cssi/SciSciGPT-SciSciNet huggingface dataset:
A geometric approach to Orlov’s theorem

A famous theorem of D. Orlov describes the derived bounded category of coherent sheaves on projective hypersurfaces in terms of an algebraic construction called graded matrix factorizations. In this article, I implement a proposal of E. Segal to prove Orlov’s theorem in the Calabi–Yau setting using a globalization of the category of graded matrix factorizations (graded D-branes). Let X⊂ℙ be a projective hypersurface. Segal has already established an equivalence between Orlov’s category of graded matrix factorizations and the category of graded D-branes on the canonical bundle Kℙ to ℙ. To complete the picture, I give an equivalence between the homotopy category of graded D-branes on Kℙ and Dbcoh(X). This can be achieved directly, as well as by deforming Kℙ to the normal bundle of X⊂Kℙ and invoking a global version of Knorrer periodicity. We also discuss an equivalence between graded D-branes on a general smooth quasiprojective variety and on the formal neighborhood of the singular locus of the zero fiber of the potential.
Sharp entropy bounds for self-shrinkers in mean curvature flow

Let M ⊂ ℝ m + 1 be a smooth, closed, codimension-one self-shrinker (for mean curvature flow) with nontrivial k th homology. We show that the entropy of M is greater than or equal to the entropy of a round k -sphere, and that if equality holds, then M is a round k -sphere in ℝ k + 1 .
On the E2-term of the bo-Adams spectral sequence

The E_1-term of the (2-local) bo-based Adams spectral sequence for the sphere spectrum decomposes into a direct sum of a v_1-periodic part, and a v_1-torsion part. Lellmann and Mahowald completely computed the d_1-differential on the v_1-periodic part, and the corresponding contribution to the E_2-term. The v_1-torsion part is harder to handle, but with the aid of a computer it was computed through the 20-stem by Davis. Such computer computations are limited by the exponential growth of v_1-torsion in the E_1-term. In this paper, we introduce a new method for computing the contribution of the v_1-torsion part to the E_2-term, whose input is the cohomology of the Steenrod algebra. We demonstrate the efficacy of our technique by computing the bo-Adams spectral sequence beyond the 40-stem.
Metallicity Differences in Type Ia Supernova Progenitors Inferred from Ultraviolet Spectra

Two ''twin'' Type Ia supernovae (SNe Ia), SNe 2011by and 2011fe, have extremely similar optical light-curve shapes, colors, and spectra, yet have different ultraviolet (UV) continua as measured in Hubble Space Telescope spectra and measurably different peak luminosities. We attribute the difference in the UV continua to significantly different progenitor metallicities. This is the first robust detection of different metallicities for SN Ia progenitors. Theoretical reasoning suggests that differences in metallicity also lead to differences in luminosity. SNe Ia with higher progenitor metallicities have lower {sup 56}Ni yields and lower luminosities for the same light-curve shape. SNe 2011by and 2011fe have different peak luminosities ({Delta}M{sub V} Almost-Equal-To 0.6 mag), which correspond to different {sup 56}Ni yields: M{sub 11fe}({sup 56}Ni) / M{sub 11by}({sup 56}Ni) = 1.7{sup +0.7}{sub -0.5}. From theoretical models that account for different neutron-to-proton ratios in progenitors, the differences in {sup 56}Ni yields for SNe 2011by and 2011fe imply that their progenitor stars were above and below solar metallicity, respectively. Although we can distinguish progenitor metallicities in a qualitative way from UV data, the quantitative interpretation in terms of abundances is limited by the present state of theoretical models.
On the Inference of a Star's Inclination Angle from its Rotation Velocity and Projected Rotation Velocity

It is possible to learn about the orientation of a star's rotation axis by combining measurements of the star's rotation velocity ($v$) and its projection onto our line of sight ($v\sin i$). This idea has found many applications, including the investigation of the obliquities of stars with transiting planets. Here, we present a method for the probabilistic inference of the inclination of the star's rotation axis based on independent data sets that constrain $v$ and $v\sin i$. We also correct several errors and misconceptions that appear in the literature.
Vicious Circle Principle and Logic Programs with Aggregates

The paper presents a knowledge representation language $\mathcal{A}log$ which extends ASP with aggregates. The goal is to have a language based on simple syntax and clear intuitive and mathematical semantics. We give some properties of $\mathcal{A}log$ , an algorithm for computing its answer sets, and comparison with other approaches.
The Trigonometric Parallax of the Brown Dwarf Planetary System 2MASSW J1207334–393254

We have measured a trigonometric parallax to the young brown dwarf 2MASSW J1207334-393254. The distance (54.0 pc) and space motion confirm membership in the TW Hydrae Association. The primary is a ~25 MJup brown dwarf. We discuss the "planetary mass" secondary, which is certainly below the deuterium-burning limit but whose colors and absolute magnitudes pose challenges to our current understanding of planetary-mass objects.
Prompt neutrinos and intrinsic charm at SHiP

We present a new evaluation of the far-forward neutrino plus antineutrino flux and number of events from charm hadron decays in a 400 GeV proton beam dump experiment like the Search for Hidden Particles (SHiP). Using next-to-leading order perturbative QCD and a model for intrinsic charm, we include intrinsic transverse momentum effects and other kinematic angular corrections. We compare this flux to a far-forward flux evaluated with next-to-leading order perturbative QCD, without intrinsic transverse momentum, that used the angular distribution of charm quarks rather than the neutrinos from their decays. The tau neutrino plus antineutrino number of events in the perturbative QCD evaluation is reduced by a factor of about three when intrinsic transverse momentum and the full decay kinematics are included. We show that intrinsic charm contributions can significantly enhance the number of events from neutrinos from charm hadron decays. Measurements of the number of events from tau neutrino plus antineutrino interactions and of the muon charge asymmetry as a function of energy can be used to constrain intrinsic charm models.
EzGal: A Flexible Interface for Stellar Population Synthesis Models

We present EzGal, a flexible Python program designed to easily generate observable parameters (magnitudes, colors, and mass-to-light ratios) for arbitrary input stellar population synthesis (SPS) models. As has been demonstrated by various authors, for many applications the choice of input SPS models can be a significant source of systematic uncertainty. A key strength of EzGal is that it enables simple, direct comparison of different model sets so that the uncertainty introduced by choice of model set can be quantified. Its ability to work with new models will allow EzGal to remain useful as SPS modeling evolves to keep up with the latest research (such as varying IMFs). EzGal is also capable of generating composite stellar population models (CSPs) for arbitrary input star-formation histories and reddening laws, and it can be used to interpolate between metallicities for a given model set. To facilitate use, we have created an online interface to run EzGal and quickly generate magnitude and mass-to-light ratio predictions for a variety of star-formation histories and model sets. We make many commonly used SPS models available from the online interface, including the canonical Bruzual & Charlot models, an updated version of these models, the Maraston models, the BaSTI models, and the Flexible Stellar Population Synthesis (FSPS) models. We use EzGal to compare magnitude predictions for the model sets as a function of wavelength, age, metallicity, and star-formation history. From this comparison we quickly recover the well-known result that the models agree best in the optical for old solar-metallicity models, with differences at the ~0.1 mag level. Similarly, the most problematic regime for SPS modeling is for young ages (2 Gyr) and long wavelengths (λ 7500 A), where thermally pulsating AGB stars are important and scatter between models can vary from 0.3 mag (Sloan i) to 0.7 mag (Ks). We find that these differences are not caused by one discrepant model set and should therefore be interpreted as general uncertainties in SPS modeling. Finally, we connect our results to a more physically motivated example by generating CSPs with a star-formation history matching the global star-formation history of the universe. We demonstrate that the wavelength and age dependence of SPS model uncertainty translates into a redshift-dependent model uncertainty, highlighting the importance of a quantitative understanding of model differences when comparing observations with models as a function of redshift.
FREELY DECAYING TURBULENCE IN FORCE-FREE ELECTRODYNAMICS

Freely decaying relativistic force-free turbulence is studied for the first time. We initiate the magnetic field at a short wavelength and simulate its relaxation toward equilibrium on two and three dimensional periodic domains, in both helical and non-helical settings. Force-free turbulent relaxation is found to exhibit an inverse cascade in all settings, and in 3D to have a magnetic energy spectrum consistent with the Kolmogorov $5/3$ power law. 3D relaxations also obey the Taylor hypothesis; they settle promptly into the lowest energy configuration allowed by conservation of the total magnetic helicity. But in 2D, the relaxed state is a force-free equilibrium whose energy greatly exceeds the Taylor minimum, and which contains persistent force-free current layers and isolated flux tubes. We explain this behavior in terms of additional topological invariants that exist only in two dimensions, namely the helicity enclosed within each level surface of the magnetic potential function. The speed and completeness of turbulent magnetic free energy discharge could help account for rapidly variable gamma-ray emission from the Crab Nebula, gamma-ray bursts, blazars, and radio galaxies.
Transposable regularized covariance models with an application to missing data imputation

Missing data estimation is an important challenge with high-dimensional data arranged in the form of a matrix. Typically this data matrix is transposable, meaning that either the rows, columns or both can be treated as features. To model transposable data, we present a modification of the matrix-variate normal, the mean-restricted matrix-variate normal, in which the rows and columns each have a separate mean vector and covariance matrix. By placing additive penalties on the inverse covariance matrices of the rows and columns, these so called transposable regularized covariance models allow for maximum likelihood estimation of the mean and non-singular covariance matrices. Using these models, we formulate EM-type algorithms for missing data imputation in both the multivariate and transposable frameworks. We present theoretical results exploiting the structure of our transposable models that allow these models and imputation methods to be applied to high-dimensional data. Simulations and results on microarray data and the Netflix data show that these imputation techniques often outperform existing methods and offer a greater degree of flexibility.
Estimating Graphlet Statistics via Lifting

Exploratory analysis over network data is often limited by the ability to efficiently calculate graph statistics, which can provide a model-free understanding of the macroscopic properties of a network. We introduce a framework for estimating the graphlet count---the number of occurrences of a small subgraph motif (e.g. a wedge or a triangle) in the network. For massive graphs, where accessing the whole graph is not possible, the only viable algorithms are those that make a limited number of vertex neighborhood queries. We introduce a Monte Carlo sampling technique for graphlet counts, called Lifting, which can simultaneously sample all graphlets of size up to k vertices for arbitrary k. This is the first graphlet sampling method that can provably sample every graphlet with positive probability and can sample graphlets of arbitrary size k. We outline variants of lifted graphlet counts, including the ordered, unordered, and shotgun estimators, random walk starts, and parallel vertex starts. We prove that our graphlet count updates are unbiased for the true graphlet count and have a controlled variance for all graphlets. We compare the experimental performance of lifted graphlet counts to the state-of-the art graphlet sampling procedures: Waddling and the pairwise subgraph random walk.
On free discrete subgroups of Diff(I)

In recent decades and especially in recent years, some remarkable papers devoted to the study of finitely generated subgroups of DiffCŒ0; 1 have appeared (see Bergman [1], Calegari [2], Farb and Franks [3; 4], Farb and Shalen [5], Ghys [6], Navas [7; 8; 9], Tsuboi [12] and Yoccoz [13] for some of the most current developments). In contrast, discrete subgroups of DiffCŒ0; 1 are much less studied. Very little is known in this area especially in comparison with the very rich theory of discrete subgroups of Lie groups started in the works of F Klein and H Poincare in the 19th century, and expanded enormously in the works of A Selberg, A Borel, G Mostow, G Margulis and many others in the 20th century. Many questions which are either very easy or were studied a long time ago for (discrete) subgroups of Lie groups remain open in the context of the infinite-dimensional group DiffCŒ0; 1 and its relatives. In this paper, we address a question about the existence of discrete faithful representations of nonabelian free groups into the group DiffCŒ0; 1.
The Astrosphere of the Asymptotic Giant Branch Star CIT 6

We have discovered two extended half-ring structures in a far-ultraviolet image taken with the GALEX satellite of the well-known mass-losing carbon star CIT 6 (RW LMi). The northern (southern) ring is brighter (fainter) with a diameter of ∼15' (∼18'). These structures most likely represent the astrosphere resulting from the shock interaction of CIT 6's molecular wind with the warm interstellar medium (ISM), as it moves through the latter. These data provide a direct estimate of the size of CIT 6's circumstellar envelope that is a factor ∼20 larger than previous estimates based on CO millimeter-wave line data. We find that CIT 6 has been undergoing heavy mass-loss for at least 93,000 yr and the total envelope mass is 0.29 M {sub ☉} or larger, assuming a constant mass-loss rate of 3.2 × 10{sup –6} M {sub ☉} yr{sup –1}. Assuming that the shock front has reached a steady state and CIT 6's motion relative to the ISM is in the sky plane, we measure the termination-shock standoff distance directly from the image and find that CIT 6 is moving at a speed of about ≳39 (0.17 cm{sup –3}/n {sub ISM}){sup 1/2} km s{sup –1} through the ISM around it. However,more » comparisons with published numerical simulations and analytical modeling shows that CIT 6's forward shock (the northern ring) departs from the parabolic shape expected in steady state. We discuss several possible explanations for this departureþ.« less
A Penrose-Like Inequality for General Initial Data Sets

We establish a Penrose-Like Inequality for general (not necessarily time symmetric) initial data sets of the Einstein equations which satisfy the dominant energy condition. More precisely, it is shown that the ADM energy is bounded below by an expression which is proportional to the square root of the area of the outermost future (or past) apparent horizon.
Likelihood Analysis of Repeating in the BATSE Catalogue

I describe a new likelihood technique, based on counts-in-cells statistics, that I use to analyze repeating in the BATSE 1B and 2B catalogues. Using the 1B data, I find that repeating is preferred over non-repeating by 4.3:1 odds, with a peak at 5–6 repetitions per source. I find that the post-1B data are consistent with the repeating model inferred from the 1B data, after taking into account the lower fraction of bursts with well-determined positions. Combining the two data sets, I find that the odds favoring repeating over non-repeating are almost unaffected at 4:1, with a narrower peak at 5 repetitions per source. I conclude that the data sets are consistent both with each other and with repeating, and that for these data sets the odds favor repeating.
MATRIX FUNCTIONS THAT PRESERVE THE STRONG PERRON-FROBENIUS PROPERTY ∗

In this note, matrix functions that preserve the strong Perron-Frobenius property are characterized, using the real Jordan canonical form of a real matrix.
Guaranteed Matrix Completion via Non-Convex Factorization

Matrix factorization is a popular approach for large-scale matrix completion. The optimization formulation based on matrix factorization, even with huge size, can be solved very efficiently through the standard optimization algorithms in practice. However, due to the non-convexity caused by the factorization model, there is a limited theoretical understanding of whether these algorithms will generate a good solution. In this paper, we establish a theoretical guarantee for the factorization-based formulation to correctly recover the underlying low-rank matrix. In particular, we show that under similar conditions to those in previous works, many standard optimization algorithms converge to the global optima of a factorization-based formulation and recover the true low-rank matrix. We study the local geometry of a properly regularized objective and prove that any stationary point in a certain local region is globally optimal. A major difference of this paper from the existing results is that we do not need resampling (i.e., using independent samples at each iteration) in either the algorithm or its analysis.
The Low Earth Orbit Satellite Population and Impacts of the SpaceX Starlink Constellation

I discuss the current low Earth orbit artificial satellite population and show that the proposed "megaconstellation" of circa 12,000 Starlink Internet satellites would dominate the lower part of the Earth orbit, below 600 km, with a latitude-dependent areal number density of between 0.005 and 0.01 objects per square degree at airmass <2. Such large, low-altitude satellites appear visually bright to ground observers, and the initial Starlinks are naked-eye objects. I model the expected number of illuminated satellites as a function of latitude, time of year, and time of night and summarize the range of possible consequences for ground-based astronomy. In winter at lower latitudes typical of major observatories, the satellites will not be illuminated for six hours in the middle of the night. However, at low elevations near twilight at intermediate latitudes (45°–55°, e.g., much of Europe) hundreds of satellites may be visible at once to naked-eye observers at dark sites.
Vibrational signatures in the THz spectrum of 1,3-DNB: A first-principles and experimental study

Understanding the fundamental processes of light-matter interaction is important for detection of explosives and other energetic materials, which are active in the infrared and terahertz (THz) region. We report a comprehensive study on electronic and vibrational lattice properties of structurally similar 1,3-dinitrobenzene (1,3-DNB) crystals through first-principles electronic structure calculations and THz spectroscopy measurements on polycrystalline samples. Starting from reported x-ray crystal structures, we use density-functional theory (DFT) with periodic boundary conditions to optimize the structures and perform linear response calculations of the vibrational properties at zero phonon momentum. The theoretically identified normal modes agree qualitatively with those obtained experimentally in a frequency range up to 2.5 THz and quantitatively at much higher frequencies. The latter frequencies are set by intra-molecular forces. Our results suggest that van der Waals dispersion forces need to be included to improve the agreement between theory and experiment in the THz region, which is dominated by intermolecular modes and sensitive to details in the DFT calculation. An improved comparison is needed to assess and distinguish between intra- and intermolecular vibrational modes characteristic of energetic materials.
The Astrolabe Project: Identifying and Curating Astronomical ‘Dark Data’ through Development of Cyberinfrastructure Resources

As research datasets and analyses grow in complexity, data that could be valuable to other researchers and to support the integrity of published work remain uncurated across disciplines. These data are especially concentrated in the “Long Tail” of funded research, where curation resources and related expertise are often inaccessible. In the domain of astronomy, it is undisputed that uncurated "dark data" exist, but the scope of the problem remains uncertain. The “Astrolabe” Project is a collaboration between University of Arizona researchers, the CyVerse cyberinfrastructure environment, and the American Astronomical Society, with a mission to identify and ingest previously-uncurated astronomical data, and to provide a robust computational environment for analysis and sharing of data, as well as services for authors wishing to deposit data associated with publications. Following expert feedback obtained through two workshops held in 2015 and 2016, Astrolabe is funded in part by National Science Foundation. The system is being actively developed within CyVerse, and Astrolabe collaborators are soliciting heterogeneous datasets and potential users for the prototype system. Astrolabe team members are currently working to characterize the properties of uncurated astronomical data, and to develop automated methods for locating potentially-useful data to be targeted for ingest into Astrolabe, while cultivating a user community for the new data management system.
A Model of Controlled Growth

We consider a free boundary problem for a system of PDEs, modeling the growth of a biological tissue. A morphogen, controlling volume growth, is produced by specific cells and then diffused and absorbed throughout the domain. The geometric shape of the growing tissue is determined by the instantaneous minimization of an elastic deformation energy, subject to a constraint on the volumetric growth. For an initial domain with $${\mathcal{C}^{2,\alpha}}$$ boundary, our main result establishes the local existence and uniqueness of a classical solution, up to a rigid motion.
Reality or Mirage? Observational Test and Implications for the Claimed Extremely Magnified Quasar at z = 6.3

In the last two decades, approximately 200 quasars have been discovered at $z>6$, hosting active super-massive black holes with masses $M_{\bullet} \gtrsim 10^9 M_{\odot}$. While these sources reflect only the tip of the iceberg of the black hole mass distribution, their detection challenges standard growth models. The most massive $z>6$ black hole that was inferred thus far (J0100+2802, $M_{\bullet} \approx 1.2\times 10^{10} M_{\odot}$) was recently claimed to be lensed, with a magnification factor $\mu=450$. Here, we perform a consistency check of this claim, finding that the detection of such source requires a bright-end slope $\beta \geq 3.7$ for the intrinsic quasar luminosity function, $\Phi(L) \propto L^{-\beta}$. Commonly used values of $\beta \sim 2.8$ are rejected at $>3\sigma$. If the claim is confirmed, it is very unlikely that all the remaining $51$ sources in the SDSS sample are not magnified. Furthermore, it suffices that $\gtrsim 25\%$ of the remaining sources are lensed for the intrinsic luminosity function to differ significantly (i.e., $>3\sigma$) from the observed one. The presence of additional extremely magnified sources in the sample would lower the requirement to $\sim 4\%$. Our results urge the community to perform more extended multi-wavelength searches targeting $z>6$ lensed quasars, also among known samples. This effort could vitally contribute to solving the open problem of the growth of the brightest $z\sim 7$ quasars.
A Spectroscopic Study of Type Ibc Supernova Host Galaxies From Untargeted Surveys

We present the first spectroscopic study of the host environments of Type Ibc supernovae (SNe Ibc) discovered exclusively by untargeted SN searches. Past studies of SN Ibc host environments have been biased toward high-mass, high-metallicity galaxies by focusing on SNe discovered in galaxy-targeted SN searches. Our new observations more than double the total number of spectroscopic stellar population age and metallicity measurements published for untargeted SN Ibc host environments. For the 12 SNe Ib and 21 SNe Ic in our metallicity sample, we find median metallicities of 0.62 Z ☉ and 0.83 Z ☉, respectively, but determine that the discrepancy in the full distribution of metallicities is not statistically significant. This median difference would correspond to only a small difference in the mass loss via metal-line-driven winds ( 30%), suggesting this does not play the dominant role in distinguishing SNe Ib and Ic progenitors. However, the median metallicity of the seven broad-lined SNe Ic (SNe Ic-BL) in our sample is significantly lower, 0.45 Z ☉. The age of the young stellar population of SN Ic-BL host environments also seems to be lower than for SNe Ib and Ic, but our age sample is small. Combining all SN Ibc host environment spectroscopy from the literature to date does not reveal a significant difference in SN Ib and Ic metallicities, but reinforces the significance of the lower metallicities for SNe Ic-BL. This combined sample demonstrates that galaxy-targeted SN searches introduce a significant bias for studies seeking to infer the metallicity distribution of SN progenitors, and we identify and discuss other systematic effects that play smaller roles. We discuss the path forward for making progress on SN Ibc progenitor studies in the Large Synoptic Survey Telescope era. This paper includes data gathered with the 6.5 m Magellan Telescopes located at Las Campanas Observatory, Chile.
Prospects of direct growth boron nitride films as substrates for graphene electronics

We present a route for direct growth of boron nitride via a polyborazylene to h-BN conversion process. This two-step growth process ultimately leads to a >25x reduction in the root-mean-square surface roughness of h-BN films when compared to a high temperature growth on Al2O3(0001) and Si(111) substrates. Additionally, the stoichiometry is shown to be highly dependent on the initial polyborazylene deposition temperature. Importantly, chemical vapor deposition (CVD) graphene transferred to direct-grown boron nitride films on Al2O3 at 400 °C results in a >1.5x and >2.5x improvement in mobility compared to CVD graphene transferred to Al2O3 and SiO2 substrates, respectively, which is attributed to the combined reduction of remote charged impurity scattering and surface roughness scattering. Simulation of mobility versus carrier concentration confirms the importance of limiting the introduction of charged impurities in the h-BN film and highlights the importance of these results in producing optimized h-BN substrates for high performance graphene and TMD devices.
Pain Intensity Assessment in Sickle Cell Disease Patients Using Vital Signs During Hospital Visits.

Pain in sickle cell disease (SCD) is often associated with increased morbidity, mortality, and high healthcare costs. The standard method for predicting the absence, presence, and intensity of pain has long been self-report. However, medical providers struggle to manage patients based on subjective pain reports correctly and pain medications often lead to further difficulties in patient communication as they may cause sedation and sleepiness. Recent studies have shown that objective physiological measures can predict subjective self-reported pain scores for inpatient visits using machine learning (ML) techniques. In this study, we evaluate the generalizability of ML techniques to data collected from 50 patients over an extended period across three types of hospital visits (i.e., inpatient, outpatient and outpatient evaluation). We compare five classification algorithms for various pain intensity levels at both intra-individual (within each patient) and inter-individual (between patients) level. While all the tested classifiers perform much better than chance, a Decision Tree (DT) model performs best at predicting pain on an 11-point severity scale (from 0–10) with an accuracy of 0.728 at an inter-individual level and 0.653 at an intra-individual level. The accuracy of DT significantly improves to 0.941 on a 2-point rating scale (i.e., no/mild pain: 0–5, severe pain: 6–10) at an inter-individual level. Our experimental results demonstrate that ML techniques can provide an objective and quantitative evaluation of pain intensity levels for all three types of hospital visits.
Predicting changes in protein thermodynamic stability upon point mutation with deep 3D convolutional neural networks

Predicting mutation-induced changes in protein thermodynamic stability (ΔΔG) is of great interest in protein engineering, variant interpretation, and protein biophysics. We introduce ThermoNet, a deep, 3D-convolutional neural network (3D-CNN) designed for structure-based prediction of ΔΔGs upon point mutation. To leverage the image-processing power inherent in CNNs, we treat protein structures as if they were multi-channel 3D images. In particular, the inputs to ThermoNet are uniformly constructed as multi-channel voxel grids based on biophysical properties derived from raw atom coordinates. We train and evaluate ThermoNet with a curated data set that accounts for protein homology and is balanced with direct and reverse mutations; this provides a framework for addressing biases that have likely influenced many previous ΔΔG prediction methods. ThermoNet demonstrates performance comparable to the best available methods on the widely used Ssym test set. In addition, ThermoNet accurately predicts the effects of both stabilizing and destabilizing mutations, while most other methods exhibit a strong bias towards predicting destabilization. We further show that homology between Ssym and widely used training sets like S2648 and VariBench has likely led to overestimated performance in previous studies. Finally, we demonstrate the practical utility of ThermoNet in predicting the ΔΔGs for two clinically relevant proteins, p53 and myoglobin, and for pathogenic and benign missense variants from ClinVar. Overall, our results suggest that 3D-CNNs can model the complex, non-linear interactions perturbed by mutations, directly from biophysical properties of atoms.
Methods to Recover Unknown Processes in Partial Differential Equations Using Data

We study the problem of identifying unknown processes embedded in time-dependent partial differential equation (PDE) using observational data, with an application to advection-diffusion type PDE. We first conduct theoretical analysis and derive conditions to ensure the solvability of the problem. We then present a set of numerical approaches, including Galerkin type algorithm and collocation type algorithm. Analysis of the algorithms are presented, along with their implementation detail. The Galerkin algorithm is more suitable for practical situations, particularly those with noisy data, as it avoids using derivative/gradient data. Various numerical examples are then presented to demonstrate the performance and properties of the numerical methods.
Sufficient conditions for forward invariance and contractivity in hybrid inclusions using barrier functions

Abstract This paper studies set invariance and contractivity in hybrid systems modeled by hybrid inclusions using barrier functions. After introducing the notion of barrier function, we investigate sufficient conditions to guarantee different forward invariance and contractivity notions of a closed set for hybrid systems with nonuniqueness of solutions and solutions terminating prematurely. We consider forward (pre-)invariance of sets, which guarantees that the maximal solutions starting from the set stay in it, and (pre-)contractivity, which further requires that the solutions starting from the boundary of the set evolve immediately (continuously or discretely) towards its interior. Our conditions for forward invariance and contractivity are infinitesimal and in terms of the proposed barrier functions. Examples illustrate the results.
Has COVID-19 Hurt Resident Education? A Network-Wide Resident Survey on Education and Experience During the Pandemic

Purpose:As the COVID-19 pandemic continues to evolve, the healthcare system has been forced to adapt in myriad ways. Residents have faced significant changes in work schedules, deployment to COVID-...
Comparing Covariate Prioritization via Matching to Machine Learning Methods for Causal Inference Using Five Empirical Applications

When investigators seek to estimate causal effects, they often assume that selection into treatment is based only on observed covariates. Under this identification strategy, analysts must adjust fo...
Effect of Margin Status on Survival After Resection of Hilar Cholangiocarcinoma in the Modern Era of Adjuvant Therapies.

IntroductionStudies have shown that for patients with hilar cholangiocarcinoma (HC), survival is associated with negative resection margins (R0). This requires increasingly proximal resection, putt...
MLSNet: A Policy Complying Multilevel Security Framework for Software Defined Networking

Ensuring that information flowing through a network is secure from manipulation and eavesdropping by unauthorized parties is an important task for network administrators. Many cyber attacks rely on a lack of network-level information flow controls to successfully compromise a victim network. Once an adversary exploits an initial entry point, they can eavesdrop and move laterally within the network (e.g., scan and penetrate internal nodes) to further their malicious goals. In this article, we propose a novel multilevel security (MLS) framework to enforce a secure inter-node information flow policy within the network and therein vastly reduce the attack surface available to an adversary who has penetrated it. In contrast to prior work on multilevel security in computer networks which relied on enforcing the policy at network endpoints, we leverage the centralization of software-defined networks (SDNs) by moving the task to the controller and providing this service transparently to all network nodes. Our framework, MLSNet , formalizes the generation of a policy compliant network configuration (i.e., set of flow rules on the SDN switches) as network optimization problems, with the objectives of (1) maximizing the number of flows satisfying all security constraints and (2) minimizing the security cost of routing any remaining flows to guarantee availability. We demonstrate that MLSNet can securely and efficiently route flows that satisfy the security constraints and route the remaining flows with a minimal security cost (e.g., route >85% of flows, where the heuristic achieves 89% and 87% of the optimal solutions for the optimization problems).
The Keck Planet Imager and Characterizer: Phase I fiber injection unit early performance and commissioning

The Keck Planet Imager and Characterizer (KPIC) is an upgrade to the Keck II adaptive optics system and instrument suite with the goal of improving direct imaging and high-resolution spectroscopic characterization capabilities for giant exoplanets. KPIC Phase I includes a fiber injection unit (FIU) downstream of a new pyramid wavefront sensor, coupling planet light to a single mode fiber fed into NIRSPEC, Keck’s high-resolution infrared spectrograph. This enables high-dispersion spectroscopy (HDS) of directly imaged exoplanets at smaller separation and higher contrast, improving our spectral characterization capabilities for these objects. Here, we report performance results from the KPIC Phase I FIU commissioning, including analysis of throughput, stability, and sensitivity of the instrument.
Congenital Diaphragmatic Hernia: Demographics and 30-day Outcomes in Adults.

BACKGROUND Congenital diaphragmatic hernia (CDH) is a pathology most often affecting the pediatric population, although adults can also be affected. Few studies exist of adults undergoing repair of this defect. Using a national database, we sought to determine demographics and outcomes of this population. METHODS An analysis of the American College of Surgeons National Surgical Quality Improvement Program (ACS NSQIP) database (2015-2018) was performed, capturing patients with postoperative diagnosis of CDH, distinct from ventral hernia. Two groups were created based upon surgical approach of open or minimally invasive (MIS) repair. Baseline demographics and outcomes were compared. RESULTS 110 patients undergoing surgical correction of CDH were captured in the database. We found rates of return to the operating room (4.55%), postoperative respiratory failure (5.45%), and reintubation (3.64%) with no difference between groups. There was no mortality and no difference between groups in length of operation, discharge to home, or postoperative complications. Patients undergoing open repair had a longer length of stay than patients in the MIS group (6.47 ± 10.76 days vs. 3.68 ± 3.74 days, P = .0471). Mesh was used in MIS more often than the open group (47.30% vs. 5.56%, P < .0001). DISCUSSION This study describes rates of postoperative complications in patients undergoing repair of CDH, and suggests outcomes those are equivalent between patients receiving open or MIS approaches. Further case series or retrospective studies are needed to further describe this population of patients.
Guaranteed Reachability for Systems with Unknown Dynamics

The problem of computing the reachable set for a given system is a quintessential question in nonlinear control theory. Motivated by prior work on safety-critical online planning, this paper considers an environment where the only available information about system dynamics is that of dynamics at a single point. Limited to such knowledge, we study the problem of describing the set of all states that are guaranteed to be reachable regardless of the unknown true dynamics. We show that such a set can be underapproximated by a reachable set of a related known system whose dynamics at every state depend on the velocity vectors that are available in all control systems consistent with the assumed knowledge. Complementing the theory, we discuss a simple model of an aircraft in distress to verify that such an underapproximation is meaningful in practice.
Staged investments in entrepreneurial financing

Abstract Venture capitalists deliver investments to entrepreneurs in stages. This paper shows staged financing is efficient. Staging lets investors abandon ventures with low early returns, and thus sorts good projects from bad. The primary implication from staging is that it is efficient to invest more in later rounds. The model yields a number of predictions on how the ratio of early to late round financing varies with uncertainty, the outside options of both parties, the value of the venture, the costs of investment, and project difficulty. We test these predictions against data on venture capital financings and find significant empirical support for the theory.
Measuring the Benefit of Offering Auxiliary Services: Do Bag‐Checkers Differ in Their Sensitivities to Airline Itinerary Attributes?

When firms evaluate their service system design choices, there is typically more uncertainty surrounding the value that a particular auxiliary service provides than there is on the cost of providing that service. To help inform this decision, we propose an approach where we compare the relative value of the segment of passengers who use an auxiliary service to the relative value of the segment that does not use it. We demonstrate this approach for a typical auxiliary service common to the airline industry. In 2008, most US airlines implemented checked baggage fee policies to decrease their costs by reducing the number of customer service agents needed in the check-in and baggage handling processes. The success of this change has led to a current debate at many of these airlines on whether to make further staffing cuts in these areas, essentially making it even less attractive for passengers to check their baggage. Our proposed methodology helps answer whether passengers who continue to check bags in today's baggage-fee era are more or less valuable than passengers who do not check bags. We explore this question empirically by examining, through a stated preference survey, if a history of checking or not checking bags can be used to segment passengers based on how their itinerary choices are influenced by common airline service attributes (on-time performance, itinerary time, number of connections, airfare, and schedule delay). Contrary to the opinions of some top airline executives, we find that the passengers who continue to check bags at airlines that charge baggage fees are generally less sensitive to differences in three of these important service attributes and are less likely to switch airlines when a competing airline improves its offerings along these dimensions. Thus, airlines that charge for checked bags should consider improving the customer experience for their bag-checking passengers, as they represent a potentially more valuable segment class to the airline.
Moral Hazard and the Optimality of Debt

I show that, in a benchmark model, debt securities minimize the welfare losses associated with the moral hazards of excessive risk-taking and lax effort. For any security design, the variance of the security payoff is a statistic that summarizes these welfare losses. Debt securities have the least variance, among all limited liability securities with the same expected value. In other models, mixtures of debt and equity are exactly optimal, and pure debt securities are approximately optimal. I study both static and dynamic security design problems, and show that these two types of problems are equivalent. I use moral hazard in mortgage lending as a recurring example, but my results apply to other corporate finance and principal-agent problems.
First mover advantages and optimal patent protection

This paper examines the economic logic underlying so-called “first mover advantages” as alternatives to patent protection in allowing innovators protection from immediate imitation and time to recoup their research and development investments. These include a head start, lower costs due to learning by doing, and product-differentiating reputational advantages. William Nordhaus’ theory of optimal patent protection is extended to cases of product, as distinguished from cost-saving, innovation. Over the parameters covered by a simulation analysis, profit potentials sufficient to induce R&D investment are found much more frequently than R&D incentive failures. R&D failures occur most commonly in small markets and situations in which imitators’ erosion of the innovator’s market share is particularly rapid. Implications for patent policy are drawn.
Parenthood in a Time of Transition: Tensions Between Legal, Biological, and Social Conceptions of Parenthood

The law of parentage, long seemingly immune from the revolutionary changes affecting other aspects of family law, is now being reconsidered as never before. On one front, the growing number of families raising children in informal or unconventional settings has put pressure on law to recognize parentage outside its traditional boundaries, on the basis of caregiving wholly apart from biology, marriage, and adoption. At the same time, the ready availability of DNA testing has spurred efforts to place new weight on biology, pushing parentage back toward a narrower and more traditional core. Courts and legislatures have responded to these developments often impulsively and in isolation, introducing a new and fundamental incoherence into the law's conception of parenthood. Just as states are beginning to deemphasize genetics as an essential determinant of parenthood in the contexts of assisted reproduction and same-sex partnerships - recognizing as parents, for example, unmarried partners who undertake to "co-parent" a child with a legal parent - there is simultaneous movement to permit men to "disestablish" longstanding paternal bonds on the basis of a single DNA test. This article, written as a national report for the Congress of the International Academy of Comparative Law, examines these cross-currents and contends that parentage law is likely to remain unstable until society produces greater consensus about the respective roles of biology, consent, and caregiving in defining what it means to be a parent.
Body Blow: Boxer Chases Ambulance and Wins Judgment

Case analysis and discussion of Maldonado v. Gateway Hotel Holdings, L.L.C., 2003 Mo. App. LEXIS 1577, in which the Missouri appellate court upheld a trial court decision as a professional boxer was awarded $13.7 million in compensatory damages for a hotel's failure to provide an ambulance on site after the match was over even though it had subcontracted responsibility for the event with a promoter.
Does Stock Market Performance Influence Retirement Intentions

Media reports predicted that the stock market decline in October 2008 would cause changes in retirement intentions, due to declines in retirement assets. We use panel data from the Health and Retirement Study to investigate the relationship between stock market performance and retirement intentions during 1998–2008, a period that includes the recent crisis. While we find a weak negative correlation between stock returns and retirement intentions, further investigation suggests that this relationship is not driven by wealth shocks brought about by stock market fluctuations, but by other factors that are correlated with both the stock market and retirement intentions.
Financial knowledge overconfidence and early withdrawals from retirement accounts

Early distributions from retirement accounts could endanger future retirement income security, and the U.S. has restrictions to discourage them, including possible tax penalties. On the other hand, tapping one's retirement assets may be rational when an individual encounters financial hardship. With the 2020 Coronavirus Aid, Relief, and Economic Security Act, early distribution from retirement accounts became an even more attractive option to individuals. In this study, we examined factors related to individuals' decision of taking hardship withdrawals and plan loans, focusing on financial knowledge and overconfidence in financial knowledge, using the 2018 National Financial Capability Study dataset. We found evidence that people may be making early withdrawals without understanding possible consequences. Objective financial knowledge was negatively related to hardship withdrawals and plan loans, but the subjective assessment of financial knowledge was positively related to hardship withdrawals. Respondents with financial knowledge overconfidence (high subjective and low objective knowledge) were more likely to take early withdrawals than those with other combinations of objective and subjective knowledge. We discuss implications for public policy and financial education and advice. Full Text Available Here: https://doi.org/10.1002/cfp2.1091