Miracle-dz/UniFAR-FTUs huggingface dataset:
The Effect of Network Width on Stochastic Gradient Descent and Generalization: an Empirical Study

We investigate how the final parameters found by stochastic gradient descent are influenced by over-parameterization. We generate families of models by increasing the number of channels in a base network, and then perform a large hyper-parameter search to study how the test error depends on learning rate, batch size, and network width. We find that the optimal SGD hyper-parameters are determined by a "normalized noise scale," which is a function of the batch size, learning rate, and initialization conditions. In the absence of batch normalization, the optimal normalized noise scale is directly proportional to width. Wider networks, with their higher optimal noise scale, also achieve higher test accuracy. These observations hold for MLPs, ConvNets, and ResNets, and for two different parameterization schemes ("Standard" and "NTK"). We observe a similar trend with batch normalization for ResNets. Surprisingly, since the largest stable learning rate is bounded, the largest batch size consistent with the optimal normalized noise scale decreases as the width increases.
Fast and Efficient Zero-Learning Image Fusion

We propose a real-time image fusion method using pre-trained neural networks. Our method generates a single image containing features from multiple sources. We first decompose images into a base layer representing large scale intensity variations, and a detail layer containing small scale changes. We use visual saliency to fuse the base layers, and deep feature maps extracted from a pre-trained neural network to fuse the detail layers. We conduct ablation studies to analyze our method's parameters such as decomposition filters, weight construction methods, and network depth and architecture. Then, we validate its effectiveness and speed on thermal, medical, and multi-focus fusion. We also apply it to multiple image inputs such as multi-exposure sequences. The experimental results demonstrate that our technique achieves state-of-the-art performance in visual quality, objective assessment, and runtime efficiency.
Nucleoid-Associated Protein HU: A Lilliputian in Gene Regulation of Bacterial Virulence

Nucleoid-associated proteins belong to a group of small but abundant proteins in bacterial cells. These transcription regulators are responsible for many important cellular processes and also are involved in pathogenesis of bacteria. The best-known nucleoid-associated proteins, such as HU, FIS, H-NS, and IHF, are often discussed. The most important findings in research concerning HU protein are described in this mini review. Its roles in DNA compaction, shape modulation, and negative supercoiling induction have been studied intensively. HU protein regulates bacteria survival, growth, SOS response, virulence genes expression, cell division, and many other cell processes. Elucidating the mechanism of HU protein action has been the subject of many research projects. This mini review provides a comprehensive overview of the HU protein.
Does Movement Matter? Prefrontal Cortex Activity During 2D vs. 3D Performance of the Tower of Hanoi Puzzle

In the current study, we used functional near-infrared spectroscopy (fNIRS) to compare prefrontal cortex (PFC) activity in adults as they performed two conditions of the Tower of Hanoi (ToH) disk-transfer task that have equivalent executive function (EF) but different motor requirements. This study explored cognitive workload, here defined as the cognitive effort utilized while problem-solving by performance output. The first condition included a two-dimensional (2D) computerized ToH where participants completed trials using a computer mouse. In contrast, our second condition used a traditional, three-dimensional (3D) ToH that must be manually manipulated. Our aim was to better understand the role of the PFC in these two conditions to detect if PFC activity increases as a function of motor planning. Twenty right-handed, neurotypical adults (10M/10F, x¯ = 24.6, SD ± 2.8 years old) participated in two blocks (one per condition) of three 1-min trials where they were asked to solve as many puzzles as possible. These data were analyzed using a mixed effects ANOVA with participants nested within blocks for 2D vs. 3D conditions, presentation order (leading block), individual participants, and regions and additional follow-up statistics. Results showed that changes in oxygenated hemoglobin, ΔHbO, were significantly higher for 3D compared to 2D condition (p = 0.0211). Presentation order and condition interacted significantly (p = 0.0015). Notably, a strong correlation between performance and ΔHbO existed between blocks 1 and 2 (r = −0.69, r2 = 0.473, p < 0.01) when the 3D condition was initially performed, in contrast to the 2D condition where no significant correlation was seen. Findings also showed a significant decrease in ΔHbO between the first and second block (p = 0.0015) while performance increased significantly for both 3D and 2D conditions (p < 0.005). We plan to use this information in the future to narrow the potential points of impairment on the perception-cognition-action continuum in certain developmental disabilities.
Unification of inflation with dark energy in 
f(R)
 gravity and axion dark matter

In this work we introduce an effective model of $f(R)$ gravity containing a nonminimal coupling to the axion scalar field. The axion field is described by the misalignment model, in which the primordial $U(1)$ Peccei-Quin symmetry is broken during inflation and the $f(R)$ gravity is described by the ${R}^{2}$ model, and in addition, the nonminimal coupling has the form $\ensuremath{\sim}h(\ensuremath{\phi}){R}^{\ensuremath{\gamma}}$, with $0l\ensuremath{\gamma}l0.75$. By appropriately constraining the nonminimal coupling at early times, the axion field remains frozen in its primordial vacuum expectation value, and the ${R}^{2}$ gravity dominates the inflationary era. As the Universe expands, when $H$ equals the axion mass ${m}_{a}$ and for cosmic times for which ${m}_{a}\ensuremath{\gg}H$, the axion field oscillates. By assuming a slowly varying evolution of the axion field, the axion energy density scales as ${\ensuremath{\rho}}_{a}\ensuremath{\sim}{a}^{\ensuremath{-}3}$, where $a$ is the scale factor, regardless of the background Hubble rate, thus behaving as cold dark matter. At late times, the axion still evolves as ${\ensuremath{\rho}}_{a}\ensuremath{\sim}{a}^{\ensuremath{-}3}$, however, the Hubble rate of the expansion and thus the dynamical evolution of the Universe is controlled by terms containing the higher derivatives of $\ensuremath{\sim}{R}^{\ensuremath{\gamma}}$, which are related to the nonminimal coupling, and as we demonstrate, the resulting solution of the Friedman equation at late times is an approximate de Sitter evolution. The late-time de Sitter Hubble rate scales as $H\ensuremath{\sim}{\mathrm{\ensuremath{\Lambda}}}^{1/2}$, where $\mathrm{\ensuremath{\Lambda}}$ is an integration constant of the theory, which has its allowed values very close to the current value of the cosmological constant. Finally, the theory has a prediction for the existence of a preinflationary primordial stiff era, in which the energy density of the axion scales as ${\ensuremath{\rho}}_{a}\ensuremath{\sim}{a}^{\ensuremath{-}6}$.
Absence of Protein A Expression Is Associated With Higher Capsule Production in Staphylococcal Isolates

Staphylococcus aureus is a major human pathogen, and a leading cause of soft tissue and blood stream infections. One of the causes of its success as a pathogen is the peculiar array of immune evasion factors through which the bacterium avoids host defenses, where the staphylococcal protein A (SpA) plays a major role thanks to its IgG binding activities. Moreover, SpA has recently been proposed as a promising vaccine antigen. In this study, we evaluated the expression of SpA in a collection of staphylococcal strains, about 7% of which did not express SpA (SpA- strains), despite the presence of the gene. By a comparative genomic analysis, we identified that a mutation in the spa 5′ UTR sequence affecting the RBS is responsible for the loss of SpA in a subset of SpA- strains. Using a high-throughput qRT-PCR approach on a selected panel of virulence-related genes, we identified that the SpA- phenotype is associated with lower spa transcript levels and increased expression and production of capsule as well as other changes in the transcription of several key virulence factors. Our data suggest that the SpA- phenotype has occurred in geographically distinct strains through different molecular mechanisms including both mutation, leading likely to translation alterations, and transcriptional deregulation. Furthermore, we provide evidence that SpA- strains are highly susceptible to phagocytic uptake mediated by anti-capsule antibodies. These data suggest that S. aureus may alter its virulence factor expression pattern as an adaptation to the host or environment. Vaccination strategies targeting both SpA and capsule could therefore result in broader coverage against staphylococcal isolates than SpA alone.
The geometry of null rotation identifications

The geometry of flat spacetime modded out by a null rotation (boost + rotation) is analysed. When embedding this quotient spacetime in String/M-theory, it still preserves one half of the original supersymmetries. Its connection with the BTZ black hole, supersymmetric dilatonic waves and one possible resolution of its singularity in terms of nullbranes are also discussed.
ABC: A Simple Explicit Congestion Control Protocol for Wireless Networks

We propose Accel-Brake Control (ABC), a simple and deployable explicit congestion control protocol for network paths with time-varying wireless links. ABC routers mark each packet with an "accelerate" or "brake", which causes senders to slightly increase or decrease their congestion windows. Routers use this feedback to quickly guide senders towards a desired target rate. ABC requires no changes to header formats or user devices, but achieves better performance than XCP. ABC is also incrementally deployable; it operates correctly when the bottleneck is a non-ABC router, and can coexist with non-ABC traffic sharing the same bottleneck link. We evaluate ABC using a Wi-Fi implementation and trace-driven emulation of cellular links. ABC achieves 30-40% higher throughput than Cubic+Codel for similar delays, and 2.2X lower delays than BBR on a Wi-Fi path. On cellular network paths, ABC achieves 50% higher throughput than Cubic+Codel.
Beyond cDC1: Emerging Roles of DC Crosstalk in Cancer Immunity

Dendritic cells (DCs) efficiently process and present antigens to T cells, and by integrating environmental signals, link innate and adaptive immunity. DCs also control the balance between tolerance and immunity, and are required for T-cell mediated anti-tumor immunity. One subset of classical DCs, cDC1, are particularly important for eliciting CD8 T cells that can kill tumor cells. cDC1s are superior in antigen cross-presentation, a process of presenting exogenous antigens on MHC class I to activate CD8+ T cells. Tumor-associated cDC1s can transport tumor antigen to the draining lymph node and cross-present tumor antigens, resulting in priming and activation of cytotoxic T cells. Although cross-presenting cDC1s are critical for eliciting anti-tumor T cell responses, the role and importance of other DC subsets in anti-tumor immunity is not as well-characterized. Recent literature in other contexts suggests that critical crosstalk between DC subsets can significantly alter biological outcomes, and these DC interactions likely also contribute significantly to tumor-specific immune responses. Therefore, antigen presentation by cDC1s may be necessary but not sufficient for maximal immune responses against cancer. Here, we discuss recent advances in the understanding of DC subset interactions to maximize anti-tumor immunity, and propose that such interactions should be considered for the development of better DC-targeted immunotherapies.
DistillHash: Unsupervised Deep Hashing by Distilling Data Pairs

Due to storage and search efficiency, hashing has become significantly prevalent for nearest neighbor search. Particularly, deep hashing methods have greatly improved the search performance, typically under supervised scenarios. In contrast, unsupervised deep hashing models can hardly achieve satisfactory performance due to the lack of supervisory similarity signals. To address this problem, in this paper, we propose a new deep unsupervised hashing model, called DistilHash, which can learn a distilled data set, where data pairs have confident similarity signals. Specifically, we investigate the relationship between the initial but noisy similarity signals learned from local structures and the semantic similarity labels assigned by the optimal Bayesian classifier. We show that, under a mild assumption, some data pairs, of which labels are consistent with those assigned by the optimal Bayesian classifier, can be potentially distilled. With this understanding, we design a simple but effective method to distill data pairs automatically and further adopt a Bayesian learning framework to learn hashing functions from the distilled data set. Extensive experimental results on three widely used benchmark datasets demonstrate that our method achieves state-of-the-art search performance.
Recovering the unsigned photospheric magnetic field from Ca II K observations

Context. A number of studies have aimed at defining the exact form of the relation between magnetic field strength and Ca II H and K core brightness. All previous studies have however been restricted to isolated regions on the solar disc or to a limited set of observations. Aims. We reassess the relationship between the photospheric magnetic field strength and the Ca II K intensity for a variety of surface features as a function of the position on the disc and the solar activity level. This relationship can be used to recover the unsigned photospheric magnetic field from images recorded in the core of Ca II K line. Methods. We have analysed 131 pairs of high-quality, full-disc, near-co-temporal observations from the Helioseismic and Magnetic Imager (SDO/HMI) and Precision Solar Photometric Telescope (Rome/PSPT) spanning half a solar cycle. To analytically describe the observationally determined relation, we considered three different functions: a power law with an offset, a logarithmic function, and a power-law function of the logarithm of the magnetic flux density. We used the obtained relations to reconstruct maps of the line-of-sight component of the unsigned magnetic field (unsigned magnetograms) from Ca II K observations, which were then compared to the original magnetograms. Results. We find that both power-law functions represent the data well, while the logarithmic function is good only for quiet periods. We see no significant variation over the solar cycle or over the disc in the derived fit parameters, independently of the function used. We find that errors in the independent variable, which are usually not accounted for, introduce attenuation bias. To address this, we binned the data with respect to the magnetic field strength and Ca II K contrast separately and derived the relation for the bisector of the two binned curves. The reconstructed unsigned magnetograms show good agreement with the original ones. Root mean square differences are less than 90 G. The results were unaffected by the stray-light correction of the SDO/HMI and Rome/PSPT data. Conclusions. Our results imply that accurately processed and calibrated Ca II K observations can be used to reconstruct unsigned magnetograms by using the relations derived in our study.
Networks, communities and markets in sub-Saharan Africa: implications for firm growth and investment

This paper examines how relationships and networks affect market exchange in Sub-Saharan Africa. After noting that market exchange arguably plays a larger role in Africa than in developed economies, we show that the presence of transactions costs naturally leads market participants to enter in long-term trading relationships. These relationships form business networks that shape market outcomes. We argue that network segmentation can have large efficiency and equity costs, particularly in international trade. Because of network externalities, groups and countries that are familiar with a particular activity tend to continue investing in that activity. The presence of networks and non-convex transactions costs also complicates the analysis of market competition. Implications for future research are briefly discussed.
Proteomic Profiling Unravels a Key Role of Specific Macrophage Subtypes in Sporadic Inclusion Body Myositis

Unbiased proteomic profiling was performed toward the identification of biological parameters relevant in sIBM, thus giving hints about the pathophysiological processes and the existence of new reliable markers. For that purpose, skeletal muscle biopsies from 13 sIBM and 7 non-diseased control patients were analyzed with various methods, including liquid chromatography coupled to tandem mass spectrometry (four patients). Subsequent data analysis identified key molecules further studied in a larger cohort by qPCR, immunostaining, and immunofluorescence in situ. Proteomic signature of muscle biopsies derived from sIBM patients revealed the chaperone and cell surface marker CD74, the macrophage scavenger molecule CD163 and the transcription activator STAT1 to be among the highly and relevantly expressed proteins suggesting a significant contribution of immune cells among the myofibers expressing these markers. Moreover, in silico studies showed that 39% of upregulated proteins were involved in type I or mixed type I and type II interferon immunity. Indeed, further studies via immunohistochemistry clearly confirmed the prominent involvement of the key type I interferon signature-related molecules, ISG15 as well as IRF8 with MHC class II+ myofibers. Siglec1 colocalized with CD163+ macrophages and MHC class II molecules also co-localized with CD74 on macrophages. STAT1 co-localized with Siglec1+ macrophages in active myofibre myophagocytosis while STAT6 colocalized with endomysial macrophages. These combined results show involvement of CD74, CD163, and STAT1 as key molecules of macrophage activation being crucially involved in mixed and specific type I interferon, and interferon gamma associated-pathways in sIBM. On a more general note, these results also highlight the type of immune-interaction between macrophages and myofibers in the etiopathology of sIBM.
The Fe Line Flux Ratio as a Diagnostic of the Maximum Temperature and the White Dwarf Mass of Cataclysmic Variables

The flux ratio of Fe xxvi–Lyα to Fe xxv–Heα lines (I7.0/I6.7) is a sensitive indicator of the maximum temperature (Tmax), and therefore the mass of white dwarf stars (MWD) in cataclysmic variables (CVs). To examine and calibrate the theoretical I7.0/I6.7–Tmax–MWD relations, reliable measurements of Tmax and I7.0/I6.7 are necessary. In this work, we conduct a thorough investigation of 3–50 keV X-ray spectra of 25 solar neighborhood magnetic and nonmagnetic CVs based on archival NuSTAR and Suzaku observations. The measured Tmax are compared to the I7.0/I6.7 and MWD. The results show that the sampled CVs closely follow the theoretical I7.0/I6.7–Tmax relation. Moreover, all the MWD estimated from I7.0/I6.7 are consistent with the dynamically measured ones. We conclude that I7.0/I6.7 can be used as a good diagnostic for Tmax and MWD in both magnetic and nonmagnetic CVs.
The Vickrey Auction with a Single Duplicate Bidder Approximates the Optimal Revenue

Bulow and Klemperer's well-known result states that, in a single-item auction where the n bidders' values are independently and identically drawn from a regular distribution, the Vickrey auction with one additional bidder (a duplicate) extracts at least as much revenue as the optimal auction without the duplicate. Hartline and Roughgarden, in their influential 2009 paper, removed the requirement that the distributions be identical, at the cost of allowing the Vickrey auction to recruit n duplicates, one from each distribution, and relaxing its revenue advantage to a 2-approximation. In this work we restore Bulow and Klemperer's number of duplicates in Hartline and Roughgarden's more general setting. We show that recruiting a duplicate from one of the distributions suffices for the Vickrey auction to $10$-approximate the optimal revenue. We also show that in a k-unit auction, recruiting k duplicates suffices for the VCG auction to $O(1)$-approximate the optimal revenue. We also tighten the analysis for Hartline and Roughgarden's Vickrey auction with n duplicates. We show that, for two distributions, the Vickrey auction with two duplicates obtains at least $3/4$ of the optimal revenue. This is tight by meeting a lower bound by Hartline and Roughgarden. En route, we obtain a transparent analysis of their $2$-approximation, by a natural connection to Ronen's lookahead auction.
QSO2 outflow characterization using data obtained with OSIRIS at the Gran Telescopio Canarias

Context. Ionized outflows are ubiquitous in non-radio-loud obscured quasars (QSO2s) at different redshifts. However, the actual size of the outflows and their efficiency for gas ejection and star formation truncation are controversial. Large-scale (exceeding several kiloparsec) extended radio structures might be necessary to identify (even to trigger) outflow signatures across such large spatial scales. Aims. We search for large-scale ionized outflows associated with six optically selected QSO2 (five non-radio-loud and one radio-loud) at z ∼ 0.2−0.5, targeting objects with extended radio structures. We also investigate the dynamical state of the QSO2 host galaxies. Methods. We obtained data with the optical imager and long-slit spectrograph (OSIRIS) mounted on the 10.4m Gran Telescopio Canarias Spanish telescope (GTC) for these six QSO2 with the slit located along the radio axis. We traced the gas kinematics with the [OIII]λλ4959,5007 lines to investigate ionized outflows and characterize the dynamical state of the host galaxies. This second study was complemented with previously published spectroscopic data obtained with the multimode focal reducer and low dispersion spectrograph (FORS2) mounted on the Very Large Telescope (VLT) of 13 more QSO2 at similar z. Results. We identify ionized outflows in four out of the six QSO2 observed with the GTC. The outflows are spatially unresolved in two QSO2 and compact in a third (radial size of R = 0.8 ± 0.3 kpc). Of particular interest is the radio-quiet QSO2 SDSS 0741+3020 at z = 0.47. It is associated with a giant ∼112 kpc nebula. An ionized outflow probably induced by the radio structures has been detected along the axis defined by the central ∼1″ radio structure, extending up to at least ∼4 kpc from the active galactic nucleus (AGN). Turbulent gas (σ ∼ 130 km s−1) has also been detected across the giant gas nebula up to ∼40 kpc from the AGN. This turbulence may have been induced by outflows triggered by the interaction between a so-far undetected large-scale radio source and the nebula. Regarding the dynamical state of the host galaxies, we find that the majority of the QSO2 show v/σ < 1, implying that they are dominated by random motions (so-called dispersion-dominated systems). Most (17 of 19) fall in the area of the E/S0 galaxies in the dynamical diagram v/σ versus σ. None are consistent with spiral or disk galaxies.