stables depuis ~10 Ma sur la coupe Kuitun. Nous avons egalement realise des etudes de la mineralogie magnetique et des mesures de l'ASM qui montrent des changements importants de la susceptibilite magnetique (Κ) et du parametre de forme (T) a 21, 15 et 11 Ma sur les deux piemonts. A partir des changements de vitesses de sedimentation, contraint par ailleurs par ceux des parametres magnetiques, nous pensons que la surrection du Tianshan a probablement debute vers 15 Ma puis s'est acceleree a ~11 Ma, ce qui est coherent avec les etudes precedentes realisees sur la zone suivant d'autres methodes. A partir de modeles structuraux des piemonts et des basins de la Junggarie et de Kuche, associes aux âges magnetostratigraphiques et a des datations U-Th/He de grains d'apatites et zircons detritiques , nous determinons egalement: (1) l'âge d'activation et les vitesses de deformation de certaines structures des piemonts, (2) les flux et vitesses sedimentaires et (3) l'evolution des taux d'erosion. Nous discutons et decrivons ainsi l'evolution cinetique et cinematique des piemonts et de la haute chaine.