Miracle-dz/UniFAR-FTUs huggingface dataset:
Using Galactic Cepheids to verify Gaia parallaxes

Context. The Gaia satellite will measure highly accurate absolute parallaxes of hundreds of millions of stars by comparing the parallactic displacements in the two fields of view of the optical instrument. The requirements on the stability of the "basic angle" between the two fields are correspondingly strict, and possible variations (on the microarcsec level) are therefore monitored by an on-board metrology system. Nevertheless, since even very small periodic variations of the basic angle might cause a global offset of the measured parallaxes, it is important to find independent verification methods. Aims. We investigate the potential use of Galactic Cepheids as standard candles for verifying the Gaia parallax zero point. Methods. We simulate the complete population of Galactic Cepheids and their observations by Gaia. Using the simulated data, simultaneous fits are made of the parameters of the period-luminosity relation and a global parallax zero point. Results. The total number of Galactic Cepheids is estimated at about 20 000, of which nearly half could be observed by Gaia. In the most favourable circumstances, including negligible intrinsic scatter and extinction errors, the determined parallax zero point has an uncertainty of 0.2 microarcsec. With more realistic assumptions the uncertainty is several times larger, and the result is very sensitive to errors in the applied extinction corrections. Conclusions. The use of Galactic Cepheids alone will not be sufficient to determine a possible parallax zero-point error to the full potential systematic accuracy of Gaia. The global verification of Gaia parallaxes will most likely depend on a combination of many different methods, including this one. (Less)
Fine-tuning of CNN models for Instance Search with Pseudo-Relevance Feedback

CNN classification models trained on millions of labeled images have been proven to encode “general purpose” descriptors in their intermediate layers. These descriptors are useful for a diverse range of computer vision problems [1]. However, the target task of these models is substantially different to the instance search task. While classification is concerned with distinguishing between different classes, instance search is concerned with identifying concrete instances of a particular class.
Classification of atomic-scale multipoles under crystallographic point groups and application to linear response tensors

Four types of atomic-scale multipoles, electric, magnetic, magnetic toroidal, and electric toroidal multipoles, give a complete set to describe arbitrary degrees of freedom for coupled charge, spin, and orbital of electrons. We here present a systematic classification of these multipole degrees of freedom towards the application in condensed matter physics. Starting from the multipole description under the rotation group in real space, we generalize the concept of multipoles in momentum space with the spin degree of freedom. We show how multipoles affect the electronic band structures and linear responses, such as the magneto-electric effect, magneto-current (magneto-gyrotropic) effect, spin conductivity, Piezo-electric effect, and so on. Moreover, we exhibit a complete table to represent the active multipoles under 32 crystallographic point groups. Our comprehensive and systematic analyses will give a foundation to identify enigmatic electronic order parameters and a guide to evaluate peculiar cross-correlated phenomena in condensed matter physics from microscopic point of view.
Anti-Lenz Supercurrents in Superconducting Spin Valves

Here, we present a study on Si(111)/\-Ta($150$\AA )/\-IrMn($150$\AA )/\-NiFe($50$\AA )/\-Nb($x$)/\-NiFe($50$\AA )/\-Ta($50$\AA ) and Si(111)/\-Ta($150$\AA )/\-NiFe($50$\AA )/\-Nb($x$)/\-NiFe($50$\AA )/\-IrMn($150$\AA )/\-Ta($50$\AA ) spin-valves with $x=100$ to $500$\AA . For both sample families, above a specific critical thickness of the Nb-layer and below $T_c$, the superconducting Nb-layer contributes strongly to the magnetization. These systems show an anomalous hysteresis loop in the magnetization of the superconducting layer; the hysteresis loop is similar to what is generally expected from hard superconductors and many superconductor/ferromagnet hybrid systems, but the direction of the hysteresis loop is inverted, compared to what is generally observed (paramagnetic for up sweeping fields and diamagnetic for down sweeping fields). This means that the respective samples exhibit a magnetization, which is contrary to what should be expected from the Lenz' rule.
Multipacting studies of beta_g=0.61 and beta_g =0.9, 650 MHz Elliptical SRF Cavities

Multipacting is seen as a performance limiting phenomenon for the superconducting radio frequency (SRF) cavities. Numerical simulations are essential to pre-empt the experimentally observed multipacting conditions. Readily available codes(e.g. FISHPACT, MULTIPACT,CST etc.) are widely used to simulate the phenomenon of multipacting in such cases. Most of the contemporary two dimensional (2D) codes are unable to detect multipacting in the elliptical cavities because they use a simplistic secondary emission model, where a constant value of emission kinetic energy of secondary electrons is assumed. Some three-dimensional (3D) codes, which use a more realistic and sophisticated secondary emission model (Furman model) by following a probability distribution for the emission kinetic energy of secondary electrons, are able to correctly predict the occurance of multipacting. These 3D softwares however require large data handling and are slower than contemporary 2D codes. We have developed a 2D code for the multipacting analysis for axisymmetric structures, which is based on the Furman model. Since our code is 2D, it is faster than the 3D codes. This makes it possible to perform an accurate multipacting analysis of multipacting within a resaonalble computational time, thus achieving an accuracy as good as in the case of 3D codes, but requiring significantly less computing time. We have used our code for determining the multipacting prone range of values for Eacc in beta_g =0.61 and beta_g =0.9, 650 MHz mid-cell elliptical cavities that we have recently designed for the medium and high energy section of the proposed Indian Spallation Neutron Source (ISNS) project.
Radiative stellar feedback in galaxy formation: Methods and physics

Radiative feedback (RFB) from stars plays a key role in galaxies, but remains poorly understood. We explore this using high-resolution, multifrequency radiation-hydrodynamics (RHD) simulations from the Feedback In Realistic Environments (FIRE) project. We study ultrafaint dwarf through Milky Way mass scales, including H+He photoionization; photoelectric, Lyman Werner, Compton, and dust heating; and single+multiple scattering radiation pressure (RP). We compare distinct numerical algorithms: ray-based LEBRON (exact when optically thin) and moments-based M1 (exact when optically thick). The most important RFB channels on galaxy scales are photoionization heating and single-scattering RP: in all galaxies, most ionizing/far-UV luminosity (∼1/2 of lifetime-integrated bolometric) is absorbed. In dwarfs, the most important effect is photoionization heating from the UV background suppressing accretion. In MW-mass galaxies, metagalactic backgrounds have negligible effects; but local photoionization and single-scattering RP contribute to regulating the galactic star formation efficiency and lowering central densities. Without some RFB (or other ‘rapid’ FB), resolved GMCs convert too-efficiently into stars, making galaxies dominated by hyperdense, bound star clusters. This makes star formation more violent and ‘bursty’ when SNe explode in these hyperclustered objects: thus, including RFB ‘smoothes’ SFHs. These conclusions are robust to RHD methods, but M1 produces somewhat stronger effects. Like in previous FIRE simulations, IR multiple-scattering is rare (negligible in dwarfs, $\sim 10{{\ \rm per\ cent}}$ of RP in massive galaxies): absorption occurs primarily in ‘normal’ GMCs with AV ∼ 1.
Spatially Resolved Millimeter Interferometry of SMM J02399–0136: A Very Massive Galaxy at z = 2.8

We report high-resolution millimeter mapping with the IRAM Plateau de Bure interferometer of rest-frame 335 μm continuum and CO (3-2) line emission from the z = 2.8 submillimeter galaxy SMM J02399-0136. The continuum emission comes from a ~3'' diameter structure whose elongation is approximately east-west and whose centroid is coincident within the astrometric errors with the brightest X-ray and rest-UV peak (L1). The line data show that this structure is most likely a rapidly rotating disk. Its rotation velocity of ≥420 km s-1 implies a total dynamical mass of ≥3 × 1011 sin−2 i h M☉ within an intrinsic radius of 8 h kpc, most of which is plausibly in the form of stars and gas. SMM J02399-0136 is thus a very massive system, whose formation at z ~ 3 is not easy to understand in current cold dark matter hierarchical merger cosmogonies.
Investigation of lock release gravity currents in an upslope valley

The sun heats the land faster than it heats the ocean, causing the air to be warmer over land than over the sea during the day. Convection over land keeps these air masses apart. However, as convection weakens in the afternoon and evening, a pressure gradient causes the cold dense air over the ocean to flow under the warm air on the land in a “sea breeze. ” In areas where sea breezes occur, they cool the region of land adjacent to the ocean and bring in moisture. In the Santa Barbara region, where valleys penetrate into coastal mountain ranges, sea breezes propagate to high inland plateaus, enabling grapes to be grown; in the absence of sea breezes, the climate would otherwise be too hot and dry. In general, it is of interest to study the flow of dense fluids into valleys and up hills. The results presented here may be applicable not only to coastal agriculture, but also to tidal flows in submarine canyons and estuaries. Sea breezes are a type of gravity current, and gravity currents are often studied by performing lock-release experiments. This is the approach we take here. A dense fluid is held at one end of the tank by a gate, and the rest of the tank is filled with a lighter fluid. When the gate is removed, the dense fluid, driven by the pressure gradient, flows under the lighter fluid as a gravity current. The experiments, numerics, and theory in this manuscript explore full-depth lock-release at high Reynolds numbers in the parameter range available when a tank is tilted in the x and y directions, as shown in Figure 1. The aim is to look at the behaviour of gravity currents up slopes and in symmetric and asymmetric V -shaped valleys, and in particular to measure the speed, the time-dependence, and the shape of the currents we observe. We wish to understand what factors control these parameters in order to make general predictions for the initial speed and time dependence of a gravity current in a valley. The timescale of sea breezes is much shorter than one day, and so we do not expect the rotation of the Earth to be important. In Section 2 of this manuscript we describe previous work on gravity currents, particularly those in valleys and up slopes. In Section 3, we extend Benjamin’s analysis to predict the speed and height of a gravity current in a V -shaped valley. A prediction for the speed of upslope flow as a function of slope is also made based on local water depth at the front. In Section 4, we perform laboratory experiments to explore the speed and time dependence
DNA methylation-based biomarkers and prediction models for the survival of patients with colorectal cancer: systematic review and external validation study

Objectives To identify existing DNA methylation-based prognostic biomarkers and prediction models for colorectal cancer (CRC) prognosis and to validate them in a large external cohort. Design Systematic review and external validation study. Data source Systematic search in PubMed and Web of Science until October 2022 to identify epigenome-wide studies reporting methylation at CpG sites (CpGs) associated with survival among CRC patients. Validation data were drawn from the 2310 CRC patients of the DACHS study recruited from 22 hospitals in the Rhine-Neckar region in the southwest of Germany. Main outcome measures Overall survival (OS) in CRC patients. Results We identified 200 unique CpGs and 10 CpG-based prognostic models derived from 15 studies. In the external validation analysis, 1252 of 2310 patients died during follow-up (median 10.4 years). Thirty-nine CpGs (20%) and five prognostic models (50%) were independently associated with overall survival after adjustment for clinical variables. The five models had unsatisfactory discrimination ability, with the area under the receiver operating characteristic curves at five years ranging from 0.54 to 0.60. The calibration accuracy of the five models using recalibrated baseline survival was also poor, and no relevant added prognostic value to traditional clinical variables was observed. Based on the Prediction Model Risk of Bias Assessment Tool, all models were rated as high risk of bias. Conclusions Only 20% of published CpGs associated with survival in CRC patients could be externally validated. So far derived published CpG-based prognostic models for CRC do not seem to be useful for clinical practice.
Isolation efficiency of collagenase and EDTA for the culture of corneal endothelial cells

Purpose Tissue engineering of the corneal endothelium, as well as cell therapy, has been proposed as an alternative approach for the treatment of corneal endotheliopathies. These approaches require in vitro amplification of functional corneal endothelial cells (CECs). The goal of this study was to compare two common isolation methods, collagenase A and EDTA (EDTA), and determine whether they influence cell viability, morphology, and barrier function. Methods Human eye bank research-grade corneas were used to isolate and cultivate CECs. All donors were more than 40 years old. Two Descemet membranes from the same donor were used separately to compare the collagenase A and EDTA cell isolation methods. The number of isolated cells, cell viability, morphology, and barrier functionality were compared. Results A higher isolation efficiency of viable CECs and a higher circularity index (endothelial morphology) were obtained using collagenase A. Passage 3 cells presented similar barrier functionalities regardless of the isolation method. Conclusions This study showed that isolation of CECs using collagenase A yields higher isolation efficiency than EDTA, delaying the loss of endothelial morphology for early passage cells.
Ethylene represses the promoting influence of cytokinin on cell division and expansion of cotyledons in etiolated Arabidopsis thaliana seedlings

The plant hormones ethylene and cytokinin influence many processes; sometimes they act cooperatively, other times antagonistically. To study their antagonistic interaction, we used the cotyledons of etiolated, intact seedlings of Arabidopsis thaliana. We focused on cell division and expansion, because both processes are quantified readily in paradermal sections. Here, we show that exogenous cytokinins modestly stimulate cell division and expansion in the cotyledon, with a phenyl-urea class compound exerting a larger effect than benzyl-adenine. Similarly, both processes were stimulated modestly when ethylene response was inhibited, either chemically with silver nitrate or genetically with the eti5 ethylene-insensitive mutant. However, combining cytokinin treatment with ethylene insensitivity was synergistic, strongly stimulating both cell division and expansion. Evidently, ethylene represses the growth promoting influence of cytokinin, whether endogenous or applied. We suggest that the intact etiolated cotyledon offers a useful system to characterize how ethylene antagonizes cytokinin responsiveness.
DGRanker: Cancer Driver Gene Detection in Human Transcriptional Regulatory Network

Background: Cancer is a group of diseases that have received much attention in biological research because of its high mortality rate and the lack of accurate identification of its root causes. In such studies, researchers usually try to identify cancer driver genes (CDGs) that start cancer in a cell. The majority of the methods that have ever been proposed for the identification of CDGs are based on gene expression data and the concept of mutation in genomic data. Recently, using networking techniques and the concept of influence maximization, some models have been proposed to identify these genes. Objectives: We aimed to construct the cancer transcriptional regulatory network and identify cancer driver genes using a network science approach without the use of mutation and genomic data. Materials and Methods: In this study, we will employ the social influence network theory to identify CDGs in the human gene regulatory network (GRN) that is based on the concept of influence and power of webpages. First, we will create GRN Networks using gene expression data and Existing nodes and edges. Next, we will implement the modified algorithm on GRN networks being studied by weighting the regulatory interaction edges using the influence spread concept. Nodes with the highest ratings will be selected as the CDGs. Results: The results show our proposed method outperforms most of the other computational and network-based methods and show its superiority in identifying CDGs compared to many other methods. In addition, the proposed method can identify many CDGs that are overlooked by all previously published methods Conclusions: Our study demonstrated that the Google’s PageRank algorithm can be utilized and modified as a network-based method for identifying cancer driver gene in transcriptional regulatory network. Furthermore, the proposed method can be considered as a complementary method to the computational-based cancer driver gene identification tools.
Evaluation of the Biodistribution of Arginine, glycine, aspartic acid peptide-modified Nanoliposomes Containing Curcumin in Rats

Background: Liposomes, as a biological membrane, is successfully used for drug delivery, reduces toxicity in normal cells and improves bio-accessibility of the drug to the target cells. Curcumin, as a bioactive substance with pleiotropic biological activities, is an anti-inflammatory compound and has several anticancer effects in different cancers such as pancreatic and breast cancer. Objectives: This study was conducted to determine the bio-distribution of arginine-glycine-aspartic acid (RGD)-modified nanoliposomes containing curcumin in different tissues of rats. Materials and Methods: The amount of curcumin in each tissue was examined by HPLC analysis. The distribution of liposomal Hoechst in the rats was evaluated by using fluorescence spectrophotometry, live animal imaging analyses and histological methods. Results: HPLC analysis showed the mean of curcumin in the blood significantly increased in the liposomal curcumin modified with RGD compared to free curcumin. These results were confirmed by fluorescence measurement for RGD modified liposome containing Hoechst dye. There was negligible fluorescent intensity in the blood rats, which received Hoechst alone. Live animal imaging analysis showed the presence of fluorescent color in heart tissue for all groups. It was also detected in kidney tissue for liposomal Hoechst modified with RGD group. Conclusions: The present study demonstrated that RGD-modified nano-liposomes can significantly improve drug retention time in the blood of rats.
Ab initio calculation of the G peak intensity of graphene: Laser-energy and Fermi-energy dependence and importance of quantum interference effects

We present the results of a diagrammatic, fully ab initio calculation of the $G$ peak intensity of graphene. The flexibility and generality of our approach enables us to go beyond the previous analytical calculations in the low-energy regime. We study the laser and Fermi energy dependence of the $G$ peak intensity and analyze the contributions from resonant and non-resonant electronic transitions. In particular, we explicitly demonstrate the importance of quantum interference and non-resonant states for the $G$ peak process. Our method of analysis and computational concept is completely general and can easily be applied to study other materials as well.
CC chemokine CCL 5 plays a central role impacting infarct size and post-infarction heart failure in mice

Methods and Results C57Bl/6 mice were submitted to left coronary artery permanent ligature. Then, various parameters were monitored for up to 21 days. At5 min and 3 days after coronary occlusion, mice received one intravenous injection of the rat anti-mouse CCL5 mAb or isotype IgG control. Infarct size was assessed histologically and by measuring serum cardiac troponin I levels. Kinetics of CCL5 tissue expression, leucocyte infiltration, matrix metalloproteinase (MMP) levels, and collagen deposition were histologically assessed. Serum chemokine levels were measured by enzyme-linked immunosorbent assay. Cardiac function and dimensions were assessed by magnetic resonance imaging (MRI). Chronic ischaemia increased both circulating and intracardiac levels of CCL5. At 24 h, treatment with the anti-CCL5 mAb resulted in a smaller infarct size and reduced circulating levels of chemokines. This effect was associated with reduction of neutrophil and macrophage infiltration within the infarcted myocardium. After 3 days of chronic ischaemia, anti-CCL5 mAb treatment reduced cardiac MMP-9. At 7 days, collagen content was significantly lower. At 21 days, neutralizing CCL5 improved mouse survival, cardiac myocyte size, and cardiac function.
The bispectral problem

Part 1. Bispectrality: Automorphisms of the Weyl algebra and bispectral operators by B. Bakalov, E. Horozov, and M. Yakimov Huygens' principle and the bispectral problem by Y. Berest Some bispectral musings by F. A. Grunbaum Beyond the classical orthogonal polynomials by L. Haine Bispectral operators, dual isomondromic deformations and the Riemann-Hilbert dressing method by J. Harnad Darboux transformations and the bispectral problem by A. Kasman The discrete version of the bispectral problem by F. Levstein and L. F. Matusevich Explicit formulas for the Airy and Bessel bispectral involutions in terms of Calogero-Moser pairs by M. Rothstein Bispectrality and Darboux transformations in the theory of orthogonal polynomials by V. Spiridonov, L. Vinet, and A. Zhedanov Baker-Akhiezer functions and the bispectral problem in many dimensions by A. P. Veselov Bispectral algebras of ordinary differential operators by G. Wilson The bispectral problem, rational solutions of the master symmetry flows, and bihamiltonian systems by J. P. Zubelli Part 2. Related Topics: The geometry of spinors and the multicomponent BKP and DKP hierarchies by V. Kac and J. van de Leur The Hamiltonian route to Sato Grassmannian by F. Magri Darboux transformations in associative rings and functional-difference equations by V. B. Matveev Remarks about the Calogero-Moser system and the KP equation by A. Y. Orlov Subject index.