Miracle-dz/UniFAR-FTUs huggingface dataset:
The Somatic Mutation Landscape of UDP-Glycosyltransferase (UGT) Genes in Human Cancers

Simple Summary The human UDP-glycosyltransferase (UGT) superfamily is involved in the metabolism of numerous anticancer drugs and endobiotic signaling molecules with pro/anti-cancer activities. Previous studies have shown abundant expression of UGT genes in many human cancers, indicative of the active intratumoral metabolism of drugs and endobiotics through the UGT conjugation pathway. Mutations of UGT genes in tumors that can affect this pathway have not yet been reported. In the present study, our analysis of somatic mutations in 10,069 tumors from 33 different cancer types identified 3427 somatic mutations in UGT genes, over half of which have been predicted to code for variant UGT proteins with no or reduced activity. As a result, somatic mutations of UGT genes may reduce the capacity of cancer cells to metabolize anticancer drugs and pro/anti-cancer endobiotics, and hence, they are likely to alter therapeutic efficacy and cancer growth, highlighting their potential utility as biomarkers predicting therapeutic efficacy and clinical outcomes. Abstract The human UDP-glycosyltransferase (UGTs) superfamily has a critical role in the metabolism of anticancer drugs and numerous pro/anti-cancer molecules (e.g., steroids, lipids, fatty acids, bile acids and carcinogens). Recent studies have shown wide and abundant expression of UGT genes in human cancers. However, the extent to which UGT genes acquire somatic mutations within tumors remains to be systematically investigated. In the present study, our comprehensive analysis of the somatic mutation profiles of 10,069 tumors from 33 different TCGA cancer types identified 3427 somatic mutations in UGT genes. Overall, nearly 18% (1802/10,069) of the assessed tumors had mutations in UGT genes with huge variations in mutation frequency across different cancer types, ranging from over 25% in five cancers (COAD, LUAD, LUSC, SKCM and UCSC) to less than 5% in eight cancers (LAML, MESO, PCPG, PAAD, PRAD, TGCT, THYM and UVM). All 22 UGT genes showed somatic mutations in tumors, with UGT2B4, UGT3A1 and UGT3A2 showing the largest number of mutations (289, 307 and 255 mutations, respectively). Nearly 65% (2260/3427) of the mutations were missense, frame-shift and nonsense mutations that have been predicted to code for variant UGT proteins. Furthermore, about 10% (362/3427) of the mutations occurred in non-coding regions (5′ UTR, 3′ UTR and splice sites) that may be able to alter the efficiency of translation initiation, miRNA regulation or the splicing of UGT transcripts. In conclusion, our data show widespread somatic mutations of UGT genes in human cancers that may affect the capacity of cancer cells to metabolize anticancer drugs and endobiotics that control pro/anti-cancer signaling pathways. This highlights their potential utility as biomarkers for predicting therapeutic efficacy and clinical outcomes.
Psilocybin as a Treatment for Psychiatric Illness: A Meta-Analysis

Psilocybin is an emerging potential therapy for the treatment of psychiatric illnesses. Microdosing has been shown to result in an overall improvement in patients with anxiety, depression, obsessive-compulsive disorder, post-traumatic stress disorder, and substance abuse. This meta-analysis explores and compiles prior research to make further inferences regarding psilocybin and its use for the treatment of psychiatric illness along with its safety and efficacy. Database searches were conducted to identify peer-reviewed randomized controlled trials and clinical trials mentioning psilocybin use and psychiatric illness. A Preferred Reporting Items for Systematic Reviews and Meta-Analyses flow diagram was created and analysis was run on the nine articles that met all established inclusion criteria. An event is defined as a participant who showed improvement, in a quantitative method, from baseline after the use of psilocybin. Another analysis was done using depression severity (Quick Inventory of Depressive Symptomatology 16-Item Self Report, QIDS-SR16) at baseline and after the use of psilocybin. Analyses of the original data and the nine articles showed a great deal of heterogeneity with an I2 value of 73.68%, suggesting that the studies in this meta-analysis cannot be considered to be studies of the same population. The Q value of 30.4 was higher than 15.507, which is the critical value for eight degrees of freedom found in a chi-square distribution. This Q value showed a high degree of variation and lacked significance. The second meta-run on QIDS-SR16 scores from three studies showed a Q value of 1.16 which was lower than 5.991, the critical value for two degrees of freedom found in a chi-square distribution. The I2 statistic for this second meta-analysis was -73% which can be equated to zero. This indicated that the data were homogeneous or that there was no observed heterogeneity. Due to low heterogeneity, the fixed-effects model was used. Based on this meta-analysis, psilocybin seems to show symptom improvement in some psychiatric illnesses. The effectiveness of psilocybin microdosing and the use of psilocybin, in general, need to be studied further to determine the efficacy and safety of potential applications in psychiatry.
Rates of convergence of powered order statistics from general error distribution

Let be a sequence of independent random variables with common general error distribution with shape parameter v>0, and let denote the r-th largest order statistics of . With different normalizing constants the distributional expansions and the uniform convergence rates of normalized powered order statistics are established. An alternative method is presented to estimate the probability of the r-th extremes. Numerical analyses are provided to support the main results.
Narrow Diffuse Interstellar Bands: A Survey with Precise Wavelengths

We present an atlas of 271 diffuse interstellar bands (DIBs) between 4460 and 8800 Å based on echelle spectra (R = 45,000), of which more than 100 are new DIBs discovered in this survey. The atlas is restricted mostly to narrow features, and we describe the tests for an interstellar origin. The rest wavelength of each DIB was determined in a high‐quality composite spectrum of the star HD 23180 using the interstellar Na i (D1 and D2) lines to establish the radial velocity of the single intervening cloud. DIB wavelengths are quoted to 0.01 Å and are probably accurate to ∼0.1 Å. Other, weak DIBs found in the spectra of heavily reddened stars are included with a lower wavelength precision.
Quasi-Invariance under Flows Generated by Non-Linear PDEs

The paper is concerned with the quasi-invariance of probability measures $\mu$ under probability measure valued flows. Typically, solutions to non-linear PDEs modeling spatial development as time progresses generate such flows. In particular, it is shown that under additional conditions on $\mu$, Fr\'echet differentiability of the solution map of the PDE is sufficient for the quasi-invariance. This result is applied to the Boltzmann equation of cutoff type. The second application is a PDE related to the asymptotic behavior of a Fleming-Viot type system. Here it is demonstrated how the quasi-invariance result can be used to establish a corresponding integration by parts formula.
Reduction of off-state drain leakage in InGaAs-based metal-oxide-semiconductor field-effect transistors

Off-state drain leakage current has been investigated for InGaAs-based metal-oxide-semiconductor field-effect transistors with different drain configurations, InGaAs, and InP, respectively. The introduction of an InP drain presents a lower leakage current compared to InGaAs drain devices. From temperature dependent measurements, the leakage current mechanisms have been differentiated, and the role of drain direct band-to-band tunneling, as well as gate-induced drain leakage, has been identified.
Integral sliding‐mode‐based robust output‐regulation for constrained and uncertain linear systems

This article proposes a solution to the output regulation problem for uncertain linear systems with input saturation, state constraints, and external disturbances. The proposed robust control is composed of a linear and a nonlinear part. Each part of the control can be designed independently due to the use of an integral sliding‐mode control approach. The linear control, whose design is based on the barrier Lyapunov function and the attractive ellipsoid method, considers the input saturation, the state constraints, and the parameter uncertainties. The nonlinear part is based on an integral sliding‐mode control approach and it can compensate the effect of some matched disturbances. Also, a safe set where the system trajectories do not transgress the state constraints and input saturation, is provided. The proposed scheme guarantees asymptotic convergence to zero of the output regulation error coping with the system constraints and disturbances. A constructive and simple method, based on linear matrix inequalities, is proposed to compute the controller gains. Some simulation results illustrate the feasibility of the proposed scheme.
A coarse Cartan–Hadamard theorem with application to the coarse Baum–Connes conjecture

We establish a coarse version of the Cartan–Hadamard theorem, which states that proper coarsely convex spaces are coarsely homotopy equivalent to the open cones of their ideal boundaries. As an application, we show that such spaces satisfy the coarse Baum–Connes conjecture. Combined with the result of Osajda–Przytycki, it implies that systolic groups and locally finite systolic complexes satisfy the coarse Baum–Connes conjecture.
Electropolishing of thin-cruciform gimbal flexure of gyroscope fabricated by electrical discharge machining

ABSTRACT Electric discharge machining (EDM), a non-traditional process, is widely used for micro-fabrication, such as the thin-cruciform gimbal flexure of a gyroscope. Due to the thermoelectric process of EDM, it induces surface defects and alters the base material’s property, degrading its performance. In the present study, electropolishing (EP) has been performed on a cruciform-shaped ~119.75 µm thin gimbal flexure to remove its surface defects. The gimbal flexure is made by maraging steel 300. It is electropolished with an electrolyte mixture of acetic acid and perchloric acid in a volume ratio of 3:1. The main EP process parameters, namely electrolyte temperature, agitation of magnetic bid, and polishing time, are optimized using the response surface method of statistical design of experiments (DOE). Also, experiments are performed at optimum process parameter conditions to validate the model obtained from DOE. Surface elemental composition changes after EDM, which regain its base composition after EP. The formation of the recast layer on the surface after EDM, which increases hardness, is removed after EP and brings the surface hardness below the base material due to the formation of an oxide layer. Surface morphology after EDM contains several defects, which are entirely removed after EP.
Social force model with explicit collision prediction

We introduce a new specification of the social force model in which pedestrians explicitly predict the place and time of the next collision in order to avoid it. This and other specifications of the social force model are calibrated, using genetic algorithms, on a set of pedestrian trajectories, obtained tracking with laser range finders the movement of pedestrians in controlled experiments, and their performance is compared. The results show that the proposed method has a better performance in describing the trajectory set.
A FE-ADMM algorithm for Lavrentiev-regularized state-constrained elliptic control problem

In this paper, Elliptic control problems with pointwise box constraints on the state is considered, where the corresponding Lagrange multipliers in general only represent regular Borel measure functions. To tackle this difficulty, the Lavrentiev regularization is employed to deal with the state constraints. To numerically discretize the resulted problem, full piecewise linear finite element discretization is employed. Estimation of the error produced by regularization and discretization is done. The error order of full discretization is not inferior to that of variational discretization because of the Lavrentiev-regularization. Taking the discretization error into account, algorithms of high precision do not make much sense. Utilizing efficient first-order algorithms to solve discretized problems to moderate accuracy is sufficient. Then a heterogeneous alternating direction method of multipliers (hADMM) is proposed. Different from the classical ADMM, our hADMM adopts two different weighted norms in two subproblems respectively. Additionally, to get more accurate solution, a two-phase strategy is presented, in which the primal-dual active set (PDAS) method is used as a postprocessor of the hADMM. Numerical results not only verify error estimates but also show the efficiency of the hADMM and the two-phase strategy.
Virtual Screening of Artemisia annua Phytochemicals as Potential Inhibitors of SARS-CoV-2 Main Protease Enzyme

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a human coronaviruses that emerged in China at Wuhan city, Hubei province during December 2019. Subsequently, SARS-CoV-2 has spread worldwide and caused millions of deaths around the globe. Several compounds and vaccines have been proposed to tackle this crisis. Novel recommended in silico approaches have been commonly used to screen for specific SARS-CoV-2 inhibitors of different types. Herein, the phytochemicals of Pakistani medicinal plants (especially Artemisia annua) were virtually screened to identify potential inhibitors of the SARS-CoV-2 main protease enzyme. The X-ray crystal structure of the main protease of SARS-CoV-2 with an N3 inhibitor was obtained from the protein data bank while A. annua phytochemicals were retrieved from different drug databases. The docking technique was carried out to assess the binding efficacy of the retrieved phytochemicals; the docking results revealed that several phytochemicals have potential to inhibit the SARS-CoV-2 main protease enzyme. Among the total docked compounds, the top-10 docked complexes were considered for further study and evaluated for their physiochemical and pharmacokinetic properties. The top-3 docked complexes with the best binding energies were as follows: the top-1 docked complex with a −7 kcal/mol binding energy score, the top-2 docked complex with a −6.9 kcal/mol binding energy score, and the top-3 docked complex with a −6.8 kcal/mol binding energy score. These complexes were subjected to a molecular dynamic simulation analysis for further validation to check the dynamic behavior of the selected top-complexes. During the whole simulation time, no major changes were observed in the docked complexes, which indicated complex stability. Additionally, the free binding energies for the selected docked complexes were also estimated via the MM-GB/PBSA approach, and the results revealed that the total delta energies of MMGBSA were −24.23 kcal/mol, −26.38 kcal/mol, and −25 kcal/mol for top-1, top-2, and top-3, respectively. MMPBSA calculated the delta total energy as −17.23 kcal/mol (top-1 complex), −24.75 kcal/mol (top-2 complex), and −24.86 kcal/mol (top-3 complex). This study explored in silico screened phytochemicals against the main protease of the SARS-CoV-2 virus; however, the findings require an experimentally based study to further validate the obtained results.
Wideband Versatile Receiver for CubeSat Microwave Front-Ends

One of the main features of CubeSats is represented by their extreme versatility, e.g., maintaining the same overall structure for different purposes. This requires high technological flexibility achievable in a cost-effective way while maintaining compact sizes. In this contribution, a microwave receiver specifically designed for CubeSat applications is proposed. Due to the wide input operating bandwidth, i.e., 2 GHz–18 GHz, it can be exploited for different purposes, e.g., satellite communication, radars, and electronic warfare systems. This is beneficial for CubeSat systems, whereby the possibility to share the same front-end circuit for different purposes is a key feature in reducing the overall size and weight. The downconverter was designed to minimize the spurious contributions at low frequency by taking advantage, at the same time, of commercial off-the-shelf components due to their cost-effectiveness. The idea behind this work is to add flexibility to the CubeSat communication systems in order to be reusable in different contexts. This feature enables new applications but also provides the largest bandwidth if required from the ground system. An accurate experimental characterization was performed to validate the downconverter performance with the aim of allowing easy system integration for the new frontier of CubeSat technologies. This paves the way for the most effective implementation of the Internet of Things (IoT), machine-to-machine (M2M) communications, and smart-everything services.
Effect of slope on lateral bearing capacity of nearshore large-diameter monopiles in cohesive soil

Abstract This study investigates the effect of slope on the lateral bearing capacity of nearshore large-diameter monopiles in cohesive soil by the finite element limit analysis (FELA) method. The reduction coefficient is introduced to quantify the capacity reduction due to the slope effect, and the critical distance making the slope-induced capacity reduction negligible is normalized for generalization. After the validations by cases of different soils, an alternative way to quickly and straightforwardly assess the pile bearing capacity in sloping stratum for the most frequently-encountered cases in engineering practice is provided by multiplying the reduction coefficients in several design tables with the capacity in level stratum. The subsequent parametric studies indicate that the reduction coefficient and critical dimensionless distance are mainly governed by the internal friction angle, slope angle, and pile embedded length-diameter ratio but are almost insensitive to dimensionless cohesion and slope height-pile embedded length ratio. In addition, the failure mode of the pile-slope system would develop from local failure to transitional failure and global failure with a significant drop in pile bearing capacity while the pile-slope parameters cannot guarantee slope stability.
Value distribution theory of $q$-differences in several complex variables

In this paper, $q$-difference analogues of several central results in value distribution theory of several complex variables are obtained. The main result is the $q$-difference second main theorem for hypersurfaces. In addition, $q$-difference versions of the logarithmic derivative lemma, the second main theorem for hyperplanes, Picard's theorem, and the Tumura-Clunie theorem, are included.
Fibrations of $\infty$-categories.

We construct a flagged $\infty$-category ${\sf Corr}$ of $\infty$-categories and bimodules among them. We prove that ${\sf Corr}$ classifies exponentiable fibrations. This representability of exponentiable fibrations extends that established by Lurie of both coCartesian fibrations and Cartesian fibrations, as they are classified by the $\infty$-category of $\infty$-categories and its opposite, respectively. We introduce the flagged $\infty$-subcategories ${\sf LCorr}$ and ${\sf RCorr}$ of ${\sf Corr}$, whose morphisms are those bimodules which are \emph{left final} and \emph{right initial}, respectively. We identify the notions of fibrations these flagged $\infty$-subcategories classify, and show that these $\infty$-categories carry universal left/right fibrations.
A decomposition for additive functional of Levy processes

Motivated by the recent results of Nualart and Xu \cite{Nualart} concerning limits laws for occupation times of one dimensional symmetric stable processes, this paper proves a decomposition for functionals of one dimensional symmetric L\'evy processes under certain conditions on the characteristic exponent and computes the moments of the decomposition.
Hyperspectral anomaly detection: a performance comparison of existing techniques

ABSTRACT Anomaly detection in Hyperspectral Imagery (HSI) has received considerable attention because of its potential application in several areas. Numerous anomaly detection algorithms for HSI have been proposed in the literature; however, due to the use of different datasets in previous studies, an extensive performance comparison of these algorithms is missing. In this paper, an overview of the current state of research in hyperspectral anomaly detection is presented by broadly dividing all the previously proposed algorithms into eight different categories. In addition, this paper presents the most comprehensive comparative analysis to-date in hyperspectral anomaly detection by evaluating 22 algorithms on 17 different publicly available datasets. Results indicate that attribute and edge-preserving filtering-based detection (AED), local summation anomaly detection based on collaborative representation and inverse distance weight (LSAD-CR-IDW) and local summation unsupervised nearest regularized subspace with an outlier removal anomaly detector (LSUNRSORAD) perform better as indicated by the mean and median values of area under the receiver operating characteristic (ROC) curves. Finally, this paper studies the effect of various dimensionality reduction techniques on anomaly detection. Results indicate that reducing the number of components to around 20 improves the performance; however, any further decrease deteriorates the performance.
An inverse problem for localization operators

A classical result of time–frequency analysis, obtained by Daubechies in 1988, states that the eigenfunctions of a time–frequency localization operator with circular localization domain and Gaussian analysis window are the Hermite functions. In this contribution, a converse of Daubechies’ theorem is proved. More precisely, it is shown that, for simply connected localization domains, if one of the eigenfunctions of a time–frequency localization operator with Gaussian window is a Hermite function, then its localization domain is a disc. The general problem of obtaining, from some knowledge of its eigenfunctions, information about the symbol of a time–frequency localization operator is denoted as the inverse problem, and the problem studied by Daubechies as the direct problem of time–frequency analysis. Here, we also solve the corresponding problem for wavelet localization, providing the inverse problem analogue of the direct problem studied by Daubechies and Paul.
Truncations in stellar disks

The presence of radial truncations in stellar disks is reviewed. There is ample evidence that many disk galaxies have relatively shaprt truncations in their disks. These often are symmetric and independent of the wavelength band of the observations. The ratio of the truncation radius R_{max} to the disk scalelength h appears often less then 4.5, as expected on a simple model for the disk collapse. Current samples of galaxies observed may however not be representative and heavily biased towards disks with the largest scalelengths. Many spiral galaxies also have HI warps and these generally start at the truncation radius of the stellar disk. The HI surface density suddenly becomes much flatter with radius. In some galaxies the start of the warp and the position of the disk truncation radius is accompanied by a drop in the rotation velocity. In the regiosn beyond the dis truncation in the HI layer some star formation does occur, but the heavy element abundance and the dust content are very low. All evidence is consistent with the notion that the outer gas parts of the disks constitute recently accreted material, at least accreted after formation of what is now the stellar thin disk. Although various models exist for the origin of the truncations in the stellar disks, this at present remains unclear.