Miracle-dz/UniFAR-FTUs huggingface dataset:
Computational nanoplasmonics for biosensing applications using PyGBe-LSPR

This work uses the long-wavelength limit to compute LSPR response of biosensors, expanding the open-source PyGBe code to compute the extinction cross-section of metallic nanoparticles in the presence of any target for sensing. The target molecule is represented by a surface mesh, based on its crystal structure. PyGBe is research software for continuum electrostatics, written in Python with computationally expensive parts accelerated on GPU hardware, via PyCUDA. It is also accelerated algorithmically via a treecode that offers O(N log N) computational complexity. These features allow PyGBe to handle problems with half a million boundary elements or more. Using a model problem consisting of an isolated silver nanosphere in an electric field, our results show grid convergence as 1/N, and accurate computation of the extinction cross-section as a function of wavelength (compared with an analytical solution). For a model of a sensor-analyte system, consisting of a spherical silver nanoparticle and a set of bovine serum albumin (BSA) proteins, our results again obtain grid convergence as 1/N (with respect to the Richardson extrapolated value). Computing the LSPR response as a function of wavelength in the presence of BSA proteins captures a red-shift of 0.5 nm in the resonance frequency due to the presence of the analytes at 1-nm distance. The final result is a sensitivity study of the biosensor model, obtaining the shift in resonance frequency for various distances between the proteins and the nanoparticle. All results in this paper are fully reproducible, and we have deposited in archival data repositories all the materials needed to run the computations again and re-create the figures. PyGBe is open source under a permissive license and openly developed. Documentation is available at http://barbagroup.github. io/pygbe/docs/.
THE HIDDEN MAGNETIC FIELD OF THE YOUNG NEUTRON STAR IN KESTEVEN 79

Recent observations of the central compact object in the Kesteven 79 supernova remnant show that this neutron star (NS) has a weak dipole magnetic field (a few × 1010 G) but an anomalously large (∼64%) pulse fraction in its surface X-ray emission. We explore the idea that a substantial sub-surface magnetic field exists in the NS crust, which produces diffuse hot spots on the stellar surface due to anisotropic heat conduction, and gives rise to the observed X-ray pulsation. We develop a general-purpose method, termed “Temperature Template with Full Transport” (TTFT), that computes the synthetic pulse profile of surface X-ray emission from NSs with arbitrary magnetic field and surface temperature distributions, taking into account magnetic atmosphere opacities, beam pattern, vacuum polarization, and gravitational light bending. We show that a crustal toroidal magnetic field of order a few × 1014 G or higher, varying smoothly across the crust, can produce sufficiently distinct surface hot spots to generate the observed pulse fraction in the Kes 79 NS. This result suggests that substantial sub-surface magnetic fields, much stronger than the “visible” dipole fields, may be buried in the crusts of some young NSs, and such hidden magnetic fields can play an important role in their observational manifestations. The general TTFT tool we have developed can also be used for studying radiation from other magnetic NSs.
On the local variation of the Hubble constant

We have carefully studied how local measurements of the Hubble constant, H0, can be influenced by a variety of different parameters related to survey depth, size, and fraction of the sky observed, as well as observer position in space. Our study is based on N-body simulations of structure in the standard ΛCDM model and our conclusion is that the expected variance in measurements of H0 is far too small to explain the current discrepancy between the low value of H0 inferred from measurements of the cosmic microwave background (CMB) by the Planck collaboration and the value measured directly in the local universe by use of Type Ia supernovae. This conclusion is very robust and does not change with different assumptions about effective sky coverage and depth of the survey or observer position in space.
Evidence of Environmental Quenching at Redshift z ≈ 2

We report evidence of environmental quenching among galaxies at redshifts of ≈2, namely the probability that a galaxy quenches its star formation activity is enhanced in the regions of space in proximity of other quenched, more massive galaxies. The effect is observed as strong clustering of quiescent galaxies around quiescent galaxies on angular scales of θ ≤ 20 arcsec, corresponding to a proper (comoving) scale of 168 (502) kpc at z = 2. The effect is observed only for quiescent galaxies around other quiescent galaxies; the probability to find star-forming galaxies around quiescent or around star-forming ones is consistent with the clustering strength of galaxies of the same mass and at the same redshift, as observed in dedicated studies of galaxy clustering. The effect is mass dependent in the sense that the quenching probability is stronger for galaxies of smaller masses (M* < 1010M☉) than for more massive ones, i.e., it follows the opposite trend with mass relative to gravitational galaxy clustering. The spatial scale where the effect is observed suggests that these environments are massive halos, in which case the observed effect would likely be satellite quenching. The effect is also redshift dependent in that the clustering strength of quiescent galaxies around other quiescent galaxies at z ¯ = 1.6 is ≈1.7× larger than that of the galaxies with the same stellar mass at z ¯ = 2.6 . This redshift dependence allows for a crude estimate of the timescale of environmental quenching of low-mass galaxies, which is in the range of 1.5 ∼ 4 Gyr, in broad agreement with other estimates and with our ideas on satellite quenching.
Behavior of Signal Harmonics in Magnetic Particle Imaging Based on a Lock-in-Amplifier Model

We previously presented a lock-in-amplifier model for analyzing the behavior of signal harmonics in magnetic particle imaging (MPI). In that study, the magnetization and particle size distribution of magnetic nanoparticles (MNPs) were assumed to obey the Langevin theory of paramagnetism and a log-normal distribution, respectively, and a drive magnetic field was assumed to be applied parallel to a selection magnetic field. The purpose of the current study was to investigate the behavior of signal harmonics in MPI with the drive magnetic field being applied to the selection magnetic field in an arbitrary direction using the lock-in-amplifier model. In the lock-in-amplifier model, the signal induced by MNPs in a receiving coil was multiplied with a reference signal, and was then fed through a low-pass filter to extract the DC component of the filtered signal (MPI signal). The strength of the selection magnetic field in MPI was assumed to be given by the product of the gradient strength of the selection magnetic field and the distance from the field-free region (x). The relationships between the MPI signal and x were calculated for odd- and even-numbered harmonics and were investigated for various angles between the axis of a receiving coil and the selection magnetic field. The behavior of signal harmonics in MPI largely depended on the angle between them. This study will be useful for improved understanding, optimization, and development of MPI.
Molecular cloud evolution – IV. Magnetic fields, ambipolar diffusion and the star formation efficiency

We investigate the formation and evolution of giant molecular clouds (GMCs) by the collision of convergent warm neutral medium (WNM) streams in the interstellar medium, in the presence of magnetic fields and ambipolar diffusion (AD), focusing on the evolution of the star formation rate (SFR) and efficiency (SFE), as well as of the mass-to-magnetic-flux ratio (M2FR) in the forming clouds. We find that: 1) Clouds formed by supercritical inflow streams proceed directly to collapse, while clouds formed by subcritical streams first contract and then re-expand, oscillating on the scale of tens of Myr. 2) Our suite of simulations with initial magnetic field strength of 2, 3, and 4�G show that only supercritical or marginal critical streams lead to reasonable star forming rates. This result is not altered by the inclusion of ambipolar diffusion. 3) The GMC’s M2FR is a generally increasing function of time, whose growth rate depends on the details of how mass is added to the GMC from the WNM. 4) The M2FR is a highly fluctuating function of position in the clouds. This implies that a significant fraction of a cloud’s mass may remain magnetically supported, while SF occurs in the supercritical regions that are not supported. 5) In our simulations, the SFE approaches stationarity, because mass is added to the GMC at a similar rate at which it converts mass to stars. In such an approximately stationary regime, we find that the SFE provides a proxy of the supercritical mass fraction in the cloud. 6) We observe the occurrence of buoyancy of the low-M2FR regions within the gravitationally-contracting GMCs, so that the latter naturally segregate into a high-density, high-M2FR “core” and a low-density, low-M2FR “envelope”, without the intervention of AD.
Sensitive imaging of electromagnetic fields with paramagnetic polar molecules

We propose a method for sensitive parallel detection of low-frequency electromagnetic fields based on the fine structure interactions in paramagnetic polar molecules. Compared to the recently implemented scheme employing ultracold $^{87}$Rb atoms [B{\"o}hi \textit{et al.}, Appl. Phys. Lett. \textbf{97}, 051101 (2010)], the technique based on molecules offers a 100-fold higher sensitivity, the possibility to measure both the electric and magnetic field components, and a probe of a wide range of frequencies from the dc limit to the THz regime.
FRB 121102: A Starquake-induced Repeater?

Since its initial discovery, the fast radio burst (FRB) FRB 121102 has been found to be repeating with millisecond-duration pulses. Very recently, 14 new bursts were detected by the Green Bank Telescope during its continuous monitoring observations. In this paper, we show that the burst energy distribution has a power-law form which is very similar to the Gutenberg–Richter law of earthquakes. In addition, the distribution of burst waiting time can be described as a Poissonian or Gaussian distribution, which is consistent with earthquakes, while the aftershock sequence exhibits some local correlations. These findings suggest that the repeating FRB pulses may originate from the starquakes of a pulsar. Noting that the soft gamma-ray repeaters (SGRs) also exhibit such distributions, the FRB could be powered by some starquake mechanisms associated with the SGRs, including the crustal activity of a magnetar or solidification-induced stress of a newborn strangeon star. These conjectures could be tested with more repeating samples.
Bose-Einstein condensate as a quantum memory for a photonic polarization qubit

A scheme based on electromagnetically induced transparency is used to store light in a Bose-Einstein condensate. In this process, a photonic polarization qubit is stored in atomic Zeeman states. The performance of the storage process is characterized and optimized. The average process fidelity is 1.000 +/- 0.004. For long storage times, temporal fluctuations of the magnetic field reduce this value, yielding a lifetime of the fidelity of 1.1 +/- 0.2 ms. The write-read efficiency of the pulse energy can reach 0.53 +/- 0.05.
Cross-sectional study and Building a Geographical Information System for Brucellosis in Monufiya

Background/ Aim : Brucellosis is a communicable disease with highly significance in human and veterinary practices as well as responsible forsubstantial economic losses in cattle. This study aimed to detect the incidence of brucellosis for three successive years from 2016–2018 in Monufiya governorate using Rose Bengal test. In addition to apply the Geographic Information System (GIS) 10.1 to investigate the patterns of the disease and to identify high-risk areas of the disease . Methods: A total of 75,697 animals (43,274 cattle, 19,974 buffaloes, 8,684 sheep, and 3,765 goats) were tested by RBPT and the obtained data were subjected to the Geographic Information System (GIS) 10.1 to investigate the patterns of the disease over the period from 2016-2018 and to identify high-risk areas of the disease. Results: The reported results indicated that the highest incidence rate of brucellosis in Ashmoun center 3% other than in other cities in cattle and buffaloes. In the other side, the incidence rates in both sheep and goats varied widely between cities and even in the same city within the three years. Conclusion: The animal's movement represent a major source of infection dissemination in Monufiya governorate. Strict measures and preventive strategies must be regulating to prevent the dissemination of brucellosis in Monufiya, especially in moveable flocks.
Semileptonic decays of $\Lambda_b$ baryons in the relativistic quark model

Semileptonic Λb decays are investigated in the framework of the relativistic quark model based on the quasipotential approach and the quark-diquark picture of baryons. The decay form factors are expressed through the overlap integrals of the initial and final baryon wave functions. All calculations are done without employing nonrelativistic and heavy quark expansions. The momentum transfer dependence of the decay form factors is explicitly determined in the whole accessible kinematical range without any extrapolations or model assumptions. Both the heavy-to-heavy Λb→Λclνl and heavy-to-light Λb→plνl decay branching fractions are calculated. The results agree within error bars with the experimental value of the branching fraction of the Λb→Λc+l-ν¯l decay. From the recent LHCb data on the ratio of the branching fractions of the heavy-to-light and heavy-to-heavy semileptonic Λb decays the ratio of the Cabibbo-Kobayashi-Maskawa matrix elements |Vub|/|Vcb| is obtained. It is consistent with the corresponding ratio determined from the inclusive B meson decays.
The discovery of the 401 Hz accreting millisecond pulsar IGR J17498-2921 in a 3.8 h orbit

We report on the detection of a 400.99018734(1) Hz coherent signal in the Rossi X-ray Timing Explorer (RXTE) light curves of the recently discovered X-ray transient, IGR J17498−2921. By analysing the frequency modulation caused by the orbital motion observed between August 13 and September 8, 2011, we derive an orbital solution for the binary system with a period of 3.8432275(3) h. The measured mass function, f (M2, M1,i) = 0.00203807(8) M� , allows to set a lower limit of 0.17 Mon the mass of the companion star, while an upper limit of 0.48 Mis set by imposing that the companion star does not overfill its Roche lobe. We observe a marginally significant evolution of the signal frequency at an average rate of −(6.3 ± 1.9) × 10 −14 Hz s −1 . The low statistical significance of this measurement and the possible presence of timing noise hampers a firm detection of any evolution of the neutron star spin. We also present an analysis of the spectral properties of IGR J17498−2921 based on the observations performed by the Swift-X-ray Telescope and the RXTE-Proportional Counter Array between August 12 and September 22, 2011. During most of the outburst, the spectra are modeled by a power-law with an index Γ ≈ 1.7−2, while values of ≈3 are observed as the source fades into quiescence.
GAME: GAlaxy Machine learning for Emission lines

We present an updated, optimized version of GAME (GAlaxy Machine learning for Emission lines), a code designed to infer key interstellar medium physical properties from emission line intensities of UV/optical/far infrared galaxy spectra. The improvements concern: (a) an enlarged spectral library including Pop III stars; (b) the inclusion of spectral noise in the training procedure, and (c) an accurate evaluation of uncertainties. We extensively validate the optimized code and compare its performance against empirical methods and other available emission line codes (PYQZ and HII-CHI-MISTRY) on a sample of 62 SDSS stacked galaxy spectra and 75 observed HII regions. Very good agreement is found for metallicity. However, ionization parameters derived by GAME tend to be higher. We show that this is due to the use of too limited libraries in the other codes. The main advantages of GAME are the simultaneous use of all the measured spectral lines, and the extremely short computational times. We finally discuss the code potential and limitations.
AOS: Anti-Obesity System With Deep Learning-based Classification Model Using a Novel Data Augmentation Technique

Obesity has been a worldwide leading cause of associated health risks for decades, yet not much is being done to solve this issue. Previously, minimal efforts have been made to address this issue in regards to mandating nutrition labels on the back of packaged foods. However, the mundane and growingly elusive packing labels have diminished the proper effects of this constitution as people rarely ever take the time nor effort to thoroughly read through the labels. Moreover, most dishes served from restaurants do not serve with any nutritional information, which places many of the people dining out in complete darkness of what they are truly consuming. To solve this problem, we propose the deep learning-based AOS (Anti-Obesity System), which analyzes images of common junk foods and unhealthy meals to classify the category of food. The proposed system consists of a deep learning-based classifier and a post-processing module that outputs relevant nutritional information regarding each category of food. In addition, we propose a novel data augmentation technique in order to make the trained model produce better results. We also conduct the ablation study to experimentally prove that the proposed method enforces the model to work better in real-world situations. We achieve an AP of 59.30% on the proposed food dataset. Code will be available at https://github.com/smkim0508/ObesityNutritionClassifier.git.
Atomic states in optical traps near a planar surface

In this paper, we discuss the atomic states in a vertical optical lattice in proximity of a surface. We study the modifications to the ordinary Wannier-Stark states in the presence of a surface, and we characterize the energy shifts produced by the Casimir-Polder interaction between atom and mirror. In this context, we introduce an effective model describing the finite size of the atom in order to regularize the energy corrections. In addition, the modifications to the energy levels due to a hypothetical non-Newtonian gravitational potential as well as their experimental observability are investigated.
Significant Shifts in Microbial Communities Associated with Scleractinian Corals in Response to Algae Overgrowth

Microbes play a key role in reef dynamics, mediating the competition between scleractinian corals and benthic algae; however, major shifts in bacterial communities among coral species in response to increases in the abundance of algae are not well understood. We investigated the taxonomic composition of coral-associated microbial communities under algae-overgrowth conditions using 16S rRNA gene sequencing. The results showed that non-algal (i.e., healthy) tissue (HH) had lower bacterial abundance and diversity than tissue collected from the coral–algae interface boundary (HA) and areas of algae growth (AA). Specifically, the HA and AA samples had higher relative abundances of Saprospiraceae, Rhodobacteraceae, and Alteromonadaceae. Compared with Platygyra sp. and Montipora sp. , the physiological response of Pocillopora sp. was more intense under algae-induced stress based on microbial gene function prediction. Our results indicate that algal pressure can significantly alter the microbial community structure and function of coral ecosystems. Our data thus provide new insight into the relationship between corals and their microbiome under environmental stress.
Perturbative reheating and gravitino production in inflationary models

The low reheat temperature at the end of inflation from the gravitino bound constrains the creation of heavy Majorana neutrinos associated with models of leptogenesis. However, a detailed view of the reheating of the Universe at the end of inflation implies that the maximum temperature during reheating, T{sub max}, can be orders of magnitude higher than the final reheat temperature. This then allows for the production of the heavy Majorana neutrinos needed for leptogenesis. We carry out the complementary calculation of the gravitino production during reheating and its dependence on T{sub max}. We find that the gravitino abundance generated during reheating for a quartic potential is comparable to the standard estimate of the abundance generated after reheating and study its consequences for leptogenesis.
Holographic duals of black holes in five-dimensional minimal supergravity

We examine the dual conformal field theory for extremal charged black holes in five-dimensional minimal supergravity with two independent angular momenta. The conformal field theory Virasoro algebra, central charge and temperature are calculated. Additionally the conformal field theory entropy is calculated using the Cardy formula and agrees with the Bekenstein–Hawking black hole entropy. The central charges are directly proportional to the angular momentum components of the black hole. In five and higher dimensions, rotations of the spacetime correspond to rotations of the central charges leading to an apparent symmetry relating the conformal field theories dual to each black hole. A rotationally invariant central charge, which is proportional to the total angular momentum, is used to discuss the supersymmetric Breckenridge–Myers–Peet–Vafa black hole limits.
Imagery and long‐slit spectroscopy of the polar ring galaxy AM 2020–504

Interactions between galaxies are very common. There are special types of interactions that produce systems called polar ring galaxies (PRGs), composed of a lenticular, elliptical or spiral host galaxy, surrounded by a ring of stars and gas, orbiting in an approximately polar plane. In this paper, we study AM 2020–504, a PRG with an elliptical host galaxy, and a narrow and well-defined ring, probably formed by accretion of material from a donor galaxy, collected by the host galaxy. Our observational study is based on BVRI broad-band imagery as well as long-slit spectroscopy in the wavelength range 4100–8600 A, performed at the 1.6-m telescope at the Observatorio do Pico dos Dias, Brazil. We have estimated a redshift of z = 0.01683, corresponding to a heliocentric radial velocity of 5045 ± 23 km s−1. The (B − R) colour map shows that the ring is bluer than the host galaxy, which indicates that the ring is a younger structure. Standard diagnostic diagrams have been used to classify the main ionizing source of selected emission-line regions (nucleus, host galaxy and ring). We find that the ring regions are mainly ionized by massive stars, while the nucleus presents the characteristics of an active galactic nucleus. Using two empirical methods, we have found oxygen abundances for the H ii regions located in the ring in the range 12+log(O/H) = 8.3–8.8 dex. We have also found the presence of an oxygen gradient across the ring, and it appears that AM 2020–504 follows the metallicity–luminosity relation of spiral galaxies. These results support the accretion scenario for this object and they rule out cold accretion as the source for the H i gas in the polar ring.