Miracle-dz/UniFAR-FTUs huggingface dataset:
Radar and Radiation Properties of Ice Clouds

Abstract The authors derive relations of the equivalent radar reflectivity Ze and extinction coefficient α of ice clouds and confirm the theory by in situ aircraft observations during the First International Satellite Cloud Climatology Project Regional Experiment. Equivalent radar reflectivity Ze is a function of ice water content W and a moment of the size distribution such as the median volume diameter D0. Stratification of the data by D0 provides a set of W − Ze relations from which one may deduce the dependence of particle density on size. This relation is close to that of Brown and Francis and provides confidence in the methodology of estimating particle size and mass. The authors find that there is no universal W − Ze relation, due both to large scatter and systematic shifts in particle size from day to day and cloud to cloud. These variations manifest the normal changes in ice crystal growth. The result is that, with the exception of temperatures less than −40°C, temperature cannot be used to relia.
Smearing of a beaming pattern by an isotropic cloud: an analysis with applications to nonpulsing X-ray sources and cosmic rays

There is increasing observational and theoretical evidence to suggest that many low-mass X-ray binaries contain neutron stars shrouded by optically thick plasma. The diffusion approximation was used to examine the effect of an isotropic, spherical scattering cloud on anisotropic or periodic emission from an embedded source. Compton scattering is treated by extending the 'scattering time' method of Sunyaev and Titarchuk (1980) to include the contribution of higher angular harmonics. Applications to cosmic-ray diffusion are also discussed. It is shown that: the smearing-out of a beaming pattern is largely determined by the ratio of the cloud radius to that of the source; that periodic variations of the source are damped exponentially, and a phase lag is introduced, if the oscillation period is short compared with the time for a photon to diffuse through the cloud; that Comptonization is accompanied by isotropization, so that any underlying modulation of the source is most likely to survive in the spectral range corresponding to its intrinsic radiation temperature. 32 references.
Response-surface designs for quantitative and qualitative variables

When some variables are quantitative and some qualitative in a response-surface context, standard designs may not be suitable. The reasons for this are illuminated. Some alternative designs are discussed. Every n-point design provides n linearly independent estimation contrasts. Some of these, p say, are needed to estimate the p parameters of the postulated model. The remaining n — p linearly independent estimation contrasts are available to estimate pure error (if used) and to test for lack of fit, either overall or in particular ways. The key to choosing a good design is to use the available degrees of freedom well, given certain assumptions about the model to be fitted. When there is also uncertainty about the model assumptions, dogmatic design advice is not possible. Sound guidelines are available, however, and these are presented and illustrated.
A Cooperative Atmosphere–Surface Exchange Study (CASES) Dataset for Analyzing and Parameterizing the Effects of Land Surface Heterogeneity on Area-Averaged Surface Heat Fluxes

Abstract A multiscale dataset that includes atmospheric, surface, and subsurface observations obtained from an observation network covering a region that has a scale order comparable to mesoscale and general circulation models is described and analyzed. The dataset is half-hourly time series of forcing and flux response data developed from the one-month Cooperative Atmosphere–Surface Exchange Study (CASES-97) experiment, located in the Walnut Watershed near Wichita, Kansas. The horizontal complexity of this dataset was analyzed by looking at the sensible and latent heat flux response of station data from the three main land surface types of winter wheat, grass/pastureland, and bare soil/sparse vegetation. The variability in the heat flux response at and among the different sites points to the need for a spatially distributed, time-varying atmospheric-forcing dataset for use in land surface modeling experiments. Such a dataset at horizontal spacings of 1, 5, and 10 km was developed from the station data an.
Vegetation activity enhanced in India during the COVID-19 lockdowns: evidence from satellite data

Abstract The Severe Acute Respiratory Syndrome-COronaVIrus Diseases 2019 (SARS-COVID-19) has sternly affected the entire world in terms of human health, loss of lives, and huge economic losses. However, pandemic-triggered lockdown (LD) events (as a preventive measure) have compelled to stop or reduce major economic activities, exerting positive impacts on the terrestrial environment. We deployed a variety of satellite products (i.e., normalized difference vegetation index (NDVI), solar-induced chlorophyll fluorescence (SIF), and aerosol optical depth (AOD)) along with gridded climatic dataset (temperature (TEMP), precipitation (PREC), and net radiation (NR)) to quantify the changes in vegetation activity (greenness and productivity) during the LD period over the Indian biogeographic provinces (BGPs) as compared to the average conditions over the previous three years (2017-2019). The analysis of the NDVI and SIF data revealed that vegetation greenness and productivity significantly enhanced during LD periods (by up to 37 to 55%, respectively). The influence of climatic drivers (PREC, TEMP, and NR) on vegetation activity was also investigated. We found that the enhancement in the vegetation activity (over BGPs) during the LD period was not entirely driven by the climatic parameters, and was therefore inferred to be also influenced by the LD events. Moreover, vegetation activity around the mining clusters were largely improved during the LD period (by up to 78%) over the coal mining, followed by iron ore mining (up to 63%), and stone mining (up to 41%) clusters) regions. In a nutshell, it can be deliberated that COVID-triggered preventive measures (i.e., country-level LD, travel bans, industry ban, curtail in mining capacity, among others) likely enhanced vegetation health and productivity. Thereby, regulatory measures can be seen as a viable option for improving the terrestrial environmental conditions in the context of climate change in the near future.
Massive Remnant of Evolved Cometary Dust Trail Detected in the Orbit of Halley-Type Comet 55P/Tempel-Tuttle

There is a subpopulation of Leonid meteoroid stream particles that appear to form a region of enhanced numbers density along the path of the stream. This structure has been detected in the vicinity of the parent comet, and its variation from one apparition to the next has been traced. A significant amount of known comet 55P/Tempel-Tuttle debris is in this component, called a "filament," which has dimensions exceeding by an order of magnitude that expected for a cometary dust trail. As filament particles are of a size comparable to those found in trails, the emission ages of the particles comprising the filament must be intermediate between the age of the current trail particles (which have not been observed) and the age of the background particles comprising the annual showers. The most likely explanation for this structure is planetary perturbations acting differently on the comet and large particles while at different mean anomalies relative to each other.
An integrated framework to identify and map gullies in a Mediterranean region of Turkey

Abstract This research introduces a scientific methodology to identify areas affected by gully erosion using Geographic Object Based Image Analysis (GEOBIA) and Random Forest (RF) supervised machine learning. The GEOBIA and RF were applied in Besni district, which has a Mediterranean climate, of Adiyaman province in Turkey by including many factors in the model. Estimation Scale Parameter (ESPII) algorithm was used in the segmentation phase. The novelty of this study is the implementation of RF supervised classification algorithm to classify a large number of objects determined after the segmentation process, due to the large size of the study area. Therefore, open access data has been evaluated with high classification accuracy without the need for labor. Precision, Recall and F1-Score values were calculated using true positive (TP), true negative (TN), false positive (FP) and false negative (FN) values based on field observations and Google Earth images of the study area. The TP, TN, FP and FN values were 0.90, 0.95 and 0.92, respectively. In addition, a Kappa-index was calculated as 0.88. The gully erosion map obtained using aforementioned methodology can be used to take necessary measures to prevent further degradation and plan sustainable land uses.
Uremic toxin indoxyl sulfate induces trained immunity via the AhR-dependent arachidonic acid pathway in ESRD

Trained immunity is the long-term functional reprogramming of innate immune cells, which results in altered responses toward a secondary challenge. Despite indoxyl sulfate (IS) being a potent stimulus associated with chronic kidney disease (CKD)-related inflammation, its impact on trained immunity has not been explored. Here, we demonstrate that IS induces trained immunity in monocytes via epigenetic and metabolic reprogramming, resulting in augmented cytokine production. Mechanistically, the aryl hydrocarbon receptor (AhR) contributes to IS-trained immunity by enhancing the expression of arachidonic acid (AA) metabolism-related genes such as Arachidonate 5-Lipoxygenase (ALOX5) and ALOX5 Activating Protein (ALOX5AP). Inhibition of AhR during IS training suppresses the induction of IS-trained immunity. Monocytes from end-stage renal disease (ESRD) patients have increased ALOX5 expression and after 6-day training, they exhibit enhanced TNF-α and IL-6 production to LPS. Furthermore, healthy control-derived monocytes trained with uremic sera from ESRD patients exhibit increased production of TNF-α and IL-6. Consistently, IS-trained mice and their splenic myeloid cells had increased production of TNF-α after in vivo and ex vivo LPS stimulation compared to that of control mice. These results provide insight into the role of IS in the induction of trained immunity, which is critical during inflammatory immune responses in CKD patients.
Culture Based Development in the Regions of China

Abstract Is culture a relevant factor for the development of the Chinese regions and is this culture different from the institutional settings of China? The Culture Based Development (CBD) paradigm has been collecting evidence from the Western world about the impact of local cultural capital (a quantitative expression of culture) on the productivity of places throughout the EU and United States. The current article aims to replicate the CBD approach for the first time for the institutional setting of China. It does so by using a unique panel dataset for Chinese provinces over a seven-year period (2013–2019), which contains over sixty cultural indicators and employing factor analysis, 3SLS, and k-mean clustering estimation techniques. The main contribution of the article is the distinction that it draws conceptually and empirically between culture as a proto institution and the rest of the institutional settings in a country. Revealing part of the differences and the interaction between culture and institutions, this study sheds light on many important, still-unanswered-in-the-economic-literature questions about culture and local development in China.
Automated Side-Channel Attacks using Black-Box Neural Architecture Search

The application of convolutional neural networks (CNNs) to break cryptographic systems through hardware side-channels facilitated rapid and adaptable attacks on cryptographic systems like smart cards and Trusted Platform Modules (TPMs). However, current approaches rely on manually designed CNN architectures by domain experts, which are time-consuming and impractical for attacking new systems. To overcome this, recent research has delved into the use of neural architecture search (NAS) to discover appropriate CNN architectures automatically. This approach aims to alleviate the burden on human experts and facilitate more efficient exploration of new attack targets. However, these works only optimize the architecture using the secret key information from the attack dataset and explore limited search strategies with one-dimensional CNNs. In this work, we propose a fully black-box NAS approach that solely utilizes the profiling dataset for optimization. Through an extensive experimental parameter study, we investigate which choices for NAS, such as using 1-D or 2-D CNNs and various search strategies, produce the best results on 10 state-of-the-art datasets for identity leakage model. Our results demonstrate that applying the Random search strategy on 1-D inputs achieves a high success rate, enabling retrieval of the correct secret key using a single attack trace on two datasets. This combination matches the attack efficiency of fixed CNN architectures and outperforms them in 4 out of 10 datasets. Our experiments also emphasize the importance of repeated attack evaluations for ML-based solutions to avoid biased performance estimates.
Parameter Change Test for Poisson Autoregressive Models

In this paper, we consider the problem of testing for a parameter change in Poisson autoregressive models. We suggest two types of cumulative sum (CUSUM) tests, namely, those based on estimates and residuals. We first demonstrate that the conditional maximum likelihood estimator (CMLE) is strongly consistent and asymptotically normal and then construct the CMLE‐based CUSUM test. It is shown that under regularity conditions, its limiting null distribution is a function of independent Brownian bridges. Next, we construct the residual‐based CUSUM test and derive its limiting null distribution. Simulation results are provided for illustration. A real‐data analysis is performed on data for polio incidence and campylobacteriosis infections.
Singularity formation in chemotaxis systems with volume-filling effect

A parabolic–elliptic model of chemotaxis which takes into account volume-filling effects is considered under the assumption that there is an a priori threshold for the cell density. For a wide range of nonlinear diffusion operators including singular and degenerate ones it is proved that if the taxis force is strong enough with respect to diffusion and the initial data are chosen properly then there exists a classical solution which reaches the threshold at the maximal time of its existence, no matter whether the latter is finite or infinite. Moreover, we prove that the threshold may even be reached in finite time provided the diffusion of cells is non-degenerate.
Human immune phenotyping reveals accelerated aging in type 1 diabetes

The composition of immune cells in peripheral blood is dramatically remodeled throughout the human lifespan, as environmental exposures shape the proportion and phenotype of cellular subsets. These dynamic shifts complicate efforts to identify disease-associated immune signatures in type 1 diabetes (T1D), which is variable in age of onset and rate of β-cell decline. Herein, we conducted standardized flow cytometric immune profiling on peripheral blood from a cross-sectional cohort of T1D participants (n=240), their first-degree relatives (REL, n=310), those at increased risk with two or more islet autoantibodies (RSK, n=24), and autoantibody negative healthy controls (CTR, n=252). We constructed an immune-age predictive model in healthy subjects and developed an interactive data visualization portal (ImmScape; https://ufdiabetes.shinyapps.io/ImmScape/). When applied to the T1D cohort, this model revealed accelerated immune aging (p<0.001) as well as phenotypic signatures of disease after age correction. Of 192 investigated flow cytometry and complete blood count readouts, 46 were significantly associated with age only, 25 with T1D only, and 23 with both age and T1D. Phenotypes associated with T1D after age-correction were predictive of T1D status (AUROC=82.3%). Phenotypes associated with accelerated aging in T1D included increased CXCR3+ and PD-1+ frequencies in naïve and memory T cell subsets, despite reduced PD-1 expression levels (mean fluorescence intensity) on memory T cells. Additionally, quantitative trait locus analysis linked an increase in HLA-DR expression on monocytes with the T1D-associated HLA-DR4/DQ8 genotype, regardless of clinical group. Our findings demonstrate advanced immune aging in T1D and highlight disease-associated phenotypes for biomarker monitoring and therapeutic interventions. One Sentence Summary Peripheral blood characterization reveals accelerated immune-age and age-adjusted proinflammatory immune phenotypes in type 1 diabetes.
Genetic features and genomic targets of human KRAB-zinc finger proteins

Krüppel-associated box (KRAB) domain-containing zinc finger proteins (KZFPs) are one of the largest groups of transcription factors encoded by tetrapods, with 378 members in human alone. KZFP genes are often grouped in clusters reflecting amplification by gene and segment duplication since the gene family first emerged more than 400 million years ago. Previous work has revealed that many KZFPs recognize transposable element (TE)-embedded sequences as genomic targets, and that KZFPs facilitate the co-option of the regulatory potential of TEs for the benefit of the host. Here, we present a comprehensive survey of the genetic features and genomic targets of human KZFPs, notably completing past analyses by adding data on more than a hundred family members. General principles emerge from our study of the TE-KZFP regulatory system, which point to multipronged evolutionary mechanisms underlaid by highly complex and combinatorial modes of action with strong influences on human speciation.
ABCG2 and SLCO1B1 gene polymorphisms in the Croatian population

Abstract Background Organic anion-transporting polypeptide 1B1 (OATP1B1) and the ATP-binding cassette subfamily G member 2, ABCG2, are important transporters involved in the transport of endogenous substrates and xenobiotics, including drugs. Genetic polymorphisms of these transporters have effect on transporter activity. There is significant interethnic variability in the frequency of allele variants. Aim To determined allele and genotype frequencies of ABCG2 and SLCO1B1 genes in Croatian populations of European descent. Subjects and methods A total of 905 subjects (482 women) were included. Genotyping for ABCG2 c.421C > A (rs2231142) and for SLCO1B1 c.521T > C (rs4149056), was performed by real-time polymerase chain reaction (PCR) using TaqMan® DME Genotyping Assays. Results For ABCG2 c.421C > A, the frequency of CC, CA and AA genotypes was 81.4%, 17.8% and 0.8% respectively. The frequency of variant ABCG2 421 A allele was 9.7%. For SLCO1B1 c.521T > C, the frequency of TT, TC and CC genotypes was 61.7%, 34.8% and 3.5% respectively. The frequency of variant SLCO1B1 521 C allele was 20.9%. Conclusion The frequency of the ABCG2 and SLCO1B1 allelic variants and genotypes in the Croatian population is in accordance with other European populations. Pharmacogenetic analysis can serve to individualise drug therapy and minimise the risk of developing adverse drug reactions.
Modelling red blood cell optical trapping by machine learning improved geometrical optics calculations

Optically trapping red blood cells allows to explore their biophysical properties, which are affected in many diseases. However, because of their nonspherical shape, the numerical calculation of the optical forces is slow, limiting the range of situations that can be explored. Here we train a neural network that improves both the accuracy and the speed of the calculation and we employ it to simulate the motion of a red blood cell under different beam configurations. We found that by fixing two beams and controlling the position of a third, it is possible to control the tilting of the cell. We anticipate this work to be a promising approach to study the trapping of complex shaped and inhomogeneous biological materials, where the possible photodamage imposes restrictions in the beam power.
Toxin/antitoxin systems induce persistence and work in concert with restriction/modification systems to inhibit phage

ABSTRACT Myriad bacterial anti-phage systems have been described and often the mechanism of programmed cell death is invoked for phage inhibition. However, there is little evidence of “suicide” under physiological conditions for these systems. Instead of death to stop phage propagation, we show here that persister cells, i.e., transiently-tolerant, dormant, antibiotic-insensitive cells, are formed and survive using the Escherichia coli C496_10 tripartite toxin/antitoxin system MqsR/MqsA/MqsC to inhibit T2 phage. Specifically, MqsR/MqsA/MqsC inhibited T2 phage by 105-fold and reduced T2 titers by 3,000-fold. During T2 phage attack, in the presence of MqsR/MqsA/MqsC, evidence of persistence includes the single-cell physiological change of reduced metabolism (via flow cytometry), increased spherical morphology (via transmission electron microscopy), and heterogeneous resuscitation. Critically, we found restriction-modification systems (primarily EcoK McrBC) work in concert with the toxin/antitoxin system to inactivate phage, likely while the cells are in the persister state. Hence, a phage attack invokes a stress response similar to antibiotics, starvation, and oxidation, which leads to persistence, and this dormant state likely allows restriction/modification systems to clear phage DNA. IMPORTANCE To date, there are no reports of phage infection-inducing persistence. Therefore, our results are important since we show for the first time that a phage-defense system, the MqsRAC toxin/antitoxin system, allows the host to survive infection by forming persister cells, rather than inducing cell suicide. Moreover, we demonstrate that the MqsRAC system works in concert with restriction/modification systems. These results imply that if phage therapy is to be successful, anti-persister compounds need to be administered along with phages. To date, there are no reports of phage infection-inducing persistence. Therefore, our results are important since we show for the first time that a phage-defense system, the MqsRAC toxin/antitoxin system, allows the host to survive infection by forming persister cells, rather than inducing cell suicide. Moreover, we demonstrate that the MqsRAC system works in concert with restriction/modification systems. These results imply that if phage therapy is to be successful, anti-persister compounds need to be administered along with phages.