Miracle-dz/UniFAR-FTUs huggingface dataset:
Modular multiwell viscoelastic hydrogel platform for two- and three-dimensional cell culture applications

Hydrogels have gained significant popularity as model platforms to study the reciprocal interactions between cells and their microenvironment. While hydrogel tools to probe many characteristics of the extracellular space have been developed, fabrication approaches remain challenging and time-consuming, limiting multiplexing or widespread adoption. Thus, we have developed a modular fabrication approach to generate distinct hydrogel microenvironments within 96-well plates for increased throughput of fabrication as well as integration with existing high-throughput assay technologies. This approach enables in situ hydrogel mechanical characterization and was used to generate both elastic and viscoelastic hydrogels across a range of stiffnesses. Additionally, this fabrication method enabled a 3-fold reduction in polymer and up to an 8-fold reduction in fabrication time required per hydrogel replicate. The feasibility of this platform for cell culture applications was demonstrated by measuring both population-level and single cell-level metrics via microplate reader and high-content imaging. Finally, the 96-well hydrogel array was utilized for 3D cell culture, demonstrating the ability to support high cell viability. Together, this work demonstrates a versatile and easily adoptable fabrication approach that can support the ever-expanding tool kit of hydrogel technologies for cell culture applications.
Temperature elevation synergises with and enhances the type-I IFN-mediated restriction of MPXV

Fever is an evolutionary conserved host pro-inflammatory immune response that governs the regulation of multiple biological processes to control the outcome of infection. In January 2022, the World Health Organization (WHO) reported a global outbreak in mpox cases with a high incidence of human-to-human transmission. A frequent prodromal symptom of monkeypox virus (MPXV) infection is fever, with a febrile temperature range of 38.3 to 40.5 °C. However, the outcome of temperature elevation on MPXV infection remains poorly defined. Here, we isolated a circulating strain of MPXV from a patient who presented with fever (38.5 °C) and rash from the 2022 outbreak. Genomic sequencing identified this isolate to belong to the epidemic Clade IIb.B1. Transcriptomic analysis of infected cells demonstrated this virus to induce a strong IL6 pro-inflammatory immune response, consistent with a role for this pyrogen in the regulation of fever. We identify host-cell temperature at both physiological skin (33 °C) and clinical febrile temperatures (38.5 and 40 °C) to be a key determinant in the outcome of infection through the differential regulation of MPXV transcription and associated amplitude of host cytokine response to infection. Incubation of infected cells at 38.5 or 40 °C led to a restriction or ablation in MPXV replication, respectively. Importantly, this thermal inhibition was reversible upon temperature downshift to 37 °C without detriment to viral replication fitness. Co-stimulation of the type-I interferon (IFN) response led to a dose- and temperature-dependent inhibition in MPXV replication that restricted the re-establishment of infection upon temperature downshift and withdrawal of IFN as an immune stimulus. Our data identify febrile temperatures associated with mpox disease to be a critical component of the host pro-inflammatory immune response to infection which can synergise with the type-I IFN response to enhance the host-cell mediated restriction of MPXV.
Acute avoidance of hydrogen sulfide is modulated by external and internal states in C. elegans

Hydrogen sulfide (H2S) can act as an energy source, a poison and a gasotransmitter in organisms. We used the robust locomotory responses to H2S in Caenorhabditis elegans to delineate the molecular mechanisms governing sensory and adaptive responses to H2S exposure. We found that C. elegans exhibited transiently increased locomotory activity and turning behavior as a strategy to escape the noxious H2S stimulation. The behavioral responses to H2S were modulated by a complex network of signaling pathways, including cyclic GMP signaling in ciliated sensory neurons, calcineurin, nuclear hormone receptors, to the major starvation regulators such as insulin and TGF-β signaling. The response to H2S was substantially affected by the ambient O2 levels and their prior experience in low O2 environments, suggesting an intricate interplay between O2 and H2S sensing mechanisms. Prolonged exposure to H2S robustly evoked H2S detoxification coupled with reduced locomotory response to the subsequent H2S challenges. Intriguingly, the expression of genes involved in iron homeostasis, including ftn-1 and smf-3, was substantially modified in exposure to H2S, implying that labile iron levels are affected by H2S. In support of this, iron supplement significantly bolstered the behavioral response to H2S. In addition, mitochondria, one of the central hubs for H2S metabolism, played a crucial role in adaptive responses to H2S. In summary, our study provides molecular insights into the mechanisms through which C. elegans detects, modulates, and adapts its response to H2S.
Activation of the P2RX7/IL-18 pathway in immune cells attenuates lung fibrosis

Idiopathic pulmonary fibrosis (IPF) is an aggressive interstitial lung disease associated with progressive and irreversible deterioration of respiratory functions that lacks curative therapies. Despite IPF being associated with a dysregulated immune response, current antifibrotics aim only at limiting fibroproliferation. We show here that the P2RX7/IL-18/IFNG axis is downregulated in IPF patients and that P2RX7 has immunoregulatory functions. Using our positive modulator of P2RX7, we show that activation of the P2RX7/IL-18 axis in immune cells limits lung fibrosis progression in a mouse model by favoring an anti-fibrotic immune environment, with notably an enhanced IL-18-dependent IFN-γ production by lung T cells leading to a decreased production of IL-17 and TGFβ. Overall, we show the ability of the immune system to limit lung fibrosis progression by targeting the immunomodulator P2RX7. Hence, treatment with a small activator of P2RX7 may represent a promising strategy to help patients with lung fibrosis.
PsychoNet 2 - Contextualized and Enriched Psycholinguistic Commonsense Ontology

PsychoNet 1 has demonstrated the feasibility of integrating psycholinguistic taxonomy, represented in LIWC, and its semantic textual representation in the form of commonsense ontology, represented in ConceptNet. However, various limitations exist in PsychoNet 1, including the lack of concluding context of the concept annotation. In this paper, we address most of those limitations and introduce a new enhanced and enriched version, PsychoNet 2. PsychoNet 2 utilizes WordNet, in addition to LIWC and ConceptNet, to produce an integrated contextualized psycholinguistic ontology. The first and the main contribution is that, in PsychoNet 2, each concept is annotated by the potential (most representative) contextual psycholinguistic categories, rather than all applicable categories. The second contribution is the enrichment of LIWC through utilizing WordNet. This in fact produced an enriched version of LIWC that may also be used independently in other applications. This has contributed to substantial enrichment of PsychoNet 2 as it facilitated including additional number of concepts that were not included in PsychoNet 1 due to lack of corresponding words in the original LIWC. A sample application of text classification, for a mood prediction task, is presented to demonstrate the introduced enhancements. The results confirm the improved performance of the new PsychoNet 2 against PsychoNet 1.
Synthesis Lectures on Data Mining and Knowledge Discovery

This book offers a comprehensive overview of the various concepts and research issues about blogs or weblogs. It introduces techniques and approaches, tools and applications, and evaluation methodologies with examples and case studies. Blogs allow people to express their thoughts, voice their opinions, and share their experiences and ideas. Blogs also facilitate interactions among individuals creating a network with unique characteristics. Through the interactions individuals experience a sense of community. We elaborate on approaches that extract communities and cluster blogs based on information of the bloggers. Open standards and low barrier to publication in Blogosphere have transformed information consumers to producers, generating an overwhelming amount of ever-increasing knowledge about the members, their environment and symbiosis. We elaborate on approaches that sift through humongous blog data sources to identify influential and trustworthy bloggers leveraging content and network information. Spam blogs or splogs is an increasing concern in Blogosphere, which is discussed in detail with the approaches leveraging supervised machine learning algorithms and interaction patterns. We elaborate on data collection procedures, provide resources for blog data repositories, mention various visualization and analysis tools in Blogosphere, and explain conventional and novel evaluation methodologies, to help perform research in the Blogosphere. The book is supported by additional material, including lecture slides as well as the complete set of figures used in the book, and the reader is encouraged to visit the book website for the latest information: http://tinyurl.com/mcp-agarwal
The role of diagenisis in the hydrogeological stratification of carbonate aquifers: an example from the chalk at Fair Cross, Berkshire, UK

Carbonate rocks form important aquifers in many parts of the world and in north-west Europe the Chalk is a primary source of potable water. When flushed with relatively fresh groundwaters, the Chalk may undergo significant diagenetic alteration at relatively shallow depths resulting in a physically and hydrogeochemically stratified aquifer. Diagenetic affects may have important implications for the effective exploitable thickness of the Chalk aquifer and for water quality. In order to assess the affects of diagenesis on the properties of carbonate aquifers, matrix porosity, permeability, pore water and rock chemistry profiles have been analysed for a 300 m deep borehole through the Chalk at the western end of the London Basin. An abrupt change in the matrix porosity profile at 155 mbgl indicates a change in dominant mode of historic diagenesis from mechanical compaction above 155 mbgl to predominantly pressure solution compaction below 155 mbgl. Pore water and rock chemistry profiles also change abruptly across this depth interval, suggesting that the present day hydrogeology is controlled by historic diagenetic trends. Below 155 mbgl, pore waters are relatively saline and there is no evidence for groundwater flow; above 155 mbgl pore waters are relatively fresh and geochemical evidence for incon-gruent carbonate dissolution indicates contemporary groundwater circulation. Possible physical and chemical evolution paths for the Chalk at Fair Cross are discussed. The results provide a hydrogeological context for other studies of the long-term response of carbonate aquifers to base-line changes in sea-level and pore water chemistry and also enable studies with relatively short time-frames or of localized phenomena to be placed in the broader context of the evolution of carbonate aquifers.
A THERMO-PORO-VISCO-PLASTIC SHEAR BAND MODEL FOR SEISMIC TRIGGERING AND EVOLUTION OF CATASTROPHIC LANDSLIDES

The goal of this paper is to develop a constitutive model for the rapid deformation of clay-rich shear zones. Such a model would be necessary to describe the seismic triggering and evolution of catastrophic landslides. The model is based on: (a) the well-documented in the literature strain-softening and viscoplastic behaviour of saturated clays, and (b) the concept of frictional softening due to heat generated pore-water pressures. The inelastic stress-strain relationship is described with a 1-dimensional cyclic constitutive model of the (Bouc-Wen) type, coupled with a Cam-Clay frictional law with hardening and a set of equations that govern the mechanism of heat-generated pore-water pressure build up. Calibration of the model parameters is accomplished through laboratory tests, with the help of artificial neural network analysis. The influence of key variables on the behaviour of a rapidly deforming shear band is thoroughly investigated and the results of the analysis are critically discussed.
A relation extraction method of Chinese named entities based on location and semantic features

Named Entity Relations are a foundation of semantic networks, ontology and the semantic Web, and are widely used in information retrieval and machine translation, as well as automatic question and answering systems. Relation feature selection and extraction are two key issues. The location features possess excellent computability and operability, and the semantic features have strong intelligibility and reality. Currently, relation extraction of Chinese named entities mainly adopts the Vector Space Model (VSM) or a traditional semantic computing method, and these two methods use either the location features or the semantic features only, resulting in unsatisfactory extraction. To improve the extraction results, we propose a method that combines the information gain of the positions of words and the semantic computing based on HowNet to extract Chinese named entity relations, and present a relation extraction method of Chinese named entities, called LSE, which is scalable, semi-supervised and domain independent. Extensive experiments have been performed to show that our approach is superior, with an F-score of 0.881, which is at least 0.115 better than existing extraction methods that use either the location features or the semantic features.
Minimization of artifacts due to surface effects in laser CT images reconstructed by FBP method

Optical tomography for biomedical target is an evolving research area with emerging potential applications. In transillumination optical tomography, the filtered back projection (FBP) method is generally used for image reconstruction and the images represent a distribution of the optical attenuation coefficient. However, in practical optical imaging systems, refractive index mismatch at boundaries, such as the tissue surface, strongly affects optical attenuation. The surface effects are not constant even at the same part of the sample at different incident angles. Therefore, the surface effects introduce artifacts that obscure the internal structure and functional information in the laser CT images reconstructed by the FBP method. In this paper, we propose a simple correction method that could minimize the surface effects in laser CT images. The experiments were performed with the coherent detection imaging system based on the optical heterodyne detection technique. Experimentally determined attenuation coefficient corresponding to different incident angles was used to correct the surface effects. Improved target structures were demonstrated in the reconstructed laser CT images. Our correction method for laser CT image reconstruction is quite effective for visualizing internal structures with small variations in attenuation coefficients that would otherwise be masked by the dominant surface attenuation.
Enhancing Information Security and Privacy: Combining Biometrics & Cryptography

This book deals with "crypto-biometrics", a relatively new and multi-disciplinary area of research (started in 1998). Combining biometrics and cryptography provides multiple advantages, such as, revocability, template diversity, better verification accuracy, and generation of cryptographically usable keys that are strongly linked to the user identity. In this text, a thorough review of the subject is provided and then some of the main categories are illustrated with recently proposed systems by the authors. Beginning with the basics, this text deals with various aspects of crypto-biometrics, including review, cancelable biometrics, cryptographic key generation from biometrics, and crypto-biometric key sharing protocols. Because of the thorough treatment of the topic, this text will be highly beneficial to researchers and industry professionals in information security and privacy. Table of Contents: Introduction / Cancelable Biometric System / Cryptographic Key Regeneration Using Biometrics / Biometrics-Based Secure Authentication Protocols / Concluding Remarks
Phrase Mining from Massive Text and Its Applications Synthesis Lectures on Data Mining and Knowledge Discovery

A lot of digital ink has been spilled on “big data” over the past few years.Most of this surge owes its origin to the various types of unstructured data in the wild, among which the proliferation of textheavy data is particularly overwhelming, attributed to the daily use of web documents, business reviews, news, social posts, etc., by so many people worldwide. A core challenge presents itself: How can one efficiently and effectively turn massive, unstructured text into structured representation so as to further lay the foundation for many other downstream text mining applications? In this book, we investigated one promising paradigm for representing unstructured text, that is, through automatically identifying high-quality phrases from innumerable documents. In contrast to a list of frequent n-grams without proper filtering, users are often more interested in results based on variable-length phrases with certain semantics such as scientific concepts, organizations, slogans, and so on. We propose new principles and powerful methodologies to achieve this goal, from the scenario where a user can provide meaningful guidance to a fully automated setting through distant learning. is book also introduces applications enabled by the mined phrases and points out some promising research directions.
Combinations of processes responsible for Martian impact crater “layered ejecta structures” emplacement

[1] We utilized images and stereo-derived topographic data acquired by the High Resolution Stereo Camera (HRSC) and Thermal Emission Imaging System (THEMIS) images together with other data in order to study the geology of “layered ejecta structures” associated with relatively pristine Martian impact craters. The geomorphology and morphometric properties indicate their origin as complex combinations of a variety of impact processes. The studied (inner) layered ejecta structures often exhibit ground-hugging characteristics, and many of them do not have topographic profiles expected from simple ballistic emplacement. Such profiles include ones that are plateau-shaped or thickening outward. We think that water-rich fluidized flows driven by the momentum due to the impact and by gravity, together with ballistic emplacement and vortex produced by the atmosphere-ejecta curtain interaction, were essential to the (inner) layered ejecta structure formation. We hypothesize that the thinner outer layered ejecta structures were formed by various combinations of shockwave-induced liquefaction of water-rich near-surface sediments, ballistic emplacement of ejecta-entraining water, and strong winds (expanding vapor, vortex, base surge) related to the impact. The contribution of each proposed layered ejecta structure formation mechanism should have been variable depending on the condition of the impact.
Caching and Materialization for Web Databases

Database systems have been driving dynamic websites since the early 1990s; nowadays, even seemingly static websites employ a database back-end for personalization and advertising purposes. In order to keep up with the high demand fuelled by the rapid growth of the Internet, a number of caching and materialization techniques have been proposed for web databases over the years. The main goal of these techniques is to improve performance, scalability, and manageability of database-driven dynamic websites, in a way that the quality of data is not compromised. Although caching and materialization are well-understood concepts in the traditional database and networking/operating systems literature, the Web and web databases bring forth unique characteristics that warrant new techniques and approaches. In this monograph, we adopt a data management point of view to describe the system architectures of web databases, and analyze the research issues related to caching and materialization in such architectures. We also present the state-of-the-art in caching and materialization for web databases and organize current approaches according to the fundamental questions, namely how to store, how to use, and how to maintain cached/materialized web data. Finally, we associate work in caching and materialization for web databases to similar techniques in other related areas, such as data warehousing, distributed systems, and distributed databases.
Privacy-Preserving Data Publishing : A Survey on Recent Developments

The collection of digital information by governments, corporations, and individuals has created tremendous opportunities for knowledgeand information-based decision making. Driven by mutual benefits, or by regulations that require certain data to be published, there is a demand for the exchange and publication of data among various parties. Data in its original form, however, typically contains sensitive information about individuals, and publishing such data will violate individual privacy. The current practice in data publishing relies mainly on policies and guidelines as to what types of data can be published, and agreements on the use of published data. This approach alone may lead to excessive data distortion or insufficient protection. Privacy-preserving data publishing (PPDP) provides methods and tools for publishing useful information while preserving data privacy. Recently, PPDP has received considerable attention in research communities, and many approaches have been proposed for different data publishing scenarios. In this survey, we will systematically summarize and evaluate different approaches to PPDP, study the challenges in practical data publishing, clarify the differences and requirements that distinguish PPDP from other related problems, and propose future research directions.
AugUndo: Scaling Up Augmentations for Unsupervised Depth Completion

Unsupervised depth completion methods are trained by minimizing sparse depth and image reconstruction error. Block artifacts from resampling, intensity saturation, and occlusions are amongst the many undesirable by-products of common data augmentation schemes that affect image reconstruction quality, and thus the training signal. Hence, typical augmentations on images viewed as essential to training pipelines in other vision tasks have seen limited use beyond small image intensity changes and flipping. The sparse depth modality have seen even less as intensity transformations alter the scale of the 3D scene, and geometric transformations may decimate the sparse points during resampling. We propose a method that unlocks a wide range of previously-infeasible geometric augmentations for unsupervised depth completion. This is achieved by reversing, or ``undo"-ing, geometric transformations to the coordinates of the output depth, warping the depth map back to the original reference frame. This enables computing the reconstruction losses using the original images and sparse depth maps, eliminating the pitfalls of naive loss computation on the augmented inputs. This simple yet effective strategy allows us to scale up augmentations to boost performance. We demonstrate our method on indoor (VOID) and outdoor (KITTI) datasets where we improve upon three existing methods by an average of 11.75% across both datasets.