Miracle-dz/UniFAR-FTUs huggingface dataset:
Guardians of immunity: NK cell-mediated defense in COVID-19 and post-COVID scenarios.

The COVID-19 pandemic has left a lasting impact on global health, challenging communities, healthcare systems, and researchers worldwide. As we navigate this unprecedented crisis, this paper embarks on a multifaceted exploration of the pivotal role played by natural killer (NK) cells in the context of COVID-19. A significant portion of this paper is devoted to dissecting the nuanced role that NK cells assume in the context of COVID-19. From the initial acute infection to post-recovery immunity, NK cells emerge as critical players. We scrutinize the activation and dysregulation of NK cells during SARS-CoV-2 infection, shedding light on their potential contribution to disease severity. Moreover, we explore the fascinating landscape of post-COVID immunity, where NK cells are known to interact with adaptive immune responses, providing a foundation for long-term protection. In light of their central role, we investigate therapeutic strategies targeting NK cells in COVID-19 management, presenting an overview of current research efforts and their promise in mitigating disease progression. Lastly, we draw attention to research gaps, emphasizing the need for further investigation into NK cell dynamics during COVID-19. These gaps represent opportunities for advancing our understanding of NK cell biology and, by extension, enhancing our strategies for combating this global health crisis. This comprehensive exploration not only highlights the intricate interplay between NK cells and the COVID-19 pandemic but also underscores the importance of these innate immune warriors in shaping both the acute response and long-term immunity, ultimately contributing to the broader discourse surrounding the pandemic's pathophysiology and therapeutic approaches.
BRAZILIAN SEISMICITY: ONLINE NEWS AND SOCIAL MEDIA THAT HELP US

ABSTRACT. Historically, the earthquake studies was based on reports and records of newspapers, which referred to the estimation of the measure of the intensity of events. The advance of seismological instrumentation improved the calculation of magnitudes of earthquakes, which became a priority measure, to the detriment of intensity estimates. With the growth of access to information and communication technologies, the volume of relevant information for intensity estimation has become feasible and representative. We present the Brazilian Macroseismic Intensity Map between the years of 2006 to 2017, based on records of digital newspapers and blogs, and compare with the map of magnitudes recorded by the Brasília Seismological Observatory in the same period. The Brazilian Macroseismic Intensity Map contributes to the improvement of the Seismic Hazard Map. The results show the importance of preserving the information of seismic events published in digital media.Keywords: Macroseism, seismicity, intensity, digital newspapers, Brazilian Macroseismic Intensity Map.RESUMO. Historicamente, o estudo de terremotos era feito a partir de relatos e registros de jornais, que referenciam a estimativa da medida da intensidade dos eventos. O avanço da instrumentação sismológica aprimorou o cálculo das magnitudes dos terremotos, que tornou-se uma medida priorizada, em detrimento das estimativas de intensidade. Com o crescimento do acesso à informação e às tecnologias da comunicação, o volume de informações pertinentes para a estimativa da intensidade tornou-se viável e representativo. Apresentamos o Mapa Brasileiro de Intensidade Macrossísmica entre os anos de 2006 a 2017, baseado em registros de jornais digitais e blogs, e comparamos com o mapa de magnitudes registradas pelo Observatório Sismológico de Brasília no mesmo período. O Mapa Brasileiro de Intensidade Macrossísmica contribui para a melhora o Mapa de Risco Sísmico. Os resultados indicam a importância de preservar a informação de eventos sísmicos publicados em mídias digitais. Palavras-chave: Macrossismo, sismicidade, intensidade, jornais digitais, Mapa Brasileiro de Intensidade.
Satellite‐Based Drought Reporting on the Navajo Nation

In data scarce regions of the world, co‐produced management tools that combine remote sensing, modeled, and in situ data provide the information needed to support ground‐based monitoring systems for improved water and natural resource management. On the Navajo Nation (N.N.), in the Four Corners of the southwestern United States, there is a need for data‐driven management of water resources as the region is prone to water scarcity and emergency drought declarations, which have become more common under a changing climate. The current tools used by the N.N. Department of Water Resources largely lack the spatial detail, consistent measurements, and political and administrative information specific to their needs for determining appropriate response actions. The Drought Severity Evaluation Tool (DSET), a cloud‐based web application that harnesses the capabilities of Google Earth Engine, is a user‐friendly tool that pairs remotely sensed, modeled, and in situ data on the N.N. The DSET computing capabilities include on‐the‐fly generation of regional to field scale maps, time series figures, and reporting metrics that can assist in drought emergency declarations and the assistance to local communities through the subsequent allocation of relief dollars across the N.N. to the regions that need it most.
Double Trouble : Foraminiferal calcification in a changing ocean

Within the project ‘Double Trouble: Foraminiferal Calcification in a Changing Ocean’, I tried to illuminate mechanisms determining element incorporation in foraminifera with different calcification strategies. In particular, I aimed to assess the interplay between ocean acidification and biomineralization processes. Insight in processes in calcification likely improves foraminifera as reconstruction tools for past environmental changes, as well as it increases the accuracy of predictions regarding future carbonate production by these organisms. Constraining the mechanisms involved in foraminiferal (trace) elements uptake is pivotal for improving existing proxies and potentially discovering new proxies to reconstruct past ocean chemistry. The incorporation of certain elements in foraminiferal calcite is correlated to carbonate ion concentration ([CO32-]) of the surrounding seawater and these elements can therefore be used as proxies to reconstruct past changes in marine carbonate chemistry. We studied incorporation of Na, Mg, S, Sr, Zn and Ba as a function of changes in seawater carbonate chemistry. Modelling the chemical speciation of Ba2+ and Zn2+ shows that the amount of free ions in seawater strongly depends on changes in seawater [CO32-]. The amount of incorporated Zn and Ba (in contrast to Na, Mg and Sr) in foraminiferal carbonate changes as a function of [CO32-], suggesting only free ions are taken up and incorporated during calcification. Zn/CaCALCITE might be used as a pH-independent proxy to reconstruct inter-glacial to glacial changes in seawater [CO32-], whereas Ba/Ca shows potential as a proxy for [CO32-] over a relatively limited range. Furthermore, we observed foraminiferal S/Ca to change with seawater SO42-/CO32-, which is probably due to be substitution of sulphate for carbonate in the crystal lattice. Both hyaline and miliolid foraminiferal shells show the same sensitivity to changes in [CO32-] (resp. 19% and 21% per 100 µmol/kg [CO32-]), but the absolute values differ, indicating a superimposed bio-calcification effect. We investigated differences in trends in element incorporation between hyaline (perforate) and porcelaneous (imperforate) foraminifera in order to unravel processes involved in element uptake and subsequent foraminiferal calcification. In hyaline foraminifera we observed a correlation of element incorporation of different elements between species, reflected by a general higher built-in of elements in species with higher Mg content. Between porcelaneous species inter-element differences are much smaller. Besides these contrasting trends in element incorporation, however, similar trends are observed in element incorporation (e.g. Ba/Ca and Zn/Ca) as a function of seawater carbonate chemistry in both hyaline and porcelaneous species. This hints at similar mechanisms responsible for the transportation of ions to the site of calcification for these groups of foraminifera, although the contribution of these processes might differ across species.
Psychological Factors Associated with Firesetting : Evidence of a Treatment Effect from a Non-Randomized Trial with Male Prisoners

Despite huge societal costs associated with firesetting, no standardized therapy has been developed to address this hugely damaging behavior. This study reports the evaluation of the first standardized CBT group designed specifically to target deliberate firesetting in male prisoners (the Firesetting Intervention Programme for Prisoners; FIPP). Fifty-four male prisoners who had set a deliberate fire were referred for FIPP treatment by their prison establishment and psychologically assessed at baseline, immediately post treatment, and three-months post treatment. Prisoners who were treatment eligible yet resided at prison establishments not identified for FIPP treatment were recruited as Treatment as Usual controls and tested at equivalent time-points. Results showed that FIPP participants improved on one of three primary outcomes (i.e., problematic fire interest and associations with fire), and made some improvement on secondary outcomes (i.e., attitudes towards violence and antisocial attitudes) post treatment relative to controls. Most notable gains were made on the primary outcome of fire interest and associations with fire and individuals who gained in this area tended to self-report more serious firesetting behavior. FIPP participants maintained all key improvements at three-month follow up. These outcomes suggest that CBT should be targeted at those holding the most serious firesetting history.
EAT-UpTF: Enrichment Analysis Tool for Upstream Transcription Fctors of a gene group

EAT-UpTF (Enrichment Analysis Tool for Upstream Transcription Factors of a gene group) is an open-source Python script that analyzes the enrichment of upstream transcription factors (TFs) in a group of genes-of-interest (GOIs). EAT-UpTF utilizes genome-wide lists of TF-target genes generated by DNA affinity purification followed by sequencing (DAP-seq) or chromatin immunoprecipitation followed by sequencing (ChIP-seq). Unlike previous methods based on the two-step prediction of cis-motifs and DNA-element-binding TFs, our EAT-UpTF analysis enabled a one-step identification of enriched upstream TFs in a set of GOIs using lists of empirically determined TF-target genes. Contact sangreashim@gmail.com or pjseo1@snu.ac. kr Availability https://github.com/sangreashim/EAT-UpTF
Using Eclogite Retrogression to Track the Rapid Exhumation of the Pliocene Papua New Guinea UHP Terrane

The D’Entrecasteaux Islands of eastern Papua New Guinea (PNG) host the youngest known ultrahigh-pressure terrane on Earth and represent the only location where ultrahigh-pressure (UHP) rocks have been exhumed in an active rift. The PNG (U)HP rocks, consisting of Pliocene eclogites, garnet amphibolites and migmatitic gneisses, are exposed in five domal structures across the Islands. Zirconium-in-rutile thermometry records peak temperatures of 780 C from the eastern Oiatabu and nearby central Mailolo Domes, and hotter temperatures of 825–865 C within the western Goodenough Dome. Uranium–lead (U–Pb) and trace element zircon compositions from a suite of eclogite, host gneiss, felsic dikes and pegmatite from three domes document the rapid exhumation history of the PNG UHP terrane. High-spatial resolution laser-ablation split-stream inductively coupled plasma-mass spectrometry (LASS ICP-MS) analyses of select eclogite zircons exhibit no resolvable age zoning within single crystals. The same eclogite zircons, combined with separate zircons extracted from additional eclogite, host gneiss and felsic intrusions, were subsequently analysed by high-precision U–Pb chemical-abrasion isotope-dilution thermal ionization mass spectrometry and solution ICP-MS trace element analysis (TIMS-TEA). The results record discrete tectonic events across the three domes at sub-million year timescales: (1) (re)crystallization of host gneiss within the lower crust exposed in the eastern Oiatabu Dome from c.5 7–4 5 Ma; (2) initial retrogression and local decompression melting of eclogites from the Oiatabu and Mailolo Domes at c.4 6–4 3 Ma; (3) melt crystallization of weakly deformed felsic dikes of the Oiatabu Dome at c.3 0–2 9 Ma; and (4) retrogression and melt crystallization within eclogite–amphibolite-facies rocks in the western Goodenough Dome at c.2 9–2 6 Ma. In comparison to Zr-in-rutile peak temperature estimates, Ti-in-zircon temperatures >800 C may reflect increased temperatures during exhumation that resulted in partial melting of the eclogites. Inclusions of crystallized hydrous melt consisting of Na-rich plagioclase 6 K-feldspar þ quartz within eclogite zircons document this process. The elevated temperatures and the presence of the polyphase inclusions are the first documentation of partial melting of the (U)HP eclogites within PNG during initial retrogression from c.4 6–4 3 Ma. Overall, U–Pb zircon geochronology and geochemistry track both the timing of retrogressive overprinting within the lower-to-middle crust and final upper crustal emplacement over a VC The Author(s) 2018. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com 2017 J O U R N A L O F P E T R O L O G Y Journal of Petrology, 2018, Vol. 59, No. 10, 2017–2042 doi: 10.1093/petrology/egy088 Advance Access Publication Date: 18 September 2018
Phase Transitions and Dynamics in Mixed Three- and Low-Dimensional Lead Halide Perovskites

Lead halide perovskites are extensively investigated as efficient solution-processable materials for photovoltaic applications. The greatest stability and performance of these compounds are achieved by mixing different ions at all three sites of the APbX3 structure. Despite the extensive use of mixed lead halide perovskites in photovoltaic devices, a detailed and systematic understanding of the mixing-induced effects on the structural and dynamic aspects of these materials is still lacking. The goal of this review is to summarize the current state of knowledge on mixing effects on the structural phase transitions, crystal symmetry, cation and lattice dynamics, and phase diagrams of three- and low-dimensional lead halide perovskites. This review analyzes different mixing recipes and ingredients providing a comprehensive picture of mixing effects and their relation to the attractive properties of these materials.
A Combination Model of Shifting Joint Angle Changes With 3D-Deep Convolutional Neural Network to Recognize Human Activity

Research in the field of human activity recognition is very interesting due to its potential for various applications such as in the field of medical rehabilitation. The need to advance its development has become increasingly necessary to enable efficient detection and response to a wide range of movements. Current recognition methods rely on calculating changes in joint distance to classify activity patterns. Therefore, a different approach is required to identify the direction of movement to distinguish activities exhibiting similar joint distance changes but differing motion directions, such as sitting and standing. The research conducted in this study focused on determining the direction of movement using an innovative joint angle shift approach. By analyzing the joint angle shift value between specific joints and reference points in the sequence of activity frames, the research enabled the detection of variations in activity direction. The joint angle shift method was combined with a Deep Convolutional Neural Network (DCNN) model to classify 3D datasets encompassing spatial-temporal information from RGB-D video image data. Model performance was evaluated using the confusion matrix. The results show that the model successfully classified nine activities in the Florence 3D Actions dataset, including sitting and standing, obtaining an accuracy of (96.72 ± 0.83)%. In addition, to evaluate its robustness, this model was tested on the UTKinect Action3D dataset, obtaining an accuracy of 97.44%, proving that state-of-the-art performance has been achieved.
Calculation of slowness vectors from ray directions for qP-, qSV-, and qSH-waves in tilted transversely isotropic media

Kinematic ray tracing is an effective way to simulate the seismic wave propagation in isotropic and anisotropic media. It is essential to know the ray velocity when tracing seismic rays. But in anisotropic media, the ray velocity is a function of the direction of the slowness vector instead of the ray direction and it often deviates from the phase velocity. In this case, it causes a critical problem for ray tracing, which is how to calculate the ray velocity from a known ray direction. If we could calculate the phase slowness vector from ray directions, the ray velocity could be computed. We have evaluated a previous method in the first place. Then, we developed two new methods to solve two existing problems of the previous method: (1) It leads to complex and multiple solutions of the slowness vector and (2) it mixes up the qP- and qSV-wave modes. Our first method solves the two problems by applying eigenvalues to separate the wave modes and decrease the two unknowns ([Formula: see text] and [Formula: see text]) to only one unknown in two equations. Our second method is based on the general relationship between the slowness and ray-velocity vectors and shows that only one unknown is involved in one equation for tilted transversely isotropic (TTI) media. After obtaining the slowness vector, the ray velocity can be computed easily. A 2D model is designed to test the feasibility of the new methods. Using the results for the model, we found that the presented approaches were applicable for ray tracing in TTI media.
Bisphenol A exposure affects specific gut taxa and drives microbiota dynamics in childhood obesity

ABSTRACT Cumulative xenobiotic exposure has an environmental and human health impact which is currently assessed under the One Health approach. Bisphenol A (BPA) exposure and its potential link with childhood obesity that has parallelly increased during the last decades deserve special attention. It stands during prenatal or early life and could trigger comorbidities and non-communicable diseases along life. Accumulation in the nature of synthetic chemicals supports the “environmental obesogen” hypothesis, such as BPA. This estrogen-mimicking xenobiotic has shown endocrine disruptive and obesogenic effects accompanied by gut microbiota misbalance that is not yet well elucidated. This study aimed to investigate specific microbiota taxa isolated and selected by direct BPA exposure and reveal its role on the overall children microbiota community and dynamics, driving toward specific obesity dysbiosis. A total of 333 BPA-resistant isolated species obtained through culturing after several exposure conditions were evaluated for their role and interplay with the global microbial community. The selected BPA-cultured taxa biomarkers showed a significant impact on alpha diversity. Specifically, Clostridium and Romboutsia were positively associated promoting the richness of microbiota communities, while Intestinibacter, Escherichia-Shigella, Bifidobacterium, and Lactobacillus were negatively associated. Microbial community dynamics and networks analyses showed differences according to the study groups. The normal-weight children group exhibited a more enriched, structured, and connected taxa network compared to overweight and obese groups, which could represent a more resilient community to xenobiotic substances. In this sense, subnetwork analysis generated with the BPA-cultured genera showed a correlation between taxa connectivity and more diverse potential enzymatic BPA degradation capacities. IMPORTANCE Our findings indicate how gut microbiota taxa with the capacity to grow in BPA were differentially represented within differential body mass index children study groups and how these taxa affected the overall dynamics toward patterns of diversity generally recognized in dysbiosis. Community network and subnetwork analyses corroborated the better connectedness and stability profiles for normal-weight group compared to the overweight and obese groups.
Thiamine as adjunctive therapy for diabetic ketoacidosis (DKAT) trial protocol and statistical analysis plan: a prospective, single-centre, double-blind, randomised, placebo-controlled clinical trial in the USA

Introduction Diabetic ketoacidosis (DKA) is a potentially life-threatening diabetic complication. Despite the high prevalence of DKA and the substantial associated healthcare burden, limited research on strategies to improve outcomes currently exists. Thiamine (vitamin B1) is a cofactor of pyruvate dehydrogenase, which plays a key role in aerobic glucose metabolism. Thiamine deficiency is common in patients with DKA, resulting in a shift to anaerobic metabolism and hyperlactatemia, which can prolong and complicate recovery. Therefore, we hypothesise that thiamine administration will improve aerobic metabolism and lead to faster resolution of acidemia in patients with DKA. Methods and analysis In this single centre, double-blind, randomised, placebo-controlled, parallel group interventional trial, 100 patients admitted to the hospital with DKA will be randomised to receive either intravenous thiamine (200 mg in 50 mL 0.9% saline) or placebo (0.9% saline identical in appearance and volume) two times per day for 2 days. The primary outcome will be the change in bicarbonate level over 24 hours as compared between the two treatment groups. Additional secondary outcomes include the change over time in anion gap, lactate levels, oxygen consumption by circulating mononuclear cells, intensive care unit and hospital length-of-stay and hospital resource usage when comparing the two study arms. Ethics and dissemination This trial was approved by the Committee on Clinical Investigations, the institutional review board of Beth Israel Deaconess Medical Center (protocol number 2018P000475). Findings will be disseminated through peer-reviewed publications and professional conference presentations. Trial registration number NCT03717896; clinicaltrials.gov.
Entropy ventilation in an axisymmetric tropical cyclone model

Ventilation of a tropical cyclone’s inner core by low entropy environment air has been hypothesized to constrain tropical cyclone (TC) intensity (Simpson and Riehl 1958). The low entropy air is fluxed inward by asymmetries, such as vortex Rossby waves excited by environmental vertical wind shear. However, there is ambiguity as to the layer over which ventilation occurs and how ventilation precisely affects TC intensity. Frank and Ritchie (2001) hypothesized that the upper portion of the circulation is ventilated first, causing the TC to weaken from the top-down. On the other hand, Cram et al. (2007) found in their 3D numerical simulations of a sheared TC that the eyewall entropy is reduced by midlevel ventilation. The goals of this study are to assess the sensitivity of TC intensity to the location and amplitude of the ventilation and to study how ventilation induces axisymmetric weakening.