Miracle-dz/UniFAR-FTUs huggingface dataset:
A Case Series Exploration of Multi-Regional Expression Heterogeneity in Triple-Negative Breast Cancer Patients

Extensive intratumoral heterogeneity (ITH) is believed to contribute to therapeutic failure and tumor recurrence, as treatment-resistant cell clones can survive and expand. However, little is known about ITH in triple-negative breast cancer (TNBC) because of the limited number of single-cell sequencing studies on TNBC. In this study, we explored ITH in TNBC by evaluating gene expression-derived and imaging-derived multi-region differences within the same tumor. We obtained tissue specimens from 10 TNBC patients and conducted RNA sequencing analysis of 2–4 regions per tumor. We developed a novel analysis framework to dissect and characterize different types of variability: between-patients (inter-tumoral heterogeneity), between-patients across regions (inter-tumoral and region heterogeneity), and within-patient, between-regions (regional intratumoral heterogeneity). We performed a Bayesian changepoint analysis to assess and classify regional variability as low (convergent) versus high (divergent) within each patient feature (TNBC and PAM50 subtypes, immune, stroma, tumor counts and tumor infiltrating lymphocytes). Gene expression signatures were categorized into three types of variability: between-patients (108 genes), between-patients across regions (183 genes), and within-patients, between-regions (778 genes). Based on the between-patient gene signature, we identified two distinct patient clusters that differed in menopausal status. Significant intratumoral divergence was observed for PAM50 classification, tumor cell counts, and tumor-infiltrating T cell abundance. Other features examined showed a representation of both divergent and convergent results. Lymph node stage was significantly associated with divergent tumors. Our results show extensive intertumoral heterogeneity and regional ITH in gene expression and image-derived features in TNBC. Our findings also raise concerns regarding gene expression based TNBC subtyping. Future studies are warranted to elucidate the role of regional heterogeneity in TNBC as a driver of treatment resistance.
Hybrid atomistic-continuum methods for multiscale hydrodynamics

We discuss hybrid atomistic-continuum methods for multiscale hydrodynamic applications. Both dense fluid and dilute gas formulations are considered. The choice of coupling method and its relation to the fluid physics is discussed. The differences in hybrid methods resulting from underlying compressible and incompressible continuum formulations as well as the importance of timescale decoupling are highlighted. We also discuss recently developed compressible and incompressible hybrid methods for dilute gases. The incompressible framework is based on the Schwarz alternating method whereas the compressible method is a multi-species, fully adaptive mesh and algorithm refinement approach which introduces the direct simulation Monte Carlo at the finest level of mesh refinement.
BRITEning up the Be Phenomenon

Observations of 25 Ori much expand the picture derived of other early-type Be stars with BRITE and SMEI. Two instead of one difference frequencies rule the variability: (a) The lower one, 0.0129 c/d, is the frequency of events with full amplitudes of 100-200 mmag which may signal mass loss possibly driven by the higher one, 0.1777 c/d. (b) Much of the entire power spectrum is a tightly woven network of combination frequencies: (i) Below 0.25\,c/d, numerous frequencies are difference frequencies. (ii) Many frequencies above 2.5 c/d can be represented as sum frequencies and in a few cases as harmonics. (iii) Many frequencies between 1.1 and 1.75\,c/d can be portrayed as parents of combination frequencies. The number and fraction of combination frequencies increases steeply with decreasing amplitude and and accuracy of the frequency matching.
Vegetation structure derived from airborne laser scanning to assess species distribution and habitat suitability: The way forward

Ecosystem structure, especially vertical vegetation structure, is one of the six essential biodiversity variable classes and is an important aspect of habitat heterogeneity, affecting species distributions and diversity by providing shelter, foraging, and nesting sites. Point clouds from airborne laser scanning (ALS) can be used to derive such detailed information on vegetation structure. However, public agencies usually only provide digital elevation models, which do not provide information on vertical vegetation structure. Calculating vertical structure variables from ALS point clouds requires extensive data processing and remote sensing skills that most ecologists do not have. However, such information on vegetation structure is extremely valuable for many analyses of habitat use and species distribution. We here propose 10 variables that should be easily accessible to researchers and stakeholders through national data portals. In addition, we argue for a consistent selection of variables and their systematic testing, which would allow for continuous improvement of such a list to keep it up‐to‐date with the latest evidence. This initiative is particularly needed not only to advance ecological and biodiversity research by providing valuable open datasets but also to guide potential users in the face of increasing availability of global vegetation structure products.
The Impact of Overweight and Obesity on Reduced-Port Laparoscopic Distal Gastrectomy for Gastric Cancer Patients: A Propensity Score Matching Analysis of a Single-Institution Data

This study aimed to investigate the short-term postoperative outcomes of reduced-port laparoscopic distal gastrectomy and demonstrate its safety and feasibility in overweight and obese patients with gastric cancer. The medical records of 211 patients who underwent reduced-port laparoscopic distal gastrectomy, between August 2014 and April 2020, were reviewed. After propensity score matching, they were divided into a non-overweight group (n = 68) and overweight group (n = 68). Operative details and short-term surgical outcomes were compared between two groups. Reduced-port laparoscopic distal gastrectomy in overweight group showed statistically longer operation time (200.59 vs. 208.68 min, p = 0.044), higher estimated bleeding volume (40.96 vs. 58.01 mL, p = 0.001), and lesser number of harvested lymph nodes (36.81 vs. 32.13, p = 0.039). However, no significant differences were found in hospital course and other surgical outcomes. There was no mortality in either group, and the postoperative morbidity rate was not significantly different (14.7% vs. 16.2%). In the subgroup analysis, overweight and obesity did not significantly affect postoperative complication rates (16.2% vs. 16.2%, p = 1). We demonstrated comparable short-term surgical outcomes of reduced-port laparoscopic distal gastrectomy between the two groups (p = 0.412~1). Reduced-port laparoscopic distal gastrectomy was safe in overweight and obese patients with gastric cancer.
THE GRAY EXTINCTION OF THE IONIZING CLUSTER IN NGC 3603 FROM ULTRAVIOLET TO OPTICAL WAVELENGTHS

We use photometry in the F220W, F250W, F330W, F435W filters from the High Resolution Channel of the Advanced Camera for Surveys and photometry in the F555W, F675W, and F814W filters from the Wide Field and Planetary Camera 2 aboard the Hubble Space Telescope to derive individual stellar reddenings and extinctions for stars in the HD 97950 cluster in the giant H ii region NGC 3603. The mean line of sight reddening for about a hundred main-sequence member stars inside the cluster is E ( F 435 W − F 555 W ) = 1.33 ± 0.12 ? > mag. After correcting for foreground reddening, the total to selective extinction ratio is R F 555 W = 3.75 ± 0.87 ? > in the cluster. Within the standard deviation associated with E ( λ − F 555 W ) / E ( F 435 W − F 555 W ) ? > in each filter, the cluster extinction curve at ultraviolet wavelengths tends to be grayer than the average Galactic extinction laws from Cardelli et al. and Fitzpatrick. It is closer to the extinction law derived by Calzetti et al. for starburst galaxies, where the 0.2175 μm bump is absent. This indicates an anomalous extinction in the HD 97950 cluster, which may due to the clumpy dust distribution within the cluster, and the size of dust grains being larger than the average Galactic ISM.
Relativistic spectroscopy of plasma-embedded Li-like systems with screening effects in two-body Debye potentials

The spectroscopic properties of Li atoms and Li-like Ca and Ti ions in the plasma environment are investigated using a relativistic coupled-cluster (RCC) method. Assuming that the plasma is of low density and very hot, we consider the Debye model with two approximations to account for the screening effects: (i) in the nuclear potential alone and (ii) in both the nuclear and the electron–electron interaction potentials. Also, calculations for the energies and the lifetimes of the atomic states are carried out for plasma-free systems to check their accuracy, after which they are investigated in the plasma environment. It is observed that screenings in the electron–electron interaction potentials stabilize the systems more than when the screenings are present only in the nuclear potential. Similarly, the blue and red shifts in the &Dgr; n = 0 ? > and &Dgr; n ≠ 0 ? > transition lines (with the principal quantum number n) of the Li-like ions observed in the (i) approximation are altered in the (ii) approximation. The level crossings among the energy levels are observed for large screening effects and are found to be prominent in the states of higher orbital angular momentum. The lifetimes of many low-lying states of the allowed transitions are estimated by considering different plasma screening strengths.
Dominant Hydro-Climatic Drivers of Water Temperature, Salinity, and Flow Variability for the Large-Scale System of the Baltic Coastal Wetlands

For the large-scale coastal wetland system of the Baltic Sea, this study develops a methodology for investigating if and to what degree the variability and changes in certain hydro-climatic drivers control key coastal–marine physical conditions. The studied physical conditions include: (a) water temperature, (b) water salinity, and (c) flow structures (magnitudes and directions of flows between marine basins and the associated coastal zones and wetlands). We use numerical simulations of three hydro-climatically distinct cases to investigate the variations in hydro-climatic drivers and the resulting physical conditions (a–c) among the cases. The studied hydro-climatic forcing variables are: net surface heat flux, wind conditions, saltwater influx from the North Sea, and freshwater runoff from land. For these variables, the available observation-based data show that the total runoff from land is significantly and positively correlated with precipitation on the sea itself, and negatively correlated with saltwater influx from the North Sea to the Baltic Sea. Overall, the physical condition (a–c) variability in the Baltic Sea and its coastal zones is found to be pairwise well-explained by simulation case differences as follows: (a) Net heat flux is a main control of sea water temperature. (b) Runoff from land, along with the correlated salt water influx from the North Sea, controls average sea salinity; with the variability of local river discharges shifting some coastal zones to deviate from the average sea condition. (c) Wind variability and change control the Baltic Sea flow structure, primarily in terms of flow magnitude and less so in terms of flow direction. For specific coastal wetland zones, considerable salinity differences from average Baltic Sea conditions (due to variability in local river discharges) are found for the coasts of Finland and Estonia, while the coastal wetland zones of south-eastern Sweden, and of Estonia and Latvia, emerge as particularly sensitive to wind shifts.
Magnetic fields during galaxy mergers

Galaxy mergers are expected to play a central role for the evolution of galaxies, and may have a strong impact on their magnetic fields. We present the first grid-based 3D magneto-hydrodynamical simulations investigating the evolution of magnetic fields during merger events. For this purpose, we employ a simplified model considering the merger event of magnetized gaseous disks in the absence of stellar feedback and without a stellar or dark matter component. We show that our model naturally leads to the production of two peaks in the evolution of the average magnetic field strength within 5 kpc, within 25 kpc and on scales in between 5 and 25 kpc. The latter is consistent with the peak in the magnetic field strength reported by Drzazga et al. (2011) in a merger sequence of observed galaxies. We show that the peak on the galactic scale and in the outer regions is likely due to geometrical effects, as the core of one galaxy enters the outskirts of the other one. In addition, there is a physical enhancement of the magnetic field within the central ~5 kpc, reflecting the enhancement in density due to efficient angular momentum transport. We conclude that high-resolution observations of the central regions will be particularly relevant to probe the evolution of magnetic field structures during merger events.
Massive Dead Galaxies at z ∼ 2 with HST Grism Spectroscopy. I. Star Formation Histories and Metallicity Enrichment

Observations have revealed massive ( ) galaxies that were already dead when the universe was only ∼2 Gyr. Given the short time before these galaxies were quenched, their past histories and quenching mechanism(s) are of particular interest. In this paper, we study star formation histories (SFHs) of 24 massive galaxies at 1.6 < z < 2.5. A deep slitless spectroscopy and imaging data set collected from multiple Hubble Space Telescope surveys allows robust determination of their spectral energy distributions and SFHs with no functional assumption on their forms. We find that most of our massive galaxies had formed >50% of their extant masses by ∼1.5 Gyr before the time of observed redshifts, with a trend where more massive galaxies form earlier. Their stellar-phase metallicities are already compatible with those of local early-type galaxies, with a median value of and scatter of ∼0.15 dex. In combination with the reconstructed SFHs, we reveal their rapid metallicity evolution from z ∼ 5.5 to ∼2.2 at a rate of ∼0.2 dex Gyr−1 in . Interestingly, the inferred stellar-phase metallicities are, when compared at half-mass time, ∼0.25 dex higher than observed gas-phase metallicities of star-forming galaxies. While systematic uncertainties remain, this may imply that these quenched galaxies have continued low-level star formation, rather than abruptly terminating their star formation activity, and kept enhancing their metallicity until recently.
A Non-conventional Wine from Stem of Syzygium cumini and Statistical Optimization of its Fermentation Conditions for Maximum Bioactive Extraction

Keeping in view the increased demand of functional foods and the therapeutic potential associated with the stem of Syzygium cumini, a novel wine was produced from it. The wine was found to possess an ethanol content of 8.0±0.03% v/v. The wine had high total phenolic content (331.5μg/mL) and consequently, high total anti-oxidant capacity (27.09±0.1 μM/mL.). Statistical modeling was employed to the wine production for increasing ethanol, total phenolic and total anti oxidant capacity of the wine. Primarily, the three most significant factors affecting the process were identified by Plackett-Burman design. In the second phase, the concentration and interaction of the factors identified (KH2PO4, yeast extract and ZnSO4) was studied and optimized to achieve maximum response. The model was found to be significant (p<0.005) and ethanol concentration increased significantly to 11.59% (v/v), total anti-oxidant capacity to 186.0 μM/mL and total phenolic content to 1049.87 μg/mL in the optimized media. Further, for the identification of major bioactive compounds of the wine, LC-MS analysis of the wine was carried out which revealed the presence of various phyto-chemicals including malvidin, dephnidin, petunidin, gallic acid etc.
Unconventional superconductivity in the cage-type compound 
Sc5Rh6Sn18

We have examined the superconducting ground state properties of the caged type compound Sc$_5$Rh$_6$Sn$_{18}$ using magnetization, heat capacity, and muon-spin relaxation or rotation ($\mu$SR) measurements. Magnetization measurements indicate type-II superconductivity with an upper critical field $\mu_0H_{c2}(0)$ = 7.24 T. The zero-field cooled and field cooled susceptibility measurements unveil an onset of diamagnetic signal below $T_{\bf c}$ = 4.4 K. The interpretation of the heat capacity results below $T_{\bf c}$ using the $\alpha-$BCS model unveils the value of $\alpha$ = 2.65, which gives the dimensionless ratio 2$\Delta(0)/k_B T_{\bf c}$ = 5.3, intimating that Sc$_5$Rh$_6$Sn$_{18}$ is a strong-coupling BCS superconductor. The zero-field $\mu$SR measurements in the longitudinal geometry exhibit a signature of a spontaneous appearance of the internal magnetic field below the superconducting transition temperature, indicating that the superconducting state is characterized by the broken time-reversal symmetry (TRS). We have compared the results of broken TRS in Sc$_5$Rh$_6$Sn$_{18}$ with that observed in R$_5$Rh$_6$Sn$_{18}$ (R = Lu and Y).
A mid-IR interferometric survey with MIDI/VLTI: resolving the second-generation protoplanetary disks around post-AGB binaries

We present a mid-IR interferometric survey of the circumstellar environment of a specific class of post-Asymptotic Giant Branch (post-AGB) binaries. For this class the presence of a compact dusty disk has been postulated on the basis of various spatially unresolved measurements. Our interferometric survey was performed with the MIDI instrument on the VLTI. In total 19 different systems were observed using variable baseline configurations. Combining all the visibilities at a single wavelength at 10.7 micron, we fitted two parametric models to the data: a uniform disk (UD) and a ring model mimicking a temperature gradient. We compared our observables of the whole sample, with synthetic data computed from a grid of radiative transfer models of passively irradiated disks in hydrostatic equilibrium. These models are computed with a Monte Carlo code that has been widely applied to describe the structure of protoplanetary disks around young stellar objects (YSO). The spatially resolved observations show that the majority of our targets cluster closely together in the distance-independent size-colour diagram, and have extremely compact N-band emission regions. The typical uniform disk diameter of the N-band emission region is about 40 mass which corresponds to a typical brightness temperature of 400-600~K. The resolved objects display very similar characteristics in the interferometric observables and in the spectral energy distributions. Therefore, the physical properties of the disks around our targets must be similar. The grid of protoplanetary disk models covers very well the observed objects. Much like for young stars, the spatially resolved N-band emission region is determined by the hot inner rim of the disk. Continued comparisons between post-AGB and protoplanetary disks will help to understand grain growth and disk evolution processes,
State of the Amphibia 2020: A Review of Five Years of Amphibian Research and Existing Resources

Amphibians are a clade of over 8,400 species that provide unique research opportunities and challenges. With amphibians undergoing severe global declines, we posit that assessing our current understanding of amphibians is imperative. Focusing on the past five years (2016–2020), we examine trends in amphibian research, data, and systematics. New species of amphibians continue to be described at a pace of ∼150 per year. Phylogenomic studies are increasing, fueling a growing consensus in the amphibian tree of life. Over 3,000 species of amphibians are now represented by expert-curated accounts or data in AmphibiaWeb, AmphibiaChina, BIOWEB, or the Amphibian Disease Portal. Nevertheless, many species lack basic natural history data (e.g., diet records, morphological measurements, call recordings) and major gaps exist for entire amphibian clades. Genomic resources appear on the cusp of a rapid expansion, but large, repetitive amphibian genomes still pose significant challenges. Conservation continues to be a major focus for amphibian research, and threats cataloged on AmphibiaWeb for 1,261 species highlight the need to address land use change and disease using adaptive management strategies. To further promote amphibian research and conservation, we underscore the importance of database integration and suggest that other understudied or imperiled clades would benefit from similar assessments of existing data.
Nonequilibrium states of a quenched Bose gas

Yin and Radzihovsky [1] recently developed a self-consistent extension of a Bogoliubov theory, in which the condensate number density $n_c$ is treated as a mean field that changes with time, in order to analyze a JILA experiment by Makotyn et al. [2] on a $^{85}$Rb Bose gas following a deep quench to a large scattering length. We apply this theory to construct a closed set of equations that highlight the role of $\dot{n}_c$, which is to induce an effective interaction between quasiparticles. We show analytically that such a system supports a steady state characterized by a constant condensate density and a steady but periodically changing momentum distribution, whose time average is described exactly by the generalized Gibbs ensemble. We discuss how the $\dot{n}_{c}$-induced effective interaction, which cannot be ignored on the grounds of the adiabatic approximation for modes near the gapless Goldstone mode, can significantly affect condensate populations and Tan's contact for a Bose gas that has undergone a deep quench.
Effect of Nitrogen and Potassium on Yield and Quality of Pearl Millet ( Pennisetum glaucum L . )

A field experiment was carried out during to study the effect of nitrogen and potassium on yield and quality of pearl millet during kharif 2013. Eight nutrient management practices were imposed with three replic ations using RBD. All the yield, yield attributing parameters and grain quality parameters were recorded accordingly. The significantly highest grain yield was recorded with T7 followed by T4. Similar trend was seen with grain quality parameters viz., total protein, total amino acid and total carbohydrate content. Based on the results, it may be concluded that for higher production with good qual ity grain, pearl millet crop has to be supplied with 100 kg N ha + 30 kg P2O5 ha -1 + 40 kg K2O ha -1 (T7). However, for optimum and economic production, pearl millet has to be sup plied with 100 kg N ha + 30 kg P2O5 ha -1 + 20 kg K2O ha -1 (T4).