Miracle-dz/UniFAR-FTUs huggingface dataset:
Different Color Union for Single Sensor Interpolation

This paper introduces a single sensor interpolation method for a different color assigned single sensor color camera. The presented method especially describes the performance among three different color combinations, such as RRGB, RGGB, and RGGB. The Bayer pattern has been widely used, and nowadays the research on X-Trans pattern is well studied. The proposed method substitutes the dominant color to the other color of two, and evaluates the performance. In any case, the three color potion is one of three, 2:1:1, 1:2:1, or 1:1:2. Simulation results display the MSE and PSNR results and the obtained images.
Uncovering Vulnerabilities in Smartphone Cryptography: A Timing Analysis of the Bouncy Castle RSA Implementation

Modern day smart phones are used for performing several sensitive operations, including online payments. Hence, the underlying cryptographic libraries are expected to adhere to proper security measures to ensure that there are no exploitable leakages. In particular, the implementations should be constant time to prevent subsequent timing based side channel analysis which can leak secret keys. Unfortunately, we unearth in this paper a glaring timing variation present in the Bouncy-Castle implementation of RSA like ciphers which is based on the BigIn-teger Java library to support large number theoretic computations. We follow up the investigation with a step-by-step procedure to exploit the timing variations to retrieve the complete secret of windowed RSA-2048 implementation. The entire analysis is possible with a single set of timing observation, implying that the timing observation can be done at the onset, followed by some post processing which does not need access to the phone. We have validated our analysis on Android Marshmallow 6.0, Nougat 7.0 and Oreo 8.0 versions. Interestingly, we note that for newer phones the timing measurement is more accurate leading to faster key retrievals.
Three-dimensional thinning algorithm using subfields

A three-dimensional parallel thinning algorithm is presented. This algorithm works in cubic grid with the 26-connectivity. It is based upon two topological numbers introduced elsewhere. These numbers allow us to check if a point is simple or not and to detect end points. The strategy which is used for removing points in parallel without altering the topology of the image is a strategy based upon subfields: the cubic grid is divided into 8 subfields which are successively activated. The use of 4 subfields is also considered. One major interest of the subfield approach is that it is `complete,' i.e., all simple points which are not considered as skeletal points are removed. The proposed algorithm allows us to get a curve skeleton, a surface skeleton as well as a topological kernel of the objects. Furthermore it is possible to implement it by using only Boolean conditions.
Generalized diffraction enhanced imaging to retrieve absorption, refraction and scattering effects

A simple algorithm that generalizes the diffraction enhanced imaging (DEI) technique is introduced and discussed by means of simulated and experimental data. While the original DEI algorithm by Chapman et al (1997 Phys. Med. Biol. 42 2015) is limited to objects featuring absorption and refraction only, also ultra-small-angle scattering is considered here. Utilizing only three images in input three parametric images are produced conveying information relative to the three effects. The quality of the parametric images depends on the choice of the input images, as is demonstrated by means of a Monte Carlo simulation. With an appropriate choice, the algorithm gives accurate results on simulated and experimental datasets, as long as the refraction and scattering angles introduced by the object are small compared with the width of the rocking curve. The proposed algorithm can be implemented in several applications, as a valid alternative to multiple-image methods, particularly when time and dose constraints are relevant.
Transient Te Scattering From a Cylinder Above an Infinite Periodic Surface Using a Decomposition Method

A cylindrical target above a periodic surface is illuminated by a short-pulse electromagnetic wave to study the effect of multipath on radar measurements of targets above the sea. A decomposition method is outlined for TE scattering from a cylinder above an infinite, periodic surface. The basis of this method is that if a target is close to the sea, the current induced on the sea surface will be nearly identical to that induced by a plane wave without the target present, except within a region of finite extent immediately beneath the target. A set of coupled Electric-Field Integral Equations (EFIEs) for the current induced on the cylinder and the perturbation current (the difference between the current with the target present and with the target absent) on the surface has been derived in which the perturbation current is approximated to zero outside a finite region beneath the cylinder. The EFIEs are solved in the frequency domain using the Method of Moments and transformed into the time domain using the inverse Fourier transform. Use of this technique for studying the transient multipath phenomenon of a target located near a disturbed surface is discussed.
Phylogenomic analysis of the Lake Kronotskoe species flock of Dolly Varden charr reveals genetic signatures of sympatric radiation

Recent adaptive radiations provide evolutionary case studies which can be parsed to reveal the relationship between genomic variation and the origins of distinct phenotypes. Sympatric radiations of the charr complex (genus Salvelinus) present a trove for comparative genomics as charrs have repeatedly diversified into multiple morphs with distinct feeding specializations. However, stereotypical species flocks are assemblages of only two to three lineages. However, a species flock of Dolly Varden charr (Salvelinus malma) in Lake Kronotskoe contains at least seven lineages, each with defining morphological and ecological traits. This is the most extensive radiation described for the genus. Here, we perform the first genome-wide analysis of this species flock to parse the genetic foundations of adaptive change. Our data support distinct, reproductively isolated lineages with little hybridization. We also find that specific selection on thyroid and craniofacial genes forms a shared basis for the radiation. The data also implicate thyroid signaling in subsequent lineage specification. These results delineate a clear genetic basis for the diversification of specialized lineages, and highlight the role of developmental mechanisms in shaping the forms generated during adaptive radiation.
AN ACCURATE IMAGING ALGORITHM FOR MILLIMETER WAVE SYNTHETIC APERTURE IMAGING RADIOMETER IN NEAR-FIELD

Due to the fact that the imaging distance is similar to the dimension of synthetic aperture antenna in near-fleld, the Fourier imaging theory used in the traditional synthetic aperture imaging radiometer (SAIR), which is based on the far-fleld approximation, is invalid for near-fleld synthetic aperture imaging. This paper is devoted to establishing an accurate imaging algorithm for near- fleld millimeter wave SAIR. Firstly, the near-fleld synthetic aperture imaging theory is deduced and its relationship to the far-fleld imaging theory analyzed. Then, an accurate imaging algorithm based on the near-fleld imaging theory is established. In this method, the quadratic phase item and antenna pattern are taken into consideration, and the image reconstruction is performed by minimizing the Total- Variation norm of brightness temperature image, which reduces the in∞uence of the visibility observation error and improves imaging precision. Finally, the efiectiveness of the proposed imaging algorithm has been tested by means of several simulation experiments, and the superiority is also demonstrated by the comparison between it and the existing Fourier transform methods. The results demonstrate that the proposed method is an e-cient, feasible imaging algorithm for near- fleld millimeter wave SAIR.
Lynx: Family of Lightweight Authenticated Encryption Schemes based on Tweakable Blockcipher

The widespread deployment of low-power and handheld devices opens an opportunity to design lightweight authenticated encryption schemes. The schemes so proposed must also prove their resilience under various security notions. Romulus -N1 is an authenticated encryption scheme with associated data based on a tweakable blockcipher, a primary variant of Romulus -N family which is NIST (National Institute of Standards and Technology) lightweight cryptography competition finalist; provides beyond birthday bound security for integrity security in nonce respecting scenario but fails to provide the integrity security in nonce misuse and RUP (release of unverified plaintext) scenarios. In this paper, we propose lynx , a family with 14 members of 1-pass and rate-1 lightweight authenticated encryption schemes with associated data based on a tweakable blockcipher, that provides birthday bound security for integrity security in both nonce respecting as well as nonce misuse and RUP scenarios and birthday bound security for privacy in nonce respecting scenario. For creating such a family of schemes we propose a family of function F that provides a total of 72 cases out of which we show that only 14 of them can be used for creating authenticated encryption schemes. We provide the implementation of one of the members of lynx family on six different hardware platforms and compare it with Romulus-N1 . The comparison clearly shows that the lynx member outperforms Romulus-N1 on all the six platforms.
The Kinase Module of the Mediator regulates cell cycle re-entry and transcriptional response following DNA damage

When faced with a DNA double strand break, cells activate an elaborate signaling cascade called the DNA damage response to protect genomic integrity. To identify novel factors that modulate the DNA damage response to DNA double strand breaks, we performed an epistatic miniarray profile (E-MAP) analysis of Mec1 and Rad53, two essential kinases that coordinate the DNA damage response in budding yeast. Through this analysis, we discovered a genetic interaction between the kinase module (CKM) of the Mediator of transcription and Rad53. We find that all four subunits of the CKM, as well as CKM’s kinase activity are critical for cell cycle re-entry following a DNA break, whereas the core Mediator subunits are dispensable. Notably, CKM mutants do not impair DNA repair by homologous recombination or confer sensitivity to DNA damaging reagents, suggesting that CKM specifically impinges on DNA damage signaling. In support of this, we find that Rad53 and CKM physically interact in response to DNA damage. Following the induction of a DNA break, CKM is a critical regulator of global transcription inhibition. In addition to this global effect, we illustrate that CKM functions locally at DNA breaks together with the core Mediator. In the absence of catalytically active CKM, the CKM-Mediator complexes at DNA breaks are replaced by RNAPII. Taken together, our results reveal a previously uncharacterized role for CKM in the DNA damage response.
Heat stress response and transposon control in plant shoot stem cells

Post-embryonic plant development must be coordinated in response to and with environmental feedback. Development of above-ground organs is orchestrated from stem cells in the center of the shoot apical meristem (SAM). Heat can pose significant stress to plants and induces a rapid heat response, developmental alterations, chromatin decondensation, and activation of transposable elements (TEs). However, most plant heat-stress studies are conducted with whole plants, not resolving cell-type-specific responses. Heat stress consequences in stem cells are of particular significance, as they can potentially influence the next generation. Here we use fluorescent-activated nuclear sorting to isolate and characterize stem cells after heat exposure and after a recovery period in wild type and mutants defective in TE defense and chromatin compaction. Our results indicate that stem cells can suppress the heat response pathways that dominate surrounding somatic cells and maintain their developmental program. Furthermore, mutants defective in DNA methylation recover less efficiently from heat stress and persistently activate heat response factors and heat-inducible TEs. Heat stress also induces epimutations at the level of DNA methylation, and we find hundreds of DNA methylation changes three weeks after stress. Our results underline the importance of disentangling cell type-specific environmental responses for understanding plant development.
Immediate targeting of host ribosomes by jumbo phage encoded proteins

Bacteriophages must seize control of the host gene expression machinery to promote their own protein synthesis. Since the bacterial hosts are armed with numerous anti-phage defence systems, it is essential that mechanisms of host take-over act immediately upon infection. Although individual proteins that modulate components of the bacterial gene expression apparatus have been described in several different phages, systematic approaches which capture the phage’s arsenal for immediate targeting of host transcription and translation processes have been lacking. In particular, there are no known phage factors that associate directly with host ribosomes to modulate protein synthesis. Here, we take an integrative high-throughput approach to uncover numerous new proteins encoded by the jumbo phage ΦKZ that target the gene expression machinery of the Gram-negative human pathogen Pseudomonas aeruginosa immediately upon infection. By integrating biochemical and structural analyses, we identify a conserved phage factor that associates with the large ribosomal subunit by binding the 5S ribosomal RNA. This highly abundant factor is amongst the earliest ΦKZ proteins expressed after infection and stays bound to ribosomes during the entire translation cycle. Our study provides a general strategy to decipher molecular components of phage-mediated host take-over and argues that phage genomes represent a large discovery space for proteins that modulate the host gene expression machinery.
MeCP2 Represses the Activity of Topoisomerase IIβ in Long Neuronal Genes

A unique signature of neuronal transcriptomes is the high expression of the longest genes in the genome (e.g. >100 kilobases). These genes encode proteins with essential functions in neuronal physiology, and disruption of long gene expression has been implicated in neurological disorders. DNA topoisomerases resolve topological constraints that arise on DNA and facilitate the expression of long genes in neurons. Conversely, methyl-CpG binding protein 2 (MeCP2), which is disrupted in Rett syndrome, can act as a transcriptional repressor to downregulate the expression of long genes. The molecular mechanisms underlying the regulation of long genes by these factors are not fully understood, however, and whether or not they directly influence each other is not known. Here, we identify a functional interaction between MeCP2 and Topoisomerase II-beta (TOP2β) in neurons. We show that MeCP2 and TOP2β physically interact in vivo and map protein sequences sufficient for their physical interaction in vitro. We profile TOP2β activity genome-wide in neurons and detect enrichment at regulatory regions and gene bodies of long neuronal genes, including long genes regulated by MeCP2. Further, we find that knockdown and overexpression of MeCP2 leads to altered TOP2β activity at MeCP2-regulated genes. Our findings uncover a mechanism by which MeCP2 inhibits the activity of TOP2β at long genes in neurons and suggest that this mechanism is disrupted in neurodevelopment disorders caused by mutation of MeCP2.
Clonal phylogenies inferred from bulk, single cell, and spatial transcriptomic analysis of cancer

Epithelial cancers are typically heterogeneous with primary prostate cancer being a typical example of histological and genomic variation. Prostate cancer is the second most common male cancer in western industrialized countries. Prior studies of primary prostate cancer tumor genetics revealed extensive inter and intra-patient tumor heterogeneity. Recent advances have enabled extensive single-cell and spatial transcriptomic profiling of tissue specimens. The ability to resolve accurate prostate cancer tumor phylogenies at high spatial resolution would provide tools to address questions in tumorigenesis, disease progression, and metastasis. Recent advances in machine learning have enabled the inference of ground-truth genomic single-nucleotide and copy number variant status from transcript data. The inferred SNV and CNV states can be used to resolve clonal phylogenies, however, it is still unknown how faithfully transcript-based tumor phylogenies reconstruct ground truth DNA-based tumor phylogenies. We sought to study the accuracy of inferred-transcript to recapitulate DNA-based tumor phylogenies. We first performed in-silico comparisons of inferred and directly resolved SNV and CNV status, from single cancer cells, from three different cell lines. We found that inferred SNV phylogenies accurately recapitulate DNA phylogenies (entanglement = 0.097). We observed similar results in iCNV and CNV based phylogenies (entanglement = 0.11). Analysis of published prostate cancer DNA phylogenies and inferred CNV, SNV and transcript based phylogenies demonstrated phylogenetic concordance. Finally, a comparison of pseudo-bulked spatial transcriptomic data to adjacent sections with WGS data also demonstrated recapitulation of ground truth (entanglement = 0.35). These results suggest that transcript-based inferred phylogenies recapitulate conventional genomic phylogenies. Further work will need to be done to increase accuracy, genomic, and spatial resolution.
Can CA describe collective effects of polluting agents

Pollution represents one of the most relevant issues of our time. Several studies are on stage but, generally, they do not consider competitive effects, paying attention only to specific agents and their impact. In this paper, it is suggested a different scheme. At first, it is proposed a formal model of competitive noxious effects. Second, by generalizing a previous algorithm capable of describing urban growth, it is developed a cellular automata (CA) model that provides the effective impact of a variety of pollutants. The final achievement is a simulation tool that can model pollution combined effects and their dynamical evolution in relation to anthropized environments.
Inverse problem for biomedical applications: use of prior information on target and forward model parameters

We propose the use of a retrieval operator for biomedical applications in near-infrared spectroscopy. The proposed retrieval operator is based on the "Optimal Estimation" method. The main characteristic of this method relates to the possibility to include prior information both on target and on forward model parameters of the inversion procedure. The possibility of the retrieval operator to elaborate a-priori information can in principle be a benefit for the whole retrieval procedure. This means that a larger number of target parameters can be retrieved, or that a better accuracy can be achieved in retrieving the target parameters. The final goal of this inversion procedure is to have an improved estimate of the target parameters. The procedure has been tested on time-resolved simulated experiments obtained with a Monte Carlo code. The results obtained show that an improved performance of the inversion procedure is achieved when prior information on target and forward model parameters is available. With the use of a priori information on target parameters we have in average a lower difference between the retrieved values of the parameters and their true values, and the error bars determined by the inversion procedure on the retrieved parameters are significantly lower. At the same time a good estimate of the errors on the forward model parameters can significantly improve the retrieval of the target parameters.
A Wideband Circularly Polarized Candy-Like Patch Antenna

The paper demonstrates a new means to achieve a broad impedance bandwidth and circularly polarized bandwidth with a suspended candy-like antenna and a T-shaped feeding probe. By incorporating a long probe inside a high substantial cavity (∼ 0.16λ), a circularly polarized (CP) antenna in broadside direction is achieved. The horizontal arm of the probe is implemented by means of a printed monopole that is diagonally coupled to a small candy-like copper plate. The CP antenna features a wide operating bandwidth of 15.2% ranging from 1.47 Hz to 1.71 GHz (VSWR < 2 and axial ratio < 3 dB). The maximum gain of this antenna is recorded as no less than 7.2 dBic across the bandwidth. The dimension of the candy-like patch is 0. 3λ × 0. 3λ, whereas the ground plane size is 1. 8λ × 1. 8λ. The measured results are presented.
Lines in Random Effects Plots from the Linear Mixed-Effects Model

Abstract After fitting a linear mixed-effects model to a set of repeated-measures or longitudinal data, it is common practice to plot the estimated random effects. On occasion it may be observed that in these plots a straight line may appear. How did this line arise? What influence does it have on the interpretation of the results from the model? This article demonstrates an artifact that can occur in the plots of random effects. If a cluster has exactly one observation, the plot of any estimated random effect against any other estimated random effect will fall on a straight line. The line in the plot of a pair of estimated random effects may even lie in the opposite direction of the direction suggested by the correlation from the random effects covariance matrix. For clusters with two observations at the same design points of the variables for the random effects, the estimated random effects will lie on a plane. Using an example, we demonstrate the patterns in the plots of the estimated random effects. This illustrates that care must be taken when using plots of the estimated random effects.
Obfuscating Decision Trees

We construct a new encoder for hiding parameters in an interval membership function. As an interesting application, we design a simple and efficient virtual black-box obfuscator for evasive decision tree classifiers. The security of our construction relies upon random oracle paradigm. Our exclusive goal behind designing the obfuscator is that, not only will the solution increase the class of functions that has cryp-tographically secure obfuscators, but also address the open problem of non-interactive prediction in privacy-preserving classification using computationally
A model for OH masers in star-forming regions

A new model of the OH maser environment in star-forming regions is described in detail and the predictions of the model are compared with observational data. After reviewing the status of OH maser observations, the ingredients which such a model requires are outlined. Among these we highlight rate coefficients for energy transfer, the nature of the FIR dust radiation field and the treatment of line and continuum radiation transport in the presence of FIR line overlap where the latter is based on a new theoretical description