Miracle-dz/UniFAR-FTUs huggingface dataset:
DYNAMICAL STUDY OF A PIECEWISE-SMOOTH MODEL IN TAPPING MODE ATOMIC FORCE MICROSCOPE

This paper deals with the dynamics of a piecewise-smooth model used to represents the Tapping Mode Atomic Force Microscope behavior. Created by Binning et al (1986), Atomic Force Microscopy became a powerful tool in scanning probe process. A micro-cantilever vibrates, excited by a piezo electric transducer and its vibration is detected by a photo detector. Working close from its resonance, the micro-cantilever has a nonlinear behavior, due to this, chaotic behavior may occur. Represented by a piecewise SDOF system, the dynamics of the model are investigate via numerical simulations and the study of figures like, phase portrait, FFT, time history and Lyapunov exponent show evidences of chaotic oscillations of micro-cantilever tips in dynamic atomic force microscopy (AFM). This irregular behavior appears in a defined interval of time. Palavras-Chave: Atomic force microscopy, chaos.
Comparing the Effects of Environmental Enrichment, Seasonality, and Soft Release on Site Retention and Survivorship of Captive-Reared Eastern Hellbenders (Cryptobranchus alleganiensis alleganiensis)

Abstract: Translocations of captive-reared animals are commonly used to stabilize declining wildlife populations. However, captive-reared animals are often raised in conditions dissimilar to their release sites and lacking natural characteristics, which could alter movement patterns and postrelease survivorship. These patterns can be further altered by season of release and soft-release conditions. We reared juvenile Eastern Hellbenders (Cryptobranchus alleganiensis alleganiensis) for 18 mo in captivity in one of two conditions: a control condition with low-velocity water flow (unconditioned) or a treatment condition with moving water (conditioned) that simulated natural flow velocities at their intended release site. We divided 4-yr-old Hellbenders (n = 118) into six treatment groups to determine the effects of release season (fall or summer), release type (standard soft release or enhanced soft release), and conditioning (unconditioned or conditioned) on the number of days until first movement, release site retention, and survival. In November 2017, we released 80 radio-tagged individuals (40 conditioned and 40 unconditioned) into soft-release structures in the Blue River, Indiana. In July 2018, we released another 38 radio-tagged individuals (18 conditioned and 20 unconditioned) into soft-release structures at the same site. After release, we tracked each individual one to three times weekly for 10 mo (fall release) or 12 mo (summer release). We found that treatment groups released into caged cobble beds (i.e., enhanced soft release) delayed their first movement and had higher release site retention relative to groups released under caged shelter rocks (i.e., standard soft release). We found that conditioning had a positive effect on survival but only in the treatment group released in the summer. By combining techniques and releasing conditioned individuals in the summer using enhanced soft releases, we increased annual survival of captive-reared Hellbenders from a probability of 0.50 (95% confidence interval [CI] = 0.31–0.79) to 0.74 (95% CI = 0.55–0.99). Our results provide important information about techniques that can be adopted across captive-rearing programs to help maximize the conservation success of Eastern Hellbenders.
Fast iterative solution of integral equation with matrix decomposition algorithm and multilevel simple sparse method

In order to efficiently solve large dense complex linear systems arising from the electric field integral equations formulation of electromagnetic problems, matrix decomposition algorithm–singular value decomposition (MDA–SVD) is used to accelerate the matrix–vector product (MVP) operation. Based on the symmetry of the impedance matrix, a modified multilevel simple sparse method (M-MLSSM) is proposed. Combining MDA and M-MLSSM, the authors obtain a sparse representation of the impedance matrix and construct a fast MVP operation. A perfectly electrically conducting sphere and the series-fed microstrip antenna array are simulated to demonstrate the validity of the proposed method. Moreover, numerical experiments demonstrate that combined MDA and M-MLSSM can accelerate the MVP operation and reduce memory requirements by at least half an order of magnitude compared to MDA–SVD.
Distortion effects in a switch array UWB radar for time-lapse imaging of human heartbeats

Cardiovascular diseases (CVD) are a major cause of deaths all over the world. Microwave radar can be an alternative sensor for heart diagnostics and monitoring in modern healthcare that aids early detection of CVD symptoms. In this paper measurements from a switch array radar system are presented. This UWB system operates below 3 GHz and does time-lapse imaging of the beating heart inside the human body. The array consists of eight fat dipole elements. With a switch system, every possible sequence of transmit/receive element pairs can be selected to build a radar image from the recordings. To make the radar waves penetrate the human tissue, the antenna array is placed in contact with the body. Removal of the direct signal leakage through the antennas and body surface are done by high-pass (HP) filtering of the data prior to image processing. To analyze the results, measurements of moving spheres in air and simulations are carried out. We see that removal of the direct signal introduces amplitude distortion in the images. In addition, the effect of small target motion between the collection times of data from the individual elements is analyzed. With low pulse repetition frequency (PRF) this motion will distort the image. By using data from real measurements of heart motion in simulations, we analyze how the PRF and the antenna geometry influence this distortions.
Working together when the problem is multi-faceted: understanding inter-agency working for the benefit of people with hoarding problems

Abstract Hoarding disorder is a surprisingly common problem which impacts on most areas of life. People who hoard typically have multiple agencies involved in their care due to the complex health and safety impact and risks associated with hoarding. ‘Treatment’ involves finding ways of supporting discarding large amounts, typically underpinned by CBT principles. We evaluated the impact and outcomes of a conference designed to boost professionals’ confidence and understanding in working with hoarding problems, both individually and with other agencies with a view to improving inter-agency service provision. Changes in professionals’ confidence and understanding were evaluated immediately before and after the conference. Conference participants’ qualitative responses related to service improvements were analysed using content analysis. People with personal experience of hoarding issues subsequently participated in a focus group where the results of the conference were presented. These data were analysed using thematic analysis. Confidence and understanding in working with hoarding problems substantially increased from pre- to post-conference. Professionals identified a range of possible improvements, most commonly working more closely and improving communication with other agencies. People with personal experience suggested improvements across three over-arching themes: developing an improved understanding of hoarding, the need for improved resources, and improved multi-agency working. A multi-agency conference increased confidence and understanding in professionals working with hoarding problems, and improvements specified by both people with personal experience and professionals provide a useful guide to service improvement. Results provide a framework in which CBT approaches should be embedded. Key learning aims (1) To assess the effectiveness of a multi-agency hoarding conference at improving understanding and confidence in working with hoarding problems. (2) To explore professionals’ perceptions of improvements to multi-agency service provision. (3) To explore perceptions of improvements that could be made to multi-agency service provision from people with personal experience of hoarding problems.
Two cases of MEGDHEL syndrome diagnosed with hyperammonemia

Abstract Objectives MEGDHEL [3-methylglutaconic aciduria (MEG), deafness (D), hepatopathy (H), encephalopathy (E), and Leigh-like disease (L)] syndrome is an autosomal recessive disorder caused by mutations in the serine active site-containing protein 1 (SERAC1) gene. MEGDHEL syndrome is clinically characterized by sensorineural hearing loss, encephalopathy, hepatopathy, 3-methylglutaconic aciduria, and Leigh-like lesions on cranial magnetic resonance imaging. During the neonatal period, it has been reported to present with hypoglycemia, hyperammonemia, impaired liver functions, cholestasis, metabolic acidosis, and sepsis-like clinical findings. However, clinical findings in the neonatal period were reported as a result of the retrospective evaluation of patients diagnosed at an older age. Herein we reported two cases diagnosed as MEGDHEL syndrome during neonatal period in two different clinics with sepsis-like findings, impaired liver functions, and ammonia levels high enough to require dialysis. Case presentation One of the cases was born 37 weeks of gestation with a birth weight of 2,060 g and initially presented with respiratory distress and feeding difficulties. The other case admitted to the neonatal intensive care unit had fed problems together with respiratory distress and circulatory failure within the first 24 h after initiation of parenteral nutrition. Conclusions MEGDHEL syndrome should be suspected in patients with sepsis-like clinical features and hyperammonemia.
Cross correlations of quantum key distribution based on single-photon sources

We theoretically analyze the second-order correlation function in a quantum key distribution system with real single-photon sources. Based on single-event photon statistics, the influence of the modification caused by an eavesdropper's intervention and the effects of background signals on the cross correlations between authorized partners are presented. On this basis, we have shown a secure range of correlation against the intercept–resend attacks.
Quantum Random Bit Generators

The importance of random number generators has increased over the years. This follows from the fact that contemporary research methods rely more and more on simulation and the increased importance of encryption technology. The output of a random number generator is created by either an algorithm or a physical device. The most popular method for random number generation is through the use of an algorithm. This article presents a new category of physical random bit generator that is packaged by several manufacturers. A statistical analysis of the output from the generators is given.
Inverse Born approximation for the nonlinear two-dimensional Schrödinger operator

This work deals with the inverse Born approximation for the nonlinear two-dimensional Schrödinger equation with cubic nonlinearity where the real-valued unknown functions q and α belong to with some behaviour at infinity. The following problem is studied: to estimate the smoothness of the terms from the Born sequence which corresponds to the scattering data with all arbitrary large energies and all angles in the scattering amplitude. These smoothness estimates allow us to conclude that the leading order singularities of the sum of unknown functions q and α can be obtained exactly by the Born approximation. Especially, we show for the functions in Lp, for certain values of p, that the approximation agrees with the true sum up to the functions from the Sobolev spaces. In particular, for the sum being the characteristic function of a smooth bounded domain this domain is uniquely determined by these scattering data.
Contributions of citizen scientists to monitoring alien species: the case study on Giant Asian Mantes, Hierodula tenuidentata and H. patellifera (Mantodea: Mantidae)

Many alien species directly affect humans by damaging agricultural crops and threatening the health of humans and domestic animals. Today, with the widespread use of social media, posts made by citizen scientists provide valuable data about alien species very quickly. This study reveals the importance of online databases for our knowledge on the spread of the Giant Asian Mantes Hierodula tenuidentata and H. patellifera. The data provided by citizen scientists through social media such as iNaturalist, Observation.org, and Alciphron (the latter only for Serbia) provide comprehensive baseline data for monitoring the distribution of these alien species. While 16% of the records of these species were obtained from the literature, 84% consisted of data from social media and personal observations. Our study supports the findings of previous studies stating that citizen scientists make important contributions in monitoring alien species and providing data for early prevention.
Ecological niche modeling uncovered that Holocene warming is responsible for disjoint distribution of Zamenis persicus (Werner, 1913) (Squamata: Colubridae)

Zamenis persicus (Werner, 1913) is near-endemic to the “South Caspian Circumscripation”, which is covered by Hyrcanian forests, a critical biodiversity hot spot in western Eurasia in terms of their origin and evolutionary history. The present study aims to evaluate the changes in the distribution of Zamenis persicus in the past, current, and future periods. For this purpose, 51 points of presence of species and eight climatic variables were analysed with Maxent software. We used four presence points outside the typical habitat of the species to test the presence of this species in the past in those areas. The most important variable affecting the distribution of the species is annual precipitation. The distribution of this species was more extensive in the past than today and included four test points, Miyaneh, Qom, Sabzevar, and Sarakhs. It seems that with the decline of Hyrcanian forests in the past, this species has shifted to higher latitudes. Predictions also forecasted a possible shrinkage of this species’ range. Climate change and habitat change can have a more severe effect on the remaining habitats of this species.
Shedding light on motor premanifest myotonic dystrophy type 1: A molecular, muscular and central nervous system follow‐up study

Myotonic dystrophy type 1 (DM1) is a hereditary and multisystemic disease that is characterized by heterogeneous manifestations. Although muscular impairment is central to DM1, a premanifest DM1 form has been proposed for those characterized by the absence of muscle signs in precursory phases. Nevertheless, subtle signs and/or symptoms related to other systems, such as the central nervous system (CNS), may emerge and progress gradually. This study aimed to validate the premanifest DM1 concept and to characterize and track affected individuals from a CNS centred perspective.
SWAMPy: Simulating SARS-CoV-2 Wastewater Amplicon Metagenomes with Python

Motivation Tracking SARS-CoV-2 variants through genomic sequencing has been an important part of the global response to the pandemic. As well as whole-genome sequencing of clinical samples, this surveillance effort has been aided by amplicon sequencing of wastewater samples, which proved effective in real case studies. Because of its relevance to public healthcare decisions, testing and benchmarking wastewater sequencing analysis methods is also crucial, which necessitates a simulator. Although metagenomic simulators exist, none are fit for the purpose of simulating the metagenomes produced through amplicon sequencing of wastewater. Results Our new simulation tool, SWAMPy (Simulating SARS-CoV-2 Wastewater Amplicon Metagenomes with Python), is intended to provide realistic simulated SARS-CoV-2 wastewater sequencing datasets with which other programs that rely on this type of data can be evaluated and improved. Availability The code for this project is available at https://github.com/goldman-gp-ebi/SWAMPy It can be installed on any Unix-based operating system and is available under the GPL-v3 license.
Cryo-EM map anisotropy can be attenuated by map post-processing and a new method for its estimation

One of the most important challenges in cryogenic electron microscopy (cryo-EM) is the substantial number of samples that exhibit preferred orientations, which leads to an uneven coverage of the projection sphere. As a result, the overall quality of the reconstructed maps can be severely affected, as manifested by the presence of anisotropy in the map resolution. Several methods have been proposed to measure the directional resolution of maps in tandem with experimental protocols to address the problem of preferential orientations in cryo-EM. Following these works, in this manuscript we identified one potential limitation that may affect most of the existing methods and we proposed an alternative approach to evaluate the presence of preferential orientations in cryo-EM reconstructions. In addition, we also showed that some of the most recently proposed cryo-EM map post-processing algorithms can attenuate map anisotropy, thus offering alternative visualization opportunities for cases affected by moderate levels of preferential orientations.
IIIandMe: An Algorithm for Chromosome-scale Haplotype Determination Using Genome-wide Variants of Three Haploid Reproductive Cells

Our recent algorithm, Hapi, infers chromosome-scale haplotypes using genomic data of a small number of single gametes. Its advanced version, IIIandMe, is proposed here to achieve comparable phasing accuracy with as few as three gametes, pushing the analysis to its limit. The new method is validated with simulation and a citrus gamete dataset. The rapid advances in genotyping technologies promise a broad application of IIIandMe in disclosing important genetic information.
Molecular Dynamics Simulation of Helium Cluster Formation in Ferrous-Chromium Alloy

Abstract Understanding helium transport and clustering is important for full understanding of fusion material degradation due to neutron irradiation. Molecular dynamics simulations are carried out to study the clustering of He in FeCr alloy. The simulations are performed for He fractions from 0.1 to 0.4 in FeCr alloy at temperatures ranging from 300 to 800 K. It is observed that a minimum of five He atoms is required to form a stable cluster at temperatures in the range 700 to 800 K. An He5-(Fe/Cr)2-V2 complex is found to exist at 300 K. At higher temperatures, the cluster displaces the Fe and Cr atoms from their lattice sites, forming an He5-V complex. The constituent element of the displaced material is then found to migrate inside the system, depending upon the conditions prevailing there.
Mechanisms for stability and welfare: increasing cooperation among self-interested agents (עם תקציר בעברית ושער נוסף: מנגנונים ליציבות ורווחה : הגברת שיתוף פעולה בין סוכנים אנוכיים.)

Too often an interaction among self-interested parties—be it human decision makers, firms, or automated agents—leads to an outcome that is not in the best interest of any of them. Examples include group decisions that are biased due to personal interests, collapse of public projects, congestion of roads and online networks, and so on. In this thesis I look at such interactions as games, so that the loss of stability and welfare can be measured and studied using the standard concepts of game theory (such as equilibrium and utility). I then study and design mechanisms that alter these games in order to induce more cooperation, stable outcomes, and higher utility for the participants—who are still assumed to each pursue their best personal interests. My research spans multiple domains, aiming for two primary goals. Part I of the thesis is about mechanisms that increase stability. This part covers subsidies in cooperative games, restricted cooperation with and without explicit social models, and iterative models of voting. New notions of individual and coalitional stability are introduced, in order to better understand the likely outcomes of studied interactions, and mechanisms are presented in order to achieve higher stability in corresponding games. Part II of the thesis is dedicated to welfare. I look for mechanisms that are truthful on the one hand (i.e. where all participants are better off reporting their true preferences), and approximately optimal on the other hand. I start with mechanisms for public facility location, supervised learning and other domains, showing the best approximation ratio of the optimal outcome (for society) that a truthful mechanism can achieve. Finally, several approximately optimal pricing mechanisms for parking allocation are presented, that are practical and simple to implement. In the closing chapter I discuss some of the global questions that arise throughout the work, and suggest some directions that could promote the design of mechanisms for stability and welfare.
On the control of the variable length pendulum

A new notion of differential flatness of infinite order is used to approximately regulate, along an off-line prescribed oscillatory trajectory, a mechanical system, which is nonlinear in the control input, it is not feedback linearizable by means of dynamical, or static, state feedback, and it is also non-minimum phase.
On the Complexity of Tree Edit Distance with Variables

In this paper, we propose tree edit distance with variables , which is an extension of the tree edit distance to handle trees with variables and has a potential application to measuring the similarity between mathematical formulas. We analyze the computational complexity of several variants of this model. In particular, we show that the problem is NP-complete for ordered trees. We also show for unordered trees that the problem of deciding whether or not the distance is 0 is graph isomorphism complete but can be solved in polynomial time if the maximum outdegree of input trees is bounded by a constant. We also present parameterized and exponential-time algorithms for ordered and unordered cases, respectively
Entropy Matters: Understanding Performance of Sparse Random Embeddings

This work shows how the performance of sparse random embeddings depends on the Renyi entropy-like property of data, improving upon recent works from NIPS’18 and NIPS’19. While the prior works relied on involved combinatorics, the novel approach is simpler and modular. As the building blocks, it develops the following probabilistic facts of general interest: (a) a comparison inequality between the linear and quadratic chaos (b) a comparison inequality between heterogenic and homogenic linear chaos (c) a simpler proof of Latala’s strong result on estimating distributions of IID sums (d) sharp bounds for binomial moments in all parameter regimes.
Efficient Sensitivity Analysis of Structures with Local Modifications. I: Time Domain Responses

AbstractThe time evolution of the parameter sensitivity of a nonlinear dynamical system is essential to its successful design, control, and identification. For an important class of systems, the governing equations of motion can be expressed as a linear system of ordinary differential equations augmented with a low-rank parameter-dependent (generally nonlinear) vector function. This paper builds on previous efforts by the authors to devise an approach for computing not only the responses of such systems but also the sensitivities of their responses to changes in design parameters in a computationally efficient manner. The proposed solution procedure first segregates the degrees of freedom appearing in the augmented functions from those that involve only linear deterministic operations. Second, the responses and sensitivities of the augmented terms are determined by solving the Volterra integral equations of reduced dimension. Finally, the responses and sensitivities of all remaining desired outputs are co.