Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of right heart function changes in patients with pulmonary hypertension via two-dimensional speckle tracking imaging: a retrospective study

Abstract Objective: To realize the changes in pulmonary hypertension (PH) patients’ right ventricular function.Methods: A total number of 74 patients with PH were included, and the parameters of standard echocardiographic were measured as well as the strain of peak longitudinal of each segment during the systole of the right ventricle to calculate the global longitudinal strain (LS) during systole of the right ventricular free wall.Results: ① As pulmonary arterial pressure increased, the right ventricular area gradually increased, and the case group showed the decreased right ventricular fractional area change (RVFAC), tricuspid annular plane systolic excursion (TAPSE), and tricuspid annular peak systolic velocity (S’) (p < 0.05). They, RVFAC, and TAPSE depicted significant differences that were statistical (p < 0.05) from the other groups. ② With increasing pulmonary arterial pressure, the right ventricular free wall’s LS gradually reduced (p < 0.05). Conclusion: ① LS right ventricular free wall is useful in detecting changes in right ventricular systolic function early on with greater sensitivity than RVFAC, TAPSE, and S’. In addition, increased right ventricular pressure loading can result in a subsequent impairment of right ventricular myocardial mechanics. ② As right ventricular pressure loading increases, right ventricular strain decreases. ③ In mild PH, the right ventricular free wall’s. LS is more sensitive than standard measures in spotting early alterations in myocardial mechanics.
Taxogenomic placement of Rasporella oleae and Rasporella dianae gen. and spp. nov., two insect associated yeast species

During the course of independent studies in Europe, North America, and Africa, seven yeast strains were isolated from insect frass, decaying wood, tree flux, and olive oil sediment. Phylogenetic analysis of two barcoding DNA regions (internal transcribed spacer and the D1/D2 domain of the LSU rRNA gene) revealed that they belong to two closely related undescribed species distinct from all genera in the family Debaryomycetaceae. For reliable taxonomic placement the genomes of four strains of the two novel species and six type strains of closely related species were sequenced. Orthologous genes from 54 genomes of representatives of the Pichiomycetes and 23 outgroup taxa were concatenated to construct a fully supported phylogenetic tree. Consistent with the assumptions, we found that the two new species belong to a novel genus. In addition, the delimitation of the novel species was supported by genetic distance calculations from average nucleotide identity (ANI) and digital DNA:DNA hybridization (dDDH) values. The physiological characterization of the novel species was generally consistent with their genomic content. All strains had two alleles encoding secretory lipase in either two or three copies depending on the species. However, lipolytic activity was detected only in strains with three copies of the secretory lipase gene. Nevertheless, lipolytic activity might be related to their association with the insect gut. Based on these results, formal descriptions of the new genus Rasporella gen. nov. and of two new species Rasporella dianae sp. nov. (holotype UCDFST 68‐643T, MycoBank no.: 850238) and Rasporella oleae sp. nov. (holotype ZIM 2471T, MycoBank no.: 850126) are provided.
Acute Heart Failure Is a Malignant Process: But We Can Induce Remission

ABSTRACT Acute heart failure is a common and increasingly prevalent condition, affecting >10 million people annually. For those patients who survive to discharge, early readmissions and death rates are >30% everywhere on the planet, making it a malignant condition. Beyond these adverse outcomes, it represents one of the largest drivers of health care costs globally. Studies in the past 2 years have demonstrated that we can induce remissions in this malignant process if therapy is instituted rapidly, at the first acute heart failure episode, using full doses of all available effective medications. Multiple studies have demonstrated that this goal can be achieved safely and effectively. Now the urgent call is for all stakeholders, patients, physicians, payers, politicians, and the public at large to come together to address the gaps in implementation and enable health care providers to induce durable remissions in patients with acute heart failure.
Allan William Cripps: a mucosal immunologist and mentor from beginning to end

Allan Cripps was internationally recognized in the field of mucosal immunology, in particular the relationship between respiratory diseases and mucosal immunization strategies. Allan's career spanned scientific and applied research, commercialization, health education, and evolved into leadership roles in public‐health and academic administration. Allan published over 400 papers and mentored over 40 research higher degree candidates. Allan was renowned for his mentorship, that did not end with the awarding of a PhD or Master's degree, but continued across a lifetime of professional engagement. Allan's key contributions to immunology included characterizing the ontogeny of the human mucosal immune system, understanding the impact of respiratory infections and otitis media in children, developing diagnostic technologies and mucosal vaccine strategies, and identifying the roles of the common mucosal immune system in human health. In this biography for the 100th anniversary of the Journal, we follow his journey of discovery and contributions to immunological research.
SURFACE WAVES AND SEISMIC RESPONSE OF LONG-PERIOD STRUCTURES

During an earthquake, the presence of free surface generates waves, known as surface waves, which propagate along Earth’s surface. In sedimentary basins, the conversion of seismic body waves at basin edges also generates surface waves, which travel across the basin. Surface waves are characterized by long-periods and much slower velocities than shear waves. Consequently, they are more visible in displacements than in accelerations, and show up much later in a record. In triggered seismic networks, the recorders are triggered on and off based on acceleration amplitudes. In most earthquakes, recorders are turned off before the arrival of surface waves, and the post-event memory is typically set too short to record them. This paper investigates the effects of surface waves on structural response, and presents observational and analytical confirmations of their significance. Recent data from realtime monitored structures clearly show the importance of surface waves. Because their energy is concentrated at long periods, surface waves are particularly critical for longperiod structures, such as tall buildings and base-isolated structures. Also, because of their long duration, surface waves can push a damaged structure into complete collapse because of the additional hysteretic deformation cycles that the structure goes through.
Artificial augmented dataset for the enhancement of nano-QSARs models. A methodology based on topological projections

Abstract Nanoinformatics demands accurate predictive models to assess the potential hazards of nanomaterials (NMs). However, limited data availability and the diverse nature of NMs physicochemical properties and their interaction with biological media, hinder the development of robust nano-Quantitative Structure-Activity Relationship (QSAR) models. This article proposes an approach that combines artificially data generation techniques and topological projections to address the challenges of insufficient dataset sizes and their limited representativeness of the chemical space. By leveraging the rich information embedded in the topological features, this methodology enhances the representation of the chemical space, enabling a more an exploration of the structure-activity relationships. We demonstrate the efficacy of our approach through extensive experiments, employing various machine learning regression algorithms to validate the methodology. Finally, we compare two different resampling approaches based on different modeling scenarios. The results showcase a significant improved predictive performance of QSAR models demonstrating a promising strategy to overcome the limitations of small datasets in the field of nanoinformatics. The proposed approach offers noteworthy potential for advancing nanoinformatics research within the nanosafety domain by enabling the development of more accurate predictive models for assessing the potential hazards associated with NMs.
Chitosan tamarind-based nanoparticles as a promising approach for topical application of curcumin intended for burn healing: in vitro and in vivo study

Abstract One of the most prevalent worldwide problems that affect all ages and genders is skin burn. The goal of our study was to assess the ability of curcumin nanoparticles to cure a rat burn model. Three formulations were selected after several tests were performed including investigation of encapsulation efficiency, particle size and zeta potential measurements. In vitro release was achieved on the three selected formulations. The effectiveness of the chosen formulation for healing was evaluated. The induced burn wound was smeared, starting just after excision, once daily with curcumin nanoparticles for 18 days. Our findings revealed that curcumin nanoparticles improved the burn healing potential by augmenting the skin regeneration indices as evidenced by enhancing the new production of hyaluronic acid and collagen type I. Additionally, curcumin nanoparticles could increase levels of vascular endothelial growth factor and alpha smooth muscle activity while drastically reducing the skin’s tumour necrosis factor content, revealing a significant potential for burn healing process that is also reflected in the histopathological and immunohistochemical studies. Finally, our results demonstrated that curcumin nanoparticles revealed a significant potential for burn healing than curcumin alone due to its potent antimicrobial, antioxidant and anti-inflammatory properties.
PROBING LUMINESCENCE DATING OF ARCHAEOLOGICALLY SIGNIFICANT CARVED ROCK TYPES

The thermoluminescence (TL) and Optically Stimulated Luminescence (OSL) dating of crystalline materials, first applied to calcites (limestone buildings), has been extended to carved megalithic monuments made of granites, basalt and sandstones derived from archaeological sites. Various applied criteria for potential dating included pulsed blue light stimulation, different preheating and solar simulator bleaching, while the single (and multiple) aliquot regeneration and additive dose procedures were used for equivalent dose determination. The decay curves of signal loss follow a power law, n -p ; for blue stimulation the signal loss of quartz and feldspar is better approached by an exponential law, 1-aln(n).
Clustered and diverse transcription factor binding underlies cell type specificity of enhancers for housekeeping genes

Housekeeping genes are considered to be regulated by common enhancers across different tissues. Here we report that most of the commonly expressed mouse or human genes across different cell types, including more than half of the previously identified housekeeping genes, are associated with cell type–specific enhancers. Furthermore, the binding of most transcription factors (TFs) is cell type–specific. We reason that these cell type specificities are causally related to the collective TF recruitment at regulatory sites, as TFs tend to bind to regions associated with many other TFs and each cell type has a unique repertoire of expressed TFs. Based on binding profiles of hundreds of TFs from HepG2, K562, and GM12878 cells, we show that 80% of all TF peaks overlapping H3K27ac signals are in the top 20,000–23,000 most TF-enriched H3K27ac peak regions, and approximately 12,000–15,000 of these peaks are enhancers (nonpromoters). Those enhancers are mainly cell type–specific and include those linked to the majority of commonly expressed genes. Moreover, we show that the top 15,000 most TF-enriched regulatory sites in HepG2 cells, associated with about 200 TFs, can be predicted largely from the binding profile of as few as 30 TFs. Through motif analysis, we show that major enhancers harbor diverse and clustered motifs from a combination of available TFs uniquely present in each cell type. We propose a mechanism that explains how the highly focused TF binding at regulatory sites results in cell type specificity of enhancers for housekeeping and commonly expressed genes.
The three-dimensional structure of the EBV genome plays a crucial role in regulating viral gene expression in EBVaGC

Abstract Epstein–Barr virus (EBV) establishes lifelong asymptomatic infection by replication of its chromatinized episomes with the host genome. EBV exhibits different latency-associated transcriptional repertoires, each with distinct three-dimensional structures. CTCF, Cohesin and PARP1 are involved in maintaining viral latency and establishing episome architecture. Epstein–Barr virus-associated gastric cancer (EBVaGC) represents 1.3–30.9% of all gastric cancers globally. EBV-positive gastric cancers exhibit an intermediate viral transcription profile known as ‘Latency II’, expressing specific viral genes and noncoding RNAs. In this study, we investigated the impact of PARP1 inhibition on CTCF/Cohesin binding in Type II latency. We observed destabilization of the binding of both factors, leading to a disrupted three-dimensional architecture of the episomes and an altered viral gene expression. Despite sharing the same CTCF binding profile, Type I, II and III latencies exhibit different 3D structures that correlate with variations in viral gene expression. Additionally, our analysis of H3K27ac-enriched interactions revealed differences between Type II latency episomes and a link to cellular transformation through docking of the EBV genome at specific sites of the Human genome, thus promoting oncogene expression. Overall, this work provides insights into the role of PARP1 in maintaining active latency and novel mechanisms of EBV-induced cellular transformation.
Integrated Molecular Modeling and Machine Learning for Drug Design

Modern therapeutic development often involves several stages that are interconnected, and multiple iterations are usually required to bring a new drug to the market. Computational approaches have increasingly become an indispensable part of helping reduce the time and cost of the research and development of new drugs. In this Perspective, we summarize our recent efforts on integrating molecular modeling and machine learning to develop computational tools for modulator design, including a pocket-guided rational design approach based on AlphaSpace to target protein–protein interactions, delta machine learning scoring functions for protein–ligand docking as well as virtual screening, and state-of-the-art deep learning models to predict calculated and experimental molecular properties based on molecular mechanics optimized geometries. Meanwhile, we discuss remaining challenges and promising directions for further development and use a retrospective example of FDA approved kinase inhibitor Erlotinib to demonstrate the use of these newly developed computational tools.
3D seismic imaging of the Lalor volcanogenic massive sulphide deposit, Manitoba, Canada

A three‐component three‐dimensional seismic data set was acquired over the Lalor volcanogenic massive sulphide deposit near Snow Lake, Manitoba, Canada, to assess the reflectivity of the ore and further validate the potential of three‐dimensional reflection seismic methods for deep mineral exploration. The Lalor deposit was chosen as a test site as it provided an intact, well‐characterized 25‐Mt‐deep ore deposit with a rich catalogue of geological and geophysical data, as well as extensive drill‐core and drill‐hole geophysical and geological logs. An analysis of physical rock properties from borehole logging data indicates that massive sulphides associated with the zinc‐rich zones could produce prominent reflections, whereas acoustic impedances of zones with disseminated gold do not sufficiently differ from the impedances of the host rocks to produce reflections. The interpretation of the seismic data is constrained with a detailed three‐dimensional lithofacies model constructed from the categorical kriging of 15 lithological units identified in borehole intersections. Processing of the seismic data included prestack dip‐moveout and poststack time migration. Final images reveal some strong reflections associated with the zinc‐rich massive sulphide zones. The most prominent reflection results from the constructive interference of thin and closely spaced massive sulphide zones and felsic–mafic volcanic rock contacts above and below the mineralization. Contacts between felsic and mafic volcanic rocks, including those that were hydrothermally altered and subsequently metamorphosed, produced prominent and continuous reflections that are used to map the main architecture of the footwall rocks. At depth, a series of continuous and conformable reflections indicate the general geometry of the volcanic sequences in the area of the three‐dimensional seismic survey.
A METHODOLOGY FOR FINDING UNIFORM REGIONS IN SPATIAL DATA AND ITS APPLICATION TO ANALYZING THE COMPOSITION OF CITIES

Cities all around the world are in constant evolution due to numerous factors, such as fast urbanization and new ways of communication and transportation. However, the evolution of the composition of a city is difficult to follow and analyze. Since understanding the evolution of cities is the key to intelligent urbanization, there is a growing need to develop urban planning and analysis tools to guide the orderly development of cities, as well as to enhance their smooth and beneficial evolution. Urban patches which represent uniform areas of a city play a key role in studying the composition of a city, as different types of urban patches typically are associated with different functions, such as recreational areas and commercial areas. In order to analyze the changes of the composition of cities, a polygon-based spatial clustering and analysis framework for studying urban evolution is proposed in this thesis. A spatial clustering algorithm named CLEVER is used to identify urban patches that are clusters of polygons representing different elements of the city based on a domain expert’s notion of uniformity, which has to be captured in a plug-in interestingness function. The analysis methodology uses polygons as models for spatial clusters and histogram-type distribution signatures to describe their characteristics. Finally, popular signatures are introduced that describe distribution characteristics, which occur frequently in contiguous sub-regions of a spatial dataset, and an approach is presented that identifies and annotates urban patches with popular signatures. Experiments on datasets of the city of Strasbourg, France serve as an example to highlight the usefulness of the methodology.
Multiplex Reverse Transcription Polymerase Chain Reaction Assessment of Sialyltransferase Expression in Human Breast Cancer 1

Increased sialv lation, especially involving the Sialyl-Lewis" and SialylLewisx determinants, has been reported in breast cancer. A multiplex reverse transcription-PCR method was used here to determine the expres sion of five sialyltransferases (ST3Gal HI, ST6Gal I, ST3Gal IV, ST3Gal I, and ST3Gal II) in 49 patients surgically treated for locoregional breast cancer. We assessed the relationship between these expressions and clin ical, pathological, and biological features. The most expressed sialyltransferase was ST3Gal III, which is involved in Sialyl-Lewis" synthesis. ST3Gal III expression was positively correlated to ST6Gal I and ST3Gal IV expressions, to tumor size, and to the number of involved axillary nodes. Patients with high ST3Gal III expression had a shorter overall survival. High ST6Gal I expression was associated with histoprognostic grade III. ST6Gal I expression was negatively correlated to expression of progesterone receptor. In conclusion, high ST3Gal III and ST6Gal I expressions in human breast tumors are associated with poor prognosis markers.
Viscous heating in silicate melts: An experimental and numerical comparison

[1] The transition from Newtonian to non-Newtonian flow of silicate melts is commonly manifested as shear thinning at conditions of high stress and strain rate. Shear thinning may strongly influence the dynamics of magmatic flows, but the details of its microscopic origins are not fully understood. Here we consider viscous heating and thermomechanical coupling as a potential cause of shear thinning. We compare the results of laboratory, uniaxial compression experiments of a silicate melt with the results of thermomechanical numerical simulations corresponding to the experimental setup. Both the experimental and numerical results concord and indicate that the reduction of the temperature-dependent viscosity in flowing silicate melts is a result of viscous heating. Viscous heating was quantified for glasses with viscosities ranging from 108 to 1011 Pa s and strain rates from 10−5 to 100 s−1. The results of 48 compression experiments indicate that the transition from Newtonian to non-Newtonian flow in the silicate melt occurs at a Brinkmann number (i.e., ratio of heat gained to heat lost) around 1 whereas brittle behavior dominates the melt deformation when the Deborah number (i.e., ratio of viscoelastic relaxation time to characteristic deformation time) is larger than around 0.01. The observed viscous heating significantly contributes to the viscosity decrease observed in high stress-strain rate experiments and questions our current understanding of the non-Newtonian deformation behavior of silicate melts.
Neuroimmunology of rabies: New insights into an ancient disease

Rabies is an ancient neuroinvasive viral (genus Lyssavirus, family Rhabdoviridae) disease affecting approximately 59,000 people worldwide. The central nervous system (CNS) is targeted, and rabies has a case fatality rate of almost 100% in humans and animals. Rabies is entirely preventable through proper vaccination, and thus, the highest incidence is typically observed in developing countries, mainly in Africa and Asia. However, there are still cases in European countries and the United States. Recently, demographic, increasing income levels, and the coronavirus disease 2019 (COVID‐19) pandemic have caused a massive raising in the animal population, enhancing the need for preventive measures (e.g., vaccination, surveillance, and animal control programs), postexposure prophylaxis, and a better understanding of rabies pathophysiology to identify therapeutic targets, since there is no effective treatment after the onset of clinical manifestations. Here, we review the neuroimmune biology and mechanisms of rabies. Its pathogenesis involves a complex and poorly understood modulation of immune and brain functions associated with metabolic, synaptic, and neuronal impairments, resulting in fatal outcomes without significant histopathological lesions in the CNS. In this context, the neuroimmunological and neurochemical aspects of excitatory/inhibitory signaling (e.g., GABA/glutamate crosstalk) are likely related to the clinical manifestations of rabies infection. Uncovering new links between immunopathological mechanisms and neurochemical imbalance will be essential to identify novel potential therapeutic targets to reduce rabies morbidity and mortality.