Miracle-dz/UniFAR-FTUs huggingface dataset:
Linear dust polarization during the embedded phase of protostar formation

Context. Measuring polarization from thermal dust emission can provide important constraints on the magnetic field structure around embedded protostars. However, interpreting the observations is challenging without models that consistently account for both the complexity of the turbulent protostellar birth environment and polarization mechanisms. Aims. We aim to provide a better understanding of dust polarization maps of embedded protostars with a focus on bridge-like structures such as the structure observed toward the protostellar multiple system IRAS 16293–2422 by comparing synthetic polarization maps of thermal reemission with recent observations. Methods. We analyzed the magnetic field morphology and properties associated with the formation of a protostellar multiple based on ideal magnetohydrodynamic 3D zoom-in simulations carried out with the RAMSES code. To compare the models with observations, we postprocessed a snapshot of a bridge-like structure that is associated with a forming triple star system with the radiative transfer code POLARIS and produced multiwavelength dust polarization maps. Results. The typical density in the most prominent bridge of our sample is about 10−16 g cm−3, and the magnetic field strength in the bridge is about 1 to 2 mG. Inside the bridge, the magnetic field structure has an elongated toroidal morphology, and the dust polarization maps trace the complex morphology. In contrast, the magnetic field strength associated with the launching of asymmetric bipolar outflows is significantly more magnetized (~100 mG). At λ = 1.3 mm, and the orientation of the grains in the bridge is very similar for the case accounting for radiative alignment torques (RATs) compared to perfect alignment with magnetic field lines. However, the polarization fraction in the bridge is three times smaller for the RAT scenario than when perfect alignment is assumed. At shorter wavelength (λ ≲ 200 μm), however, dust polarization does not trace the magnetic field because other effects such as self-scattering and dichroic extinction dominate the orientation of the polarization. Conclusions. Compared to the launching region of protostellar outflows, the magnetic field in bridge-like structures is weak. Synthetic dust polarization maps of ALMA Bands 6 and 7 (1.3 mm and 870 μm, respectively) can be used as a tracer of the complex morphology of elongated toroidal magnetic fields associated with bridges.
Exploring Quality and Generalizability in Parameterized Neural Audio Effects

Deep neural networks have shown promise for music audio signal processing applications, often surpassing prior approaches, particularly as end-to-end models in the waveform domain. Yet results to date have tended to be constrained by low sample rates, noise, narrow domains of signal types, and/or lack of parameterized controls (i.e. "knobs"), making their suitability for professional audio engineering workflows still lacking. This work expands on prior research published on modeling nonlinear time-dependent signal processing effects associated with music production by means of a deep neural network, one which includes the ability to emulate the parameterized settings you would see on an analog piece of equipment, with the goal of eventually producing commercially viable, high quality audio, i.e. 44.1 kHz sampling rate at 16-bit resolution. The results in this paper highlight progress in modeling these effects through architecture and optimization changes, towards increasing computational efficiency, lowering signal-to-noise ratio, and extending to a larger variety of nonlinear audio effects. Toward these ends, the strategies employed involved a three-pronged approach: model speed, model accuracy, and model generalizability. Most of the presented methods provide marginal or no increase in output accuracy over the original model, with the exception of dataset manipulation. We found that limiting the audio content of the dataset, for example using datasets of just a single instrument, provided a significant improvement in model accuracy over models trained on more general datasets.
Identifying galaxy groups at high redshift from incomplete spectroscopic data – I. The group finder and application to zCOSMOS

Identifying galaxy groups from redshift surveys of galaxies plays an important role in connecting galaxies with the underlying dark matter distribution. Current and future high-$z$ spectroscopic surveys, usually incomplete in redshift sampling, present both opportunities and challenges to identifying groups in the high-$z$ Universe. We develop a group finder that is based on incomplete redshift samples combined with photometric data, using a machine learning method to assign halo masses to identified groups. Test using realistic mock catalogs shows that $\gtrsim 90\%$ of true groups with halo masses $\rm M_h \gtrsim 10^{12} M_{\odot}/h$ are successfully identified, and that the fraction of contaminants is smaller than $10\%$. The standard deviation in the halo mass estimation is smaller than 0.25 dex at all masses. We apply our group finder to zCOSMOS-bright and describe basic properties of the group catalog obtained.
Random number generators produce collisions: Why, how many and more

Abstract It seems surprising that when applying widely used random number generators to generate one million random numbers on modern architectures, one obtains, on average, about 116 collisions. This article explains why, how to mathematically compute such a number, why they often cannot be obtained in a straightforward way, how to numerically compute them in a robust way and, among other things, what would need to be changed to bring this number below 1. The probability of at least one collision is also briefly addressed, which, as it turns out, again needs a careful numerical treatment. Overall, the article provides an introduction to the representation of floating-point numbers on a computer and corresponding implications in statistics and simulation. All computations are carried out in R and are reproducible with the texttt included in this article.
Visual cohort comparison for spatial single-cell omics-data

Spatially-resolved omics-data enable researchers to precisely distinguish cell types in tissue and explore their spatial interactions, enabling deep understanding of tissue functionality. To understand what causes or deteriorates a disease and identify related biomarkers, clinical researchers regularly perform large-scale cohort studies, requiring the comparison of such data at cellular level. In such studies, with little a-priori knowledge of what to expect in the data, explorative data analysis is a necessity. Here, we present an interactive visual analysis workflow for the comparison of cohorts of spatially-resolved omics-data. Our workflow allows the comparative analysis of two cohorts based on multiple levels-of-detail, from simple abundance of contained cell types over complex co-localization patterns to individual comparison of complete tissue images. As a result, the workflow enables the identification of cohort-differentiating features, as well as outlier samples at any stage of the workflow. During the development of the workflow, we continuously consulted with domain experts. To show the effectiveness of the workflow, we conducted multiple case studies with domain experts from different application areas and with different data modalities.
A new imaging technology based on Compton X-ray scattering.

A feasible implementation of a novel X-ray detector for highly energetic X-ray photons with a large solid angle coverage, optimal for the detection of Compton X-ray scattered photons, is described. The device consists of a 20 cm-thick sensitive volume filled with xenon at atmospheric pressure. When the Compton-scattered photons interact with the xenon, the released photoelectrons create clouds of secondary ionization, which are imaged using the electroluminescence produced in a custom-made multi-hole acrylic structure. Photon-by-photon counting can be achieved by processing the resulting image, taken in a continuous readout mode. Based on Geant4 simulations, by considering a realistic detector design and response, it is shown that photon rates up to at least 1011 photons s-1 on-sample (5 µm water-equivalent cell) can be processed, limited by the spatial diffusion of the photoelectrons in the gas. Illustratively, if making use of the Rose criterion and assuming the dose partitioning theorem, it is shown how such a detector would allow obtaining 3D images of 5 µm-size unstained cells in their native environment in about 24 h, with a resolution of 36 nm.
On the Existence of Shear-current Effects in Magnetized Burgulence

The possibility of explaining shear flow dynamos by a magnetic shear-current (MSC) effect is examined via numerical simulations. Our primary diagnostics is the determination of the turbulent magnetic diffusivity tensor η. In our setup, a negative sign of its component ηyx is necessary for coherent dynamo action by the SC effect. To be able to measure turbulent transport coefficients from systems with magnetic background turbulence, we present an extension of the test-field method (TFM) applicable to our setup where the pressure gradient is dropped from the momentum equation: the nonlinear TFM (NLTFM). Our momentum equation is related to Burgers’ equation and the resulting flows are referred to as magnetized burgulence. We use both stochastic kinetic and magnetic forcings to mimic cases without and with simultaneous small-scale dynamo action. When we force only kinetically, negative ηyx are obtained with exponential growth in both the radial and azimuthal mean magnetic field components. Using magnetokinetic forcing, the field growth is no longer exponential, while NLTFM yields positive ηyx. By employing an alternative forcing from which wavevectors whose components correspond to the largest scales are removed, the exponential growth is recovered, but the NLTFM results do not change significantly. Analyzing the dynamo excitation conditions for the coherent SC and incoherent α and SC effects shows that the incoherent effects are the main drivers of the dynamo in the majority of cases. We find no evidence for MSC-effect-driven dynamos in our simulations.
Fermentation of C14-Labeled Cellobiose by Cellulomonas fimi

Crude cell-free extracts from Cellulomonas fimi contain cellobiose phosphorylase which cleaves cellobiose into glucose and glucose-1-phosphate in the presence of inorganic phosphate. With the aid of this enzyme, two samples of C14-cellobiose labeled in reducing or non-reducing glucosyl moiety were prepared from uniformly labeled C14-glucose or C14-glucose-1-phosphate as substrate, respectively. The labeled preparations have been shown to be radiochemically pure. Analyses of the anaerobic fermentation products from C14-cellobiose by resting cell suspensions showed that both glucose moieties were fermented almost equivalently. However, relatively small differences in specific activities of the products revealed that significantly larger amounts of formic acid and smaller amounts of acetic acid were produced from the reducing glucose moiety than from the other half of the molecule. Succinic and lactic acids appeared to be produced almost equally from both moieties.
Water Use Efficiency and Biomass Partitioning of Three Different Miscanthus Genotypes with Limited and Unlimited Water Supply

Abstract Miscanthus species, which are C4perennial grasses, have a high biomass potential but yields at many sites in Europe can be limited by insufficient water supply and plant survival is endangered under extreme summer drought. A pot experiment was conducted to measure the influence of reduced water supply on the water use efficiency (WUE) and biomass partitioning of three Miscanthus genotypes (M. x giganteus, M. sacchariflorus, and a M. sinensis hybrid) in a controlled environment. The experiment consisted of three phases (phase 1 = 0–20 d; phase 2 = 21–39 d; phase 3 = 40–54 d) punctuated by destructive harvests. In phase 1, soil moisture was non-limiting. In the second and third phases, lowered soil moisture contents induced water deficits. Air vapour pressure deficit (VPD) was 0.49 ± 0.05 kPa. Water deficits caused leaf senescence in M. x giganteus and M. sacchariflorus, but not in the M. sinensis hybrid. Green leaf conductances were lowest in M. sinensis under water deficit, indicating stomatal regulation. Water use efficiency for whole plants of each genotype ranged from 11.5 to 14.2 g dry matter (DM) kg−1H2O but did not differ significantly between genotypes or water treatments under the conditions of this experiment. However, differences in dry matter partitioning to the shoot (the harvestable component) resulted in genotypic differences in WUE, calculated on a harvestable dry matter basis, which ranged from 4.1 g DM kg−1H2O for M. sacchariflorus to 2.2 g DM kg−1H2O for M. x giganteus.
Adapting Workflow Management Systems to BFT Blockchains – The YAWL Example

Blockchain technology provides an auditable and tamper-proof distributed infrastructure that can support distributed workflow management. Blockchains based on a Byzantine Fault Tolerance (BFT) ordering consensus protocol address many of the shortcomings of proof-of-work chains, such as latency and non-finality of consensus. They are a suitable technology to support workflow execution, in large part because applications do not need to be adapted to deal with eventual consistency and delayed consensus of proof-of-work blockchains. Moreover, in contrast to earlier work that has typically developed custom workflow engines using smart contracts, we port an existing, full-featured workflow engine, the YAWL workflow engine, to a blockchain-based workflow management system (WfMS) without smart contracts.
Estimativa da divergência entre ecótipos de braquiária baseada em descritores quantitativos e qualitativos

This study aimed to estimate the genetic divergence between Urochloa brizantha ecotypes based on quantitative, qualitative descriptors and their joint analysis to select the promising to release as cultivars of this species. Eight ecotypes (B1, B2, B3, B4, B5, B6, B8) and cultivar 'Marandu' of U. brizantha were implanted into pickets with 1000m2 each, with two repetitions. Five quantitative descriptors were evaluated [leaf area (ALF), length and width of leaf blades (CLF and LLF, respectively), dry mass (MS), mass of dry matter (MMS) and proportion of leaf blade in MS (PLF)] in two forage samples, being a representative of rainfall, in February 2000, and another in the dry period, in August 2000. It was measured the qualitative descriptors: shear strength (RC), volume of accumulated gas in fast and slow fraction (A and B, respectively), crude protein (CP), neutral detergent fiber (NDF), acid detergent fiber (ADF ), cellulose (CEL), lignin in sulfuric acid (LIG), silica (SIL) and in vitro digestibility of organic matter (IVOMD). There was considerable genetic divergence in U. brizantha ecotypes, especially regarding to quantitative descriptors. Based on the groupings of quantitative, qualitative descriptors and their joint analysis, the grouping containing of B1, B3 and B5 with 'Marandu' can result in promising U. brizantha ecotypes
Time Encoding of Bandlimited Signals: Reconstruction by Pseudo-Inversion and Time-Varying Multiplierless FIR Filtering

We propose an entirely redesigned framework of bandlimited signal reconstruction for the time encoding machine (TEM) introduced by Lazar and Tóth. As the encoding part of TEM consists in obtaining integral values of a bandlimited input over known time intervals, it theoretically amounts to applying a known linear operator on the input. We then approach the general question of signal reconstruction by pseudo-inversion of this operator. We perform this task numerically and iteratively using projections onto convex sets (POCS). The algorithm can be implemented exactly in discrete time with multiplications that are all reduced to scaling by signed powers of two, thanks to the use of relaxation coefficients. Meanwhile, the algorithm achieves a rate of convergence similar to that of Lazar and Tóth. For real-time processing, we propose an approximate time-varying FIR implementation, which avoids the splitting of the input into blocks. We finally propose some preliminary semi-convergence analysis of the algorithm under data noise.
Distributed Optimization With Event-Triggered Communication via Input Feedforward Passivity

In this letter, we address the distributed optimization problem with event-triggered communication by the notion of input feedforward passivity (IFP). First, we analyze the distributed continuous-time algorithm over uniformly jointly strongly connected balanced digraphs in an IFP-based framework. Then, we propose a distributed event-triggered communication mechanism for this algorithm. Next, we discretize the continuous-time algorithm by the forward Euler method with a constant stepsize irrelevant to network size, and show that the discretization can be seen as a stepsize-dependent passivity degradation of the input feedforward passivity. Thus, the discretized system preserves the IFP property and enables the same event-triggered communication mechanism but without Zeno behavior due to the discrete-time nature. Finally, a numerical example is presented to illustrate our results.
Predator recognition and defence strategies in crucian carp, Carassius carassius

Crucian carp from populations that lack piscivores are extremely vulnerable to predation. However, in the presence of piscivores these fish develop an inducible morphological defence, a deep body. This switch from a vulnerable, shallow-bodied morph to a morphologically defended morph makes this species very suitable for investigations of anti-predator strategies, and trade-offs between morphological and behavioural defences. To address these questions, we performed eight different experiments. We found that crucian carp exhibited fright responses to chemical cues from unfamiliar predators (northern pike, perch) when these were fed prey that contained alarm substance (for northern pike: crucian carp, roach; for perch: crucian carp). Cues from small pike that were fed prey that lacked alarm substance (swordtails) caused no significant fright response whereas cues from larger pike with the same diet did. Perch on a chironomid diet elicited weaker but significant fright responses. Starved predators caused as strong fright reactions as recently fed ones did, whereas no response was exhibited towards nonpredatory fish (roach, crucian carp). Crucian carp were able to detect the presence of pike after cues had been diluted to an equivalent of 21000 l, and larger predators elicited stronger fright responses. Prior experience of predators decreased fright responses. In particular, individuals from populations that coexisted with northern pike responded less to chemical cues from northern pike than individuals without prior experience did. Thus, crucian carp may use both alarm-substance related and predator-related cues to identify predators. Further, they were able to discriminate between large and small predators. Finally, individuals from populations that coexist with predators exhibit less pronounced fright responses. These fish have an induced morphological defence, a deep body, which most likely decreases the need for strong antipredator behaviour. (Less)
Heterogeneity in β-Adrenergic Receptor Kinase Expression in the Lung Accounts for Cell-specific Desensitization of the β2-Adrenergic Receptor*

The principal mechanism of homologous desensitization of the β-adrenergic receptor (β2AR) is phosphorylation of the receptor by the βAR kinase (βARK) or other closely related G protein-coupled receptor kinases (GRKs). However, within a single organ such as the lung where many cell types express the receptor, the presence or extent of β2AR desensitization in different cells has been noted to be highly variable. We hypothesized that such variability in desensitization is due to significant cell-type differences in βARK expression and/or function. To approach this, in situ hybridization was carried out in the lung and indeed revealed heterogeneity in βARK gene expression. Quantitative studies using ribonuclease protection assays with cell lines revealed that the level of βARK mRNA in airway smooth muscle cells was ∼20% of that in bronchial epithelial cells and ∼11% of that in mast cells (6.65 ± 0.96 versus 32.6 ± 4.0 and 60.7 ± 1.5 relative units, respectively, p < 0.001). βARK2 gene expression was not detected in any of these cells. At the protein level, βARK expression in airway smooth muscle cells was nearly undetectable, being ∼10-fold less than that expressed on mast cells. The activities of the GRKs in cell extracts were assessed in vitro by quantitating their ability to phosphorylate rhodopsin in the presence of light. Consistent with the gene and protein expression results, a marked discrepancy in activities was observed between extracts derived from mast cells (90.7 ± 0.5 relative units) as compared to airway smooth muscle cells (9.28 ± 0.6 relative units, p < 0.001). In contrast, the activities of protein kinase A (the other kinase that phosphorylates β2AR) in these extracts were not different. We predicted, then, that airway smooth muscle β2AR would undergo minimal short-term (5 min) agonist-promoted desensitization as compared to the β2AR expressed on mast cells. Mast cell cAMP reached maximal levels after 90 s and did not further increase over time, indicative of receptor desensitization in this cell. In contrast, cAMP levels of airway smooth muscle cells did not plateau, increasing at a rate of 103 ± 9% per min, consistent with little desensitization over the study period. We conclude that there is significant cell-type variation in expression of βARK and that such variation is directly related to the extent of short-term agonist-promoted desensitization of the β2AR.
Influence of pleistocene glaciations and human intervention upon mitochondrial DNA diversity in white sturgeon (Acipenser transmontanus) populations

The influence of recent genetic bottlenecks on two Northwest Pacific populations of white sturgeon (Acipenser transmontanus) was studied using restriction enzyme site differences in mitochondrial DNA (mtDNA). A total of 10 mtDNA genotypes were detected in 178 sturgeon from the Columbia and Fraser rivers. Nearly 61% of individuals from both rivers had a common genotype. However, one genotype was found only in the Fraser River. Geographical substructuring was not evident in the phylogenetic analysis. The Columbia River, a Pleistocene refugium, is suggested as the source of founders for the Fraser River following the last glacial recession, about 10 000–12 000 yr ago. MtDNA genotypic frequencies were significantly different between the rivers. Estimates of mtDNA (h) and nucleotide (π) diversity were consistently higher for the recently colonized Fraser River compared with the Columbia River refugium. This condition is the reverse of all known studies of mtDNA diversity between refugium and colonized animal p.