Miracle-dz/UniFAR-FTUs huggingface dataset:
Quasiclassical modeling of cavity quantum electrodynamics

We model a collection of $N$ two-level systems (TLSs) coupled to a multimode cavity via Meyer-Miller-Stock-Thoss (MMST) dynamics, sampling both electronic and photonic zero-point energies (ZPEs) and propagating independent trajectories in Wigner phase space. By investigating the ground state stability of a single TLS, we use MMST dynamics to separately study both electronic ZPE effects (which would naively lead to the breakdown of the electronic ground state) as well as photonic ZPE effects (which would naively lead to spontaneous absorption). By contrast, including both effects (i.e., sampling both electronic and photonic ZPEs) leads to the dynamical stability of the electronic ground state. Therefore, MMST dynamics provide a practical way to identify the contributions of self-interaction and vacuum fluctuations. More importantly, we find that MMST dynamics can predict accurate quantum dynamics for both electronic populations and electromagnetic field intensity in the high saturation limit. For a single TLS in a cavity, MMST dynamics correctly predict the initial exponential decay of spontaneous emission, Poincare recurrences, and the positional dependence of a spontaneous emission rate. For an array of $N$ equally spaced TLSs with only one TLS excited initially, MMST dynamics correctly predict the modification of spontaneous emission rate as a function of the spacing between TLSs. Finally, MMST dynamics also correctly model Dicke's superradiance and subradiance (i.e., the dynamics when all TLSs are excited initially) including the correct quantum statistics for the delay time (as found by counting trajectories, for which a full quantum simulation is hard to achieve). Therefore, this work raises the possibility of simulating large-scale collective light-matter interactions with methods beyond mean-field theory.
Spiked Laplacian Graphs: Bayesian Community Detection in Heterogeneous Networks

In the network data analysis, it is common to encounter a large population of graphs: each has a small-to-moderate number of nodes but together, they show substantial variation from one graph to another. The graph Laplacian, a linear transform of the adjacency matrix, is routinely used in community detection algorithms; however, it is limited to single graph analysis and lacks uncertainty quantification. In this article, we propose a generative graph model called `Spiked Laplacian Graph'. Viewing each graph as a transform of the degree and Laplacian, we model the Laplacian eigenvalues as an increasing sequence followed by repeats of a flat constant. It effectively reduces the number of parameters in the eigenvectors and allows us to exploit the spectral graph theory for optimal graph partitioning. The signs in these orthonormal eigenvectors encode a hierarchical community structure, eliminating the need for iterative clustering algorithms. The estimator on the communities inherits the randomness from the posterior of eigenvectors. This spectral structure is amenableto a Bayesian non-parametric treatment that tackles heterogeneity. Theory is established on the trade-off between model resolution and accuracy, as well as the posterior consistency. We illustrate the performance in a brain network study related to working memory. KEYWORDS: Hierarchical Community Detection, Isoperimetric Constant, Mixed-Effect Eigendecomposition, Normalized Graph Cut, Stiefel Manifold.
MOBSTER – III. HD 62658: a magnetic Bp star in an eclipsing binary with a non-magnetic ‘identical twin’

HD 62658 (B9p V) is a little-studied chemically peculiar star. Light curves obtained by the Kilodegree Extremely Little Telescope (KELT) and Transiting Exoplanet Survey Satellite (TESS) show clear eclipses with a period of about 4.75 d, as well as out-of-eclipse brightness modulation with the same 4.75 d period, consistent with synchronized rotational modulation of surface chemical spots. High-resolution ESPaDOnS circular spectropolarimetry shows a clear Zeeman signature in the line profile of the primary; there is no indication of a magnetic field in the secondary. PHOEBE modelling of the light curve and radial velocities indicates that the two components have almost identical masses of about 3 M⊙. The primary’s longitudinal magnetic field 〈Bz〉 varies between about +100 and −250 G, suggesting a surface magnetic dipole strength Bd = 850 G. Bayesian analysis of the Stokes V profiles indicates Bd = 650 G for the primary and Bd < 110 G for the secondary. The primary’s line profiles are highly variable, consistent with the hypothesis that the out-of-eclipse brightness modulation is a consequence of rotational modulation of that star’s chemical spots. We also detect a residual signal in the light curve after removal of the orbital and rotational modulations, which might be pulsational in origin; this could be consistent with the weak line profile variability of the secondary. This system represents an excellent opportunity to examine the consequences of magnetic fields for stellar structure via comparison of two stars that are essentially identical with the exception that one is magnetic. The existence of such a system furthermore suggests that purely environmental explanations for the origin of fossil magnetic fields are incomplete.
HATCH-OUT ANALYSIS AND REPEATABILITY ESTIMATES OF COMMON HATCHABILITY PROBLEMS IN ISA

Six thousand and three hundred (6,300) sampled hatchable eggs (from a total of 68,130 eggs) produced in two commercial farms were used to evaluate hatchout performance and repeatability of some common hatchability problems in 38-41 weeks old Isa-Brown hens. Fertility, hatchability of total egg set and hatchability of fertile eggs were generally high (>80%) for eggs from the two farms. There was significant difference (p<0.05) between the two farms in the magnitude of hatchability problems at the early (1-7 days) and late (15-17 days) stages of embryonic development. Hatchability problems were higher for eggs obtained from farm AB (16.89%) than for eggs obtained from farm AA (11.87%). The trio of early post fertility mortality, piped, and dead-in-shell were the most important hatchability problems in the two farms. The estimates of repeatability of hatchability problems were generally high (66-98%). Repeatability estimates obtained for early and late embryonic stages were higher than that obtained for the midembryonic stage. Results obtained from this study showed that farms source of hatchable eggs has effect on the type and magnitude of reproductive failures that occurred during incubation. The high repeatability of hatchability problems at the early and late embryonic stages suggest a high probability of reproductive failure at the early and late stages of embryonic development in the future except corrective breeding and management strategies are put in place.
Optimization of 3 D phase contrast venography for the assessment of the cranio-cervical venous system at 1 . 5 T

Purpose The aim of this work was to optimize a three-dimensional (3D) phase-contrast venography (PCV) product MR pulse sequence in order to obtain clinically reliable images with less artifacts for an improved depiction of the cranio-cervical venous vessels. Methods Starting from the product sequence, the 3D PCV protocol was optimized in eight steps with respect to the velocity encoding (Venc) direction and value, slice thickness, reduction of susceptibility artifacts and arterial contamination, gradient mode and radio-frequency (RF)-spoiling, B0-Shimming, asymmetric echo technique and RF-pulse type, and flip angle. The product and optimized protocol was used to perform 3D PCV in 12 healthy male volunteers with a median age of 50 years using a stateof-the-art 1.5-T MR system. For evaluation, the cranio-cervical venous system was divided into 15 segments. These segments were evaluated by three radiologists with experience in neuroradiology. An ordinal scoring system was used to access the overall diagnostic quality, arterial contamination, and the quality of visualization. Results Image quality in the optimized 3D PCVwas graded as Bexcellent^ by all readers in 65.3% of the cases (p < 0.0001). The visualization of venous segments was strongly improved: it was considered diagnostic in 81.8% of all cases using the optimized sequence and in 47.6% for the product 3D PCV (p < 0.0001), respectively. The optimized protocol improved the imaging of all venous segments (p < 0.0001). Conclusion The optimized 3D PCV pulse sequence showed superior results compared to the product 3D PCV for the visualization and evaluation of the venous system in all healthy volunteers.
Assessing protected areas management using soft systems analysis : The case of Carrasco National Park , Bolivia

The establishment of protected areas has often been a top-down process, based on elitist concepts of land use and surrounded by restrictive legislation. Many protected areas and buffer zones in Bolivia, as in other countries, exist only on paper. The objectives and guidelines for their establishment are either not viable or unclear, resulting in management plans being overly simplistic or non-existent. In this study the various problems associated with the implementation/non-implementation of protected areas and buffer zone are considered from a systemic perspective. The paper outlines the application of soft systems methods to approach a complex problematic situation and presents preliminary results for protected areas in Bolivia.
Retina Deep Learning for Predicting Refractive Error From Retinal Fundus Images

Avinash V. Varadarajan, Ryan Poplin, Katy Blumer, Christof Angermueller, Joe Ledsam, Reena Chopra, Pearse A. Keane, Greg S. Corrado, Lily Peng, and Dale R. Webster Google Research, Google, Inc., Mountain View, California, United States Google DeepMind, Google, Inc., London, United Kingdom NIHR Biomedical Research Centre for Ophthalmology, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, United Kingdom
Collective Identity in Software Development

Background Software development has progressed towards an agile approach over the last decade, which increases demand for delivering high-quality software with a short time to market. Such an environment requires good communication and teamwork within teams as well as with outside stakeholders in order to attain a state of high performance to be able to reach objectives. Therefore, social interaction is central for a software development team to be successful. Such social interactions form social identities and social structures in both teams and organizations. Objective This thesis investigates possible effects that the collective self-esteem of individuals may have on the effectiveness of software development. Method Interviews were conducted with seven individuals to gain insight and find factors that could be used to explain correlations and causalities between collective self-esteem and software development effectiveness. The qualitative data from interviews were analyzed and summarized using summative content analysis. Furthermore, the seven individuals answered a questionnaire multiple times throughout the timespan of one month. The questionnaire was based on previous research on the topic of collective self-esteem and served as a means to explain the qualitative data. The quantitative data gathered from the questionnaire was tested and analyzed with statistical tests. Results An individual’s collective self-esteem is affected by the context of their groups and perceived effectiveness also varies based on the group context. In this case, it was found that communication played an important role as a mediating effect between collective self-esteem and effectiveness. However, the quantitative results show that there were no direct correlations between the aspects of collective self-esteem and effectiveness. Conclusions We show that many social interactions interplay and affect both individuals’ collective self-esteem and group effectiveness. Specifically, communication stood out as a central factor in the qualitative data which we were not able to find in the quantitative data, as our methods focused on collective self-esteem and effectiveness. Communication should be broken down into several factors to explore the topic further as a mediating effect.
A Letter from the Editor

Editorial A. Veis Dear colleagues: I would like to bring to your attention the review article and an accompanying research article that are featured in this issue. In my long career in connective tissue studies, and with a focus on collagen structure in particular, I have had the opportunity to witness the presentation and publication of a number of notable works on the structure of collagen, from the electron microscopy that led F.O. Schmitt and Alan Hodge [1] to the quarter-stagger overlap model of the collagen fibril [2,3], and parallel in time, the X-ray diffraction studies of Ramachandran [4–6] that introduced and advanced the concept of the unique triple helix conformation of the three-stranded collagen molecule (see Ref. [7] for a complete discussion of the early work on the triple helix). The next attempts were to marry up the rigid rod structure of the collagen to the fibril packing. There were thus models, such as the limiting microfibril [8], the Smith microfibril [9], the Piez “quasi-hexagonal microfibril” [10,11], and many subsequent refinements. The problem with these models was that the X-ray diffraction of fibrils at the time did not provide enough high-resolution data on lateral arrangements, and most modeled the triple helical structure as identical to the poly (ProProGly)n structure. Over the past 10 years, a series of papers stemming from the work of Joseph Orgel and collaborators have brought profound new insights, comparable to the impact of the earlier works noted above, to the understanding of the structures of “real” collagen molecules, and how their packing and organization within the collagen fibril governs their structure, packing, and most importantly, how the fibril arrangements affect the interaction of collagen fibers with their surrounding potential ligands. These new structural insights allow us to address new questions as to which of the putative ligand binding and functional sites of collagen are available on the outside of the fibril, and which are buried within the fibril and thus inaccessible? How is the surface modulated in the dynamic in vivo situation? The concepts are provocative and an alternative model of collagen fibril structure and function has been proposed by Herr and Farndale [12] so the final answers still require more study. I hope that you find this article and the related paper to be of interest—as well as the other interesting works presented in this article.
Skala Prioritas Pemeliharaan dan Rehabilitasi Jaringan Irigasi Sederhana (Studi Kasus di Kabupaten Semarang)

Pemerintah Kabupaten Semarang memiliki 492 jaringan irigasi sederhana. Agar keberlanjutan fungsi jaringan irigasi dapat dipertahankan dan ditingkatkan, dilakukan evaluasi penilaian kinerja sistem irigasi dengan berpedoman pada Perturan Menteri Pekerjaan Umum dan Perumahan Rakyat Nomor 12/PRT/M/2015. Permasalahannya pedoman tersebut hanya untuk jaringan irigasi teknis, pedoman evaluasi untuk jaringan irigasi sederhana masih belum ada. Metode penelitian dilakukan dengan cara penelusuran pada 25 jaringan irigasi di Kecamatan Susukan untuk mendapatkan data kondisi prasarana fisik, wawancara untuk mendapatkan data produktifitas tanam, sarana penunjang, organisasi personalia, dokumentasi dan P3A, serta kuisioner untuk mendapatkan nilai derajat kepentingan antar kriteria. Dari data yang diperoleh, dibuat kriteria evaluasi penilaian kinerja sistem irigasi jaringan irigasi sederhana. Hasil evaluasi penilaian kinerja sistem irigasi di Kecamatan Susukan Kabupaten Semarang didapatkan kisaran nilai bobot 69,21%, yang berarti Indeks kinerjanya Kurang dan Perlu Perhatian. Dengan menggunakan analytical hierarchy process (AHP) yang diawali penyusunan struktur hirarki dilanjutkan perhitungan bobot tiap-tiap kriteria dan alternatif, didapat urutan skala prioritas pemeliharaan : pertama DI. Kedung Asem dan kedua DI. Kedung Bunder. Dan urutan skala prioritas rehabilitasi: pertama DI. Sitaman dan kedua DI. Dungjati. Kata kunci : Kinerja Sistem irigasi, AHP, Skala Prioritas
J-PAS: forecasts on dark energy and modified gravity theories

The next generation of galaxy surveys will allow us to test one of the most fundamental assumptions of the standard cosmology, i.e. that gravity is governed by the general theory of relativity (GR). In this paper, we investigate the ability of the Javalambre Physics of the Accelerating Universe Astrophysical Survey (J-PAS) to constrain GR and its extensions. Based on the J-PAS information on clustering and gravitational lensing, we perform a Fisher matrix forecast on the effective Newton constant, μ, and the gravitational slip parameter, η, whose deviations from unity would indicate a breakdown of GR. Similar analysis is also performed for the DESI and Euclid surveys and compared to J-PAS with two configurations providing different areas, namely an initial expectation with 4000 deg2 and the future best case scenario with 8500 deg2. We show that J-PAS will be able to measure the parameters μ and η at a sensitivity of $2\! -\! 7{{\ \rm per\ cent}}$, and will provide the best constraints in the interval z = 0.3–0.6, thanks to the large number of ELGs detectable in that redshift range. We also discuss the constraining power of J-PAS for dark energy models with a time-dependent equation-of-state parameter of the type w(a) = w0 + wa(1 − a), obtaining Δw0 = 0.058 and Δwa = 0.24 for the absolute errors of the dark energy parameters.
Modeling the Comb Filter Effect and Interaural Coherence for Binaural Source Separation

Typical methods for binaural source separation consider only the direct sound as the target signal in a mixture. However, in most scenarios, this assumption limits the source separation performance. It is well known that the early reflections interact with the direct sound, producing acoustic effects at the listening position, e.g. the so-called comb filter effect. In this article, we propose a novel source separation model, that utilizes both the direct sound and the first early reflection information to model the comb filter effect. This is done by observing the interaural phase difference obtained from the time-frequency representation of binaural mixtures. Furthermore, a method is proposed to model the interaural coherence of the signals. Including information related to the sound multipath propagation, the performance of the proposed separation method is improved with respect to the baselines that did not use such information, as illustrated by using binaural recordings made in four rooms, having different sizes and reverberation times.
Multi-Agent Reinforcement Learning for Order-dispatching via Order-Vehicle Distribution Matching

Improving the efficiency of dispatching orders to vehicles is a research hotspot in online ride-hailing systems. Most of the existing solutions for order-dispatching are centralized controlling, which require to consider all possible matches between available orders and vehicles. For large-scale ride-sharing platforms, there are thousands of vehicles and orders to be matched at every second which is of very high computational cost. In this paper, we propose a decentralized execution order-dispatching method based on multi-agent reinforcement learning to address the large-scale order-dispatching problem. Different from the previous cooperative multi-agent reinforcement learning algorithms, in our method, all agents work independently with the guidance from an evaluation of the joint policy since there is no need for communication or explicit cooperation between agents. Furthermore, we use KL-divergence optimization at each time step to speed up the learning process and to balance the vehicles (supply) and orders (demand). Experiments on both the explanatory environment and real-world simulator show that the proposed method outperforms the baselines in terms of accumulated driver income (ADI) and Order Response Rate (ORR) in various traffic environments. Besides, with the support of the online platform of Didi Chuxing, we designed a hybrid system to deploy our model.
Constraining coupled quintessence with the 21 cm signal

The 21 cm line probes the evolution of matter perturbations over a wide range of redshifts, from the dark ages to the completion of reionization, and down to the present-day Universe. Observing the 21 cm cosmological signal will extend our understanding of the evolution of the Universe and it is thus important to investigate the predictions of different cosmological models. In this paper we focus on the prospect of constraining coupled quintessence models during the Epoch of Reionization both for global signal experiments and for intensity mapping surveys. To derive the all-sky 21 cm signal and fluctuations in coupled quintessence, we simulate cosmological volumes of the 21 cm signal including the coupling between dark matter and the quintessence field, where the strength of the coupling is labeled by the parameter Q. We show that the coupling between dark matter and quintessence modifies structure formation and expedites the process of reionization. For upcoming 21 cm line surveys like SKA and a fiducial global 21 cm signal experiment, we perform a Fisher matrix analysis to constrain the coupling Q and the dark matter density parameter Ωdm. The results indicate that SKA will be able to place a 68% upper limit of 0.04 on |Q|. At the same time, our fiducial global 21 cm detector constrains the dark matter density parameter Ωdm with a predicted error of ΔΩdm≍ 0.005, whereas SKA sets a weaker constraint of ΔΩdm≍0.1. These constraints are comparable to those already obtained from the cosmic microwave background, but explore an entirely different redshift range.
Variability of the thermal conductance of gold-alkane-gold single-molecule junctions studied using ab-initio and molecular dynamics approaches

Motivated by recent experiments, we study the variability of the thermal conductance of single dithiolated alkane molecules of varying length connecting two gold electrodes. For this purpose, we examine (i) the influence of the metal-molecule contact and of the electrode orientation on the thermal conductance of straight alkane chains, (ii) the effect of molecule-internal disorder realized through torsional gauche defects and the behavior upon stretching, and (iii) the modifications resulting from temperature-dependent dynamical variations of the geometry. While we analyze the former two aspects with a combination of density functional theory (DFT) and nonequilibrium Green's function (NEGF) methods, in the latter case we use nonequilibrium molecular dynamics (NEMD). Our calculations show the size of the variation of the phonon thermal conductance due to changes in contact geometry, that gauche defects generally reduce the thermal conductance but that they vanish upon stretching of the junction, and that the thermal conductance at elevated temperatures results from an average over many junction configurations, including alkanes with thermally excited gauche defects. Overall we find a good agreement between the DFT-NEGF and NEMD approaches for our room-temperature investigations. This confirms that anharmonic effects do not play a major role in alkane chains containing between four to ten carbon atoms. The phonon heat transport thus proceeds elastically and phase-coherently through these short molecular junctions.