Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantitative Flow Cytometry to Understand Population Heterogeneity in Response to Changes in Substrate Availability in Escherichia coli and Saccharomyces cerevisiae Chemostats

Microbial cells in bioprocesses are usually described with averaged parameters. But in fact, single cells within populations vary greatly in characteristics such as stress resistance, especially in response to carbon source gradients. Our aim was to introduce tools to quantify population heterogeneity in bioprocesses using a combination of reporter strains, flow cytometry, and easily comprehensible parameters. We calculated mean, mode, peak width, and coefficient of variance to describe distribution characteristics and temporal shifts in fluorescence intensity. The skewness and the slope of cumulative distribution function plots illustrated differences in distribution shape. These parameters are person-independent and precise. We demonstrated this by quantifying growth-related population heterogeneity of Saccharomyces cerevisiae and Escherichia coli reporter strains in steady-state of aerobic glucose-limited chemostat cultures at different dilution rates and in response to glucose pulses. Generally, slow-growing cells showed stronger responses to glucose excess than fast-growing cells. Cell robustness, measured as membrane integrity after exposure to freeze-thaw treatment, of fast-growing cells was strongly affected in subpopulations of low membrane robustness. Glucose pulses protected subpopulations of fast-growing but not slower-growing yeast cells against membrane damage. Our parameters could successfully describe population heterogeneity, thereby revealing physiological characteristics that might have been overlooked during traditional averaged analysis.
Effects of Different Methionine Sources on Methionine Metabolism in the IPEC-J2 Cells

As one of the essential amino acids, methionine (Met) plays an important role in biological events such as methylation and antioxidant properties besides its function in protein synthesis. Different Met sources have been used in animal production, but their effects on Met metabolic pathways are not well understood. In the present study, we investigated the effects of different Met sources (L-Met, DL-Met, DL-2-hydroxy-4-(methylthio)butanoic acid (DL-HMTBA), and DL-methionyl-DL-methionine (DL-MM)) on the metabolism of Met in small intestinal porcine epithelial cell line (IPEC-J2) and the contents of extracellular Met sources. The results showed that concentrations of intracellular Met, S-adenosylmethionine (SAM), S-adenosylhomocysteine (SAH), and the ratio of SAM to SAH in the DL-HMTBA group were significantly lower than that in other Met source groups, while the content of 5-methyltetrahydrofolate (5-MTHF) was significantly higher. Moreover, the mRNA levels of MAT2A, AHcy, CBS, MTHFR, and MTR in the DL-HMTBA group were significantly higher than those in other Met source groups. Further study showed that the total content of extracellular Met sources was highest in the DL-HMTBA group, followed by DL-MM group, followed by L-Met and DL-Met groups. These results demonstrated that DL-HMTBA mainly affects the transmethylation and remethylation of Met and it can promote the trans-sulfur metabolism of Met when compared with other Met sources. In addition, most DL-HMTBA and a small amount of DL-MM can escape the intestinal first-pass metabolism and then provide more extracellular Met sources than L-Met and DL-Met. Therefore, this study can provide a theoretical basis for the selection of Met sources in livestock.
Magnitude of Intention to Leave and Associated Factors among Health Workers Working at Primary Hospitals of North Gondar Zone, Northwest Ethiopia: Mixed Methods

Background Human resource is the most crucial resources for the survival of an organization. Intention to leave is an employee's plan to leave their current job in the near future and is used as a proxy indicator for measuring turnover in cross-sectional surveys. In developing countries human resource shortages are not only due to production of health professionals but also because of employee turnover and instability at health facilities. Objective This study aimed to assess the magnitude of intention to leave and associated factors among health workers working at primary hospitals of North Gondar Zone, Northwest Ethiopia. Methods Institution based cross-sectional mixed methods' (both quantitative and qualitative) study design was conducted among health workers working at primary hospitals of North Gondar zone. Self-administered standardized structured questionnaires for quantitative and interview guide for qualitative were used for data collection. Variables having p-value less than 0.2 during bivariable analysis were entered into multivariable logistic regression model. Thematic analysis was done for qualitative data analysis. Results A total of 382 health workers were participated in the study with a response rate of 93.6%. Overall, 67.8% of them were intended to leave their current organization. Age of participants, 20-29 years (AOR=3.96; 95%CI: 1.04, 15.07), living out of family (AOR= 1.73; 95% CI: 1.23, 3.02), opportunity of other job (AOR= 2.04; 95% CI: 1.21, 3.45), performance appraisal system (AOR= 2.97; 95%CI: 1.64, 5.36), and affective commitment (AOR= 3.12; 95% CI: 1.64, 5.92) were the factors affecting health workers intention to leave current organization. Conclusion overall, magnitude of health workers intention to leave their current organization was high. Therefore, healthcare managers, supervisors, and policymakers need to develop and implement retention strategies that aim to improve the retaining of healthcare workers at their working organization such as unifying healthcare providers who are living separately with their families, use evidence-based performance evaluation mechanism, and make efforts to develop a sense of ownership in the health workers, which will reduce health professional's intention to leave their organization.
Transcriptome profiling of the liver among the prenatal and postnatal stages in chickens

The liver is an important organ that has pivotal functions in the synthesis of several vital proteins, the metabolism of various biologically useful materials, the detoxification of toxic substances, and immune defense. Most liver functions are not mature at a young age and many changes happen during postnatal liver development, which lead to differential functions of the liver at different developmental stages. However, the transcriptome details of what changes occur in the liver after birth and the molecular mechanisms for the regulation of the developmental process are not clearly known in chickens. Here, we used RNA-sequencing to analyze the transcriptome of chicken liver from the prenatal (at an embryonic day of 13) to the postnatal stages (at 5 wk and 42 wk of age). A total of approximately 161.17 Gb of raw data were obtained, with 4,127 putative and 539 differentially expressed lncRNAs, and with 13,949 putative and 6,370 differentially expressed mRNAs. Coexpression of lncRNAs-mRNAs in hepatic transcriptome analysis showed that the liver plays important roles in providing energy for organisms through the mitochondrial respiratory chain in chickens, meanwhile, acting as a crucial part of antioxidant stress. The developmental transcriptome date revealed that antioxidant defenses are likely to act on chicken embryo development and that significant functional changes during postnatal liver development are associated with the liver maturation of chickens. These results provide a timeline for the functional transcriptome transition from the prenatal to adult stages in chickens and will be helpful to reveal the underlying molecular mechanisms of liver development.
Suitability of dual-purpose cockerels of 3 different genetic origins for fattening under free-range conditions

The utilization of male chickens for fattening constitutes a potential advantage of the dual-purpose concept. In addition to the use of commercial hybrids, producers could introduce alternative chicken genotypes or further develop local breeds. To gain more information about the genetic effect on growth performance, carcass characteristics, physicochemical meat traits, and sensory attributes, 60 cockerels belonging to Les Bleues (developed from the French breed Bresse Gauloise), Canarian (Spanish local breed), and Dominant Red Barred D459 (DRB D459; commercial dual-purpose hybrid) genotypes were reared under free-range conditions in a warm tropical climate and slaughtered at 15 wk of age. The major findings were as follows: (i) Les Bleues chickens exhibited the best growth rate and the body weight of 2.44 kg reached by this strain at 15 wk would be gained only after 18 to 19 wk with DRB D459 and it would take even 2 wk longer for Canarian breed, according to the growth modeling using the Morgan equation, although the body weights between the latter were statistical similar at 15 wk; (ii) Les Bleues strain had a good capability in terms of meat production performance, presenting carcasses with significantly heavier commercial cuts, and higher fleshiness than the other 2 genotypes; (iii) although significant differences among genotypes appeared in the physical characteristics of the breast meat, especially those concerning the skin and meat color and water-holding capacity, which was significantly reduced for Canarian chickens, no significant differences were detected in the chemical composition and fatty acid profile of the breast meat; (iv) trained panelists (n = 8) pointed out that leg meat of none of the genotypes is better in terms of global appreciation, but untrained consumers (n = 99) perceived that the Les Bleues leg meat was significantly more palatable than the DRB D459 leg meat.
Interleaved Polar (I-Polar) Codes

By inserting interleavers between intermediate stages of the polar encoder, a new class of polar codes, termed interleaved polar (i-polar) codes, is proposed. By the uniform interleaver assumption, we derive the weight enumerating function (WEF) and the input-output weight enumerating function (IOWEF) averaged over the ensemble of i-polar codes. The average WEF can be used to calculate the upper bound on the average block error rate (BLER) of a code selected at random from the ensemble of i-polar codes. Also, we propose a concatenated coding scheme that employs <inline-formula> <tex-math notation="LaTeX">$P$ </tex-math></inline-formula> high rate codes as the outer code and <inline-formula> <tex-math notation="LaTeX">$Q$ </tex-math></inline-formula> i-polar codes as the inner code with an interleaver in between. The average WEF of the concatenated code is derived based on the uniform interleaver assumption. Simulation results show that BLER upper bounds can well predict BLER performance levels of the concatenated codes. The results show that the performance of the proposed concatenated code with <inline-formula> <tex-math notation="LaTeX">$P=Q=2$ </tex-math></inline-formula> is better than that of the CRC-aided i-polar code with <inline-formula> <tex-math notation="LaTeX">$P=Q=1$ </tex-math></inline-formula> of the same length and code rate at high signal-to-noise ratios (SNRs). Moreover, the proposed concatenated code allows multiple decoders to operate in parallel, which can reduce the decoding latency and hence is suitable for ultra-reliable low-latency communications (URLLC).
Is there a fundamental upper limit to the mass of a star cluster?

The discovery around the turn of the millennium of a population of very massive (M⋆ > 2 × 106 M⊙) compact stellar systems (CSS) with physical properties (radius, velocity dispersion, stellar mass etc.) that are intermediate between those of the classical globular cluster (GC) population and galaxies led to questions about their exact nature. Recently a consensus has emerged that these objects, usually called ultracompact dwarfs (UCDs), are a mass-dependent mixture of high-mass star clusters and remnant nuclei of tidally disrupted galaxies. The existence of genuine star clusters with stellar masses >107 M⊙ naturally leads to questions about the upper mass limit of the star cluster formation process. In this work we compile a comprehensive catalogue of CSS, and reinforce the evidence that the true ancient star cluster population has a maximum mass of M⋆ ∼ 5 × 107 M⊙, corresponding to a stellar mass at birth of close to 108 M⊙. We then discuss several physical and statistical mechanisms potentially responsible for creating this limiting mass.
StructureNet

The ability to generate novel, diverse, and realistic 3D shapes along with associated part semantics and structure is central to many applications requiring high-quality 3D assets or large volumes of realistic training data. A key challenge towards this goal is how to accommodate diverse shape variations, including both continuous deformations of parts as well as structural or discrete alterations which add to, remove from, or modify the shape constituents and compositional structure. Such object structure can typically be organized into a hierarchy of constituent object parts and relationships, represented as a hierarchy of n-ary graphs. We introduce StructureNet, a hierarchical graph network which (i) can directly encode shapes represented as such n-ary graphs, (ii) can be robustly trained on large and complex shape families, and (iii) be used to generate a great diversity of realistic structured shape geometries. Technically, we accomplish this by drawing inspiration from recent advances in graph neural networks to propose an order-invariant encoding of n-ary graphs, considering jointly both part geometry and inter-part relations during network training. We extensively evaluate the quality of the learned latent spaces for various shape families and show significant advantages over baseline and competing methods. The learned latent spaces enable several structure-aware geometry processing applications, including shape generation and interpolation, shape editing, or shape structure discovery directly from un-annotated images, point clouds, or partial scans.
Sound source detection, localization and classification using consecutive ensemble of CRNN models

In this paper, we describe our method for DCASE2019 task3: Sound Event Localization and Detection (SELD). We use four CRNN SELDnet-like single output models which run in a consecutive manner to recover all possible information of occurring events. We decompose the SELD task into estimating number of active sources, estimating direction of arrival of a single source, estimating direction of arrival of the second source where the direction of the first one is known and a multi-label classification task. We use custom consecutive ensemble to predict events' onset, offset, direction of arrival and class. The proposed approach is evaluated on the TAU Spatial Sound Events 2019 - Ambisonic and it is compared with other participants' submissions.
A common origin for the circumnuclear disc and the nearby molecular clouds in the Galactic Centre

The origin of the molecular clouds orbiting SgrA* is one of the most debated questions about our Galactic Centre. Here, we present the hydrodynamic simulation of a molecular cloud infalling towards SgrA*, performed with the adaptive-mesh-refinement code ramses. Through such simulation, we propose that the circumnuclear disc and the +20 km s−1 cloud originated from the same tidal disruption episode, occurred less than 1 Myr ago. We also show that recent star formation is to be expected in the +20 km s−1 cloud, as also suggested by recent observations.
The CANDELS/SHARDS Multiwavelength Catalog in GOODS-N: Photometry, Photometric Redshifts, Stellar Masses, Emission-line Fluxes, and Star Formation Rates

We present a WFC3 F160W (H-band) selected catalog in the CANDELS/GOODS-N field containing photometry from the ultraviolet (UV) to the far-infrared (IR), photometric redshifts, and stellar parameters derived from the analysis of the multiwavelength data. The catalog contains 35,445 sources over the 171 arcmin2 of the CANDELS F160W mosaic. The 5σ detection limits (within an aperture of radius 0.″17) of the mosaic range between H = 27.8, 28.2, and 28.7 in the wide, intermediate, and deep regions, which span approximately 50%, 15%, and 35% of the total area. The multiwavelength photometry includes broadband data from the UV (U band from KPNO and LBC), optical (HST/ACS F435W, F606W, F775W, F814W, and F850LP), near-to-mid IR (HST/WFC3 F105W, F125W, F140W, and F160W; Subaru/MOIRCS Ks; CFHT/Megacam K; and Spitzer/IRAC 3.6, 4.5, 5.8, and 8.0 μm), and far-IR (Spitzer/MIPS 24 μm, HERSCHEL/PACS 100 and 160 μm, SPIRE 250, 350 and 500 μm) observations. In addition, the catalog also includes optical medium-band data (R ∼ 50) in 25 consecutive bands, λ = 500–950 nm, from the SHARDS survey and WFC3 IR spectroscopic observations with the G102 and G141 grisms (R ∼ 210 and 130). The use of higher spectral resolution data to estimate photometric redshifts provides very high, and nearly uniform, precision from z = 0–2.5. The comparison to 1485 good-quality spectroscopic redshifts up to z ∼ 3 yields Δz/(1 + zspec) = 0.0032 and an outlier fraction of η = 4.3%. In addition to the multiband photometry, we release value-added catalogs with emission-line fluxes, stellar masses, dust attenuations, UV- and IR-based star formation rates, and rest-frame colors.
Global behaviors of defocusing semilinear wave equations

In this paper, we investigate the global behaviors of solutions to defocusing semilinear wave equations in $\mathbb{R}^{1+d}$ with $d\geq 3$. We prove that in the energy space the solution verifies the integrated local energy decay estimates for the full range of energy subcritical and critical power. For the case when $p>1+\frac{2}{d-1}$, we derive a uniform weighted energy bound for the solution as well as inverse polynomial decay of the energy flux through hypersurfaces away from the light cone. As a consequence, the solution scatters in the energy space and in the critical Sobolev space for $p$ with an improved lower bound. This in particular extends the existing scattering results to higher dimensions without spherical symmetry.
An Episodic Wide-angle Outflow in HH 46/47

During star formation, the accretion disk drives fast MHD winds, which usually contain two components, a collimated jet and a radially distributed wide-angle wind. These winds entrain the surrounding ambient gas producing molecular outflows. We report a recent observation of 12CO (2–1) emission of the HH 46/47 molecular outflow by the Atacama Large Millimeter/submillimeter Array, in which we identify multiple wide-angle outflowing shell structures in both the blueshifted and redshifted outflow lobes. These shells are highly coherent in position–position–velocity space, extending to ≳40–50 km s−1 in velocity and 104 au in space, with well-defined morphology and kinematics. We suggest these outflowing shells are the result of the entrainment of ambient gas by a series of outbursts from an intermittent wide-angle wind. Episodic outbursts in collimated jets are commonly observed, yet detection of a similar behavior in wide-angle winds has been elusive. Here we show clear evidence that the wide-angle component of the HH 46/47 protostellar outflows experiences variability similar to that seen in the collimated component.
Fast convergence of empirical barycenters in Alexandrov spaces and the Wasserstein space

This work establishes fast rates of convergence for empirical barycenters over a large class of geodesic spaces with curvature bounds in the sense of Alexandrov. More specifically, we show that parametric rates of convergence are achievable under natural conditions that characterize the bi-extendibility of geodesics emanating from a barycenter. These results largely advance the state-of-the-art on the subject both in terms of rates of convergence and the variety of spaces covered. In particular, our results apply to infinite-dimensional spaces such as the 2-Wasserstein space, where bi-extendibility of geodesics translates into regularity of Kantorovich potentials.
Homogeneous liaison and the sequentially bounded licci property

In CI-Liaison, significant effort has been made to study ideals that are in the linkage class of a complete intersection, which are called licci ideals. In a polynomial ring, recently E. Chong defined a "sequentially bounded" condition on the degrees of the forms generating the regular sequences, and used this condition to find a large class of licci ideals satisfying the Eisenbud-Green-Harris Conjecture (among them, grade $3$ homogeneous Gorenstein ideals). He raised the question of whether all homogeneous licci ideals are sequentially bounded licci. In this paper we construct a class of examples that are homogeneously licci, but not sequentially bounded licci, thus answering his question in the negative. The structure of certain Betti tables plays a central role in our proof.
The 2017 Failed Outburst of GX 339–4: Relativistic X-Ray Reflection near the Black Hole Revealed by NuSTAR and Swift Spectroscopy

We report on the spectroscopic analysis of the black hole binary GX 339−4 during its recent 2017–2018 outburst, observed simultaneously by the Swift and NuSTAR observatories. Although during this particular outburst the source failed to make state transitions, and despite Sun constraints during the peak luminosity, we were able to trigger four different observations sampling the evolution of the source in the hard state. We show that even for the lowest-luminosity observations the NuSTAR spectra show clear signatures of X-ray reprocessing (reflection) in an accretion disk. Detailed analysis of the highest signal-to-noise spectra with our family of relativistic reflection models relxill indicates the presence of both broad and narrow reflection components. We find that a dual-lamppost model provides a superior fit when compared to the standard single lamppost plus distant neutral reflection. In the dual-lamppost model two sources at different heights are placed on the rotational axis of the black hole, suggesting that the narrow component of the Fe K emission is likely to originate in regions far away in the disk, but still significantly affected by its rotational motions. Regardless of the geometry assumed, we find that the inner edge of the accretion disk reaches a few gravitational radii in all our fits, consistent with previous determinations at similar luminosity levels. This confirms a very low degree of disk truncation for this source at luminosities above ∼1% Eddington. Our estimates of Rin reinforce the suggested behavior for an inner disk that approaches the innermost regions as the luminosity increases in the hard state.