Miracle-dz/UniFAR-FTUs huggingface dataset:
The physical and chemical structure of Sagittarius B2 - II. Continuum millimeter emission of Sgr B2(M) and Sgr B2(N) with ALMA

Context. The two hot molecular cores Sgr B2(M) and Sgr B2(N), which are located at the center of the giant molecular cloud complex Sagittarius B2, have been the targets of numerous spectral line surveys, revealing a rich and complex chemistry. Aims. We seek to characterize the physical and chemical structure of the two high-mass star-forming sites Sgr B2(M) and Sgr B2(N) using high-angular resolution observations at millimeter wavelengths, reaching spatial scales of about 4000 au. Methods. We used the Atacama Large Millimeter/submillimeter Array (ALMA) to perform an unbiased spectral line survey of both regions in the ALMA band 6 with a frequency coverage from 211 GHz to 275 GHz. The achieved angular resolution is 0.4, which probes spatial scales of about 4000 au, i.e., able to resolve different cores and fragments. In order to determine the continuum emission in these line-rich sources, we used a new statistical method, STATCONT, which has been applied successfully to this and other ALMA datasets and to synthetic observations. Results. We detect 27 continuum sources in Sgr B2(M) and 20 sources in Sgr B2(N). We study the continuum emission variation across the ALMA band 6 (i.e., spectral index) and compare the ALMA 1.3 mm continuum emission with previous SMA 345 GHz and VLA 40 GHz observations to study the nature of the sources detected. The brightest sources are dominated by (partially optically thick) dust emission, while there is an important degree of contamination from ionized gas free-free emission in weaker sources. While the total mass in Sgr B2(M) is distributed in many fragments, most of the mass in Sgr B2(N) arises from a single object, with filamentary-like structures converging toward the center. There seems to be a lack of low-mass dense cores in both regions. We determine H_2 volume densities for the cores of about 10^7–10^9 cm^(-3) (or 10^5–10^7 M_⊙ pc^(-3)), i.e., one to two orders of magnitude higher than the stellar densities of super star clusters. We perform a statistical study of the chemical content of the identified sources. In general, Sgr B2(N) is chemically richer than Sgr B2(M). The chemically richest sources have about 100 lines per GHz and the fraction of luminosity contained in spectral lines at millimeter wavelengths with respect to the total luminosity is about 20%–40%. There seems to be a correlation between the chemical richness and the mass of the fragments, where more massive clumps are more chemically rich. Both Sgr B2(N) and Sgr B2(M) harbor a cluster of hot molecular cores. We compare the continuum images with predictions from a detailed 3D radiative transfer model that reproduces the structure of Sgr B2 from 45 pc down to 100 au. Conclusions. This ALMA dataset, together with other ongoing observational projects in the range 5 GHz to 200 GHz, better constrain the 3D structure of Sgr B2 and allow us to understand its physical and chemical structure.
Emergent remote stress-focusing drive submucosal collagen fiber remodeling in intestinal anastomotic surgery

Following resection of a diseased segment of intestine, a reconnection (anastomotic) geometry is chosen to reduce postoperative stress and optimize outcomes. As proper healing of an intestinal anastomosis is strongly affected by its mechanobiology, much attention has been devoted to the conical structures formed along the suture lines, where stress-focusing is expected. However, geometric considerations reveal that in addition to the obvious loci of stress-focusing, additional remote locations of stress-focusing may form. We identify conical structures that inevitably form within regions of otherwise uninterrupted tissue. In this work we use geometric analysis, finite element modeling (FEM), and in-vivo experiments to investigate these emergent stress-focusing structures, their mechanical stresses, and the resulting submucosal collagen fiber re-orientation, as these naturally arise in the side-to-side small bowel anastomosis (SBA), the most common configuration performed in patients. FEM predicts the appearance of remote high-stress regions. Allowing for tissue remodeling, our simulations also predict an increased dispersion of submucosal collagen fibers in these regions. In-vivo experiments performed on ten-week-old male C57BL/6 mice assigned the creation of side-to-side SBA or sham-laparotomy corroborate this result. Anastomoses were analyzed at sacrifice on post-operative day (POD) 14 and 88 with histologic-sectioning, staining, high magnification imaging, and submucosal collagen fiber orientation (κ) mapping. The mean and variance of κ, a measure of collagen fiber dispersion, at POD-14 far from the anastomosis show similar values to those obtained for sham-operated mice, while the FEM-predicted loci of stress-focusing display statistically significant higher values. The values at POD-88 at all loci show no statistically-significant difference, and agree with those of the sham-operated mice at POD-14.
Dense Kondo Behavior in CexLa1-xAl2

We have measured the electrical resistivity and the magnetic susceptibility of Ce x La 1- x Al 2 ( x =0–1) single crystals to study the dense Kondo phenomenon. The magnetic resistivities per molar cerium, which result from the combined effect of the crystalline field and the Kondo scattering, are found to be almost the same at higher temperatures than ca. 50 K. The Curie temperature of ca. 30 K and the effective Bohr magneton of ca. 2.5 µ B are also independent of the concentration of cerium ion. These data show that the dilute Kondo state is continuously connected to the dense Kondo state as a linear function of cerium concentration in the paramagnetic region.
Galactic Angular Momentum in Cosmological Zoom-in Simulations. I. Disk and Bulge Components and the Galaxy–Halo Connection

We investigate the angular momentum evolution of four disk galaxies residing in Milky-Way–sized halos formed in cosmological zoom-in simulations with various sub-grid physics and merging histories. We decompose these galaxies, kinematically and photometrically, into their disk and bulge components. The simulated galaxies and their components lie on the observed sequences in the j*–M* diagram, relating the specific angular momentum and mass of the stellar component. We find that galaxies in low-density environments follow the relation past major mergers, with in the case of strong feedback, when bulge-to-disk ratios are relatively constant, and in the other cases, when secular processes operate on shorter timescales. We compute the retention factors (i.e., the ratio of the specific angular momenta of stars and dark matter) for both disks and bulges and show that they vary relatively slowly after averaging over numerous but brief fluctuations. For disks, the retention factors are usually close to unity, while for bulges, they are a few times smaller. Our simulations therefore indicate that galaxies and their halos grow in a quasi-homologous way.
Scalar Fields: From Domain Walls to Nanotubes and Fulerenes

In this work we review some features of topological defects in field theory models for real scalar fields. We investigate topological defects in models involving one and two or more real scalar fields. In models involving a single field we examine two different subclasses of models, which support one or more topological defects. In models involving two or more real scalar fields, we explore the presence of defects that live inside topological defects, and junctions and networks of defects. In the case of junctions of defects we investigte structures that simulate nanotubes and fulerenes. Our investigations may also be used to describe nonlinear properties of polymers, Langmuir films and optical solitons in fibers.
In Silico, Brain Mesh Platform for Computing Topographic Dependent Internal Facets

Individualized and anatomically correct computational models of the brain can be leveraged to improve knowledge of drug dispersal following simulation of drug delivery. Using a patient’s magnetic resonance image (MRI) scans, we were able to reconstruct the pial surface of the brain of the left hemisphere with strong anatomic accuracy. We then established the major internal features, including the lateral ventricle, a tumor, and drug delivery catheters. These were able to include relevant tissue characteristics such as porosity and permeability in the Multiphysics platform COMSOL to create a platform for brain modeling. To test the performance of this platform, we simulated direct drug infusion in both a healthy patient brain and a diseased patient model, focusing on glioblastoma (GBM). Using this platform, we simulated perturbed convection enhanced delivery of a cancer medication (similar to temozolomide (TMZ) but modeled using methylene blue) to the tumor. Consequently, with our patient derived model, we are able to simulate solute dispersal and fluid flow representative of in vivo conditions.
Optogenetic control of beta-carotene bioproduction in yeast across multiple lab-scales

Optogenetics arises as a valuable tool to precisely control genetic circuits in microbial cell factories. Light control holds the promise of optimizing bioproduction methods and maximize yields, but its implementation at different steps of the strain development process and at different culture scales remains challenging. In this study, we aim to control beta-carotene bioproduction using optogenetics in Saccharomyces cerevisiae and investigate how its performance translates across culture scales. We built four lab-scale illumination devices, each handling different culture volumes, and each having specific illumination characteristics and cultivating conditions. We evaluated optogenetic activation and beta-carotene production across devices and optimized them both independently. Then, we combined optogenetic induction and beta-carotene production to make a light-inducible beta-carotene producer strain. This was achieved by placing the transcription of the bifunctional lycopene cyclase / phytoene synthase CrtYB under the control of the pC120 optogenetic promoter regulated by the EL222-VP16 light-activated transcription factor, while other carotenogenic enzymes (CrtI, CrtE, tHMG) were expressed constitutively. We show that illumination, culture volume and shaking impact differently optogenetic activation and beta-carotene production across devices. This enabled us to determine the best culture conditions to maximize light-induced beta-carotene production in each of the devices, reaching a content of up to 880 μg/gCDW. Our study exemplifies the stakes of scaling up optogenetics in devices of different lab scales and sheds light on the interplays and potential conflicts between optogenetic control and metabolic pathway efficiency. As a general principle, we propose that it is important to first optimize both components of the system independently, before combining them into optogenetic producing strains to avoid extensive troubleshooting. We anticipate that our results can help designing both strains and devices that could eventually lead to larger scale systems in an effort to bring optogenetics to the industrial scale.
Best Practices for Interpretable Machine Learning in Computational Biology

Advances in machine learning (ML) have enabled the development of next-generation prediction models for complex computational biology problems. These developments have spurred the use of interpretable machine learning (IML) to unveil fundamental biological insights through data-driven knowledge discovery. However, in general, standards and guidelines for IML usage in computational biology have not been well-characterized, representing a major gap toward fully realizing the potential of IML. Here, we introduce a workflow on the best practices for using IML methods to perform knowledge discovery which covers verification strategies that bridge data, prediction model, and explanation. We outline a workflow incorporating these verification strategies to increase an IML method’s accountability, reliability, and generalizability. We contextualize our proposed workflow in a series of widely applicable computational biology problems. Together, we provide an extensive workflow with important principles for the appropriate use of IML in computational biology, paving the way for a better mechanistic understanding of ML models and advancing the ability to discover novel biological phenomena.
Robust Time Series Chain Discovery with Incremental Nearest Neighbors

Time series motif discovery has been a fundamental task to identify meaningful repeated patterns in time series. Recently, time series chains (TSCs) were introduced as an expansion of time series motifs to identify the continuous evolving patterns in time series data. TSCs are shown to be able to reveal latent continuous evolving trends in the time series, and identify precursors of unusual events in complex systems. However, existing TSC definitions lack the ability to accurately cover the evolving part of a time series: the discovered chains can be easily cut by noise and can include non-evolving patterns, making them impractical in real-world applications. In this work, we introduce a new TSC definition based on an incremental nearest neighbor concept which can better locate the evolving patterns while excluding the non-evolving ones, and propose two new quality metrics to rank the discovered chains. With extensive empirical evaluations, we demonstrate that the proposed TSC definition is significantly more robust to noise than the state of the art, and the top ranked chains discovered can reveal meaningful regularities in a variety of real world datasets.
Optimization of Assisted Search Over Server-Mediated Peer-to-peer Networks

Accompanied by improving accessibility of data and storage and the invention of the blockchain economy, advantages of the peer-to-peer network in privacy and efficiency over server-client systems have become more significant recently. One of the most popular applications of peer-to-peer networks is file transferring, where each peer stores a partial segment of a file and the requester can aggregate each piece into a single file when downloading it. To optimize the performance of file transmission, one goal is to increase the searching speed for the file location over the network. In this paper, we analyze the server-mediated peer-to-peer networks, which is an uncommon architecture mentioned in previous works but can potentially improve the search speed, and minimize the average number of hops during flooding search.
Value Chain Analysis to Identify Internet of Things Use Cases in The Indonesian Pharmaceutical Industry

The coronavirus pandemic has not only boosted the revenue of many pharmaceutical companies, it has also boosted their reputation. The value of pharmaceutical innovation is unquestionable, after the COVID-19 vaccine was developed at such a rapid pace. Besides, the coronavirus pandemic has exposed weakness in the industry's global supply chains and while consumer confidence is recovering, it is far from normal. Businesses in this sector are likely to face a number of major risks through the end of the year. The purpose of this study is to provide insights regarding challenges faced by the Indonesian pharmaceutical industry as driver to conduct value chain analysis in order to identify the prioritized internet of things use cases so pharmaceutical companies in Indonesia will be able to drive both top-line and operational efficiencies.
A hybrid organic/inorgaic scintillator for high performance measurements

New experimental research programs in the field of neutrino physics are calling for new detectors with large masses, high energy resolution and good background rejection capabilities. This paper presents a novel hybrid organic/inorganic scintillator, which is able to improve on all three aspects simultaneously. This scintillator consists of microscopic grains of inorganic crystals suspended in an organic scintillating carrier medium. Due to multiple scattering off the crystals, this scintillator appears opaque over longer distances and is intended for use in specialized detectors. Thanks to the crystal phase it can natively incorporate a large variety of elements in large quantities, so that a sufficiently large detector can reach elemental loadings on the ton- or multiton scale. At the same time, this composition can produce very high light outputs and provides additional particle identification capabilities. This scintillator concept is expected to provide significant advantages for future neutrino experiments, like searches of neutrinoless double beta experiments and reactor antineutrino physics.
Affective Adaptation Design for Better Gaming Experiences

 Abstract— Affective adaptation is a creative way for game designers to add an extra layer of engagement to their productions. When player’s emotions are an explicit factor in mechanics design, endless possibilities for imaginative gameplay emerge. Whilst gaining popularity, existing affective game research mostly runs controlled experiments in restrictive settings and rely on one or more specialist devices for measuring player’s emotional state. These conditions albeit effective, are not necessarily realistic. Moreover, the simplified narrative and intrusive wearables may not be suitable for players. This exploratory study investigates delivering an immersive affective experience in the wild with minimal requirements, in an attempt for the average developer to reach the average player. A puzzle game is created with rich narrative and creative mechanics. It employs both explicit and implicit adaptation and only requires a web camera. Participants played the game on their own machines in various settings. Whilst it was rated feasible, very engaging and enjoyable, it remains questionable whether a fully immersive experience was delivered due to the limited sample size.
Kinematic Diagnostics of Disks around Young Stars: CO Overtone Emission from WL 16 and 1548C27

We report high spectral resolution observations of the CO vibrational overtone emission from the young stellar object 1548C27; our observations include both the CO(2-0) and CO(5-3) bandhead regions. These data and similar observations of the young stellar object WL16, reported in a previous contribution to this journal, provide some of the most compelling evidence to date for the existence of inner disks around young stars. We describe the simple procedure that we use to synthesize bandhead emission from disks including the effect of thermal dissociation of CO and non-LTE excitation of the vibrational levels. Using this spectral synthesis procedure to extract the kinematics and physical properties of the emitting gas from the overtone data, we show how these high signal-to-noise data are also powerful probes of the stellar and inner disk properties of these systems. Our modeling is consistent with the identification of WL16 and 1548C27 as Herbig AeBe stars with stellar masses of approximately 2 and 4 solar masses, respectively. Thus, the kinematic signature of rotating disks in the overtone spectra of these sources provides strong support for the role of accretion disks in the formation of intermediate mass stars. For both WL16 and 1548C27, we interpret our modeling results as indicating that the overtone emission arises from a temperature inversion region in the inner disk atmosphere. We also find evidence for suprathermally broadened lines and are able to place useful constraints on the radial temperature and column density distributions of the CO line-formation region of the disk atmosphere.
VLT observations of the z=6.28 quasar SDSS 1030+0524

We present new VLT spectroscopic observations of the most distant quasar known, SDSS J1030+0524 at z=6.28 which was recently discovered by the Sloan Digital Sky Survey. We confirm the presence of a complete Gunn-Peterson trough caused by neutral hydrogen in the intergalactic medium. There is no detectable flux over the wavelength range from 8450 to 8710 A. We set an improved limit on the drop of the flux level blueward of the Ly alpha line: a factor of > 200. Below 8450 A the spectrum shows a rise in flux, with a large fraction (> 60 %) of the total emission produced by few narrow features of transmitted flux. We discuss the obvious proximity effect around this quasar, with the presence of transmitted flux with many absorption features in a region of about 23h^{-1} comoving Mpc. If assuming the surrounding medium were completely neutral, the size of this region would imply a quasar lifetime of \~1.3x10^7 years. We also present near-IR spectroscopy of both SDSS J1030+0524 and of SDSS J1306+05, the second most distant quasar known at redshift 6.0. We combine measurements of the CIV line and limits on the HeII emission with the NV line measurements from the optical spectra to derive line ratios, and by implication the abundances of these early quasar environments. The results are indistinguishable from those of lower redshift quasars and indicate little or no evolution in the abundances from z ~ 6 to z ~ 2. The line ratios suggest supersolar metallicities, implying that the first stars around the quasars must have formed at least a few hundreds of Myrs prior to the observation, i.e. at redshift higher than 8.
Satellite observations of thought experiments close to a black hole

Since black holes are `black', methods for their identification must necessarily be indirect. Due to the very special boundary conditions on the horizon, the advective flow behaves in a particular way, which includes the formation of a centrifugal-pressure-dominated boundary layer or CENBOL where much of the infall energy is released and outflows are generated. The observational aspects of black holes must depend on the steady and time-dependent properties of this boundary layer. Several observational results are written down in this review which seem to support the predictions of thought experiments based on this advective accretion/outflow model. In future, when gravitational waves are detected, some other predictions of this model could be tested as well.
Cadmium Uptake by Biomass of Lysinibacillus sphaericus KY203810 and Enterobacter cloacae KY203811 from Steel Company Dumpsite.

Biosorption of cadmium (Cd 2+ ) was investigated using metal tolerant bacterial strains isolated from a steel company dumpsite. Various environmental conditions that can affect cadmium uptake were determined with the aim of optimizing its uptake using various isotherm models. Metal tolerant bacteria were screened using agar well diffusion technique. Isolates DNA were extracted, sequenced and identified using 16S rRNA phylogenetic approach. They were identified as Lysinibacillus sphaericus KY203810 and Enterobacter cloacae KY203811 after submitting the sequence to NCBI. Effects of biosorption conditions: pH, biomass concentration, temperature and contact time were studied. Equilibrium isotherms were also determined. The result showed that optimum sorption of Cd 2+ was achieved at pH 5.0, biomass dose of 1 g/L, temperature of 25 o C and contact time of 24 hours for L. sphaericus. Cadmium sorption by E. cloacae was at pH 9.0, biomass dose of 1 g/L, 35 o C and contact time of 12 hours. Adsorption data fitted isotherm models postulated by Langmuir and Freundlich. Maximum cadmium biosorption capacities for L. sphaericus and E. cloacae were 50.15 and 57.59 mg/g respectively, indicating higher biosorption efficiency of E. cloacae cells to heavy metals compared to L. sphaericus . This study showed that Lysinibacillus sphaericus KY203810 and Enterobacter cloacae KY203811 can effectively act as biosorbent for Cd 2+ sorption from solution.