Miracle-dz/UniFAR-FTUs huggingface dataset:
Investigation of 3‐D basin structures in the İzmit Bay area (Turkey) by single‐station microtremor and gravimetric methods

SUMMARY We investigate 3-D basin structures and site resonance frequencies in the Izmit Bay area of Turkey by new geophysical surveys based on 239 single station microtremor and 405-point gravity measurements. A fundamental resonance frequency map of the Izmit Bay was produced from the main peak in the horizontal-to-vertical component spectral ratio (HVSR) of microtremors. The HVSR analysis of the microtremor data reveals single, double, broad peaked or no peak type HVSR curves varying in accordance with the surface geology and spatial extent of the three basins present in the Izmit Bay area. In the deepest sections of the Izmit, Golcuk and Derince basins of the Izmit Bay, the fundamental resonance frequencies are dominantly 0.24–0.30 Hz. These resonance frequencies should be taken into consideration along with higher mode frequencies to construct earthquake resistant structures in the Izmit Bay area. The 3-D gravimetric bedrock depth map of the Izmit basin shows that the basin has an asymmetric shape with its deepest section coinciding with the surface trace of the North Anatolian Fault. The northern shoulder of the basin has a gentle dip on the Kocaeli Peneplain side and the southern shoulder is much steeper, and it is bounded by the Samanli Mountains. We derive a power-law relationship that correlates the fundamental site resonance frequencies with the sedimentary cover thickness obtained from the gravity and shear wave velocity data in the Izmit Bay. We use this relationship to estimate bedrock depths beneath Golcuk and Derince basins. Our estimation of maximum basin depths is 1400 m for the Izmit and is 800 m for the Golcuk and Derince basins. Finally, we have analysed a converted Sp phase from a local earthquake recording made at site CMP to calculate and verify the sediment thickness estimations obtained from our gravimetric and microtremor analyses. This calculation shows close agreement with that of the gravimetric and microtremor results. Our results show that the basins in the Izmit Bay area have a very thick sedimentary cover with very low shear velocities underlined by hard bedrock, forming a sharp impedance contrast. We anticipate that these results will be a key contribution to the quantitative assessment of seismic hazard for the Izmit Bay area before the occurrence of strong earthquakes in the Marmara region.
Independent prognostic biomarker FERMT3 associated with immune infiltration and immunotherapy response in glioma

Abstract Background Adult glioma progresses rapidly and has a poor clinical outcome. The focal adhesion protein Kindlin-3 (encoded by the FERMT3 gene) participates in tumor development, drug resistance, and progression. However, the relationship between Kindlin-3 and glioma prognosis or immune microenvironment is poorly understood. Methods We comprehensively analyzed the expression, prognostic value, mutation landscape, functional enrichment, immune infiltration, and therapeutic role of FERMT3 in glioma using multiple datasets and validated Kindlin-3 expression in clinical tissue specimens by immunohistochemistry and multiple immunofluorescence staining. Results FERMT3 is an independent predictor of glioma prognosis and is highly expressed in glioblastoma tissues. Functional enrichment analyses indicated that FERMT3 participates in multiple immune-related pathways such as immune response and cytokine production. Furthermore, FERMT3 expression was positively correlated with the infiltration of several immune cells, immune scores, and the expression of genes related to immune checkpoints. Further analyses revealed that overexpression of FERMT3 was linked to a better response to anti-PD1 therapy. Data from single-cell RNA-seq reveal that FERMT3 was largely expressed in microglial cells and tissue-resident macrophages. Multiple immunofluorescence staining confirmed the overexpression of Kindlin-3 in the glioma-associated microglia/macrophages (GAMs). Conclusion The findings of this study provide a new perspective on the role of Kindlin-3 in glioma and may have a significant impact on the discovery of novel biomarkers and targeting of GAMs in the future.
Visceral adipose tissue reference data computed for GE HealthCare DXA from the National Health and Nutrition Examination Survey data set

The National Health and Nutrition Examination Survey (NHANES) characterizes body composition representative of the US population using dual‐energy x‐ray absorptiometry (DXA) scans. These population‐level trends of abdominal subcutaneous and visceral adipose tissue (SAT and VAT) are useful for identifying measures associated with increased disease risk. Recently, VAT and SAT data collected by Hologic DXA in NHANES were published online; however, there are known differences in the absolute calibration of DXA systems by make. The purpose of this study was to create reference tables suitable for calculating z scores and percentile values for GE HealthCare (GEHC) DXA systems.
A late Weichselian stable isotope and Molluscan Stratigraphy from Southern Sweden

Late Weichselian and early Holocene partly carbonate-rich sediments from a small lacustrine deposit in Skane, southern Sweden, were analysed for stable carbon and oxygen isotopes and mollusc assemblages. The data from these analyses reveal a pronounced climatic warming at c. 12,400 BP, accompanied by a general change from continental to maritime conditions. Two significant climatic oscillations were identified, dated ate. 12,200-12,000 BP ande. 11,000-10,200 BP. The climatic cooling of the latter, corresponding to the Younger Dryas stadial, may have been initiated well before 11,000 BP. A climatic oscillation of minor amplitude may have occurred around 11,500 BP. Distinct variations in delta(13)C of bulk organic material and shell carbonate are discussed in terms of climatically-induced changes in lake-water chemistry. The general assumption of a positive correlation between delta(18)O of limnic carbonates and mean annual air temperature is questioned. A climatic warming may be associated with a depletion of (18)O in limnic carbonates. Comparisons of palaeoclimatic information from the stable isotope data with that provided by molluscs allow the identification of aspects of climatic and environmental change such as water temperature, water depth, and aquatic vegetation density. Changes in the mollusc assemblage reflect changes in the limnic environment and facilitates the interpretation of stable isotope data. (Less)
Estimation of wheat leaf area index from IRS LISS-III data using Price model

A satellite sensor image based model suggested by Price was investigated for the estimation of Leaf Area Index (LAI) using data acquired by Linear Imaging Self Scanner-III (LISS-III) onboard Indian Remote Sensing Satellite-1C (IRS-1C) over two wheat growing sites in India (Karnal and Delhi) for crop seasons 1996-97 and 1997-98, respectively. Besides red and near-infrared (NIR) measurements over vegetation canopy, the model only requires a priori crop specific attentuation constants. These constants were computed for wheat using published and field ground reflectance measurements. Application of the model over 36 fields on which ground estimates of LAI were available, indicated a RMSE of 1.28 and 1.07 for the Karnal and Delhi sites, respectively.
Pharmacology of viable mechanism agnostic respiratory stimulants for the reversal of drug-induced respiratory depression in humans

ABSTRACT Introduction Drug-induced respiratory depression is potentially fatal and can be caused by various drugs such as synthetic opioids and tranquilizers. The only class of respiratory depressants that has a specific reversal agent are opioids, such as naloxone. These reversal agents have limited utility in situations of polysubstance ingestion with agents from multiple respiratory depressant classes. Hence, there is an unmet need for drugs that stimulate breathing irrespective of the underlying cause of respiratory depression, i.e. mechanism agnostic respiratory stimulants. Areas Covered In this review, we discuss agnostic respiratory stimulants, tested in humans with promising results, i.e. ampakines, drugs that act at the carotid bodies, N-methyl-D-aspartate receptor antagonist ketamine, and orexin receptor-2-agonist danavorexton, and others that demonstrated positive effects in animals but not yet in humans. Expert Opinion Rapid, effective rescuing of individuals who overdosed on respiratory depressants saves lives. While naloxone is the preferred drug for reversing opioid-induced respiratory depression, its effectiveness is limited in cases involving non-opioids. While several agnostic respiratory stimulants showed promise in humans, further research is needed to optimize dosing, evaluate safety and efficacy in deeper respiratory depression (apnea). Additionally, future studies should combine agnostic stimulants with naloxone, to improve rapid, effective rescue from drug overdoses.
Mass transport in water waves

The theory of mass transport in water waves is re-examined. Boundary-layer arguments are incorporated into the Lagrangian equations of motion, and the mass transport velocity is conveniently derived for both monochromatic and random waves. For finite depth, Longuet-Higgins' result is confirmed. Conditions at the far end of a wave tank are found to be related to a mean pressure gradient, and results are also obtained for a truly infinite channel. The nonuniformity of the solution for the deep-water limit is discussed.
Reconciliation of modeled climate responses to spectral solar forcing

The SIM (Spectral Irradiance Monitor) on SORCE (Solar Radiation and Climate Experiment) provides more spectrally complete daily SSI (spectral solar irradiance) measurements than ever before, allowing us to explore chemical and physical processes in the Earth's ocean and atmosphere system. However, the newly observed SSI instigated controversies in the Sun‐climate community on whether the SIM‐observed trends are true solar variations and on whether climate responses are in phase or out of phase with solar forcing. In this study, we focus on resolving two apparently contradictory results published on possible temperature responses to SIM‐derived solar forcing. When applying extreme scenarios of SIM‐based spectral solar forcing in a radiative‐convective model (RCM), we find that some apparently contradictory results can be explained by the different methods used to apply the SIM SSI data. It is clear that accurate SSI data are essential for accurate climate simulations and that climate modelers need to take care how they apply these data.
Transport Properties of NaCl in Aqueous Solution and Hydrogen Solubility in Brine

Ion transport properties and hydrogen solubility in brine play pivotal roles in various engineering and scientific scopes including chemical, physical, geochemical, and geothermal domains. Molecular dynamics simulations were performed to obtain transport properties of NaCl in the binary H2O + NaCl system using different force fields. Brine density, ion diffusivity, molar conductivity, conductivity, and hydrogen solubilities were obtained as functions of temperature and salt concentration. We compared the performance of different force fields against the experimental correlation model and developed three mathematical models. The first was the modified brine density model based on the simulated brine density over a wide range of salinity levels, and the second and third analytical mathematical models were derived for the ion diffusivity and molar conductivity as a function of salinity and temperature. The results of this study illustrated that the modified brine density model not only produced the same results of the previous model for lower salinity levels but also applied well to predict the brine density for a higher salinity level. The derived mathematical models indicated that the ion diffusivity and molar conductivity decreased linearly with salinity, and the slope and y-intercept of the lines of diffusivity and molar conductivity versus temperature were third-order polynomials of temperature. The developed models provided the mechanism for the behavior of decreasing molar conductivity with increasing salinity and increasing conductivity with increasing salinity. The directions of the effect of salinity on the molar conductivity and conductivity were opposite. The molar conductivity increased with a decreasing salinity level. However, the conductivity increased with increasing salinity, as the contribution of the ion concentration or salinity level to conductivity dominated over that of the ion movement.
Seasonal to decadal scale variations in the surface velocity of Jakobshavn Isbrae, Greenland: Observation and model-based analysis

[1] Using new data, we build upon the nearly two-decade long record of observations from Jakobshavn Isbrae to investigate the processes driving its dynamic evolution. While winter flow speed has not increased substantially over the last three winters, there remains a strong seasonal variation in flow speed that coincides with a cycle of summer thinning and winter thickening. We relate changes in glacier speed to geometry through variations in basal traction and horizontal stresses, using ice-flow models constrained by satellite and airborne observations. These results suggest that the bed provides little flow resistance along the main trough within about 20 km of the terminus. While the loss of buttressing from the retreat of grounded and floating ice likely contributed to the initial speedup, other processes are of comparable significance at seasonal to decadal time scales. From analysis of the models, we hypothesize that thinning-induced change in basal effective pressure is the dominant process influencing near-terminus behavior, while diffusive processes drive the upstream response. The apparent need for the terminus to thin to near flotation before it can calve may limit the rate at which retreat occurs. Our analysis of the processes controlling the speed suggests little potential for further large acceleration. Thinning and elevated speeds may continue at rates similar to present, however, putting the glacier on course to retreat to the head of its deep trough in about a century, at which point it likely would stabilize with a thinner terminus.
Outflow of dense water from the Storfjord in Svalbard: A numerical model study

Recent investigations on deep water renewal point to the important role of dense water formed on the continental shelves surrounding the Arctic Ocean. In this investigation a hydrostatic, reduced gravity, primitive equation model for the simulation of the spatial and temporal evolution of gravity plumes on a continental slope is applied and compared to the observed outflow of a plume of dense water, originally formed in Storfjorden (Svalbard), into the Greenland Sea toward Fram Strait. The vertically integrated, nonlinear, rotational model accounts for the entrainment of water mass properties from a spatially structured but stagnant ambient water body. This study reveals that part of the dense water, in accordance with earlier estimates, spreads northward along the eastern side of Fram Strait. Another branch of the plume, guided by the topography, flows into a deep trench east of the Knipovitch Ridge to the west of Svalbard. During its descent to depths of more than 2000 m the plume entrains three different water masses (East Spitsbergen Water, Atlantic Water, and Norwegian Sea Deep Water) and hence changes its water mass characteristics. The volume of deep water produced by the mechanism discussed here depends not only on the amount of initially formed brine-enriched shelf water, but also on the water mass characteristics of the latter.
Early machine learning prediction of hospitalized patients at low risk of respiratory deterioration or mortality in community-acquired pneumonia: Derivation and validation of a multivariable model

Current prognostic tools for pneumonia predominantly focus on mortality, often neglecting other crucial outcomes such as the need for advanced respiratory support. The objective of this study was to develop and validate a tool that predicts the early risk of non-occurrence of respiratory deterioration or mortality. We conducted a single-center, retrospective cohort study involving hospitalized adult patients with community-acquired pneumonia (CAP) and acute hypoxic respiratory failure from January 2009 to December 2019 (n ═ 4379). We employed the gradient boosting machine (GBM) learning to create a model that estimates the likelihood of patients requiring advanced respiratory support (high-flow nasal cannula [HFNC], non-invasive mechanical ventilation [NIMV], and invasive mechanical ventilation [IMV]) or mortality during hospitalization. This model utilized readily available data, including demographic, physiologic, and laboratory data, sourced from electronic health records and obtained within the first 6 h of admission. Out of the cohort, 890 patients (25.2%) either required advanced respiratory support or died during their hospital stay. Our predictive model displayed superior discrimination and higher sensitivity (cross-validation C-statistic ═ 0.71; specificity ═ 0.56; sensitivity ═ 0.72) compared to the pneumonia severity index (PSI) (C-statistic ═ 0.65; specificity ═ 0.91; sensitivity ═ 0.24; P value < 0.001), while maintaining a negative predictive value (NPV) of approximately 0.85. These data demonstrate that our machine-learning model predicted the non-occurrence of respiratory deterioration or mortality among hospitalized CAP patients more accurately than the PSI. The enhanced sensitivity of this model holds the potential for reliably excluding low-risk patients from pneumonia clinical trials.
Candida albicans induces neutrophil extracellular traps and leucotoxic hypercitrullination via candidalysin

The peptide toxin candidalysin, secreted by Candida albicans hyphae, promotes stimulation of neutrophil extracellular traps (NETs). However, candidalysin alone triggers a distinct mechanism for NET‐like structures (NLS), which are more compact and less fibrous than canonical NETs. Candidalysin activates NADPH oxidase and calcium influx, with both processes contributing to morphological changes in neutrophils resulting in NLS formation. NLS are induced by leucotoxic hypercitrullination, which is governed by calcium‐induced protein arginine deaminase 4 activation and initiation of intracellular signalling events in a dose‐ and time‐dependent manner. However, activation of signalling by candidalysin does not suffice to trigger downstream events essential for NET formation, as demonstrated by lack of lamin A/C phosphorylation, an event required for activation of cyclin‐dependent kinases that are crucial for NET release. Candidalysin‐triggered NLS demonstrate anti‐Candida activity, which is resistant to nuclease treatment and dependent on the deprivation of Zn2+. This study reveals that C. albicans hyphae releasing candidalysin concurrently trigger canonical NETs and NLS, which together form a fibrous sticky network that entangles C. albicans hyphae and efficiently inhibits their growth.
Asymmetric rupture of large aspect‐ratio faults at bimaterial interface in 3D

Normal stress perturbations accompany propagating mode II rupture along an interface separating materials of contrasting elastic compliance. The extent to which those perturbations may produce significant, observable rupture asymmetries (i.e., final slip distribution heavily weighted toward a preferred propagation direction) in earthquakes is uncertain, but previous numerical simulations predict such asymmetry when frictional resistance is velocity dependent, with sufficient post‐rupture re‐strengthening to produce pulse‐like rupture. We show, by numerical simulations in 3D, that purely geometrical effects leading to pulse‐like rupture can also induce strong asymmetries (and under very limited conditions can even evolve into strictly unilateral rupture), even when frictional rate dependence is neglected. The effect is studied here in a context that can only apply to strike‐slip earthquakes large enough to rupture the entire seismogenic thickness, but the results suggest that other geometrical effects leading to pulse‐like rupture will interact with a compliance contrast in a similar manner.
An observational study of drizzle formation in stratocumulus clouds for general circulation model (GCM) parameterizations

[1] Climate model parameterization of precipitation formation in boundary layer stratocumulus clouds is a challenge that needs to be carefully addressed for simulations of the aerosol impact on precipitation and on cloud life time and extent, the so-called second indirect effect of aerosol on climate. Existing schemes are generally tuned against global observations of the liquid water path, as very few in situ observations are available for their validation. This issue is addressed here with data collected during the second Aerosol Characterization Experiment. The methodology is different from previous experimental studies in the sense that each case study is first analyzed for retrieving properties that are representative of the observed cloud system as a whole, such as the cloud system geometrical thickness, droplet concentration, precipitation flux, etc. Special attention is given to the characterization of the droplet number concentration by deriving a value that is representative of the aerosol activation process instead of the mean value over the cloud system. The analysis then focuses on the variability of these cloud system values for eight case studies with different aerosol backgrounds. The data set reveals that precipitation forms when the maximum mean volume droplet radius in the cloud layer reaches values >10 μm, the same critical value as previously used in cloud resolving models. This maximum radius can be predicted with an adiabatic diagnostic on the basis of cloud geometrical thickness and droplet number concentration. The measured reduction rate of drizzle water content by precipitation is also compared to predictions of auto-conversion and accretion production rates derived from existing bulk parameterizations initialized with the measured values of cloud droplet and drizzle water content. The good agreement with the parameterizations suggests that the cloud layer reaches a nearly steady state characterized by a balance between the production and reduction rates of cloud and drizzle water content. Finally, it is shown that the cloud system precipitation rate can be expressed as a power law of cloud geometrical thickness and cloud droplet number concentration, hence providing a simple large-scale parameterization of the precipitation process in boundary layer clouds.