Miracle-dz/UniFAR-FTUs huggingface dataset:
Time to Cite: Modeling Citation Networks using the Dynamic Impact Single-Event Embedding Model

Understanding the structure and dynamics of scientific research, i.e., the science of science (SciSci), has become an important area of research in order to address imminent questions including how scholars interact to advance science, how disciplines are related and evolve, and how research impact can be quantified and predicted. Central to the study of SciSci has been the analysis of citation networks. Here, two prominent modeling methodologies have been employed: one is to assess the citation impact dynamics of papers using parametric distributions, and the other is to embed the citation networks in a latent space optimal for characterizing the static relations between papers in terms of their citations. Interestingly, citation networks are a prominent example of single-event dynamic networks, i.e., networks for which each dyad only has a single event (i.e., the point in time of citation). We presently propose a novel likelihood function for the characterization of such single-event networks. Using this likelihood, we propose the Dynamic Impact Single-Event Embedding model (DISEE). The \textsc{\modelabbrev} model characterizes the scientific interactions in terms of a latent distance model in which random effects account for citation heterogeneity while the time-varying impact is characterized using existing parametric representations for assessment of dynamic impact. We highlight the proposed approach on several real citation networks finding that the DISEE well reconciles static latent distance network embedding approaches with classical dynamic impact assessments.
Guidelines for Integrating Value Sensitive Design in Responsible AI Toolkits

Value Sensitive Design (VSD) is a framework for integrating human values throughout the technology design process. In parallel, Responsible AI (RAI) advocates for the development of systems aligning with ethical values, such as fairness and transparency. In this study, we posit that a VSD approach is not only compatible, but also advantageous to the development of RAI toolkits. To empirically assess this hypothesis, we conducted four workshops involving 17 early-career AI researchers. Our aim was to establish links between VSD and RAI values while examining how existing toolkits incorporate VSD principles in their design. Our findings show that collaborative and educational design features within these toolkits, including illustrative examples and open-ended cues, facilitate an understanding of human and ethical values, and empower researchers to incorporate values into AI systems. Drawing on these insights, we formulated six design guidelines for integrating VSD values into the development of RAI toolkits.
Critical scaling for dense granular flow between parallel plates near jamming

We numerically study the flow of dense granular materials between parallel plates driven by an external force. The granular materials form a jammed solid-like state when the external force is below a critical force, while they flow like fluids above the critical force. The transition is characterized by the mass flux. The critical force depends on the average packing fraction and the distance between the plates. The scaling laws for the critical force and the mass flux are predicted theoretically based on a continuum model. They are numerically verified.
Nextflow vs. plain Bash: Different Approaches to the Parallelisation of SNP Calling from the Whole Genome Sequence Data

This study compared computational approaches to parallelisation of an SNP calling workflow. Data comprised DNA from five Holstein-Friesian cows sequenced with the Illumina platform. The pipeline consisted of quality control, alignment to the reference genome, post-alignment, and SNP calling. Three approaches to parallelisation were compared: (i) a plain Bash script in which a pipeline for each cow was executed as separate processes invoked at the same time, (ii) a Bash script wrapped in a single Nextflow process, and (iii) a Nextflow script with each component of the pipeline defined as a separate process. The results demonstrated that on average, the multi-process Nextflow script performed 15% to 27% faster depending on the number of assigned threads, with the biggest execution time advantage over the plain Bash approach observed with 10 threads. In terms of RAM usage, the most substantial variation was observed for the multi-process Nextflow, for which it increased with the number of assigned threads, while RAM consumption of the other setups did not depend much on the numbers of threads assigned for computations. Due to intermediate and log files generated, disk usage was markedly higher for the multi-process Nextflow than for the plain Bash and for the single-process Nextflow.
β-Hydroxybutyrate promotes basal insulin secretion while decreasing glucagon secretion in mouse and human islets

Dietary carbohydrates raise blood glucose and limiting carbohydrate intake improves glycemia in patients with T2D. Low carbohydrate intake (< 25 g) allows the body to utilize fat as its primary fuel. As a consequence of increased fatty-acid oxidation, the liver produces ketones to serve as an alternative energy source. β-Hydroxybutyrate (βHB) is the most abundant ketone. While βHB has a wide range of functions outside of the pancreas, its effect on islet cell function remains understudied. In this study, we examined islet response to racemic βHB treatment, and observed an increase in insulin secretion in human islets treated with βHB at basal glucose concentrations (3 mM glucose). Because βHB is a chiral molecule, existing as both R and S forms, we further examined insulin and glucagon secretion following acute treatment with individual βHB enantiomers in human and C57BL6/J mouse islets. We found that acute treatment with R-βHB increases insulin secretion and decreases glucagon secretion at physiological glucose concentrations in human and mouse islets. Proteomic analysis of human islets treated with R-βHB over 72 h showed altered abundance of proteins that may promote islet cell health and survival. However, live cell imaging revealed that neither enantiomer of βHB protected dispersed mouse islet cells from cell death. Collectively, our data show that physiological concentrations of βHB influence hormone secretion and signaling within pancreatic islets.
Chromosome-scale pearl millet genomes reveal a CARLACTONOIC ACID METHYL TRANSFERASE as key determinant of strigolactone pattern and Striga susceptibility

The yield of pearl millet, a resilient cereal crop crucial for African food security, is severely impacted by the root parasitic weed Striga hermonthica, which requires host-released strigolactones (SLs) for seed germination. Herein, we identified four SLs present in the Striga-susceptible line SOSAT-C88-P10 (P10), but absent in the resistant 29Aw (Aw). We generated chromosome-scale genome assemblies including four gapless chromosomes for each line. We found the Striga-resistant Aw lacks a 0.7 Mb genome segment containing two putative CARLACTONOIC ACID METHYL TRANSFERASE1 (CLAMT1) genes. Upon transient expression, P10CLAMT1b produced methyl carlactonoate (MeCLA), an intermediate in SL biosynthesis. Feeding Aw with MeCLA resulted in the production of two P10-specific SLs. Screening a diverse pearl millet panel confirmed the pivotal role of the CLAMT1 section for SL diversity and Striga susceptibility. Our results reveal a reason for Striga susceptibility in pearl millet and pave the way for generating resistant lines through marker-assisted breeding or direct genetic modification.
Glomerular Elasticity and Gene Expression Patterns Define Two Phases of Alport Nephropathy

Rationale Mutations in COL4A3,4, or 5 cause Alport syndrome and contribute to other glomerular diseases. Potential mechanisms include abnormal GBM structure, chemistry, elasticity, or ER stress. The causes of initial podocyte injury are not fully defined in collagen IV nephropathies. Objectives We characterized renal function, structural and biophysical properties of glomerular capillaries and podocytes, and renal gene expression patterns in Col4a3-/- mice (BL6) over the 8-month course of disease. To test for a role for ER stress, we treated Col4α3-/- mice with TUDCA. Findings Col4a3-/- mice develop proteinuria and reduced renal function at 4 – 5 months, but their glomerular capillaries become abnormally deformable, and podocytes are dislodged into the urine with volume loading at 3 months. Glomeruli become maximally deformable at 4 months with loss of 40% of their podocytes, and then stiffen progressively with progression of renal disease. In parallel, kidneys become increasingly fibrotic with proteinuria and inflammatory infiltrates as renal failure progresses. Bulk renal gene expression changes from 2 and 4 months where it shows increased expression of genes related to matrix organization, cytokine signaling, and cell injury to reduction in genes coding for differentiated renal tubular and metabolic proteins. Treatment of mice with TUDCA minimized glomerular injury, loss of renal function, and increased expression of genes that inhibit MAP, tyrosine kinase, and TGF-B. Conclusion Renal disease in Col4a3-/- mice progresses in two phases, before overt proteinuria with early podocyte injury and loss, and later with overt proteinuria and progressive fibrosis. Suppression of renal injury by TUDCA implicates ER stress and MAP, tyrosine kinase, and TGF-B signaling as a disease mechanism.
Stiffness Measurement of Retinal Capillaries and Subendothelial Matrix using Atomic Force Microscopy

Retinal capillary degeneration is a clinical hallmark of the early stages of diabetic retinopathy (DR). Our recent studies have revealed that diabetes-induced increase in retinal capillary stiffness plays a crucial and previously unrecognized causal role in inflammation-mediated degeneration of retinal capillaries. Retinal capillary stiffening results from overexpression of lysyl oxidase, an enzyme that crosslinks and stiffens the subendothelial matrix. Since tackling DR at the early stage is expected to prevent or slow down DR progression and associated vision loss, subendothelial matrix and capillary stiffness represent relevant and novel therapeutic targets for early DR management. Further, direct measurement of retinal capillary stiffness can serve as a crucial preclinical validation step for the development of new imaging techniques for non-invasive assessment of retinal capillary stiffness in animal and human subjects. With this view in mind, we here provide a detailed protocol for the isolation and stiffness measurement of mouse retinal capillaries and retinal subendothelial matrix using atomic force microscopy.
A Lung Cancer Mouse Model Database

Lung cancer, the leading cause of cancer mortality, exhibits diverse histological subtypes and genetic complexities. Numerous preclinical models have been developed to study lung cancer, but data from these models are disparate, siloed, and difficult to compare in a centralized fashion. Here we established the Lung Cancer Mouse Model Database (LCMMDB), an extensive repository of 1,354 samples from 77 transcriptomic datasets. Meticulous curation and collaboration with data depositors have produced a robust and comprehensive database, enhancing the fidelity of the genetic landscape it depicts. The LCMMDB aligns 859 tumors from genetically engineered mouse models (GEMMs) with human lung cancer mutations, enabling comparative analysis and revealing a pressing need to broaden the diversity of genetic aberrations modeled in GEMMs. Accompanying this resource, we developed a web application that offers researchers intuitive tools for in-depth gene expression analysis and fostering potential collaborations. With standardized reprocessing of gene expression data, the LCMMDB serves as a powerful platform for cross-study comparison and lays the groundwork for future research, aiming to bridge the gap between mouse models and human lung cancer for improved translational relevance.
Conserved helical motifs in the Ikaros IDR mediate NuRD interaction and transcriptional repression

The transcription factor IKZF1/Ikaros is essential for B cell development, and recurrently mutated in human B-ALL. Ikaros has been ascribed both activating and repressive functions via interactions with coactivator and corepressor complexes, but the relative abundance of Ikaros-associated coregulatory complexes and their contribution to Ikaros-mediated gene regulation are not well understood. To address this issue, we performed an unbiased identification of Ikaros-interacting proteins in pre-B cells, and found that Ikaros interacts overwhelmingly with corepressors and heterochromatin-associated proteins. Time-resolved analysis of transcription and chromatin state identified transcriptional repression as the immediate response to Ikaros induction. Transcriptional repression preceded transcriptional activation by several hours, and was accompanied by a rapid loss of chromatin accessibility and reduced levels of H3K27ac particularly at enhancers. Functional characterisation of intrinsically disordered regions in the Ikaros protein identified highly conserved helical motifs that mediate Ikaros association with the NuRD corepressor complex and contribute to the silencing of target genes in pre-B cells and antiproliferative functions of Ikaros in human B-ALL.
Virus-derived Synthetic Riboswitches for Real-time Coronaviruses Sensing in Live Cells

Real-time sensing of viral infection in live cells are crucial for virology research and antiviral development. However, existing methods face challenges of low signal sensitivity and the necessity for viral manipulation and cell fixation. Here, we develop a viral riboswitch (vRibo) approach that employs the viral replicase to induce transgene expression upon viral infection. The vRibo is designed to detect viral real-time transcription and replication in live cells, which in response triggers the translation of reporter and therapeutic genes. By integrating a viral packaging sequence, vRibo can be transmitted to neighboring cells through progeny virions, effectively acting as a ‘Trojan Horse’. The negative-strand vRibo elements demonstrated effective detection of several coronaviruses, including 229E and OC43, due to the conservation of cis-acting RNA structures across coronaviruses. Notably, vRibo functions as a dual-purpose system, acting both as an infection detector and inducible antiviral system. vRibo has the potential for basic virology research applications and can be adopted in improving the inducible expression of mRNA medicines for future coronaviruses.
Mriyaviruses: Small Relatives of Giant Viruses

The phylum Nucleocytoviricota consists of large and giant viruses that range in genome size from about 100 kilobases (kb) to more than 2.5 megabases. Here, using metagenome mining followed by extensive phylogenomic analysis and protein structure comparison, we delineate a distinct group of viruses with double-stranded (ds) DNA genomes in the range of 35-45 kb that appear to be related to the Nucleocytoviricota. In phylogenetic trees of the conserved double jelly-roll major capsid proteins (MCP) and DNA packaging ATPases, these viruses do not show affinity to any particular branch of the Nucleocytoviricota and accordingly would comprise a class which we propose to name “Mriyaviricetes” (after Ukrainian Mriya, dream). Structural comparison of the MCP suggests that, among the extant virus lineages, mriyaviruses are the closest one to the ancestor of the Nucleocytoviricota. In the phylogenetic trees, mriyaviruses split into two well-separated branches, the family Yaraviridae and proposed new family “Gamadviridae”. The previously characterized members of these families, Yaravirus and Pleurochrysis sp. endemic viruses, infect amoeba and haptophytes, respectively. The genomes of the rest of the mriyaviruses were assembled from metagenomes from diverse environments, suggesting that mriyaviruses infect various unicellular eukaryotes. Mriyaviruses lack DNA polymerase, which is encoded by all other members of the Nucleocytoviricota, and RNA polymerase subunits encoded by all cytoplasmic viruses among the Nucleocytoviricota, suggesting that they replicate in the host cell nuclei. All mriyaviruses encode a HUH superfamily endonuclease that is likely to be essential for the initiation of virus DNA replication via the rolling circle mechanism. Importance The origin of giant viruses of eukaryotes that belong to the phylum Nucleocytoviricota is not thoroughly understood and remains a matter of major interest and debate. Here we combine metagenome database searches with extensive protein sequence and structure analysis to describe a distinct group of viruses with comparatively small genomes of 35-45 kilobases that appears to comprise a distinct class within the phylum Nucleocytoviricota that we provisionally named “Mriyaviricetes”. Mriyaviruses appear to be the closest identified relatives of the ancestors of the Nucleocytoviricota. Analysis of proteins encoded in mriyavirus genomes suggest that they replicate their genome via the rolling circle mechanism that is unusual among viruses with double-stranded DNA genomes and so far not described for members of Nucleocytoviricota.
Azadirachta indica: derived, red-emitting, carbon nanoparticles for cellular bioimaging and potential therapeutics

Red-emitting carbon nanoparticles (CNPs) were synthesized by the refluxed green synthesis method using ethanolic extract of neem leaves (Azadirachta indica). These nanoparticles were called as nQDs (neem quantum dots). The nQDs exhibited excellent photoluminescence properties with a maximum emission at 672nm, and the average size of nQDs was around 47nm. In the in-vitro study, Retinal Pigment epithelial (RPE1) cells and SUM159A cells showed enhanced cellular uptake. In RPE1 cells, the cellular uptake was higher than in SUM159A cells. In the biocompatibility assay, SUM159A cell viability declined with the increasing nQDs concentration. The results show that red-emissive CNPs can be synthesized from Azadirachta indica (neem) leaves using a simple method with a possible application in bioimaging and therapeutics.
Enterohemorrhagic Escherichia coli (EHEC) Disrupts Intestinal Barrier Integrity in Translational Canine Stem Cell-Derived Monolayers

This study addresses the gap in translatable in vitro models for investigating Enterohemorrhagic E. coli (EHEC) infections, particularly relevant to both canine and human health. EHEC is known to induce acute colitis in dogs, leading to symptoms like hemorrhagic diarrhea and hemolytic uremic syndrome, similar to those observed in humans. However, understanding the pathophysiology and developing treatment strategies have been challenging due to the lack of effective models that replicate the clinical disease caused by EHEC in both species. Our approach involved the development of colonoid-derived monolayers using intestinal tissues from healthy, client-owned dogs. These monolayers were exposed to EHEC and the impact of EHEC was assessed through several techniques, including trans-epithelial electrical resistance (TEER) measurement, immunofluorescence staining for junction proteins and mucus, and scanning electron microscopy for morphological analysis. Modified culture with saline, which was intended to prevent bacterial overgrowth, maintained barrier integrity and cell differentiation. EHEC infection led to significant decreases in TEER and ZO-1 expression, but not in E- cadherin levels or mucus production. Additionally, EHEC elicited a notable increase in TNF-α production, highlighting its distinct impact on canine intestinal epithelial cells compared to non-pathogenic E. coli. These findings closely replicate in vivo observations in dogs and humans with EHEC enteropathy, validating the canine colonoid-derived monolayer system as a translational model to study host- pathogen interactions in EHEC and potentially other clinically significant enteric pathogens.
The Al Hoceima earthquake sequence of 1994, 2004 and 2016: Stress transfer and poroelasticity in the Rif and Alboran Sea region

The 2016 January 25 earthquake ( M w 6.3) follows in sequence from the1994 May 26 earthquake ( M w 6.0) and the 2004 February 24 earthquake ( M w 6.4) in the Rif Mountains and Alboran Sea. The earlier two seismic events which were destructive took place on inland conjugate faults, and the third event occurred on an offshore fault. These earthquake sequences occurred within a period of 22 yr at ∼ 25 km distance and 11–16-km depth. The three events have similar strike-slip focal mechanism solutions with NNE-SSW trending left-lateral faulting for the 1994 and 2016 events and NW-SE trending right-lateral faulting for the 2004 event. This shallow seismic sequence offers the possibility (i) to model the change in Coulomb Failure Function ( (cid:2) CFF with low μ (cid:3) including the pore pressure change) and understand fault-rupture interaction, and (ii) to analyse the effect of pore ﬂuid on the rupture mechanism, and infer the clock-time advance. The variation of static stress change has a direct impact on the main shock, aftershocks and related positive lobes of the 2004 earthquake rupture with a stress change increase of 0.7–1.1 bar. Similarly, the 2004 main shock and aftershocks indicate loading zones with a stress change ( > 0.25 bar) that includes the 2016 earthquake rupture. The tectonic loading of 19–24 nanostrain yr − 1 obtained from the seismicity catalogue of Morocco is comparable to the 5.0 × 10 17 N · m yr − 1 seismic strain release in the Rif Mountains. The seismic sequence is apparently controlled by the poroelastic properties of the seismogenic layer that depend on the undrained and drained ﬂuid conditions. The short interseismic period between main shocks and higher rate of aftershocks with relatively large magnitudes (4 < M w < 5.5) implies the pore-ﬂuid physical effect in undrained and drained conditions. The stress-rate ranges between 461 and 582 Pa yr − 1 with a (cid:2) CFF of 0.2–1.1 bar. The computed clock-time advance reaches 239 ± 22 yr in agreement with the ∼ 10 yr delay between main shocks. The calculated static stress change of 0.9–1.3 bar, under pore-ﬂuid stimulus added with well-constrained geodetic and seismic strain rates are critical for any seismic hazard assessment.
River flow modeling using artificial neural networks in Kapuas river, West Kalimantan, Indonesia

Kapuas River is located in the province of West Kalimantan. Kapuas river length is 1,086 km and river basin areas about 100,000 Km2. The availability of river flow data in the Long River and very wide catchments are difficult to obtain, while river flow data are essential for planning waterworks. To predict the water flow in the catchment area requires a lot of hydrology coefficient, so it is very difficult to predict and obtain results that closer to the real conditions. This paper demonstrates that artificial neural network (ANN) could be used to predict the water flow. The ANN technique can be used to predict the incidence of water discharge that occurs in the Kapuas River based on rainfall and evaporation data. With the data available to do training on the artificial neural network model is obtained mean square error (MSE) 0.00007. The river flow predictions could be carried out after the training. The results showed differences in water discharge measurement and prediction of about 4%.
AR and Public Participation in Maputo City: An Exploratory Study

This study examines the potential of using Augmented Reality to increase urban participation to deal with identified problems in Maputo city, Mozambique, southern Africa. The study’s aim is twofold; first, it seeks to add to the nascent literature on Augmented Reality (AR) in Africa; second, to experiment with AR for public participation in urban Maputo to explore the affordances of AR and examine the possibility and limitations of deploying the technology for such purposes. The study concludes that AR can enhance public participation and engagement with public spaces in Maputo city. However, technical and economic limitations must be considered when designing projects to deploy AR technologies in the city